NATIONAL MARINE FISHERIES SERVICE 

ENDANGERED SPECIES ACT SECTION 7 

BIOLOGICAL AND CONFERENCE OPINION 

Title: Biological and Conference Opinion on the Proposed 

Implementation of a Program for the Issuance of Permits for 

Research and Enhancement Activities on Threatened and 

Endangered Sea Turtles Pursuant to Section l0(a) of the 

Endangered Species Act 

Consultation Conducted By: Endangered Species Act Interagency Cooperation Division, 

Office of Protected Resources, National Marine Fisheries 

Service, National Oceanic and Atmospheric Administration, 

U.S. Department of Commerce 

Action Agency: Permits and Conservation Division of the Office of Protected 

Resources, National Marine Fisheries Service 

Publisher: Office of Protected Resources, National Marine Fisheries 

Service, National Oceanic and Atmospheric Administration, 

U.S. Department of Commerce 

Approved: 

Date: 

Consultation Tracking number: FPR-2017-9230 

Digital Object Identifier (DOI): 

Director, Office of Protected Res 

DEC 2 1 2017 

https://doi.org/10.7289/V57S7M1R
Turtle Research Programmatic Biological Opinion FPR-2017-9230 

TABLE OF CONTENTS 

Page 

1 Introduction......................................................................................................................... 11 

1.1 Background .................................................................................................................... 12 

1.2 Consultation History ...................................................................................................... 13 

2 The Assessment Framework .............................................................................................. 15 

3 Description of the Proposed Action................................................................................... 17 

3.1 Overall Process for Issuing Sea Turtle Directed Take Permits...................................... 17 

3.2 General Permit Terms and Conditions........................................................................... 20 

3.3 Annual Permit Cycle ...................................................................................................... 26 

3.4 Sea Turtle Research Activities and Associated Mitigation Measures............................ 27 

3.4.1 Sea Turtle Parts....................................................................................................... 27 

3.4.2 Remote Visual and Acoustic Surveys..................................................................... 28 

3.4.3 Capture and Collection Methods ............................................................................ 30 

3.4.4 Research Procedures on Captured Sea Turtles ....................................................... 35 

3.4.5 New Sea Turtle Research Methods, Procedures, and Mitigation Measures........... 47 

3.5 Authorizing Take Under the Sea Turtle Research Permitting Program......................... 48 

3.5.1 Sea Turtle Take Levels Authorized ........................................................................ 48 

3.5.2 Allocating Authorized Lethal Take Among Research Permits............................... 50 

3.5.3 Monitoring Sea Turtle Take.................................................................................... 52 

3.5.4 Addressing Scenarios When a Lethal Take Limit Has Been Exceeded ................. 53 

3.5.5 Incidental Take of Non-target Species.................................................................... 54 

3.6 Internal Program Review ............................................................................................... 54 

3.7 Adaptive Management ................................................................................................... 55 

3.8 Reporting to the Interagency Cooperation Division ...................................................... 56 

4 Interrelated and Interdependent Actions ......................................................................... 57 

5 Action Area.......................................................................................................................... 58 

6 Status of Endangered Species Act (ESA) Protected Resources ...................................... 61 

6.1 Species and Designated Critical Habitat Not Likely to be Adversely Affected ............ 66 

6.1.1 ESA-listed and Proposed Cetacean Species ........................................................... 68 

6.1.2 Cetacean Designated and Proposed Critical Habitat .............................................. 69 

6.1.3 Sea Turtle Designated Critical Habitat ................................................................... 71 

6.1.4 ESA-listed Pinniped Species................................................................................... 72 

6.1.5 Pinniped Designated Critical Habitat...................................................................... 73 

6.1.6 ESA-listed and Proposed Fish Species ................................................................... 74 

6.1.7 Fish Species Designated Critical Habitat................................................................ 75 

6.1.8 ESA-listed Abalone Species ................................................................................... 76 

6.1.9 Abalone Designated Critical Habitat ...................................................................... 76 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

6.1.10 ESA-listed Coral Species........................................................................................ 77 

6.1.11 Coral Species Designated Critical Habitat.............................................................. 77 

6.1.12 Johnson’s Seagrass.................................................................................................. 78 

6.1.13 Johnson’s Seagrass Designated Critical Habitat..................................................... 78 

6.2 Species Likely to be Adversely Affected....................................................................... 79 

6.2.1 Green Sea Turtle ..................................................................................................... 81 

6.2.2 Hawksbill Sea Turtle............................................................................................... 99 

6.2.3 Kemp’s Ridley Sea Turtle..................................................................................... 103 

6.2.4 Leatherback Sea Turtle ......................................................................................... 106 

6.2.5 Loggerhead Sea Turtle.......................................................................................... 112 

6.2.6 Olive Ridley Sea Turtle ........................................................................................ 122 

6.2.7 Gulf of Maine Atlantic Salmon............................................................................. 127 

6.2.8 Smalltooth Sawfish, U.S. Portion of Range.......................................................... 131 

6.2.9 Atlantic Sturgeon .................................................................................................. 135 

6.2.10 Shortnose Sturgeon ............................................................................................... 143 

6.2.11 Green Sturgeon, Southern Distinct Population Segment...................................... 148 

6.2.12 Gulf Sturgeon........................................................................................................ 152 

6.2.13 Nassau Grouper..................................................................................................... 156 

6.2.14 Scalloped Hammerhead ........................................................................................ 159 

7 Environmental Baseline.................................................................................................... 165 

7.1 Global Climate Change ................................................................................................ 165 

7.2 Habitat Degradation ..................................................................................................... 168 

7.2.1 Terrestrial Habitat ................................................................................................. 169 

7.2.2 Aquatic Habitat ..................................................................................................... 170 

7.3 Marine Debris............................................................................................................... 172 

7.4 Pollutants...................................................................................................................... 173 

7.5 Oil Spills....................................................................................................................... 175 

7.6 Vessel Strikes ............................................................................................................... 178 

7.7 Anthropogenic Sound................................................................................................... 179 

7.8 Disease ......................................................................................................................... 185 

7.9 Industrial and Power Generating Plants....................................................................... 187 

7.10 Dredging....................................................................................................................... 189 

7.11 Hydromodification ....................................................................................................... 190 

7.11.1 Dams ..................................................................................................................... 190 

7.11.2 Water Diversions .................................................................................................. 192 

7.12 Scientific Research and Enhancement Permits ............................................................ 193 

7.12.1 Sea Turtle Research .............................................................................................. 194 

7.12.2 Research on Other ESA-listed Species................................................................. 196 

7.13 Directed Harvest of Sea Turtles ................................................................................... 197 

7.14 Fisheries Bycatch ......................................................................................................... 199 

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7.14.1 Bycatch of Sea Turtles.......................................................................................... 199 

7.14.2 Bycatch of Other ESA-Listed Species.................................................................. 215 

7.15 Sea Turtle Strandings ................................................................................................... 219 

7.15.1 Sea Turtle Stranding and Salvage Network.......................................................... 222 

8 Effects of the Action.......................................................................................................... 224 

8.1 Stressors Associated with the Proposed Action ........................................................... 224 

8.2 Mitigation to Minimize or Avoid Exposure................................................................. 225 

8.3 Sea Turtle Exposure to Stressors.................................................................................. 226 

8.4 Sea Turtle Responses to Stressors................................................................................ 229 

8.4.1 Research Vessel Interactions ................................................................................ 229 

8.4.2 Surveys by Manned and Unmanned Aircraft........................................................ 230 

8.4.3 Underwater Tracking by Remotely Operated and Autonomous Vehicles............ 231 

8.4.4 Acoustic Surveys and Sonar Transducers............................................................. 231 

8.4.5 Capture.................................................................................................................. 232 

8.4.6 Recapture .............................................................................................................. 238 

8.4.7 Holding, Handling, and Transport ........................................................................ 239 

8.4.8 Morphometrics and Monitoring of Vital Parameters............................................ 240 

8.4.9 Shell Marking........................................................................................................ 241 

8.4.10 Oral and Ophthalmic Examination ....................................................................... 241 

8.4.11 Flipper and Passive Integrated Transponder Tagging .......................................... 241 

8.4.12 Oxytetracycline ..................................................................................................... 242 

8.4.13 Biological Sampling.............................................................................................. 243 

8.4.14 Gastric Lavage ...................................................................................................... 246 

8.4.15 Laparoscopy, Internal Tissue Sampling, and Anesthesia ..................................... 247 

8.4.16 Transmitter Attachments....................................................................................... 249 

8.4.17 Drilling through Carapace..................................................................................... 251 

8.4.18 Stomach Pills ........................................................................................................ 254 

8.4.19 Non-invasive Imaging........................................................................................... 254 

8.5 Sea Turtle Risk Analysis.............................................................................................. 255 

8.5.2 Research Mortality................................................................................................ 256 

8.5.3 Delayed Mortality ................................................................................................. 258 

8.5.4 Summary............................................................................................................... 260 

8.6 Non-Target Species Exposure and Response Analysis................................................ 260 

8.6.2 Capture by Entanglement, Pound, Seine, or Trawl Nets ...................................... 262 

8.7 Non-Target Species Risk Analysis............................................................................... 269 

8.7.1 Atlantic Salmon, Gulf of Maine Distinct Population Segment............................. 270 

8.7.2 Smalltooth Sawfish, U.S. Portion of Range Distinct Population Segment........... 271 

8.7.3 Sturgeon Species................................................................................................... 272 

8.7.4 Nassau Grouper..................................................................................................... 274 

8.7.5 Scalloped Hammerhead Shark.............................................................................. 274 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

9 Cumulative Effects............................................................................................................ 276 

10 Integration and Synthesis................................................................................................. 278 

10.1 Sea Turtles.................................................................................................................... 278 

10.1.1 Sea Turtle Research Permitting Program: Summary............................................ 278 

10.1.2 Current Status and Threats: Summary.................................................................. 280 

10.1.3 Sea Turtle Exposure, Response, and Risk Analyses: Summary ........................... 280 

10.1.4 Overall Summary.................................................................................................. 281 

10.2 Gulf of Maine Atlantic Salmon.................................................................................... 282 

10.3 Smalltooth Sawfish, U.S. Portion of Range ................................................................. 283 

10.4 Sturgeon: Atlantic, Shortnose, Green, and Gulf........................................................... 283 

10.5 Nassau Grouper............................................................................................................ 285 

10.6 Scalloped Hammerhead................................................................................................ 286 

11 Conclusion ......................................................................................................................... 287 

12 Incidental Take Statement ............................................................................................... 290 

13 Conservation Recommendations ..................................................................................... 296 

14 Reinitiation Notice ............................................................................................................ 298 

15 References.......................................................................................................................... 301 

Appendices 

Appendix A. Endangered Species Scientific Research and Enhancement Permit Application 

Instructions 

Appendix B. Application Review Checklist for Section 10(a)(1)(A) and NEPA Criteria 

Appendix C. Section 10(a)(1)(A) Permit Template 

Appendix D. Permits Division Annual Report Form for Section 10(a)(1)(A) Permit Holders 

Appendix E. Locations of Active Section 10(a)(1)(A) Sea Turtle Research Permits in the Atlantic 

(with Florida Inset) and Pacific Oceans as of June 30, 2017 

Appendix F. NMFS Sawfish Handling and Release Guidelines 

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LIST OF TABLES 

Page 

Table 1. Proposed ten-year lethal take limits for observed mortalities over the 

term of the programmatic consultation......................................................................................... 51 

Table 2. Threatened and endangered species that may be affected by the proposed 

action............................................................................................................................................. 61 

Table 3. ESA-listed sea turtle species abundance trends, and recovery priority 

numbers (through September 20, 2016)........................................................................................ 80 

Table 4. Summary of green sea turtle listing and recovery plan information............................... 82 

Table 5. Green sea turtle nesting abundance in each distinct population segment 

(Seminoff et al. 2015). .................................................................................................................. 83 

Table 6. Summary of hawksbill sea turtle listing and recovery plan information...................... 100 

Table 7. Summary of Kemp’s ridley sea turtle listing and recovery plan 

information.................................................................................................................................. 104 

Table 8. Summary of leatherback sea turtle listing and recovery plan information................... 107 

Table 9. Summary of loggerhead sea turtle listing and recovery plan information.................... 113 

Table 10. Loggerhead sea turtle abundance estimates for distinct population 

segments and recovery units. ...................................................................................................... 115 

Table 11. Summary of olive ridley sea turtle listing and recovery plan 

information.................................................................................................................................. 123 

Table 12. Summary of Atlantic salmon listing and recovery plan information.......................... 128 

Table 13. Summary of smalltooth sawfish listing and recovery plan information..................... 132 

Table 14. Summary of Atlantic sturgeon listing and recovery plan information. ...................... 137 

Table 15. Summary of shortnose sturgeon listing and recovery plan information..................... 144 

Table 16. Summary of green sturgeon listing and recovery plan information. .......................... 149 

Table 17. Summary of Gulf sturgeon listing and recovery plan information............................. 153 

Table 18. Summary of Nassau grouper listing and recovery plan information.......................... 157 

Table 19. Summary of scalloped hammerhead shark listing and recovery plan 

information.................................................................................................................................. 160 

Table 20. Average annual reported captures by turtle species and capture method 

from 2007 to 2017....................................................................................................................... 195 

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Table 21. Number of lethal takes authorized and reported, by species, from June 

2007 to July 2017........................................................................................................................ 196 

Table 22. Total authorized takes of sea turtles by capture method in permits from 

June 2007 to May 2017............................................................................................................... 227 

Table 23. Number of sea turtle exposures by capture type projected over the next 

ten years based on previously authorized takes and future growth estimates for 

each method. ............................................................................................................................... 228 

Table 24. ESA-listed sea turtle species with abundance estimates, abundance 

trends, ten-year lethal take limits and population impact. .......................................................... 257 

Table 25. Proportion of all trawl captures, anticipated trawl captures, ten-year 

lethal take limits, estimated delayed mortalities, abundance estimates and 

population impact for each turtle species or distinct population segment. ................................. 261 

Table 26. Authorized incidental take of sea turtles due to delayed mortality and of 

incidentally captured non-target ESA-listed species resulting from the Program 

over any given ten-year period. .................................................................................................. 292 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

LIST OF FIGURES

Page 

Figure 1. Flow chart of the overall process for issuing directed take permits under 

section 10(a)(1)(A) of the Endangered Species Act (NMFS 2017a)............................................ 18 

Figure 2. Standard otter trawl design (Source: 

http://www.grantontrawlers.com/steam%20trawler.html)............................................................ 34 

Figure 3. Direct carapace attachment on leatherback. Photo courtesy of Sandra 

Ferraroli, Centre National de la Recherche Scientifique. ............................................................. 46 

Figure 4. Average Annual Authorized and Reported Takes of Sea Turtles, June 

2007 through May 2017 (NMFS 2017a). ..................................................................................... 50 

Figure 5. Scope of the action area of research in the Pacific Ocean (shaded area), 

including United States territories. ............................................................................................... 58 

Figure 6. Scope of the action area of research in the Atlantic Ocean (shaded area), 

including the Gulf of Mexico, and Caribbean waters. .................................................................. 59 

Figure 7. Map depicting range and distinct population segment boundaries for 

green turtles................................................................................................................................... 81 

Figure 8. Green sea turtle. Photos: Mark Sullivan, NOAA (left), Andy Bruckner, 

NOAA (right)................................................................................................................................ 81 

Figure 9. Map of all Chelonia mydas nesting sites indicating delineation of 

distinct population segments (Seminoff et al. 2015). ................................................................... 87 

Figure 10. Close up of nesting distribution of green turtles in the western North 

Atlantic distinct population segment (water body labeled ‘1’). Size of circles 

indicates estimated nester abundance. Locations marked with an ‘x’ indicate sites 

lacking abundance information (Seminoff et al. 2015). ............................................................... 88 

Figure 11. Nesting distribution of green turtles in the South Atlantic distinct 

population segment (water body labeled ‘3’). Size of circles indicates estimated 

nester abundance. Locations marked with an ‘x’ indicate sites lacking abundance 

information (Seminoff et al. 2015). .............................................................................................. 89 

Figure 12. Nesting distribution of green turtles in the East Indian-West Pacific 

distinct population segment (water body labeled ‘6’). Size of circles indicates 

estimated nester abundance. Locations marked with an ‘x’ indicate sites lacking 

abundance information (Seminoff et al. 2015). ............................................................................ 90 

Figure 13. Nesting distribution of green turtles in the Central West Pacific distinct 

population segment (water body labeled ‘7’). Size of circles indicates estimated 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

nester abundance. Locations marked with an ‘x’ indicate sites lacking abundance 

information (Seminoff et al. 2015). .............................................................................................. 91 

Figure 14. Nesting distribution of green turtles in the Southwest Pacific distinct 

population segment (water body labeled ‘8’). Size of circles indicates estimated 

nester abundance. Locations marked with an ‘x’ indicate sites lacking abundance 

information (Seminoff et al. 2015). .............................................................................................. 92 

Figure 15. Nesting distribution of green turtles in the Central South Pacific 

distinct population segment (water body labeled ‘9’). Size of circles indicates 

estimated nester abundance. Locations marked with an ‘x’ indicate sites lacking 

abundance information (Seminoff et al. 2015). ............................................................................ 93 

Figure 16. Nesting distribution of green turtles in the Central North Pacific 

distinct population segment (water body labeled ‘10’). Size of circles indicates 

estimated nester abundance (Seminoff et al. 2015). ..................................................................... 94 

Figure 17. Nesting distribution of green turtles in the East Pacific distinct 

population segment (water body labeled ‘11’). Size of circles indicates estimated 

nester abundance. Locations marked with an ‘x’ indicate sites lacking abundance 

information (Seminoff et al. 2015). .............................................................................................. 95 

Figure 18. Map depicting green turtle designated critical habitat in Culebra Island, 

Puerto Rico.................................................................................................................................... 98 

Figure 19. Map identifying the range of the endangered hawksbill sea turtle.............................. 99 

Figure 20. Hawksbill sea turtle. Photos: Tom Moore, NOAA (left), Jordan 

Wilkerson (right)........................................................................................................................... 99 

Figure 21. Map depicting hawksbill sea turtle critical habitat; the coastal waters 

surrounding Mona and Monito Islands, Puerto Rico.................................................................. 102 

Figure 22. Map identifying the range of the Kemp’s ridley sea turtle........................................ 103 

Figure 23. Kemp’s ridley sea turtle. Photos: National Oceanic and Atmospheric 

Administration (left), National Park Service (right)................................................................... 104 

Figure 24. Map identifying the range of the leatherback sea turtle with the seven 

subpopulations and nesting sites. Adapted from (Wallace et al. 2010a). ................................... 106 

Figure 25. Leatherback sea turtle adult and hatchling. Photos: R. Tapilatu (left), 

N. Pilcher (right). ........................................................................................................................ 107 

Figure 26. Map depicting leatherback sea turtle designated critical habitat in the 

United States Virgin Islands. ...................................................................................................... 110 

Figure 27. Map depicting leatherback sea turtle designated critical habitat along 

the United States Pacific coast.................................................................................................... 111 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Figure 28. Map identifying the range and distinct population segment boundaries 

of the loggerhead sea turtle......................................................................................................... 112 

Figure 29. Loggerhead sea turtle. Photos: National Oceanic and Atmospheric 

Administration (left), Marco Giuliano, Fondazione Cetacea (right). ......................................... 113 

Figure 30. Map depicting loggerhead turtle designated critical habitat...................................... 121 

Figure 31. Map identifying the range of the olive ridley sea turtle. ........................................... 122 

Figure 32. Olive ridley sea turtle. Photo: Reuven Walder (left), Michael Jensen 

(right). ......................................................................................................................................... 122 

Figure 33. Atlantic salmon. Photo: William Hartley, United States Fish and 

Wildlife Service (left), Betty Holmes, NOAA Northeast Fisheries Science Center 

(right). ......................................................................................................................................... 127 

Figure 34. Map identifying the range of Gulf of Maine Atlantic salmon................................... 128 

Figure 35. Smalltooth sawfish. Photo: Florida Museum of Natural History (left), 

R. Dean Grubbs (right). .............................................................................................................. 131 

Figure 36. Smalltooth sawfish range and designated critical habitat.......................................... 132 

Figure 37. Atlantic sturgeon. Photo: Robert Michelson (left), NOAA (right). .......................... 135 

Figure 38. Range and boundaries of the five Atlantic sturgeon Distinct Population 

Segments..................................................................................................................................... 136 

Figure 39. Shortnose sturgeon. Photo: Nancy Haley, NOAA (left), University of 

Maine (right). .............................................................................................................................. 143 

Figure 40. Geographic range of shortnose sturgeon. .................................................................. 145 

Figure 41. Adult green sturgeon. Photo: Thomas Dunklin......................................................... 149 

Figure 42. Geographic range (within the contiguous US) and designated critical 

habitat for green sturgeon, southern distinct population segment. ............................................. 150 

Figure 43. Geographic range and designated critical habitat of the Gulf sturgeon. ................... 153 

Figure 44. Nassau grouper. Photo: C. Dahlgren ......................................................................... 156 

Figure 45. Map identifying the range of the Nassau grouper. From NMFS 

Biological Report (NMFS 2013). ............................................................................................... 156 

Figure 46. Scalloped hammerhead shark. Photo: NOAA (left), Brian Skerry, 

National Geographic (right)........................................................................................................ 160 

Figure 47. Map depicting the distinct population segments for the scalloped 

hammerhead shark. ..................................................................................................................... 161 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Figure 48. Frequency of Capture Methods Authorized in Sea Turtle Research 

Permits from June 2007 to May 2017 (N = 43 permits)............................................................. 194 

Figure 49. Map of global documented bycatch records of sea turtles from 1990 to 

2008, across gillnets, longlines, and trawls where bycatch intensity of each record 

is ranked from high (red) to low (blue). Symbol size corresponds to the amount of 

fishing effort for each data record (Lewison et al. 2013). .......................................................... 203 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

1 INTRODUCTION 

The Endangered Species Act of 1973, as amended (ESA; 16 U.S.C. §1531 et seq.) establishes a 

national program for conserving threatened and endangered species of fish, wildlife, plants, and 

the habitat they depend on. Section 7(a)(2) of the ESA requires Federal agencies to insure that 

any actions they authorize, fund or carry out are not likely to jeopardize the continued existence 

of endangered or threatened species or adversely modify or destroy their designated critical 

habitat. Federal agencies must do so in consultation with the National Marine Fisheries Service 

(NMFS) for threatened or endangered species (i.e., ESA-listed), or designated critical habitat that 

may be affected by the action that are under NMFS jurisdiction (50 C.F.R. §402.14(a)). If a 

Federal action agency determines that an action “may affect, but is not likely to adversely affect” 

endangered species, threatened species, or designated critical habitat under NMFS jurisdiction 

and NMFS, concurs with that determination, consultation concludes informally (50 CFR 

§402.14(b)). 

The Federal action agency shall confer with the NMFS for species under NMFS jurisdiction on 

any action which is likely to jeopardize the continued existence of any proposed species or result 

in the destruction or adverse modification of proposed critical habitat (50 CFR §402.10). If 

requested by the Federal agency and deemed appropriate, the conference may be conducted in 

accordance with the procedures for formal consultation in §402.14. 

Section 7(b)(3) of the ESA requires that at the conclusion of consultation (or conference) NMFS 

provides an opinion stating whether the Federal agency’s action is likely to jeopardize ESAlisted species (or species proposed for listing) or destroy or adversely modify their designated (or 

proposed) critical habitat. If NMFS determines that the action is likely to jeopardize ESA-listed 

species or destroy or adversely modify critical habitat, NMFS provides a reasonable and prudent 

alternative that allows the action to proceed in compliance with section 7(a)(2) of the ESA. If an 

incidental take is expected, section 7(b)(4) of the ESA requires NMFS to provide an incidental 

take statement (ITS) that specifies the impact of any incidental taking and includes reasonable 

and prudent measures to minimize such impacts and terms and conditions to implement the 

reasonable and prudent measures. 

The action agency for this consultation is NMFS, Office of Protected Resources (OPR), Permits 

and Conservation Division (hereafter referred to as the Permits Division). The Permits Division 

proposes to implement a program for the issuance of permits for research and enhancement 

activities on ESA-listed sea turtles. 

Consultation in accordance with section 7(a)(2) of the ESA, associated implementing regulations 

(50 C.F.R. §402), and agency policy and guidance was conducted by the NMFS OPR ESA 

Interagency Cooperation Division (hereafter referred to as the Interagency Cooperation 

Division). This biological and conference opinion (opinion) and ITS were prepared by the 

Interagency Cooperation Division in accordance with section 7(b) of the ESA and implementing 

regulations at 50 CFR §402. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

This document represents NMFS’s opinion on the effects of these actions on endangered and 

threatened species and designated critical habitat for those species. A complete record of this 

consultation is on file at the NMFS OPR in Silver Spring, Maryland. 

1.1 Background 

The ESA mandates the protection and conservation of threatened and endangered species, and 

prohibits the taking0 F

1

, import, and export of these species, with limited exceptions for scientific 

research and enhancement of propagation or survival, pursuant to ESA section 10(a)(1)(A) and 

its implementing regulations (50 CFR §222). 

The Permits Division issues 10(a)(1)(A) permits authorizing activities that result in either 

directed take or incidental take of other ESA-listed species (i.e., not the targeted research 

species). Since 1977, NMFS and the U.S. Fish and Wildlife Service (USFWS) have shared 

jurisdiction for the recovery and conservation of sea turtles listed under the ESA as codified in 

regulations at 50 CFR 222.309. NMFS leads the conservation and recovery of sea turtles in the 

marine environment, and the USFWS has the lead for the conservation and recovery of sea 

turtles in the terrestrial environment including nesting beaches and rehabilitation facilities. 

Hence, the Permits Division processes and manages permits for research on sea turtles when they 

are in the marine environment, from when they enter the sea as post-hatchlings through adult life 

stages. This includes permitting the temporary holding and transport of sea turtles taken in the 

water to a land-based facility for research procedures, before returning the animal to the marine 

environment near the point of capture. 

Since January 1, 2005, approximately 103 scientific research and enhancement permits have 

been issued by the Permits Division. At present there are 41 existing section 10(a)(1)(A) 

scientific research permits issued by the Permits Division for sea turtles (NMFS 2017a). Sea 

turtle research permits often use similar techniques and research activities which have been 

modified over time to improve the scientific understanding of sea turtle biology and ecology. 

Adjustments in research techniques have also been made to reduce adverse impacts to sea turtles 

being researched. Considering the large number of individual permits, including the section 

7(a)(2) consultations over a substantial number of years, NMFS high level of understanding of 

the potential effects to sea turtles under a variety of research techniques, and the workload to 

consider and issue permits individually, the Permits Division has proposed to implement a new 

sea turtle research and enhancement permitting program (hereafter referred to as the Program). 

The Program would set an annual permit cycle, fixed reporting schedule, programmatic mortality 

1 “Take” under the ESA means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to 

attempt to engage in any such conduct (§4(19)). "Harass” is further defined as an act that “creates the likelihood of 

injury to wildlife by annoying it to such an extent as to significantly disrupt normal behavioral patterns which 

include, but are not limited to, breeding, feeding, or sheltering” (NMFSPD 02-110-19). 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

limits for the lethal take of sea turtles, programmatic incidental take limits for the take of nontarget ESA-listed species, and the ability to issue individual permits for up to ten years (NMFS 

2017a). Evaluating all permits at the same time each year and having a programmatic 

consultation in place is expected to: 1) enhances species conservation and management via a 

holistic assessments of impacts which should minimize impacts to species from duplication of 

research effort, 2) reduces the Permits Division processing time for scientific research and 

enhancement permit applications, and 3) create efficiency by consolidating multiple section 7 

consultations into one programmatic process. 

The Permits Division requested a formal programmatic ESA section 7 consultation to ensure that 

the Program is not likely to jeopardize ESA-listed species or to destroy or adversely modify 

designated critical habitat. 

1.2 Consultation History 

This opinion is based on information obtained from (1) the NMFS Permits Division biological 

assessment (BA), and supporting documents, on the implementation of a permitting program for 

the issuance of permits for research activities on ESA-listed sea turtles, (2) correspondence and 

discussions between the Permits Division and the Interagency Cooperation Division, and (3) the 

available scientific information for analyzing the effects of the proposed action on ESA-listed 

species. Our communication with the Permits Division regarding this consultation is summarized 

as follows: 

• April 28, 2016: The Permits Division and the Interagency Cooperation Division finalized 

an internal NMFS document titled Terms of Reference for ESA section 7 Programmatic 

Consultations on the Scientific Research and Enhancement Permitting Program. 

• September 28, 2017: The Permits Division submitted a sea turtle programmatic 

consultation initiation package (including the BA and supporting documents) to the 

Interagency Cooperation Division. 

• October 30, 2017: The Permits Division requested adding three distinct population 

segments (DPSs) (East Indian-West Pacific and Southwest Pacific green turtle and South 

Pacific loggerhead) to the consultation based on new information. 

• November 1, 2017: The Interagency Cooperation Division responded with an email 

indicating that they agreed with the addition of the three sea turtle DPSs mentioned 

above. 

• November 3, 2017: In an email to the Permits Division, the Interagency Cooperation 

Division recommended conferencing on the recently proposed critical habitat for the 

main Hawaiian islands insular DPS of false killer whale. The Permits Division responded 

that they agreed to conferencing on this proposed critical habitat as part of the 

programmatic consultation. 

• November 2, 2017: The Interagency Cooperation Division and Permits Division met to 

discuss the major issues with the draft BA. Discussion revolved around three main issues: 

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(1) estimating delayed (unobserved) sea turtle mortality, (2) the effects of trawling as a 

sea turtle capture method, and (3) the Program sunset date (i.e., 20 years). 

• November 14, 2017: The Interagency Cooperation Division and Permits Division met to 

discuss minor issues and requests for clarification with the draft BA. Agreement was 

reached on all points raised. Agreement was also reached on removal of the Program 

sunset date. 

• November 15, 2017: The Permits Division emailed the Interagency Cooperation 

Division requesting the addition of turtle research procedures involving acoustics to the 

Program. These include studies of Auditory Evoked Potential (AEP) and Acoustic 

Deterrent Devices (ADD) to reduce sea turtle bycatch in fishing gear. 

• November 21, 2017: In a meeting, the Interagency Cooperation Division indicated that 

adding the requested acoustics research would delay the completion of the consultation 

substantially because of the additional time and analysis needed to consider acoustic 

effects. The Permits Division agreed to address acoustic research either separately or as a 

reinitiation of this consultation Program at a later date. 

• November 21, 2017: The Permits Division provided a written response to the 

Interagency Cooperation Division regarding the issues with the BA that were raised 

during the November 2, 2017 meeting (see above). The Permits Division reiterated the 

rationale for the estimated delayed mortality rate and assessment of the effects of 

research trawling on sea turtles provide in the BA. 

• November 21, 2017: The Interagency Cooperation Division officially accepted the 

initiation package, including supplementary information provided and program changes 

agreed to after BA submittal. The Interagency Cooperation Division notified the Permits 

Division that formal consultation has been initiated in a memo titled “Initiation of formal 

consultation pursuant to section 7 of the ESA on a proposed sea turtle research and 

enhancement permitting program.” 

• November 28, 2017: The Interagency Cooperation Division provided the Permits 

Division with the Description of Action and Action Area sections of the draft opinion, 

and a draft incidental take table for non-target ESA-listed species, for review. 

• December 13, 2017: The Interagency Cooperation Division provided the Permits 

Division with a revised draft ITS, including incidental take of sea turtles, for review. The 

Interagency Cooperation Division also requested minor additional information. 

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2 THE ASSESSMENT FRAMEWORK 

Section 7(a)(2) of the ESA requires Federal agencies, in consultation with NMFS, to ensure that 

their actions are not likely to jeopardize the continued existence of endangered or threatened 

species; or adversely modify or destroy their designated critical habitat. 

“Jeopardize the continued existence of” means to engage in an action that reasonably would be 

expected, directly or indirectly, to appreciably reduce the likelihood of both the survival and 

recovery of an ESA-listed species in the wild by reducing the reproduction, numbers, or 

distribution of that species” (50 C.F.R. §402.02). “Destruction or adverse modification” means a 

direct or indirect alteration that appreciably diminishes the value of designated critical habitat for 

the conservation of an ESA-listed species. Such alterations may include, but are not limited to, 

those that alter the physical or biological features essential to the conservation of a species or that 

preclude or significantly delay development of such features (50 C.F.R. §402.02). An ESA 

section 7 assessment involves the following steps: 

1. We describe the proposed action and those aspects (or stressors) of the proposed action 

that may have direct or indirect effects on the physical, chemical, and biotic 

environment within the action area, including the spatial and temporal extent of those 

stressors. We identify any interrelated and interdependent actions. 

2. We identify the ESA-listed species and designated critical habitat that are likely to cooccur with those stressors in space and time. 

3. We describe the environmental baseline in the action area including: past and present 

impacts of Federal, state, or private actions and other human activities in the action 

area; anticipated impacts of proposed Federal projects that have already undergone 

formal or early section 7 consultation, impacts of state or private actions that are 

contemporaneous with the consultation in process. 

4. We identify the number, age (or life stage), and gender of ESA-listed individuals that 

are likely to be exposed to the stressors and the populations or subpopulations to 

which those individuals belong. We also consider whether the action “may affect” 

designated critical habitat. This is our exposure analysis. 

5. We evaluate the available evidence to determine how individuals of those ESA-listed 

species are likely to respond given their probable exposure. We also consider how the 

action may affect designated critical habitat. This is our response analyses. 

6. We assess the consequences of these responses of individuals that are likely to be 

exposed to the populations those individuals represent, and the species those 

populations comprise. This is our risk analysis. 

7. The adverse modification analysis considers the impacts of the proposed action on the 

essential habitat features and conservation value of designated critical habitat. 

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8. We describe any cumulative effects of the proposed action in the action area. 

Cumulative effects, as defined in our implementing regulations (50 CFR §402.02), are 

the effects of future state or private activities, not involving Federal activities, that are 

reasonably certain to occur within the action area. Future Federal actions that are 

unrelated to the proposed action are not considered because they require separate 

section 7 consultation. 

9. We integrate and synthesize the above factors by considering the effects of the action 

to the environmental baseline and the cumulative effects to determine whether the 

action could reasonably be expected to: 

a) Appreciably reduce the likelihood of both survival and recovery of the ESA-listed 

species in the wild by reducing its numbers, reproduction, or distribution; or 

b) Reduce the conservation value of designated or proposed critical habitat. These 

assessments are made in full consideration of the status of the species and critical 

habitat. 

10. We state our conclusions regarding jeopardy and the destruction or adverse 

modification of designated critical habitat. 

If, in completing the last step in the analysis, we determine that the action under consultation is 

likely to jeopardize the continued existence of ESA-listed species or destroy or adversely modify 

designated critical habitat, then we must identify reasonable and prudent alternative(s) to the 

action, if any, or indicate that to the best of our knowledge there are no reasonable and prudent 

alternatives (50 C.F.R. §402.14). 

In addition, we include an ITS that specifies the impact of the take, reasonable and prudent 

measures to minimize the impact of the take, and terms and conditions to implement the 

reasonable and prudent measures (ESA section 7 (b)(4); 50 C.F.R. §402.14(i)). We also provide 

discretionary conservation recommendations that may be implemented by the action agency (50 

C.F.R. §402.14(j)). Finally, we identify the circumstances in which reinitiation of consultation is 

required (50 C.F.R. §402.16). 

To comply with our requirement to use the best scientific and commercial information available 

we conducted electronic and manual searches to identify information relevant to the potential 

stressors and responses of the sea turtles and other ESA-listed species that may be affected by the 

proposed action. Sources included journal articles, published reports, grey literature, internet 

sites, unpublished data, and personal communications. This information was evaluated to draw 

conclusions about the likely risks to the continued existence of these species and the 

conservation value of their designated critical habitat. 

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3 DESCRIPTION OF THE PROPOSED ACTION 

“Action” means all activities or programs of any kind authorized, funded, or carried out, in 

whole or in part, by federal agencies. The Permits Division has requested programmatic 

consultation on a Program for the issuance of research and enhancement permits for ESA-listed 

sea turtles. There is no sunset date on the Program. The Program combines elements from the 

existing approach for issuing sea turtle permits with elements that are completely new. Both the 

existing and the new features of the Program are identified and discussed in this section of the 

opinion, which is organized as follows: (1) overall process for issuing and managing directed 

take permits under section 10(a)(1)(A) of the ESA; (2) directed take permit terms and conditions 

applicable via regulation to all permits; (3) annual sea turtle permit cycle; (4) research activities 

and associated mitigation measures that will be authorized as part of the Program; (5) approach 

for processing applications and authorizing take under the Program; (6) approach for monitoring 

the effects of permitting sea turtle research; (7) the Permits Division internal program review and 

adaptive management approach; and (8) requirements for reporting on the Program to the 

Interagency Cooperation Division. 

3.1 Overall Process for Issuing Sea Turtle Directed Take Permits 

The Permits Division’s mission is to “protect and conserve marine mammals and threatened and 

endangered species by providing special exceptions for take, import, and export that maximize 

recovery value and minimize individual and cumulative impacts as directed under ESA section 

10(a)(1)(A) and its regulations” (NMFS 2017a). Permits issued pursuant to section 10(a)(1)(A) 

of the ESA must be for activities that are likely to further the conservation of the affected species 

with the ultimate goal of bringing the species to the point where listing under the ESA is no 

longer necessary. The overall process that the Permits Division follows for issuance of section 

10(a)(1)(A) permits is shown in Figure 1. 

Section 10(d) of the ESA and implementing regulations at 50 CFR 222 identify the following 

criteria specific to issuance or modification of research and enhancement permits: 

• Whether the permit was applied for in good faith 

• Whether the permit, if granted and exercised, will not operate to the disadvantage of such 

endangered species 

• Whether the permit would be consistent with the purposes and policy set forth in section 

2 of the ESA (i.e., providing a means to conserve endangered and threatened species’ 

ecosystems and providing programs for the conservation of such species 

Applicants seeking a section 10(a)(1)(A) permit must submit an application to NMFS the 

Permits Division. The ESA and NMFS implementing regulations establish information 

requirements for permit applicants. The Permits Division’s ESA section 10(a)(1)(A) application 

instructions for research and enhancement permits are provided in Appendix A. The applicant 

must provide sufficient information about the activity to allow NMFS to determine whether 

17 
Figure 1. Flow chart of the overall process for issuing directed take permits under 

section 10(a)(1)(A) of the Endangered Species Act (NMFS 2017a). 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

permit issuance would comply with all applicable statutory and regulatory issuance criteria and 

to assess the potential environmental impacts of permit issuance. Permit applications must 

include a discussion of how the proposed activities and resulting information will promote the 

conservation and recovery of ESA-listed species. 

To complete their application researchers need to address the following specific questions: 

• How the action will enhance or benefit the wild population/species 

• Whether the project has broader significance beyond the applicant’s goals 

• Why the work must take an ESA-listed species 

• How research is bona fide and likely to be published in a refereed scientific journal 

• How the work will contribute to understanding the species’ biology or ecology, 

contribute to identified objectives of a species’ recovery plan or otherwise respond to 

recommendations of a scientific body charged with management of the species, and 

contribute significantly to identifying, evaluating, or resolving conservation problems 

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• For enhancement, how the work will enhance the health the survival, conservation, and 

recovery of the species in the wild, or will enhance the propagation of the species for 

conservation and recovery purposes 

• How the research is not unnecessarily duplicative of other work 

• The anticipated effects of the activities to protected species 

• How the applicant will minimize impacts of the activities, in particular mortality 

• How the applicant will coordinate activities with other Permit Holders 

Applicants are encouraged to link research objectives to priorities identified in NMFS ESA-listed 

species recovery plans. Examples of objectives in research permits that are tied to sea turtle 

recovery plan objectives include: 

• Improve in-water abundance estimates of sea turtles; 

• Document the presence and progression of fibropapillomatosis (FP) disease in sea turtle 

populations; 

• Determine distribution and seasonal movements for all life stages; 

• Evaluate growth rates and determine age at sexual maturity; 

• Identify important marine habitats; 

• Determine breeding population origins for U.S. juvenile and subadult populations; 

• Implement large-scale in-water surveys to estimate indices of abundance and determine 

trends; 

• Assess, categorize, and map neritic habitats used by sea turtles; and 

• Develop gear modifications to prevent or minimize interactions with fishing gear. 

Permit applications that satisfy some but not all of the applicable criteria for permit issuance are 

returned to the applicant with an explanation of the deficiencies. Applicants then have 60 days to 

provide the deficient information to the Permits Division. The permit process cannot proceed 

further until the Permits Division has the necessary information to complete the application. 

Once a complete application has been received, the Permits Division reviews to determine all 

listed species that may be affected (directly or indirectly) by the research or enhancement 

activities and the nature of the effects. As part of the Program, the Permits Division will carefully 

review requested sea turtle take numbers and researcher qualifications, especially for activities 

that have an associated risk of mortality. For sea turtle permits, these include capture in trawl and 

pound net gear and procedures that require the use of general anesthesia, including certain 

imaging methods and laparoscopy. Permits Division analysts will be looking for applicants to 

demonstrate how they will minimize impacts from riskier procedures by including details such 

as: 1) how gear will be deployed and monitored; 2) whether a sea turtle veterinarian is identified 

that can perform or directly supervise the activities requiring medical credentials; and 3) 

inclusion of a veterinary-approved protocol for all medical procedures. 

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In the past, section 7(a)(2) consultations between the Permits Division and the Interagency 

Cooperation Division for sea turtle research permits were conducted either on individual section 

10 (a)(1)(A) permits or on several similar permits combined (i.e., “batched consultation”). Under 

the Program, the Permits Division will be responsible for ensuring that submitted permit 

applications that fall within the scope of this consultation are processed in accordance with the 

requirements of the opinion. Applications whose scope (area, activities, nature, etc.) or take 

levels fall outside the Program parameters will be processed separately. The Permits Division 

will seek individual consultation with the Interagency Cooperation Division for such permit 

requests. An example of such a request is gear modification research conducted by NMFS 

Science Centers that requires fishing gear be operated for tow times or at depths exceeding the 

limits specified for the Program. 

The Permits Division sends permit applications out for scientific review and publishes a Notice 

of Receipt in the Federal Register to begin a mandatory 30-day public review and comment 

period. NMFS may extend the comment period and hold public hearings on the application if 

deemed necessary. The Permits Division distributes research permit applications to several 

reviewers, who may include the NMFS Office of Law Enforcement, state agencies, and 

appropriate NMFS scientists and other federal agencies. After the close of the public comment 

period, the Permits Division reviews all comments received from reviewers and the public, and 

all substantive comments are addressed by either the Permits Division or the applicant. The 

Permits Division then re-evaluates the issuance criteria for each permit in consideration of 

comments received and responses from the applicant, and makes a final recommendation to the 

OPR Office Director on whether to issue or deny the permit. The Permits Division will use a 

checklist (Appendix B) to document whether an application does or does not meet ESA issuance 

criteria and the other requirements discussed above. 

If the permit is issued, a Federal Register Notice of Issuance is published within ten days, and the 

permit holder must date and sign the permit and return a copy of the signature page to the 

Permits Division as certification of their acceptance of the permit terms and conditions (50 CFR 

222.303). If the permit is denied, the OPR Office Director must provide the applicant with an 

explanation for the denial (50 CFR 222.303). The applicant or any party opposed to a permit may 

seek judicial review of the terms and conditions of such permit or of a decision to deny such 

permit. Review may be obtained by filing a petition for review with the appropriate U.S. District 

Court as provided for by law (50 CFR 222.303). 

3.2 General Permit Terms and Conditions 

As stated in the Permits Division’s ESA permit template (Appendix C), activities authorized in a 

permit must occur by the means, in the areas, and for the purposes set forth in the permit 

application, and are limited by the terms and conditions in a permit. Permit noncompliance 

constitutes a violation of the ESA and may be grounds for permit modification, suspension, or 

revocation, and for enforcement action. A description of the general terms and conditions 

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common to permits issued by the Permits Division for all species is provided here. Additional 

terms and conditions specific to permits issued under the Program are described in the sections to 

follow. 

All research and enhancement permits contain terms and conditions that address the following: 

• Duration of permit 

• Number and kinds of protected species, locations, and manner of taking 

• Qualifications, responsibilities, and designation of personnel 

• Possession of permit 

• Reports 

• Notification and coordination 

• Observers and inspections 

• Permit modification, suspension, and revocation 

• Penalties and permit sanctions 

• Acceptance of permit 

3.2.1.1 Duration of Permits (50 CFR 222.304) 

Each permit specifies an expiration date. Historically the Permits Division has issued ESA 

permits for up to five years, although the ESA does not limit the duration of a permit. As part of 

the Program the Permits Division may issue ESA permits for up to ten years. A permit may be 

extended if the applicant has submitted a new application for work of a continuing nature (50 

CFR 222.304). A Permit Holder operating under an extension may continue such activities as 

were authorized by the permit until a decision has been made on the renewal application. To 

ensure that environmental analyses prepared for issuance of the permit under the ESA and the 

National Environmental Policy Act (NEPA) remain valid in extending the permit, the Permits 

Division conditions the extension such that no additional take of species is authorized over the 

life of the extension. Rather, the extension allows the Permit Holder to continue take of ESAlisted species authorized in the last year of the permit over an additional 12 months or until the 

Permit Holder has reached the take limit in the last year of the permit. The permit also clarifies 

that the Permit Holder may continue to possess biological samples of the target species acquired 

under the permit after permit expiration without additional written authorization. 

3.2.1.2 Number and Kinds of Protected Species, Locations and Manner of Taking (50 CFR 

216.36, 222.301(e), and 222.308(d)) 

Each permit contains a table outlining the number of animals authorized to be taken (by species 

and listing unit), and the locations, manner, and time frame in which they may be taken. In 

addition, authorized personnel working under a permit may take photographs and video 

incidental to research or enhancement provided it does not result in take not authorized by the 

permit. 

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3.2.1.3 Qualifications, Responsibilities, and Designation of Personnel (50 CFR 216.3, 

216.35(f-i), 216.36, and 216.41(c)(iii) and (iv)) 

All research and enhancement permits identify by name the researchers (Principal Investigator 

[PI] and Co-investigators [CIs]) authorized to direct and supervise the permitted activities. 

Individuals conducting permitted activities must possess qualifications commensurate with their 

roles and responsibilities. The roles and responsibilities of personnel operating under a permit are 

as follows: 

• The Permit Holder is ultimately responsible for activities of individuals operating under 

the permit. Where the Permit Holder is an institution, the Responsible Party is the person 

at the institution who is responsible for the supervision of the PI. 

• The PI is the individual primarily responsible for the taking, import, export, and related 

activities conducted under the permit. The PI must be on site during activities conducted 

under this permit unless a CI is present to act in place of the PI. 

• CIs are individuals who are qualified to conduct activities authorized by the permit 

without the onsite supervision of the PI. CIs assume the role and responsibility of the PI 

in the PI’s absence. 

• Research Assistants work under the direct and on site supervision of the PI or CI. They 

cannot conduct permitted activities in the absence of the PI or CI and are not named in 

the permit. 

• Specific to sea turtle applications, the applicant must also identify a 24-hr on-call 

veterinarian (with sea turtle experience) and local permitted rehabilitation facility that 

researchers can contact in the event of an emergency during field activities. 

Personnel involved in permitted activities must be reasonable in number and essential to the 

conduct of the permitted activities. Essential personnel are limited to the following: 

• Individuals who perform a function directly supportive of and necessary to the permitted 

activity (including operation of vessels or aircraft) 

• Individuals included as backup for essential personnel, and 

• Individuals included for training purposes 

Persons who require state or Federal licenses to conduct activities authorized under a permit 

(e.g., veterinarians, pilots) must be duly licensed when undertaking such activities. Permitted 

activities may be conducted on vessels or aircraft or in cooperation with individuals engaged in 

commercial activities, provided the commercial activities are not conducted simultaneously with 

the permitted activities, except with written approval of the Permits Division Chief, such as for a 

news article or documentary film. The Permit Holder cannot require direct or indirect 

compensation from persons requesting to conduct activities under the permit. For permits held by 

NMFS offices, the Permits Division may allow the Responsible Party or PI to designate 

additional CIs and must provide a copy of the letter designating the individual to the Permits 

Division on the day of designation. 

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3.2.1.4 Possession of Permit (50 CFR 216.35(i) and (j), 222.301(d)(1) and (2), 222.305), and 

222.308(d)) 

Permits cannot be transferred or assigned to any other person. The Permit Holder and persons 

operating under the authority of a permit must possess a copy of the permit when engaged in a 

permitted activity. A copy of the permit must be attached to any means of containment in which 

a protected species or protected species part is placed for purposes of storage, transit, supervision 

or care. 

3.2.1.5 Reports (50 CFR 216.38, 216.41(c)(ii), 222.301(h) and (i), and 222.308(d)) 

Permit Holders must submit annual and incident reports, and papers or publications resulting 

from the activities authorized by a permit. Research results must be published or otherwise made 

available to the scientific community in a reasonable period of time. Annual reports must be 

submitted at the conclusion of each year for which a permit is valid, due 30 days after the end of 

each reporting period (either a calendar year or a 12-month period). The Permits Division will 

then have 30 days to review the reports and, if needed, request additional information from 

permit holders. The Permits Division will send reminders to any permit holder who has not sent 

in their report. After an additional 30-day grace period, if the report is not received the permit 

may be suspended until it is received and approved by the Permits Division. The Permits 

Division may take additional measures to ensure that reports are received in a timely manner 

including: (1) Suspending the permit until the report is received and approved by the Permits 

Division. (2) Deferring or returning modification requests for an active permit until the report is 

received, (3) Deferring or returning an application for a new permit until the report is received, 

and (4) Notifying the NMFS Office of Law Enforcement of a permit violation due to failure to 

report. 

As required by conditions of the permit, each annual report must include the following: 

• A table reporting the number of animals taken, by activity and location 

• Observed effects and frequency of effects from permitted activities for target and nontarget animals 

• Problems or unforeseen effects encountered and steps to resolve such problems 

• Discussion of any serious injuries, mortalities, or unauthorized species taken 

• Efforts to conduct post-research monitoring 

• Efforts to coordinate and collaborate with other Permit Holders and NMFS Regional 

Offices 

• Progress to meeting the objectives, including citations of reports, publications resulting 

from the reporting period 

• Additional information as required by the permit on a case-by-case basis to monitor 

impacts of specific activities to animal health, effectiveness of protocols, etc. 

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Appendix D includes the Permits Division’s annual report form, which has been revised to 

improve the Permits Division’s monitoring capabilities and inform other section 7 consultations. 

On a case-by-case basis, the Permits Division may determine that a permit also requires 

additional reporting to closely monitor and evaluate the impacts of specific research procedures. 

This may occur when more information is needed on the potential for harm or injury of a 

research procedure or when new scientific information (reports, publications, presentations, etc.) 

indicates that an activity may warrant closer monitoring for impacts to the target species or other 

portions of the environment. When such a report is required, the permit also will contain a 

requirement for annual reauthorization. In this scenario, the permit is temporarily suspended at 

the end of each permit year (12-month period) and the Permit Holder must report on the work 

that occurred during the year as noted above and any additional monitoring requirements, such as 

re-sighting data, photographs or tag transmissions of target animals, for the Permits Division’s 

review. Based on review of the report, veterinarian and expert opinions as warranted, and 

relevant information from the literature, the Permits Division may modify, discontinue or 

reauthorize the activities under the permit for the next permit year. 

Incident reports are required for any events of serious injury or exceeding take authorized by the 

permit. Incident reports must be submitted within two weeks of the incident and describe the 

events and steps that will be taken to reduce the potential for additional incidents. If the activity 

is not authorized or the Permit Holder reaches their mortality take limit, as required by the 

permit, researchers must immediately cease permitted activities until the Permits Division allows 

the work to resume. The Permits Division reviews the report and facts relevant to the incident, 

such as a necropsy report for mortality, and determines whether the methods and protocols 

and/or permit requirements, such as mitigation measures or take numbers, need to be modified 

before work can resume. 

• After the conclusion of research or permit expiration, the last annual report due for the 

permit must include the above details for annual reports in addition to: 

• Whether the objectives were met and what was learned; 

• An explanation of why objectives were not accomplished, if applicable; 

• A description of how the activities benefited the species, promoted recovery, or 

conserved the target species and fulfilled objectives listed in the recovery or conservation 

plan; and 

• Identification of any additional or improved mitigation measures. 

This information is merged into the annual report form for the last year that a report is due to 

streamline reporting, resulting in a combined annual/final report. 

3.2.1.6 Notification and Coordination 

Permit Holders must provide written notification of planned fieldwork to the applicable NMFS 

Assistant Regional Administrator at least two weeks prior to initiation of a field trip/season and 

must include the locations of the intended field study and/or survey routes, estimated dates of 

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research, and number and roles of participants. Permit Holders must coordinate activities with 

other Permit Holders conducting the same or similar activities on the same species, in the same 

locations, or at the same times of year to avoid unnecessary, repeated disturbance of animals. 

3.2.1.7 Observers and Inspections (50 CFR 216.36, 222.301(g), (i) and (j), and 222.308(d)) 

At the request of NMFS, the Permit Holder must allow an employee of NMFS or another 

designated other person to observe permitted activities. The Permit Holder must provide 

documents or other information relating to the permitted activities upon request. 

3.2.1.8 Modification, Suspension, and Revocation (50 CFR 216.36, 216.39, 216.40, and 

222.306; 15 CFR Part 904 Subpart D) 

Permits are subject to suspension, revocation, modification, and denial in accordance with the 

provisions of subpart D of 15 CFR part 904. The OPR Office Director may modify, suspend, or 

revoke a permit in whole or in part under the following circumstances: 

• To make the permit consistent with a change in the regulations prescribed under section 

103 of the Marine Mammal Protection Act (MMPA) or section 4 of the ESA 

• In a case in which a violation of the terms and conditions of the permit is found 

• In response to a written request from the Permit Holder 

• If NMFS determines that the application or other information pertaining to the permitted 

activities includes false information 

• If NMFS determines that the authorized activities will operate to the disadvantage of 

threatened or endangered species or are otherwise no longer consistent with the purposes 

and policy in section 2 of the ESA 

Permit Holders may also request modifications. Because ESA regulations do not distinguish 

between types of modifications, the Permits Division adopts MMPA regulations defining major 

and minor amendments (50 CFR 216.39) for issuance of ESA and joint ESA/MMPA permits. As 

such, a “major” modification to an ESA permit is a request to change any of the following: 

• The number or type of species to be taken/imported/exported 

• The location where animals are taken/imported/exported 

• The manner in which animals are taken/imported/exported such that it would result in an 

increased level of take or risk of adverse impact 

• Increase the duration for more than 12 months 

Public comment periods are required for major modifications. Minor modifications (e.g., 

modifying tag designs that result in equivalent or lesser impacts) and authorization letters (e.g., 

adding co-investigators) do not require public comment periods. Issuance of a permit does not 

guarantee or imply that NMFS will issue or approve subsequent permits or modifications for the 

same or similar activities including those of a continuing nature, requested by a Permit Holder. 

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3.2.1.9 Penalties and Permit Sanctions (50 CFR 216.36, 216.40(a), 222.301(f), and 222.306(e) 

A person who violates a provision of a permit, the ESA, or the regulations at 50 CFR 216 and 50 

CFR 222-226 is subject to civil and criminal penalties, permit sanctions, and forfeiture as 

authorized under the ESA, and 15 CFR part 904. In addition, per ESA regulation, permits shall 

not be altered, erased, or mutilated, and any permit which has been altered, erased, or mutilated 

shall immediately become invalid. OPR is the sole arbiter of whether a given activity is within 

the scope and bounds of the authorization granted in a permit. The Permit Holder must contact 

the Permits Division for verification before conducting an activity if they are unsure whether an 

activity is within the scope of the permit. Failure to verify, where the Permits Division 

subsequently determines that an activity was outside the scope of the permit, may be used as 

evidence of a violation of the permit, the ESA, and applicable regulations in any enforcement 

actions. 

3.2.1.10 Acceptance of Permit (50 CFR 216.33(e)(3)(i) and (ii)) 

When a permit is issued by signature of the OPR Office Director, the Permit Holder must date 

and sign the permit, and return a copy of the original signature to the Permits Division. The 

permit is effective upon the Permit Holder's signing of the permit. In signing an ESA permit, the 

Permit Holder 

• Agrees to abide by all terms and conditions set forth in the permit, all restrictions and 

relevant regulations under 50 CFR Parts 222-226, and all restrictions and requirements 

under the ESA 

• Acknowledges that the authority to conduct certain activities specified in the permit is 

conditional and subject to authorization by the Office Director 

• Acknowledges that the permit does not relieve the Permit Holder of the responsibility to 

obtain any other permits, or comply with other Federal, State, local, or international laws 

or regulations 

3.3 Annual Permit Cycle 

To date, the Permits Division has processed individual sea turtle research permit requests as they 

are received, batching the processing of requests that have a similar nature and scope where 

possible. However, issuing permits on a case-by-case basis provides less opportunity for 

authorizing and monitoring annual take of ESA-listed species than does a holistic program 

approach. To address this, the Permits Division will implement an annual permit cycle for the 

Program. All of the permit issuance requirements identified above will still apply. Minor permit 

modifications and authorizations, often administrative in nature, that do not increase the risk of 

adverse impacts to the species and can often be processed within a few weeks, will continue to 

be processed throughout the year as they are received. 

The Permits Division will set an application deadline for all sea turtle researchers each year. The 

Permits Division will have six months to (1) review and process all sea turtle research permit 

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requests for the upcoming year, (2) conduct an evaluation of the level of requested take for all 

permits requested for each species, DPS, and life stage, and (3) issue permits authorizing 

research activities and take, as appropriate, following the detailed procedures described herein as 

part of the proposed action. If a permit request is received after the submission deadline, at the 

Permits Division Deputy Division Chief’s discretion, the request may either be merged into the 

batch or the applicant will have to wait until the next permit cycle for the request to be 

processed. This decision will largely be based on the completeness and complexity of the 

request. 

3.4 Sea Turtle Research Activities and Associated Mitigation Measures 

The following is a description of the general activities that may be authorized by the Permits 

Division as part of the Program. The authorized research methods and protocols are commonly 

accepted by the sea turtle research community and have been reviewed by the NMFS National 

Sea Turtle Coordinator and OPR’s Veterinary Medical Officer for effects to sea turtles (NMFS 

2017a). The Permits Division will require mitigation measures to minimize impacts to protected 

species when authorizing sea turtle research activities. Associated mitigation measures for a 

given method are included within the permit template of Appendix C, with species-specific 

conditions beginning at Condition B.5. In addition to these standard protocols, researchers are 

required to consider and describe in their permit application additional precautionary measures 

they can take to further minimize potential impacts of their research on individual sea turtles. 

The Permits Division will seek individual consultation outside the scope of the programmatic for 

methodologies that are not described here or for studies with methods that by design would not 

be able to follow the standard mitigation measures. 

3.4.1 Sea Turtle Parts 

The Permits Division may authorize the collection, receipt or import of sea turtle parts, tissues, 

and carcasses when the source of the part was taken from the marine environment. This may 

include any of the following activities: 

• the import of tissues and parts from the high seas for research purposes when the Permits 

Division is authorizing the initial collection (or take) of the samples from live animals, 

• the development and maintenance of cell lines from sea turtle tissues for future research 

and study, 

• the permanent transfer or receipt of samples for research purposes from other NMFS 

Section 10 permit holders or other legal sources, and 

• the salvage of carcasses or parts when mortality of the animal is authorized under a 

NMFS Section 10(a)(1)(A) permit so that the holder may legally retain the carcass for 

transfer to the Sea Turtle Stranding and Salvage Network (STSSN) for necropsy. 

Because these activities would only involve the use of parts, they are not in and of themselves 

expected to adversely affect any sea turtle populations or species. Applicants are required to 

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demonstrate that the source of the parts (i.e., the original taking from the live animal) was legal 

in cases where the Permits Division is not authorizing the parts collection in conjunction with the 

initial sample collection from live sea turtles. 

3.4.2 Remote Visual and Acoustic Surveys 

As part of the Program, researchers may conduct visual surveys of sea turtles by vessel and 

aircraft to assess habitat and to document seasonal abundance and spatial distribution of sea 

turtle populations. Visual surveys from a vessel may be conducted from large research vessels 

and from smaller motorized vessels. Surveys are typically conducted at slow speeds ranging 

from five to ten knots. Vessel survey activities may include conducting line-transect surveys, or 

temporarily tracking animals from a distance to observe behavior or retrieve short-term 

transmitter attachments once shed. 

Manned aerial surveys predominantly use a twin- or single-engine, fixed high-wing aircraft such, 

as the DeHavilland Twin Otter, or a helicopter, such as the two-bladed, single-engine light utility 

helicopter Robinson R22 or R44. Photographs and video may be taken during flights. Surveys 

are typically flown at 500 feet or higher but may be flown as low as 300 feet depending on the 

type of aircraft, research objectives, and other factors (e.g., weather). Aircraft are flown at speeds 

ranging from 35 to 110 knots. During capture efforts, researchers may conduct aerial line 

transects, and aircraft may act as spotters to guide the capture vessel to the vicinity of turtle 

aggregations. Aerial surveys often involve limited circling (approximately two to three passes) 

from a distance only to verify sightings, although in some instances they may be used for 

activities that require longer observation and/or in closer proximity of target sea turtles. 

Unmanned aircraft system (UAS) surveys may also be authorized as part of the Program. UAS 

units can be fixed wing, such as the Puma AE, or rotary units capable of vertical take-off and 

landing (VTOL), such as the APH-22 hexacopter. The size of UAS units varies from less than 

one meter in diameter for VTOL units to the ten-foot wingspan of the Puma. UAS may be 

launched directly from the capture vessel to search for animals. Once sea turtles are sighted, the 

capture vessel will move to the vicinity of a sighted animal to permit observation and evaluation 

of behavior and condition before attempting capture. The aircraft may repeatedly circle, follow, 

or hover over an animal for an extended period of time to more accurately define and maintain 

its location. For UAS, the time spent over the animal will be limited by the UAS battery life, 

typically 15 to 30 minutes for VTOL units and 45 minutes for fixed wing units based on 

currently available models. Fixed wing UAS are typically operated at 100 feet or higher but 

VTOL units may be flown at lower altitudes of approximately 50 feet to collect images (e.g., 

photogrammetry). 

In cases where the Permits Division would authorize take for potential harassment of sea turtles 

from UAS activities, the applicants must demonstrate that the unit: 

• has an auto-return feature to prevent mid-flight failure and the potential for injury to sea 

turtles; 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

• will be piloted by a trained, qualified crew member; 

• has a ground control station with a trained, dedicated UAS visual monitor working with 

the pilot; and 

• will be operated only within line of sight. 

Remotely operated vehicles (ROVs), including autonomous underwater vehicles (AUVs), may 

also be authorized as part of the Program to closely track sea turtles and observe and record 

foraging and dive behaviors. Models in current use for turtle tracking are approximately two m in 

length and include the Ocean Server Iver II, the Benthos mini-Rover, and the REMUS 100. 

ROVs may be attached to the research vessel by a tether that can be several hundred meters long. 

Tethers would be much too rigid to present a risk of sea turtle entanglement. 

Tracking of animals with an ROV may occur upon sighting a target animal during a vessel 

survey or upon release of a captured animal outfitted with an acoustic transmitter. The ROV is 

deployed from the side of the vessel and maneuvered towards the turtle, maintaining a minimum 

distance of three to five meters. In some instances, two AUVs are deployed together when 

tracking a tagged animal to increase positional resolution of its location. AUVs are outfitted with 

sensors to detect acoustic tag transmissions and are able to then alter their path in order to follow 

a moving transmitter. The AUVs process these detections to position the acoustic tag in threedimensional space with a resolution of less than 10 meters over 30 times a minute. Working in 

tandem to increase the spatial resolution, the AUVs can communicate through an acoustic 

transducer to plan movements and exchange information. When using two units, to minimize 

influence on turtle behavior, the AUVs are programmed to not get within 15 meters of the 

estimated turtle location. This distance may vary depending on the study objectives and 

capabilities (e.g., sensors) of the unit. AUVs may be operated underwater or at the surface to 

allow for visual monitoring of their positions from the research vessel. Tracking may occur for 

ten hours or more depending on ROV battery life or turtle tag attachment duration. Throughout 

tracking operations, researchers may deploy a directional hydrophone over the side of the vessel 

monitoring the AUVs to constantly monitor the approximate location of the tagged turtle in 

reference to the AUVs. This will ensure that the AUVs do not lose the acoustically tagged turtle 

and that the AUVs are maintaining the programmed buffer distance. 

Other methods of remote detection of sea turtles that would be authorized in the Program are 

multibeam, side-scan, and imaging sonars (e.g., DIDSON). Vessels deploying these devices 

operate at low speeds (two to seven knots). High-frequency sound pulses (120 kilohertz (kHz) to 

1.8 megahertz (MHz) are transmitted by the sonar transducers and reflect off the seafloor and 

objects in the water column, producing real-time acoustic backscatter images of bottom 

topography and location of sea turtles in the study area. When testing the effectiveness of a 

particular type of acoustic gear for detecting and/or imaging sea turtles, turtles may be followed 

at a distance once they are detected, to keep them within the acoustic beam. The duration of this 

type of directed acoustic effort typically does not exceed five to ten minutes. 

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3.4.3 Capture and Collection Methods 

Researchers use a variety of sampling methods and techniques for capturing sea turtles. Capture 

methods for sea turtles include selective methods that are only likely to result in the capture of 

the target animals, and non-selective netting methods (e.g., trawls and entanglement nets) that 

may also result in capture of non-target species. The most commonly authorized sea turtle 

capture methods are by hand, dip net, and entanglement net; other methods are authorized less 

frequently. Sea turtle researchers typically request a combination of capture methods in their 

permit applications. Individual turtles may be targeted for recapture over the course of a field 

season or in subsequent years based on the study objectives (e.g., monitoring of health, life 

history studies, etc.) or to remove transmitters. This section describes the currently available 

capture methods that the Permits Division may authorize as part of the Program. Future 

improvements in capture methods over time will be evaluated and incorporated into the Program 

provided that (1) they do not increase the risk to listed species (target and non-target) or critical 

habitat above the level considered in this consultation and (2) the Permit Holder can adhere to 

the standard mitigation measures for these methods provided in Appendix C. 

There are a number of standard practices that minimize risk of injury upon capture that generally 

apply to all authorized sea turtle capture methods. For examples, turtles are fully supported 

during lifting by hand or within nets to prevent injurious distribution of weight or stress on the 

neck and appendages. Sea turtles typically are boarded through the lowest point in the gunwale 

or other area of the vessel unless fully supported within a net. Some capture vessels are modified 

(e.g., with cut-outs in the gunwale or modified bows or sterns) to facilitate boarding. Once on 

board the vessel turtles are placed onto cushioned surfaces to prevent injury. Other mitigation 

measures associated with capture using particular methods are described in more detail below. 

3.4.3.1 Hand Capture 

Most hand-capture techniques fall into one of three categories: those in which boats are directly 

involved in the pursuit and capture; those in which barrier nets of some kind are used; and those 

involving the use of SCUBA and/or snorkeling gear (Ehrhart and Ogren 1999). There are 

variations in the specific capture technique under different conditions and vessel configurations. 

One approach involves positioning a diver on the bow of the vessel and scan the water for turtles. 

When a turtle is located the vessel will pursue the turtle and maneuver into a position for the 

diver to dive into the water and capture the turtle by hand. In some cases this involves pursuing 

the animal until it begins to tire. In other cases the turtle is simply followed at a relatively slow 

speed until it stops or slows down or quiescent turtles on the bottom are searched for (Ehrhart 

and Ogren 1999). Turtles sleeping or resting quietly on the bottom can, in some instances, be 

approached stealthily and captured directly by a free diver or a SCUBA diver. Once within 

range, the diver captures the turtle by placing one hand on the leading edge of the carapace and 

the other hand on the trailing edge and guiding the turtle to the surface. Once at the surface, the 

onboard crew will lift the turtle over the gunwale with the aid of the diver in the water. 

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3.4.3.2 Selective Hand Deployed Capture Nets 

Sea turtle researchers use a variety of capture nets that are deployed by hand and target a 

particular animal or group of animals. These selective capture methods have little to no potential 

for interaction with non-target species. 

A dip net is a small-mesh net affixed to a rigid hoop that is affixed to a long pole. The hoop 

diameter can vary depending on the species and life stage targeted, but is generally one meter or 

smaller. Sea turtles are dip netted from the sea surface, typically by research personnel aboard a 

vessel. Once in the net, the turtle is carefully lifted out of the water and placed on the deck of the 

research vessel. 

A cast net, or throw net, is a circular net bordered by weights and connected to a line for 

retrieval. Nets used by turtle researchers vary in size from approximately one to four meters in 

diameter. Cast nets are manually thrown upon sighting a turtle at the surface, and immediately 

retrieved to bring the turtle onboard the vessel. 

A breakaway hoop net consists of a rigid hoop, a net fastened with breakaway stays that detach 

upon capture, a guiding pole, and line affixed around the net opening that cinches it closed and 

maintains control and attachment once deployed. The hoop diameter is wide enough to fit easily 

over the targeted turtle and keep the front flippers loosely held at the sides, which is essential for 

safe capture. A researcher positioned on the bow guides the breakaway hoop net over the turtle. 

Upon capture, the net detaches from the hoop and the opening is cinched using the line to 

enclose the turtle. Additional personnel aid in maneuvering the turtle onto the research platform, 

which may consist of a research vessel modified for boarding or other platform designed to 

safely and securely restrain the animal. The breakaway hoop net is primarily used to capture 

leatherback sea turtles but may be used to capture any sea turtle species. 

An encircle net, or strike net, is a net deployed from the research vessel in a quick fashion to 

encircle the target sea turtle (or group of turtles) upon sighting. Per established protocols 

(Ehrhart and Ogren 1999; Witzell and Schmid 2004) nets may be up to 300 meters long with a 

36 centimeter stretch-mesh nylon webbing, four meters depth, braided polyfoam float line, and 

braided leadcore line. When a turtle is sighted, the net is deployed off the stern of the research 

vessel at relatively high speed, encircling the turtle, and held closed until the turtle is observed 

entangled in the net or until 20 minutes has elapsed without sighting the animal. Upon 

entanglement in the net, a diver may enter the water to assist with disentanglement and transfer 

to the vessel. If necessary, webbing is carefully cut from animals to minimize any adverse effects 

of entanglement and to aid in their removal from the net. Encircle nets are not deployed if marine 

mammals are in the area and are immediately retrieved if marine mammals are sighted after net 

deployment. 

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3.4.3.3 Entanglement Net 

A large mesh entanglement net is a commonly used type of fixed gear for capturing turtles, 

typically in shallow waters (often referred to as “gill nets” in fisheries use). Nets are typically 

100 meters or less in length with webbing made of 18-gauge twisted nylon twine and a stretched 

mesh size ranging from 20 to 51 centimeters (knot to knot). The mesh is suspended from a foam 

core braided polyethylene top line with fixed bullet-shaped polystyrene foam floats at 

approximately ten-meter intervals. The bottom line consists of a continuous lead core line. 

Anchors attached to both ends of the net keep it in position and prevent drifting of the lead line. 

Net heights vary depending upon the depth in which the net will be set such that the netting 

extends throughout the water column and provides slack for entangled turtles to reach the surface 

to breathe. From one to four nets may be deployed for a project depending on the study design, 

study area, and applicant’s resources. As part of the Program, the Permits Division will consider 

variations in length and configuration of entanglement nets provided that the applicant has 

demonstrated that he/she has sufficient resources to adhere to standard permitting requirements 

for continuous net monitoring (see Appendix C for details) and to process and release turtles in a 

timely manner. For example, a minimum of two research vessels and eight crew members are 

typically needed to adequately monitor and tend four nets that are each 100 meters long. 

Entanglement nets are a non-selective gear type as there is potential for bycatch and incidental 

take of protected species, especially marine mammals. To mitigate this risk, the study site is 

visually surveyed for marine mammals prior to and during net deployment. If marine mammals 

are sighted near the netting sight, nets either are not be deployed or are pulled in, and netting 

activity ceases until marine mammals have left the area (see Appendix C for more details). 

Entanglement nets must be visually monitored every 30 minutes or less, as required by permit 

conditions, or whenever there is movement of the net indicating an animal may be 

entangled. When turtles encounter the net and become entangled they will be quickly removed 

from the net and boarded for processing. 

3.4.3.4 Pound Nets 

Pound nets are stationary gear that direct fish and other marine life into enclosures or “pounds” 

by means of barriers called “leads.” Most pound nets also have a middle section or “heart” 

located in between the lead and the pound. As animals swim along the lead into the heart they 

are directed into the pound by way of a mesh tunnel. Once in the pound, sea turtles can reach the 

surface to breathe. Animals captured in the net are collected by gathering up the bottom of the 

pound, working from the tunnel wall to the back wall of the pound until the catch is concentrated 

in the back of the pound. Sea turtles are then removed by hand and placed into the research 

vessel. 

As a requirement of the Program, hearts and pounds are must have 1.75 inch stretched mesh to 

minimize the risk of entanglement for sea turtles. Other than mesh size, the exact design of 

pound nets used in turtle research (e.g., lead mesh size and length, pound area, and use of escape 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

panels for small fish) could vary. The Permits Division would only authorize a particular 

proposed pound net design if the adverse effects are equivalent to or less than those analyzed in 

the scope of this consultation. Another requirement of the permit is that pound nets (including 

the entire pound, heart, and leader) would have to be checked daily by researchers, unless 

weather conditions prevented safe passage to the nets. Pound nets are not selective and catch 

numerous species, including many species of fish. Bycatch in pound nets generally remain alive 

in good condition as they can swim freely in the pound until the net is checked and they are 

released. No marine mammal interactions have ever been documented by researchers using 

pound nets (NMFS 2017a). 

3.4.3.5 Seine Nets 

Seine nets are used to capture sea turtles that are in close proximity to the shoreline. These nets 

have double float and lead lines and are deployed approximately 100 to 200 meters offshore in a 

straight or slightly curved line running parallel with the shoreline. Once the seine is set a boat at 

each end of the net pulls it toward the beach at a speed of about two to three knots. When the 

ends of the net are close to the beach the net is pulled onto the beach by hand. The boats may 

assist by doubling back out along each side of the net, and attach to the cork line about 20 meters 

from the beach and pull the net toward the beach. In some cases, entanglement nets (described 

above) can be used as a set net placed over a mud bottom substrate and/or deployed in the 

manner of a seine net from the vessel or on shore. When using an entanglement net as a seine net 

one side of the net would be set with an anchor and the other side would be deployed from the 

vessel in a circular fashion and slowly pulled in back onto the vessel or onto shore within a few 

minutes of deployment. The deployment of entanglement nets as a seine net is expected to take 

less than ten minutes. The net setting and retrieval process will be rapid, and therefore any turtles 

that might become entangled in the net will quickly be brought to water shallow enough for them 

to reach the surface to breathe, and they will be disentangled as quickly as possible. 

Seine nets are a non-selective gear type as there is potential for bycatch and incidental take of 

protected species, especially marine mammals. Similar to entanglement nets, to mitigate this risk 

the study site is visually surveyed for marine mammals prior to and during net deployment. If 

marine mammals are sighted near the netting sight, seine nets either are not be deployed or are 

pulled in, and netting activity ceases until marine mammals have left the area (see Appendix C 

for more details). 

3.4.3.6 Trawling 

Trawls are nets dragged behind vessels that are used to capture marine organisms (i.e., fish, 

shrimp, and turtles) on the sea floor or within the water column. There are many different types 

of trawl nets and deployment configurations. One example of a trawl net configuration used to 

capture sea turtles is a paired otter/flat trawl (such that one net is towed on each side) (Figure 2). 

Turtles and other marine life are captured in the cod end which consists of four inch stretch 

mesh. Trawls nets are brought on-board using winches and turtles are removed from the net in a 

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Figure 2. Standard otter trawl design (Source: 

http://www.grantontrawlers.com/steam%20trawler.html). 

 

 

 

 

 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

manner where they are safely placed on deck. Trawling is generally only used to capture hardshelled species. If a leatherback is captured and cannot be safely boarded and released, it is freed 

in the water without bringing the net on board by untying the cod end of the trawl. Due to the 

increased risk of mortality or serious injury associated with this gear, as a condition of any 

permit authorized under the Program, trawls nets cannot be towed for more than 30 minutes 

bottom time and at depths exceeding 20 meters. 

Trawls are non-selective gear that can also result in the capture of other species, including many 

species of fish, sharks, invertebrates and marine mammals. As with tangle netting, permit 

requirements are in place to minimize the risk of capturing marine mammals by monitoring for 

their presence before and during tows; trawl nets are not deployed or are immediately retrieved if 

marine mammals are sighted within the area. 

3.4.3.7 Bycatch Reduction Studies 

Bycatch reduction studies are designed to test modifications to fishing gear in an effort to reduce 

sea turtle bycatch and bycatch mortality rates. Examples include the evaluation of new or 

improved turtle excluder devices (TEDs) in trawl fisheries and deterrent devices such as lights to 

tangle nets. This type of research could be authorized as part of the Program (and covered under 

this programmatic consultation) provided that the gear type matches one described above and the 

applicant can adhere to the required mitigation measures (provided in Appendix C) for that 

particular gear type. If the applicant requests to use a capture method not described above (e.g., 

longlines) or cannot follow the standard mitigation measures (e.g., trawl in depths greater than 

20 m), the action would fall outside the scope of the Program and require individual section 7 

consultation. 

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3.4.3.8 Capture under Another Authority 

Applicants may request authorization to conduct research procedures on sea turtles that have 

already been legally taken (i.e., captured) under a separate ESA authority. This may include 

turtles captured under another researcher’s section 10 permit or the incidental take of turtles 

authorized under a previously issued section 7 biological opinion for a commercial fishery. 

Turtles may also be obtained after disentanglement from fishing gear under the authority of the 

STSSN if the animals are deemed fit for research by consultation with a veterinarian or by 

following a veterinary-approved protocol. In all cases, the applicant must demonstrate how the 

source of the turtle is legal under the ESA before the Permits Division would authorize research 

on the animals as part of the Program. Because the capture and effects of capture have already 

been analyzed when they were authorized previously, those capture methods are not addressed as 

part of this programmatic consultation. 

3.4.4 Research Procedures on Captured Sea Turtles 

This section describes the research procedures that would be authorized by the Permits Division 

as part of the Program. Standard protocols and required mitigation measures associated with 

these procedures are also discussed here and described in more detail in Appendix C. 

3.4.4.1 Handling, Transportation, and Holding 

As part of the Program, researchers are required to comply with commonly accepted handling 

practices and holding times. While an animal is on deck or on shore, precautions are taken to 

make the animal comfortable, prevent injury, and minimize stress. Each turtle is kept separate 

(especially those prone to conspecific aggression), placed on top of padding or other cushioned 

device (e.g., tire) within a confined area or container, and sheltered from the elements. The upper 

head may be covered with a wet cloth to keep the turtle calm. With the exception of sterile, 

disposable equipment (e.g, needles, scalpel blades), all gear (e.g., tag applicators, measuring 

tapes, etc.) that comes into contact with animals must be cleaned and disinfected before use and 

between animals. Disposable gloves must be used whenever possible, and are required if there is 

any risk of contact with breaches in the skin (e.g., biopsies, administering hemostasis) or to 

minimize opportunity for contamination of sterile instruments. For circumstances where 

disposable gloves are impractical, good hand sanitation (thorough washing) between animals is 

required. If sea turtles with FP may be encountered, a designated separate set of equipment for 

turtles with tumors must be available and used only for turtles with observable FP. Every effort 

must be made to minimize turtle handling time. Handling time for research procedures vary 

based on the activities the animal will receive but in most cases turtles are released within 60 

minutes and almost all will be released within a few hours. Sea turtles must be released from the 

vessel in a safe manner near the point of capture. For more details on sea turtle handling and 

holding practices see Appendix C. Appendix C also includes an additional attachment (i.e., 

Attachment 1) of protocols and requirements for handling and monitoring captured leatherbacks. 

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Attachment 1 is only included in the permit when the permit holder is targeting leatherbacks 

using selective capture methods (e.g., hand, breakaway hoop net). 

If researchers are requesting to transport turtles to a facility for temporary holding and additional 

research procedures, applicants must provide details demonstrating how the turtles will be 

monitored and cared for during transport. The type of information that must be provided is 

specified by regulation at 50 CFR 222.308. When transport and holding in a facility is 

authorized, as a condition of the permit researchers must transport, maintain and care for sea 

turtles following the USFWS’ “Standard Permit Conditions for Care and Maintenance of Captive 

Sea Turtles” (USFWS 2013). For facilities in Florida, researchers must follow the Florida Fish 

and Wildlife Conservation Commission Marine Turtle Conservation Handbook Section 4, 

Holding Marine Turtles in Captivity (FFWCC 2016). 

As described in Appendix C, researchers are required to contact their designated on-call 

veterinarian or permitted rehabilitation facility if an injured, comatose or compromised sea turtle 

is encountered. This veterinary consultation will determine whether the animal is suitable for 

research, should be returned to the water, or should be transported for rehabilitation and 

treatment. In most cases, the Permits Division will not authorize research on compromised 

animals if the procedures would further stress the animal to the degree that survival would likely 

be affected. Rare exceptions may be allowed if the research objectives are tied to health 

assessments or identified management needs to aid a species’ recovery, and only after close 

consultation with OPR’s Veterinary Medical Officer for sea turtles. In such cases, a sea turtle 

veterinarian would have to be consulted and activities would only be conducted at his/her 

discretion following an Institutional Animal Care and Use Committee- or veterinary-approved 

protocol. 

Researchers may temporarily hold turtles captured in the wild in a tank for studies that require 

multiple days to complete or controlled conditions, such as for behavioral or physiological 

studies. This most often involves transporting turtles to designated facilities with specific 

capabilities. Upon completion, animals are returned to the wild near the point of capture. Tankbased studies will be considered to fall within the scope of the Program provided that the 

research does not result in turtle injury or mortality and the researchers adhere to the standard 

protocols and mitigation measures for procedures and captive care as described in this opinion 

and detailed in Appendix C. 

3.4.4.2 Examination, Measurements and Monitoring 

External Examination and Photography 

Upon capture, each turtle is assessed (i.e., looking for signs of illness, injury, epibiont load, etc.) 

to determine its general state of health and suitability for subsequent research procedures. A 

common practice is to photograph captured turtles to document condition, physical 

characteristics, and any tags, distinguishing marks, old injuries, or lesions. 

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Oral/ophthalmic/vent examination 

The mouth, eyes, and vent may be examined for signs of injury, ingestion of hooks or marine 

debris (plastics, tar balls), and tumors. Some researchers conduct more in-depth evaluations, all 

of which included under this category are characterized as non-invasive methods of visual 

assessment and data collection. Researchers infrequently propose more involved examinations, 

which typically are conducted in collaboration with a veterinarian. For example, ophthalmic 

examinations may employ fluorescein staining (a common veterinary diagnostic) to evaluate the 

integrity of cornea, evaluation of the anterior chamber using a slit lamp (ophthalmological 

instrument), or ultrasonography. 

Morphometrics 

Measurements and weight are standard, non-invasive procedures performed on all sea turtles 

captured and provide critical information related to life stage, sexual maturation, growth rates, 

and nutritional condition. Turtles are measured using a soft measuring tape to collect curved 

carapace, plastron, and tail lengths and widths. Calipers are used to measure straight carapace 

length (SCL), width, and body depth. Less commonly, specific aspects of anatomy, such as the 

jaw and oral cavity (with the aid of a bite block or oral speculum), are measured for specific 

research interests. Sea turtles are weighed using various types of scales, depending on their size. 

In all instances, animals are supported using containers, specially-designed harnesses, or netting 

that allow safe lifting practices and provide adequate support of the body to prevent injury. 

Monitoring Vital Parameters 

Vital parameters may be measured as part of specific research objectives (e.g., physiological 

studies) or as a means of monitoring animals that appear more sensitive to the stress of capture 

(such as leatherbacks, as required in Appendix C), or as deemed prudent based on the discretion 

of an attending veterinarian. These are rapid, non-invasive or minimally invasive procedures that 

measure health parameters across tissue membranes or surfaces. 

Heart rate is monitored using a Doppler blood flow detector, electrocardiogram, or 

ultrasonography probe. For Doppler flow detectors and visual ultrasonography, ultrasound gel is 

applied to the skin and a hand-held instrument (transducer) is passed lightly over the skin to 

locate pulsatile flow within blood vessels or the heart. Electrocardiograms involve the placement 

of electrical adhesive, leads, clips, or probes in various configurations on the skin to measure 

electrical activity of the heart. A pulse oximeter is a medical device that indirectly measures the 

amount of oxygen in a patient's blood (as opposed to measuring oxygen saturation directly 

through a blood sample). Although this device is inaccurate for measuring blood oxygen levels 

in sea turtles, it can be used as an alternative measure of sea turtle heart rate. Pulse oximetry 

probes come in various configurations that can be applied to the skin or inserted into the cloaca. 

Turtle respiration rate is simply monitored by visual detection of inhalation and exhalation. Body 

temperature is measured in turtles using either a thermometer probe inserted into the cloaca or 

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externally using an infrared thermometer (typically the neck/shoulder regions or prefemoral 

areas). Cloacal thermometers consist of a flexible thermistor probe (or equivalent) that is 

lubricated and gently inserted into the cloaca to the level of the caudal plastron or until resistance 

is encountered. To estimate overall health of the animals, researchers may measure the relative 

fat content of turtles using Bioelectrical Impedance Analysis (BIA). BIA non-invasively 

measures the resistance of body tissues to the flow of a harmless, low-level electrical current. 

The percent of fat tissue is determined by measuring the speed and strength of the current. 

Researchers typically use a handheld analyzer which runs on a 9-volt battery. The instrument 

includes an Ohm resistor which allows calibration checks. During testing, small electrodes would 

be placed on the opposite limbs of the body. The test generally takes only 5 to 20 seconds and 

elicits no response from sea turtles. 

3.4.4.3 Identification Tags and Markings 

Metal Flipper Tagging 

Metal flipper tags that are uniquely numbered are used to identify individual sea turtles. When 

properly applied, metal flipper tags can remain attached for over a decade. A routine practice for 

all personnel that work with sea turtles is to carefully inspect each encountered turtle for existing 

flipper tags. If existing tags are found and are in good condition, no additional flipper tags are 

applied. If tags are damaged, detaching, or deteriorating, they may be removed and new ones 

applied. For turtles greater than 30 centimeters SCL, the standard 681 Inconel flipper tags 

(http://www.nationalband.com/) are used; smaller tags (e.g., 1005 Monel series) are used for 

turtles from 20 to 30 centimeters SCL. Turtles less than 20 centimeters SCL are not tagged. 

The specific location of tag placement depends on the tagging program and species. To 

accommodate future growth in young turtles, flipper tags are placed with additional space (about 

15 to 30 percent) between the edge of the flipper and the curve of the tag. To avoid injury and 

minimize tag loss, researchers ensure that the piercing tab of the tag is within the receiver portion 

and is securely folded (crimped). The standard practice is to apply two flipper tags (one on the 

right and one of the left) to the caudal margin of the proximal front or rear flippers. Double 

tagging minimizes the probability of complete tag loss. Single tags may be applied if only one 

tag needs to be replaced or if a flipper is missing or has any other abnormality that would pose 

increased risks from tagging. As with all invasive procedures that involve piercing the skin, 

metal flipper tagging must adhere to the Permits Division’s aseptic techniques detailed in 

Appendix C. Prior to use, tags are washed in hot, soapy water and disinfected to minimize the 

possibility of infection. Applicators are cleaned and disinfected before use and between animals. 

Passive Integrated Transponder Tagging 

PIT tags are small rice-sized microchips that emit a unique code when activated by a PIT tag 

reader. These tags provide another means of identifying individual sea turtles and are thus vital 

to sea turtle research. PIT tags are internally injected and are not subject to tag loss due to 

environmental conditions as are external tags. Since they are not self-powered, PIT tags can 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

provide life-long identification. PIT tags typically are used in combination with metal flipper 

tags because not all individuals who may encounter a tagged turtle will have access to a PIT tag 

reader (e.g., the public encountering a stranded turtle). Researchers with tag readers scan all 

encountered turtles for PIT tags and only insert a PIT tag if one is not already detected. 

Prior to insertion, each sterile PIT tag is tested by scanning it with a PIT tag reader. PIT tags are 

inserted using an injector that is provided by the manufacturer. The exact location of PIT tag 

insertion depends on the program and species. On hardshell turtles, the PIT tag would typically 

be inserted into the triceps muscle complex or within the soft, fleshy area dorsal to the wrist 

bones of the front flipper at a seam between the scales and nearly parallel with the skin of the 

flipper and with the needle directed proximally. Other locations would be authorized as part of 

the Program if determined to be appropriate and if expected to have the same effect on the 

animal as intramuscular insertion. The most commonly used locations for hard-shelled turtle 

species are the flipper blade and triceps muscle area of the front flippers. In Hawaii, it has been 

standard practice to insert the tag in a rear flipper since 1998. Leatherback turtles are tagged in 

the shoulder region (Dutton and McDonald 1994). As with all invasive procedures that involve 

piercing the skin, PIT tagging must adhere to the Permits Division’s aseptic techniques detailed 

in Appendix C. 

Turtles must be greater than 30 centimeters SCL to receive the standard 12 millimeter PIT tag 

(the size most frequently used for sea turtles), which uses a 12 gauge injector. For turtles 

between 16 to 30 centimeters SCL, a smaller 10 millimeter PIT tag (16 gauge injector) and local 

anesthetic must be used (see Appendix C for details). Additional steps to minimize impacts 

would be required for turtles between 16 to 30 centimeters SCL (see Appendix C for details). 

PIT tagging of turtles less than 16 centimeters SCL will not be not authorized as part of the 

Program. 

Shell Marking 

The carapace of hardshell sea turtles may be temporarily marked for easy identification of 

individuals during the research season to avoid recapturing animals. Researchers apply paint, 

such as a non-toxic paint stick used for livestock, to mark the carapace shell, using as little paint 

as necessary to easily identify the animal. The Permits Division will not authorize the use of 

xylene or toulene-based paints, or any other potentially harmful or toxic paints, particularly those 

containing tributyltin or cyanide. Additionally, researchers may not use paints with exothermic 

curing reactions or reflective paints. 

Etching tools (e.g., Dremel Moto-Tool with a "pear-shaped" bit) are used to place an etch or 

groove in the carapace of hardshell sea turtles. The bit is disinfected before use. The etch or 

groove is only made in the keratin layers of the scute and does not injure the underlying living 

tissue. Etching is not done on turtles with scutes that are too thin to be etched without risk of 

injury. Non-toxic paint is applied to the etched grooves in some instances to improve the 

visibility of animals post-capture. 

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For studies related to reproductive activity, the plastron of males may be marked using a 

minimally invasive protocol based on Blanvillain et al. (2008). Male sea turtles are placed in a 

recumbent position (carapace down). The entire plastron is delineated using a non-toxic marker 

and an additional line is drawn around the area of softness to highlight this area for 

photodocumentation and comparison with other parameters. 

Oxytetracycline 

Oxytetracycline injection is a means of chemically marking the bone to validate the “ring 

counting” technique of skeletochronological (aging) studies and to calibrate bone growth if the 

turtle strands dead and is recovered (Frazier 1985). Turtles are injected with the antibiotic 

tetracycline or oxytetracycline. Administration is according to a veterinary-approved protocol 

(NMFS 2008) that defines the dosage, injection site, and procedure. 

3.4.4.4 Biological Sampling 

Epibiont Collection 

Numerous organisms occur as epibiota on sea turtles and may be collected by researchers by 

various physical means, such as use of forceps, scraping devices, and swabs. All collection 

procedures, including detachment of barnacles, most be done in a manner that avoids injury to 

the underlying skin. 

Swabs 

Swabs are collected from the skin, eyelids, and orifices (mouth, nares, cloaca) of sea turtles for 

various purposes, including DNA recovery, cytology, and characterization of microbiota. This 

sampling collects surface or naturally exfoliating materials and does not injure the skin or 

mucosal surface. For oral swabbing, a bite block or speculum is used to transiently hold the 

mouth open for safe collection. For cloacal swabs, the swab is not inserted beyond the point of 

any resistance (to avoid accidental perforation). Palpebral swabs are collected with care so as not 

to abrade the sensitive cornea. The specific type of swab, gauze, or similar material/instrument 

depends on the research objective. 

Skin Biopsy 

Tissue samples (biopsies) are used for various purposes, including genetic analyses, isotope 

analyses, and disease studies. Included under skin biopsies is sampling that aims to specifically 

collect keratin (i.e., for isotopic, heavy metal or other analyses). A new, sterile biopsy punch, 

razor, or surgical blade is used on each sample. Skin biopsies are limited to two biopsies per 

animal per sampling event, and two sampling events per 12-month interval unless additional 

sampling is defined in a veterinarian-approved protocol. 

Skin biopsies typically are 6 mm in diameter or less and are collected from specific areas of the 

body, depending on their intended use. For example, samples for genetic analysis are most often 

collected from edges of the flipper webbing for hard-shelled species. Skin overlying the shoulder 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

areas or specific areas of the shell may be targeted for isotopic analysis and specific types of skin 

lesions, e.g., fibropapillomas, may be sampled for disease studies. The tissue surface would be 

cleaned and disinfected following the required aseptic technique and disposable gloves must be 

worn. Sterile biopsy punch, forceps, surgical scissors, or an additional blade may be used to 

extract and trim the sample. Analgesia (i.e., use of local anesthetics) under the direction of a 

veterinarian is encouraged when possible for biopsies of any size. A veterinarian-approved 

protocol is required for biopsies larger than 6 millimeters. 

There are instances when sea turtles cannot be safely boarded onto a vessel, but may be sampled 

using a biopsy pole. Samples are collected from anywhere on the limbs or neck (avoiding the 

head) that are most safely accessible to the researcher. Samples from leatherbacks are collected 

via shallow carapacial scrapes. The sampling gear consists of a 1-cm diameter sterile stainless 

steel corer attached to a two to four meter anodized steel sectional aluminum pole. The vessel 

comes alongside the leatherback in the water and scrapes the carapace at an oblique angle to 

collect a superficial skin sample. 

Soft Tissue Biopsy 

Soft tissue biopsies include surgical collection of samples of skeletal muscle, tumors, lesions, or 

fat, which are used for physiological and health studies. Because this is a surgical procedure, soft 

tissue biopsies must follow a veterinarian-approved protocol and are only performed by a 

veterinarian or under direct veterinary supervision. This procedure must follow the provisions in 

Appendix C, including aseptic techniques and pain management. Sampling of soft tissues may 

occur in a facility or under field conditions provided that an appropriate designated surgery area 

is used. 

Blood Sampling 

Blood sampling is a minimally invasive method to study sea turtle population genetics, sex 

ratios, health, contaminants, and stable isotopes. Sampling may only occur if directly taken by or 

supervised by experienced personnel. Blood is most frequently collected from the dorsal cervical 

sinus (external jugular vein) of the turtle’s neck, but also may be collected from other peripheral 

vessels. For example, vessels at the base of the rear flippers and adjacent to the phalanges are 

alternate collection sites in leatherbacks. Turtles are adequately restrained during the collection 

to prevent movement. The sample site is cleaned and disinfected before drawing blood following 

the required aseptic techniques. New disposable needles are used on each animal and no more 

than two attempts are allowed per needle. The needle size is dependent on the size of the animal, 

e.g., a 21 or 22 gauge, 1 to 1.5 inch needle is adequate for adults (Owens and Ruiz 1980); a 23 

gauge, 0.5 inch needle is appropriate for smaller animals; longer spinal needles are needed to 

reach the cervical sinuses of leatherbacks. Attempts (needle insertions) to extract blood would be 

limited to a total of four, two on either side of the neck or other site. During blood sampling, 

lateral movement of the needle and unnecessarily deep insertion are avoided to prevent injury. 

The needle is retracted to the level of the subcutis prior to redirection. No blood may be collected 

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should conditions on the boat preclude the safety and health of the turtle. Permits conservatively 

limit total blood volume collected to no more than three mL per one kg of turtle body mass. 

Collection of larger volumes requires a veterinarian-approved protocol. Severely compromised 

or injured turtles would not be sampled for blood unless specifically authorized by the Permits 

Division or deemed necessary to facilitate clinical assessment in the field. In addition, 

researchers would follow protocols to ensure a proper sampling period between samplings as 

outlined in Appendix C. 

Tear Collection 

Sea turtle tears are collected for physiological studies. Tear collection methods will be authorized 

as part of the Program provided that they are non-invasive, comply with required safe handling 

practices, and do not pose any risk to the turtles eyes. 

Fecal and Urine Sampling 

Fecal and urine samples are collected for sea turtle diet analyses, health evaluations, and other 

purposes. Fecal samples may be voluntarily voided following capture, collected from larger 

turtles (greater than 50 centimeters SCL) using a lubricated, gloved finger, or by fecal loops, 

swabs, or cloacal lavage (using a red rubber catheter). To avoid injury, objects inserted into the 

cloaca must never be forced beyond the point of any resistance. Cloacal lavage generally uses 

small fluid volumes (approximately 5 to 20 milliliters of saline, depending on size). Urine is 

collected opportunistically when the bladder is voided following capture. 

Gastric Lavage 

Gastric lavage is used in hardshell sea turtles to obtain samples of ingested food for diet-related 

analyses. Standard procedures generally follow those described by (Eckert et al. 1999a). This 

procedure is only done by experienced personnel or under their direct supervision. Clear, 

flexible, vinyl tubing is used for the lavage procedure. Two tubes may be used, one for 

introduction of water for lavage and another for retrieval. Prior to use, the tube ends are heat 

treated if necessary to remove any sharp edges. Tube length is compared with the turtle to 

identify the length of necessary insertion into the esophagus, which is marked for reference. The 

tubes are not inserted beyond this point or beyond the point of any resistance. The turtle is placed 

with its caudal end elevated. The mouth is opened, and a padded bite block or speculum is 

inserted to prevent the jaws from closing. Once the turtle’s position has been stabilized, the 

tubing is lubricated with vegetable oil or non-toxic water-based gel and inserted into the 

esophagus. Water is pumped into the esophagus (e.g., using a doubleaction, veterinary stomach 

pump). The forthcoming fluid and any ingesta is discharged through the retrieval tube. The 

lavage continues for approximately 30-45 seconds as the tube is passed up and down the length 

of the esophagus. Lavage does not exceed three minutes to avoid aspiration. Upon completion, 

the turtle is left with its caudal end elevated until researchers are certain that all of the fluid has 

been discharged. The tubes are then removed followed by the bite block or speculum, and the 

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head is elevated to prevent aspiration. The procedure is aborted if any element of the procedure 

becomes unstable. 

3.4.4.5 Laparoscopy and Associated Internal Tissue Sampling 

Laparoscopy involves the use of an endoscope to directly view inside the body (coelomic) 

cavity. This invasive procedure is typically used in research on sea turtle reproduction to confirm 

the sex of immature individuals, characterize stage of maturation and the reproductive cycle, and 

as a means for collecting biopsies of internal organs. As a surgical procedure, laparoscopy is 

only performed by or under the supervision of a qualified veterinarian and must follow a 

veterinarian-approved protocol that includes consideration of aseptic technique, analgesia, and a 

plan for response to any unplanned complications, as required in Appendix C. Sedation is not 

required but is recommended if conditions allow. Laparoscopy is not performed on any 

compromised animals (those that are obviously weak, lethargic, positively buoyant, emaciated, 

or that have severe injuries or other abnormalities resulting in debilitation). 

The procedure begins with a surgical incision at the port of entry, typically within the prefemoral 

area. A trocar is used to penetrate the body cavity and insert a cannula for passage of the 

endoscope. If introduction of gas (insufflation) is necessary for visualization, medical grade 

carbon dioxide is used. Upon completion of the procedure, the gas is expelled using one of 

multiple techniques and the surgical site is sutured closed using an absorbable suture. The turtle 

is monitored prior to release to ensure recovery and buoyancy control. 

As part of the laparoscopic procedure, internal organs and tissues (e.g., gonads, muscle, liver, 

kidney, spleen, and mesenteric fat), may be sampled using surgical endoscopic instruments for 

physiological and health-related studies. As with the endoscopic procedure in general, this 

sampling is performed by or directly supervised by a qualified veterinarian. 

3.4.4.6 Transmitter Attachments 

Researchers use a variety of instruments and transmitters to track turtle movements and collect 

data on habitat use, dive behavior, physiology, foraging events, and associated environmental 

parameters. Commonly used types of instruments include acoustic, radio, and satellite 

transmitters, time-depth recorders (TDRs), pop-up archival tags, animal-borne video, audio, and 

environmental data collection systems (AVEDS) also referred to as “Crittercams©”, and less 

commonly, stomach pills. While the size, weight and dimensions vary by tag type, all tracking 

devices authorized as part of the Program must meet the Permits Division’s standard mitigation 

measures (see Appendix C) to reduce drag (e.g., hydrodynamic shape, tag placement) and to 

minimize the risk of entanglement. Transmitter attachment methods will also vary based on the 

research objectives, study design, and target species (hardshells vs leatherbacks). Attachment 

methods that may be authorized as part of the Program include suction-cup, adhesive 

(epoxy/resin/putty), wired/tied attachments by drilling through the carapace or pygal region, and 

ingestion (stomach pills). Each of these methods is discussed in more detail below. Though 

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previously authorized for use on sea turtles in section 10 research permits, the Program does not 

include authorization of harnessed-based attachments. 

Depending on the study objectives, multiple tag components may be housed into one tag package 

to minimize impacts to the target sea turtle. In other cases multiple tag attachments (up to three 

maximum) that remain attached for varying durations may be needed. For example, a researcher 

may place a short-term suction-cup attached AVED and a longer-term satellite transmitter on an 

animal to collect different types of data. The use of multiple tags can also provide information 

for assessing tag accuracy, tag failure rate and turtle post-release mortality rate. In some 

instances (e.g., TDR tags), researchers would recapture the animal to remove the tag and 

download the information it recorded. These animals would be intentionally captured twice. 

When reviewing requests to attach transmitters to sea turtles under the Program, the Permits 

Division would ensure that the tag type, attachment method, and expected attachment duration 

are appropriate for and consistent with the applicant’s objectives, are not unnecessarily 

duplicative (when attaching more than one tag), and are likely to yield meaningful data. This 

ensures that the research is bona fide and meets ESA issuance criteria. 

Suction-cup Attachment 

Suction-cups are used for the short-term attachment of AVEDS, radio transmitters, TDRs or 

acoustic transmitters to monitor short-term movements, dive behavior, and foraging ecology. 

Suction-cup tags are attached upon capture and work-up of an animal or remotely by pole during 

a close approach by the vessel. Small amounts of a temporary adhesive (e.g., denture adhesive) 

may be used to lengthen the duration of attachment. Suction-cup attachments have been shown 

to last for up to nine days in studies of leatherbacks, although most typically lasted for 48 hours 

or less. 

Adhesive Attachment 

Tags requiring longer attachment times for hardshell sea turtles use an adhesive, such as an 

epoxy, marine putty, resin, and fiberglass strips. Neoprene or silicone may be used to 

accommodate the physical features of smaller, growing sea turtles (Mansfield et al. 2012). 

During the attachment process, turtles are held out of water in a well-ventilated area to prevent 

unnecessary contact with curing compounds used for the attachment. All epoxies, resin, and 

other compounds must be tested prior to use to ensure that they will not cause thermal injury 

while curing. The carapace is thoroughly cleaned and prepared using a mild abrasive and solvent 

wash to promote adhesion. Tags are applied directly to the carapace at a location that minimizes 

drag while maintaining satellite transmission quality, typically to the posterior region of turtles, 

in particular the last vertebral and costal scutes. Attachment media may also encompass sections 

of the surrounding scutes, but is minimized and applied to be as hydrodynamic as possible. All 

surfaces of the transmitter except the saltwater switch and bottom are covered with anti-fouling 

paint to prolong function. In some instances, adhesive is used to affix a metal base plate to the 

carapace on which a tag is attached so that the tag can be released from the turtle after a pre44 
 

 

 

 

 

 

 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

determined time period using a corrosive link. Battery life and duration of attachment depend on 

the species, life stage, attachment method, and individual behavior, but can last a year or more. 

Tags, or base plates, detach as the shell grows and the scutes are naturally shed, or are scraped 

off on underwater structures. These factors result in shorter attachment durations for younger 

juvenile turtles and some other life stages. 

Carapace Drilling 

Sea turtle researchers have developed methods for tag attachment that involve drilling through 

the carapace. Acoustic tags may be secured to the posterior marginal scutes using coated wire or 

zip ties in addition to or in lieu of marine epoxy products. The wire or zip tie is run through holes 

drilled into the marginal scute and secured with small aluminum clamps. A sterile drill bit is used 

for each individual turtle and cleaned with alcohol prior to drilling holes. The outermost edge of 

the posterior marginal scute is drilled to avoid damaging any tissue beyond the carapace itself. A 

putty may also be applied to the scute under the tag to prolong attachments. 

Pop-up Archival Tags (PATs) may be attached to the caudal carapace by tether. Using this 

technique, a sterilized drill bit is used to create a hole through one of the pygal bones (caudalmost carapace margin in hardshell species) or the pygal (in leatherbacks). The skin is thoroughly 

disinfected prior to drilling. The attachment tethers have a weak link to prevent accidental 

entanglement and corrodible elements that result in detachment over time. The tags themselves 

are programed to detach after a designated interval or if certain environmental parameters are 

met. PATs attached using this technique typically last a year or less. 

The medial ridge direct attachment method was designed for leatherbacks and allows 

accommodation of tags that are specifically designed for this species (Figure 3). After cleansing 

of the skin along the medial ridge, two to three small holes are drilled through the ridge using a 

sterilized drill bit. Monofilament or coated wire tether (swabbed with triple antibiotic ointment) 

is threaded through an acetal polyoxymethylene resin disk. Once passed through the hole, the 

monofilament is secured with a second acetal polyoxymethylene resin disk (swabbed with triple 

antibiotic ointment) and a metal crimp so that the tether is tight and secure. Any excess 

monofilament is cut off, and the process is repeated for the second monofilament tether. These 

tags are very low profile and pose little risk of entanglement. The tag releases once the crimp 

corrodes, and may be designed to release from as little as 30 days to up to a year. 

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Figure 3. Direct carapace attachment on leatherback. Photo courtesy of Sandra Ferraroli, 

Centre National de la Recherche Scientifique. 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Stomach Pills 

This procedure has primarily been authorized for research on leatherbacks but could be used on 

any turtle species. The stomach pill possesses a thermistor to detect stomach temperature, and a 

transmitter to relay data to a satellite-linked data recorder mounted on the turtle’s carapace to 

provide details on the foraging events and patterns of sea turtles at sea. By design, pills thus far 

used in sea turtles can only be used in conjunction with an externally attached satellite tag that 

can collect and transmit the data. The pill is coated with a dissolvable, biocompatible material 

(e.g., ethylcellulose) to temporarily increase the pill’s diameter to increase retention time in the 

stomach (Casey et al. 2010). Coating diameter is based on pill size (technology is making pills 

smaller quickly) and the size of the animal. Pills may only be used according to a veterinaryapproved protocol. The pill is inserted into the turtle’s esophagus using a lubricated flexible 

rubber tube. Once the coating dissolves, the pill would be small enough to pass through the 

pyloric sphincter, into the small intestine and then be passed by the animal, within two weeks of 

ingestion. Administration of the pill takes only one to two minutes. 

3.4.4.7 Non-invasive Imaging 

Diagnostic imaging includes multiple methods that are commonly used in veterinarian medicine 

to visualize internal structures. Though rarely performed under NMFS permits, turtles may be 

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transported to a facility for imaging or imaged in the field using portable units. If necessary, 

turtles are restrained, sedated, or anesthetized under veterinarian supervision. 

Radiography 

Radiography (X-rays) uses electromagnetic radiation to image internal structures, which are 

recognized by their shape and density. Portable units are readily available for potential field use. 

Generally, animals are manually restrained; sedation usually is not required. Radiation exposure 

during imaging is well within the safety limits set for general medical use. Intravenously or 

orally administered contrast material might be used to improve visualization of specific 

structures, evaluate function (e.g., digestive and urinary systems), or assess blood flow. Only 

contrast agents with demonstrated safety in animals are used and a veterinarian-approved 

protocol is required. 

Computed Tomography 

Computed tomography (CT) also uses electromagnetic radiation, but allows better distinction of 

specific tissue densities, as well as cross-sectional and 3-D imaging, which allows better 

visualization than standard radiography. These machines are large and require turtles to be taken 

to an imaging facility. Sedation or anesthesia are typically necessary, as the turtle must remain 

motionless during imaging. Contrast agents are used for CT as with radiography. It typically 

takes less than a minute to image a sea turtle, depending on the size of the turtle and area of 

interest. 

Magnetic Resonance Imaging 

Magnetic resonance imaging (MRI) uses magnetic fields and radio waves to image internal 

structures, and is preferred for imaging soft tissues. As with CT, MRI units are large, nonportable machines. Sea turtles must remain motionless during imaging, thus sedation or 

anesthesia is often necessary. Imaging takes longer than for CT, approximately 20-45 minutes on 

average. Duration depends on the size of the turtle and the aspect of anatomy that is being 

imaged. 

Ultrasound 

Ultrasonography uses high frequency sound waves to image internal structures. In sea turtle 

research this method is most often used to image the gonads for reproductive studies, but other 

organ systems and tissues can be imaged as well. Portable units allow ultrasonography to be 

performed under field conditions and no sedation or anesthesia is necessary with this procedure. 

An ultrasound probe is placed against the skin overlying the area of interest. A special acoustic 

coupling gel is used to facilitate transmission. 

3.4.5 New Sea Turtle Research Methods, Procedures, and Mitigation Measures 

As new technologies are developed and techniques improved, the Permits Division anticipates 

new research procedures or protocols may be proposed by sea turtle researchers. For example, 

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the use of UAS for sea turtle research is expected to grow over time as this relatively new 

technology evolves (i.e., new sensors and payload components that can collect different types of 

information are likely to be developed). Improvements in sea turtle tag design and attachment 

methods are also expected as this field of study grows and technology evolves (e.g., the 

miniaturization of solar cell technology with longer battery life), allowing units to be placed on 

smaller animals and/or for longer durations. These units would be authorized under the Program 

as long as their effects are equivalent to those analyzed in this BA, and the researcher can meet 

our standard permit mitigation measures. 

Since additional risks may be associated with new or experimental procedures, the Permits 

Division will only authorize a new procedure (i.e., one that is not explicitly discussed above) as 

part of the Program if, after reviewing the best available scientific information, they determine 

that (1) the procedure is effective at achieving the research objectives, and (2) any adverse 

effects on sea turtles resulting from the procedure are less than or equal to the adverse effects of 

any of the procedures previously authorized or described above for the same research objectives. 

Therefore, the Permits Division does not expect new research methods or changes in protocols to 

result in a level of impact not evaluated as part of this programmatic consultation. If the adverse 

effects are greater than considered in this programmatic opinion, reinitiation is required. 

Similarly, if NMFS develops new recommendations or best practices for sea turtle research, the 

Permits Division’s standard mitigation measures and permit requirements (described above and 

in Appendix C) would be revised to be consistent with such recommendations to minimize 

impacts to the extent possible. For example, as new information becomes available on the 

impacts of tag units and attachment methods, such as studies analyzing drag forces to smaller 

turtles, the Permits Division’s standard mitigation measures for the Program would be revised to 

minimize the potential impacts of transmitters and instruments to the extent possible. 

3.5 Authorizing Take Under the Sea Turtle Research Permitting Program 

As part of the Program, the Permits Division will authorize take of captured sea turtles through 

the issuance of section 10 research permits. Permits for research on turtle parts alone, such as for 

cell line development, would not authorize the take of live animals, and the numbers of parts 

could be unlimited. This section discusses the Permits Division proposed approach for 

authorizing non-lethal and lethal take for research activities on live animals in the wild. 

3.5.1 Sea Turtle Take Levels Authorized 

There is no specified limit or cap on the number of sea turtles that may be taken non-lethally for 

the Program as a whole. However, individual permits issued under the Program will have 

specified limits for non-lethal take and lethal take, as applicable. As shown in Figure 4, past sea 

turtle take numbers authorized by the Permits Division were considerably higher than reportedly 

used take on an annual basis. As part of the Program, permit applicants will be asked to provide 

additional justification for their requested take numbers in an effort to make authorized take 

levels more in line with reported take levels. Non-lethal take of unidentified/hybrid turtles would 

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be allowed under the Program. If an unidentified/hybrid sea turtle dies, then the mortality would 

be attributed to all the possible sea turtle species and DPSs (based on ocean basin) until genetic 

testing is done to confirm the identity. No lethal take would be authorized up-front in individual 

permits for unidentified/hybrid turtles. The Permits Division estimates a modest annual increase 

(approximately 10 percent) in reported take of sea turtles associated with vessel-based captures 

or research procedures on captured turtles (NMFS 2017a). Both authorized and reported take 

numbers for remote survey methods are expected to decrease significantly as a result of the 2016 

NMFS’ Interim Guidance on the ESA Term Harass (NMFS 2016c). 

As a condition of their permit, researchers will be required to follow specific protocols to avoid, 

minimize, and mitigate the unintended adverse effects that may result from research activities 

(e.g., capture, handling, and performing various invasive procedures). While these precautionary 

measures have proven highly effective at reducing the adverse impacts of research, some risk of 

sea turtle mortality still remains. Two types of lethal take may occur as a result of research 

authorized under the Program: (1) observed mortalities reported by the researcher, and (2) 

delayed or “unobserved” mortalities that occurs at some time after the sea turtle is released back 

into the wild. As part of the Program, the Permits Division would authorize lethal take within 

specified levels for the Program as a whole. Lethal take would also be authorized for individual 

permits (that are within the Program) on a case-by-case basis based on researcher requests and 

supporting justification. For individual permits, lethal take would be authorized over the permit 

duration, up to a maximum of ten years. The Permits Division’s lethal take limits for the 

Program are shown in Table 1. 

Each species would have a ten-year lethal take limit by ocean basin (Atlantic versus Pacific). For 

green and loggerhead turtles which have multiple DPSs considered in this opinion, the 10-year 

lethal take limit will represent the combined take limit for all DPSs within that particular ocean 

basin. The Permits Division would not authorize take for a species across ocean basins (i.e., in 

both the Atlantic and Pacific) as the species subjected to research under NMFS jurisdiction do 

not migrate between the Atlantic and Pacific Ocean basins. 

The proposed approach for authorizing lethal take also includes a reserve lethal take buffer that 

would not be authorized up front in research permits. The reserve buffer provides the Program 

some flexibility for unanticipated events, such as the Deepwater Horizon oil spill in 2010, that 

may result in the need for increased research effort. The reserve lethal take could also be used to 

modify a research permit for which the authorized lethal take limit has been reached (or 

exceeded) to allow research to continue. These decisions will be made on a case-by-case basis. 

The Permits Division will carefully consider the circumstances resulting in a researcher 

exceeding their turtle lethal take limit, the amount of lethal take left that could be authorized 

(initial limit and reserve) within a given ten-year period, and any other relevant factors before 

authorizing any additional lethal take through permit modification. 

49 
Fig 42. Average Annual Authorized and Reported Takes of Sea Turtles June 

2007 - May 2017 

16000 

Authorized 

Authorized 

Authorized 

Reported 

Reported 

Reported 

0 

2000 

4000 

6000 

8000 

10000 

12000 

14000 

Aerial/Vessel Survey 

Sea Turtles 

Capture Procedures only 

Figure 4. Average Annual Authorized and Reported Takes of Sea Turtles, June 2007 

through May 2017 (NMFS 2017a). 

 

 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

3.5.2 Allocating Authorized Lethal Take Among Research Permits 

As discussed in Section 3.3, the Program would establish an annual permit cycle for processing 

new sea turtle permit applications and major modifications. The annual cycle will allow Permits 

Division staff to review and evaluate all requests for directed sea turtle take, along with all 

previously authorized take under the programmatic framework, for the upcoming year at one 

time. Once the annual window for submitting new research permit applications is closed, the 

Permits Division can estimate the number of lethal takes that are anticipated in the upcoming 

year for purposes of comparison with the lethal take limit levels established for each species by 

ocean basin. In the first year that the programmatic framework is in place (i.e., 2018), the 

Program will evaluate the lethal takes requested by all applicants for that year’s annual permit 

cycle against the lethal take limits. In subsequent years under the programmatic framework, the 

pool of active permits within the Program will include both newly issued permits, and permits 

issued in previous permit application cycles. Moving forward, authorizations of sea turtle lethal 

take for a given year must consider previously authorized lethal take in permits under the 

Program. Because most existing active permits (issued prior to the Program) authorize mortality 

as a single low take number for multiple species combined per permit, such takes cannot be 

deducted from the individual species lethal take limits; rather, the lethal takes authorized under 

50 
Turtle Research Programmatic Biological Opinion FPR-2017-9230 

existing permits and which have already undergone separate section 7 consultation, are 

considered as part of the baseline for this programmatic consultation. 

Table 1. Proposed ten-year lethal take limits for observed mortalities over the term of 

programmatic consultation. 

the 

Atlantic Lethal Take Limits for Observed Research Mortality 

 Ten year Duration Limits 

Species (DPSs) 

Column A 

Authorized 

in permits 

Column B 

Reserve 

buffer 

Column C 

Total over 

10 years 

Green 

(North Atlantic, South Atlantic) 10 5 15 

Hawksbill 5 3 8 

Kemp's ridley 10 5 15 

Leatherback 10 5 15 

Loggerhead 

(Northwest Atlantic) 10 5 15 

Olive ridley 5 3 8 

Pacific Lethal Take Limits for Observed Research Mortality 

Ten year Duration Limits 

Species (DPSs) 

Column A 

Authorized 

in permits 

Column B 

Reserve 

buffer 

Column C 

Total over 

10 years 

Green 

(Central West Pacific, Central South Pacific, 

Central North Pacific, East Pacific) 

5 2 7 

Hawksbill 5 2 7 

Leatherback 1 1 2 

Loggerhead 

(North Pacific) 5 2 7 

Olive ridley 5 2 7 

Lethal take is authorized in less than ten percent of current permits for activities that would fall 

under the scope of the programmatic. Therefore, based on past permit applications, the Permits 

Division anticipates that sea turtle lethal take will not be authorized for the large majority of 

permits issued under the Program. Provided that the lethal take numbers requested by all 

applicants for the year’s permit cycle are within the ten-year lethal take limits (Column A, Table 

1) for each species and ocean basin, lethal takes would be authorized as requested. This assumes

that all applications and proposed take numbers have been deemed bona fide by the Permits

51 
Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Division and are recommended for issuance. The permit applicant must fully justify their 

requested level of lethal take to the Permits Division, particularly if the requested level exceeds 

the anticipated level based on prior research experience. The Permits Division will only 

authorize observed lethal take if the researcher can justify the numbers (e.g., past report of death, 

requesting riskier methods, etc.) and demonstrate that the research and research methodologies 

are warranted for the conservation and recovery of the species. If the request cannot be justified, 

the applicant’s request for a research mortality may be lowered or the application may be denied. 

Though not anticipated, if the pool of lethal take requests in a given year’s cycle exceeds the 

prescribed lethal take limits for a species/ocean basin, the Permits Division will contact affected 

researchers to discuss options for reducing the anticipated mortality so as not to exceed the 

Program limits. Options may include reducing the number of lethal takes, number of captures by 

gear type, or changing the protocols or procedures requested. The Permits Division will initially 

contact new applicants in a given permit cycle to reduce the anticipated mortalities for a given 

species and ocean basin to the allowable levels. Researchers with permits issued in previous 

years may also be contacted to assess their flexibility in reducing their previously authorized 

lethal take limit or in altering their research approach for the upcoming years. 

3.5.3 Monitoring Sea Turtle Take 

The Permits Division will monitor and track sea turtle take (lethal and non-lethal) from capture, 

handling, and both non-invasive and invasive procedures, as information from researchers is 

reported throughout the year. As a condition of the permit, Permit Holders must notify the 

Permits Division of each research mortality within two business days, followed by submission of 

a written incident report detailing the research mortality within two weeks. Efforts must be made 

to necropsy turtles that die as a result of research activities and results provided to the Permits 

Division for review as part of the report. Sea turtle necropsies may only be conducted by 

authorized personnel. Mortalities that are determined to have occurred prior to authorized 

activities (e.g., decomposed carcass pulled up in a trawl) would not be counted against the 

researcher’s permit or the Program’s limit as these deaths are already accounted for and 

monitored by the STSSN via the necropsy report. All other observed mortalities would count 

against the researcher’s permit and the lethal take limits. Upon review of the incident, the permit 

could be modified in a number of ways to ensure that best practices are used to minimize further 

mortality. These include options such as: 1) improving protocols and methods that likely resulted 

in or contributed to the mortality; 2) limiting authorized capture numbers or specific procedures; 

and 3) requiring additional coordination among researchers or monitoring of the species. If a 

Permit Holder reaches or exceeds their limit of observed (authorized) mortalities specified in 

their permit, they also must stop their research activities until they receive approval from the 

Permits Division to resume work. Before issuing a modification to a permit that has exceeded its 

mortality limit, the Permits Division must determine that the change will not likely result in a 

mortality level that exceeds the Program’s lethal take limits for any species/ocean basin 

combination. 

52 
 

 

 

 

 

 

 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Sea turtle observed mortalities that occur as part of the Program may include both mortality of 

the target research turtle species as well as incidental mortality of non-target sea turtles species. 

The latter scenario could occur in the event that a researcher wants to work solely on one species 

but could incidentally kill another species during fieldwork involving non-selective capture 

methods. To ensure that mortality of non-target turtle species is accounted for in the Program, 

such mortalities will be deducted from the overall Program limits as they occur. Such cases are 

expected to be extremely rare because capture mortalities are rare to begin with, and many 

researchers study the majority of the species found in their waters. 

The Permits Division will closely monitor sea turtle mortality occurring under research permits 

issued as part of the Program. Every effort will be made to avoid exceeding the lethal take limits 

established for each species and ocean basin. The online database titled Authorizations and 

Permits for Protected Species (APPS) will be used to track the annual number of authorized sea 

turtle takes allocated in issued permits and the number of takes reported as used each year. The 

Permits Division can run a report in APPS to evaluate these takes at any time for each species by 

location. 

3.5.4 Addressing Scenarios When a Lethal Take Limit Has Been Exceeded 

It is possible that a ten-year authorized lethal take limit (Column A, Table 1), as proposed for the 

Program as a whole, would be exceeded due to a combination of management uncertainty 

associated with monitoring mortality and the low lethal take limits established for some 

species/ocean basin combinations (e.g., Pacific leatherbacks). The risk of exceeding a lethal take 

limit may increase if researchers due not adhere (either intentionally or unintentionally) to the 

research techniques, procedures and mitigation measures specified as a condition of their permit. 

If a ten-year lethal take Program limit has been exceeded for a particular species/ocean basin 

combination, the Permits Division could make use of the reserve buffer (Column B, Table 1) to 

allow research to continue for that species and within that ocean basin. The lethal takes in the 

reserve buffer could be used if a mortality occurs under a permit that authorizes no lethal takes or 

if a researcher exceeds the lethal take limit authorized for their individual permit (e.g., two 

mortalities reported when only one is authorized). If, upon review of the incident, the Permits 

Division determines that additional lethal take needs to be authorized for the permit, they would 

be drawn from the reserve buffer if Column A takes are all allocated. Additional lethal take will 

be authorized only after the Permits Division has made all other efforts to reduce the likelihood 

of another mortality occurring under the permit. The reserve buffer of lethal takes will be used 

sparingly in the Program and limited to cases where the original (Column A, Table 1) lethal take 

limit was unexpectedly exceeded due to circumstances beyond the control of the researcher or 

the Permits Division (see 3.5.1 above for discussion of the use of reserve take). Reported sea 

turtle mortalities would be monitored closely to avoid exceeding the total ten-year lethal take 

limits (Column C, Table 1). The Permits Division would initiate discussions with the Interagency 

Cooperation division about reinitiation if all Column A lethal takes for a species/ocean basin 

53 
 

 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

have been authorized for a given ten-year period, and at least one authorized lethal take has been 

drawn from the buffer reserve (Column B. Table 1). 

3.5.5 Incidental Take of Non-target Species 

In addition to the effects on sea turtles, the authorized research activities may result in the 

incidental take of other ESA-listed species. Because incidental take is rare during turtle research, 

the Permits Division will manage an annual cap on incidental take for non-target species 

authorized within the ITS of this programmatic biological opinion (i.e., the ITS will not be 

included in the permits themselves, as is currently done). Because the risk of mortality of nontarget species cannot be completely eliminated, the proposed incidental take annual cap will 

include both non-lethal and lethal takes. By not authorizing incidental take by permit, the 

incidental take cap allows the Permits Division to keep the level of take for non- target species 

lower for the Program as a whole (which is included in the baseline of other section 7 

consultations). 

If a non-target ESA-listed species is incidentally taken, the permit holder must stop work and 

notify the Permits Division as described in its permit. The Permits Division will deduct the 

incidental take from the Program’s annual cap for that particular non-target species or DPS. The 

Permits Division will then evaluate the factors that caused the incidental take to occur. As 

necessary, the permit may be modified to account for any changes in protocols, methods or 

mitigation measures required to minimize the chance of additional incidental take before 

research is allowed to resume. 

On rare occasions, a sea turtle researcher may incidentally take a turtle species that is not 

included on their research permit (e.g., capture of a loggerhead under a permit that only 

authorizes take of leatherbacks). Incidental lethal take of a non-target sea turtle species will not 

be exempted under the programmatic ITS as described above for other non-target species, 

Instead, as discussed above (Section 3.5.3), it will be considered as part of the takes evaluated 

pursuant to the Program-wide lethal take limits along with the directed take for that particular 

species or DPS. 

3.6 Internal Program Review 

The Permits Division will conduct an internal review of the Program after one full annual permit 

cycle, including submission of annual reports, has been completed. The internal review will 

evaluate program operations to determine whether resources (time, staff, expertise etc.) need 

adjustment, identify challenges or problems that arose and lessons learned, and identify ways to 

improve how the Program functions. Specific aspects of the Program that will be assessed 

include: 

• Permit cycle – Are the majority of applicants submitting requests on time? Is the volume 

of requests in a cycle manageable in addition to other workload? Is the six-month 

processing window adequate? 

54 
 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

• Take allocation – Are the levels of mortality requested and authorized in line with what 

was expected based on past data? Are the lethal take limits and incidental take estimates 

sufficient or over-estimated? 

• Reporting schedule – Are Permit Holders submitting annual and incident reports on time? 

Is NMFS getting the details needed to assess the Program? 

• Lessons learned – What other challenges or problems arose and how were they resolved? 

Does the process need revision? 

• Future issues – Are there issues on the horizon based on funding announcements, 

trending research interests, species status, new information/papers, etc., that would 

require re-initiation? 

The Permits Division will continue to conduct internal reviews of the Program on a regular basis 

(approximately every 12 to 16 months), as other taxa/species programmatic consultations are 

completed, or more frequently as needed. 

3.7 Adaptive Management 

Adaptive management will be an integral component of the Program. Through adaptive 

management the Permits Division will ensure they are meeting the dual Program objectives of 

authorizing sea turtle research necessary for the conservation and recovery of ESA-listed species 

while mitigating and minimizing any adverse effects on individual turtles and turtle populations. 

At the program level, the Permits Division will continually evaluate and, as appropriate, modify 

the standard permit terms and conditions and required research protocols and mitigation 

measures based on new information received from permit holders, published papers, or other 

relevant sources. Adaptive management will also provide the Permits Division with the 

flexibility to include new sea turtle research methods, procedures, and protocols as part of the 

Program over time. Research methods, procedures, and protocols not specifically addressed in 

this consultation would be authorized as part of the Program only if they meet the specified 

criteria described in Section 3.4.5 above. The Permits Division will also continually monitor and 

evaluate available information regarding the status of each species (or DPS) to ensure that the 

basis for justification of the Program’s authorized lethal take limits is still valid. 

Reported incidences of mortality or serious injury to an ESA-listed species will be further 

investigated by the Permits Division to determine the causal factors, and additional mitigation 

measures may be added, either program–wide or to an individual permit, as warranted. The 

Permits Division can adaptively manage individual permits, through either minor or major 

modifications, as is necessary to avoid exceeding a lethal take limit or to mitigate adverse effects 

from research activities. Any aspect (e.g., species, take numbers, methods, mitigation measures, 

etc.) of a permit can be modified at any time based on new information on either the potential 

impacts of permitted activities on the species (or habitat) or the species baseline (e.g., status, 

threats, habitat range, etc.). 

55 
 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

3.8 Reporting to the Interagency Cooperation Division 

Continued close collaboration and an on-going dialogue between the Permits Division and the 

Interagency Cooperation Division will be an important component of the adaptive approach to 

managing the Program. The Permits Division will summarize and compile information from the 

annual reports submitted by sea turtle researchers (Appendix D) into an annual Program report. 

The Permits Division will submit the annual Program report to the Interagency Cooperation 

Division within 30 days of receiving and reviewing all the annual reports from permit holders. 

The annual Program report to the Interagency Cooperation Division will synthesize data such as 

the number and percentage of takes used for lethal and nonlethal activities, the frequency of 

observed effects of activities, and the number and kinds of non-target species incidentally taken. 

Annual reports will also include notifying the Interagency Cooperation Division if new 

information becomes available indicating that the estimated delayed mortality rate has changed. 

This information will be conveyed and discussed in the report, including references to literature 

and other reports that were the basis for this determination. If new information indicates that a 

procedure or capture method has greater impacts (e.g., reduced fitness, increased mortality risk) 

than those analyzed in this consultation, the Permits Division will consult (either formally or 

informally) with the Interagency Cooperation Division and use the additional documentation to 

modify individual permits as needed. The timing of the annual reporting will allow for the 

Permits Division and the Interagency Cooperation Division to confer with on such matters before 

the next year’s permit cycle begins. The Permits Division will also continue to work closely with 

the Interagency Cooperation Division to routinely check-in (e.g., every five years or more 

frequently as needed) on how the Program is functioning overall, and to determine whether new 

information indicates that the Permits Division should request re-initiation of this consultation. 

56 
Turtle Research Programmatic Biological Opinion FPR-2017-9230 

4 INTERRELATED AND INTERDEPENDENT ACTIONS 

Interrelated actions are those that are part of a larger action and depend on that action for their 

justification. Interdependent actions are those that do not have independent use, apart from the 

action under consideration. We have determined that there are no interrelated or interdependent 

actions resulting from the Permits Division implementation of the Program for the issuance of 

permits for research activities on ESA-listed sea turtles. 

57 
Figure 5. Scope of the action area of research in the Pacific Ocean (shaded area), 

including United States territories. 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

5 ACTION AREA 

Action area means all areas affected directly, or indirectly, by the Federal action, and not just the 

immediate area involved in the action (50 C.F.R. §402.02). The Permits Division proposes to 

issue ESA Section 10(a)(1)(A) scientific research permits for research activities on sea turtles 

within all U.S. waters and the high seas of the Pacific and Atlantic Oceans. 

In the Pacific, this includes the U.S. west coast from California to Washington and their 

associated embayments and estuaries, Hawaii, and all U.S. Pacific territories: Guam, 

Commonwealth of Northern Mariana Islands, Palmyra Atoll, Johnston Atoll, America Samoa, 

Bajo Nuevo Bank, Baker Island, Howland Island, Jarvis Island, Kingman Reef, Midway Islands, 

Serranilla Bank, and Wake Island (Figure 5). The shaded area in light green is an approximation 

of where research may occur. See Appendix E for locations of active Section 10(a)(1)(A) sea 

turtle research permits in the Pacific ocean as of June 30, 2017. 

In the Atlantic, this includes the U.S. east coast from Maine to Florida, Gulf of Mexico, 

Caribbean Sea, U.S. Virgin Islands, Navassa Island, and Puerto Rico and their associated 

embayments and estuaries (Figure 6). The shaded area in gray is an approximation of where 

58 
 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

research may occur. The majority of activity would occur in U.S. waters except when NMFS 

researchers are working within fisheries observer programs or in conjunction with marine 

mammal surveys on the high seas. See Appendix E for locations of active Section 10(a)(1)(A) 

sea turtle research permits in the Atlantic ocean, Gulf of Mexico, and Caribbean as of June 30, 

2017. 

 

Figure 6. Scope of the action area of research in the Atlantic Ocean (shaded area), 

including the Gulf of Mexico, and Caribbean waters. 

Although some sea turtle species have been anecdotally documented in Alaska waters, 

observations are too rare to include this area within the scope of the action area at this time. For 

example, only two loggerhead sea turtles have been reported in Alaska waters over the last fifty 

years. Therefore, the Permits Division does not believe that such an extremely low sighting 

frequency would support a research program or yield meaningful data in Alaska in the 

foreseeable future. Inclusion of Alaska would be reconsidered as part of a request to re-initiate 

the consultation should new information become available indicating an increasing trend in turtle 

sightings and interest from researchers with sufficient resources (e.g., funding) to work in 

Alaska. 

59 
Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Research would not be conducted continuously in all locations within the action area; however, 

NMFS anticipates research could occur in any sector of the action area in the foreseeable future 

as funding or valid research objectives arise. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

6 STATUS OF ENDANGERED SPECIES ACT (ESA) PROTECTED RESOURCES 

This section identifies the ESA-listed species that potentially occur within the action area that 

may be affected by the Program. It then summarizes the biology and ecology of those species 

and what is known about their life histories in the action area. The status is determined by the 

level of risk that the ESA-listed species and designated critical habitat face, based on parameters 

considered in documents such as listing decisions, status reviews, and recovery plans. This 

section also breaks down the species and designated critical habitats that may be affected by the 

proposed action, describing whether or not those species and designated critical habitats are 

likely to be adversely affected by the proposed action. The species and designated critical 

habitats deemed likely to be adversely affected by the proposed action are carried forward 

through the remainder of this opinion. This section helps to inform the description of the species’ 

current “reproduction, numbers, or distribution” as described in 50 CFR 402.02. The species 

potentially occurring within the action area that may be affected by the proposed actions are 

listed in Table 2, along with their regulatory status. 

Table 2. Threatened and endangered species that may be affected by the proposed 

action. 

Species ESA Status Critical Habitat Recovery Plan 

Marine Mammals – Cetaceans 

Blue Whale 

(Balaenoptera musculus) E – 35 FR 18319 -- -- 07/1998 

Bowhead Whale 

(Balaena mysticetes) E – 35 FR 18319 -- -- -- --

False Killer Whale 

(Pseudorca crassidens) 

Main Hawaiian Islands Insular DPS 

82 FR 51186 E – 77 FR 70915 (proposed) -- --

Fin Whale 

(Balaenoptera physalus) E – 35 FR 18319 -- -- 75 FR 47538 

Gulf of Mexico Bryde’s Whale 

(Balaenoptera edeni) 

E – 81 FR 88639 -- -- (Proposed) -- --

Humpback Whale 

(Megaptera novaeangliae) 

Central America DPS 

E – 81 FR 62259 -- -- 11/1991 

Humpback Whale 

(Megaptera novaeangliae) 

Mexico DPS 

T – 81 FR 62259 -- -- 11/1991 

Humpback Whale 

(Megaptera novaeangliae) 

Western North Pacific DPS 

E – 81 FR 62259 -- -- 11/1991 

Killer Whale 

(Orcinus orca) 

Southern Resident DPS 

E – 70 FR 69903 71 FR 69054 73 FR 4176 

North Atlantic Right Whale 

(Eubalaena glacialis) 

59 FR 28805 and E – 73 FR 12024 81 FR 4837 70 FR 32293 

Sei Whale 

(Balaenoptera borealis) E – 35 FR 18319 -- -- 12/2011 

61 
 

 

 

 

 

 

 

 

 

 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Species ESA Status Critical Habitat Recovery Plan 

Sperm Whale 

(Physeter macrocephalus) E – 35 FR 18319 -- -- 75 FR 81584 

Marine Mammals – Pinnipeds 

Guadalupe Fur Seal 

(Arctocephalus townsendi) T – 50 FR 51252 -- -- -- --

Hawaiian Monk Seal 

(Neomonachus schauinslandi) 

80 FR 50925, 53 FR E – 41 FR 51611 18988, and 51 FR 16047 72 FR 46966 

Marine Reptiles 

Green Turtle 

(Chelonia mydas) 

North Atlantic DPS 

T – 81 FR 20057 63 FR 46693 FR Not Available 

11/1991 

Green Turtle 

(Chelonia mydas) 

South Atlantic DPS 

T – 81 FR 20057 -- -- -- --

Green Turtle 

(Chelonia mydas) 

Central West Pacific DPS 

E – 81 FR 20057 -- -- 63 FR 28359 

Green Turtle 

(Chelonia mydas) 

Central South Pacific DPS 

E – 81 FR 20057 -- -- 63 FR 28359 

Green Turtle 

(Chelonia mydas) 

Central North Pacific DPS 

T – 81 FR 20057 -- -- 63 FR 28359 

Green Turtle 

(Chelonia mydas) 

East Pacific DPS 

T – 81 FR 20057 -- -- 63 FR 28359 

Hawksbill Turtle 

(Eretmochelys imbricata) E – 35 FR 8491 63 FR 46693 63 FR 28359 and 

57 FR 38818 

Kemp’s Ridley Turtle 

(Lepidochelys kempii) E – 35 FR 18319 -- -- 9/2011 

Leatherback Turtle 

(Dermochelys coriacea) 

44 FR 17710 and E – 35 FR 8491 77 FR 4170 63 FR 28359 and 

10/1991 

Loggerhead Turtle 

(Caretta caretta) 

North Pacific Ocean DPS 

E – 76 FR 58868 -- -- 63 FR 28359 

Loggerhead Turtle 

(Caretta caretta) 

Northeast Atlantic Ocean DPS 

E – 76 FR 58868 -- -- -- --

Loggerhead Turtle 

(Caretta caretta) 

Northwest Atlantic Ocean DPS 

T – 76 FR 58868 79 FR 39856 74 FR 2995 

Olive Ridley Turtle 

(Lepidochelys olivacea) 

Mexico's Pacific Coast Breeding 

Colonies 

E – 43 FR 32800 -- -- 63 FR 28359 

Olive Ridley Turtle 

(Lepidochelys olivacea) 

All Other Areas T – 43 FR 32800 -- -- -- --

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Species ESA Status Critical Habitat Recovery Plan 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

63 

Fishes 

Atlantic Salmon 

(Salmo salar) 

Gulf of Maine DPS 

E – 74 FR 29344 

and 65 FR 69459 74 FR 29300 

70 FR 75473 and 

81 FR 18639 

(Draft) 

Atlantic Sturgeon 

(Acipenser oxyrinchus oxyrinchus) 

Carolina DPS 

E – 77 FR 5913 82 FR 39160 -- -- 

Atlantic Sturgeon 

(Acipenser oxyrinchus oxyrinchus) 

Chesapeake DPS 

E – 77 FR 5879 82 FR 39160 -- -- 

Atlantic Sturgeon 

(Acipenser oxyrinchus oxyrinchus) Gulf 

of Maine DPS 

T – 77 FR 5879 82 FR 39160 -- -- 

Atlantic Sturgeon 

(Acipenser oxyrinchus oxyrinchus) 

New York Bight DPS 

E – 77 FR 5879 82 FR 39160 -- -- 

Atlantic Sturgeon 

(Acipenser oxyrinchus oxyrinchus) 

South Atlantic DPS 

E – 77 FR 5913 82 FR 39160 -- -- 

Bocaccio 

(Sebastes paucispinis) 

Puget Sound/Georgia Basin DPS 

E – 75 FR 22276 

and 82 FR 7711 79 FR 68041 81 FR 54556 (Draft) 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

California Coastal ESU 

T – 70 FR 37160 70 FR 52488 81 FR 70666 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

Central Valley Spring-Run ESU 

T – 70 FR 37160 70 FR 52488 79 FR 42504 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

Lower Columbia River ESU 

T – 70 FR 37160 70 FR 52629 78 FR 41911 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

Puget Sound ESU 

T – 70 FR37160 70 FR 52629 72 FR 2493 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

Sacramento River Winter-Run ESU 

E – 70 FR 37160 58 FR 33212 79 FR 42504 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

Snake River Fall-Run ESU 

T – 70 FR 37160 58 FR 68543 80 FR 67386 

(Draft) 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

Snake River Spring/Summer Run ESU 

T – 70 FR 37160 64 FR 57399 81 FR 74770 

(Draft) 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

Upper Columbia River Spring-Run ESU 

E – 70 FR 37160 70 FR 52629 72 FR 57303 

Chinook Salmon 

(Oncorhynchus tshawytscha) 

Upper Willamette River ESU 

T – 70 FR 37160 70 FR 52629 76 FR 52317 

Chum Salmon T – 70 FR 37160 70 FR 52629 78 FR 41911 
 

 

 

 

 

 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Species ESA Status Critical Habitat Recovery Plan 

(Oncorhynchus keta) 

Columbia River ESU 

Chum Salmon 

(Oncorhynchus keta) 

Hood Canal Summer-Run ESU 

T – 70 FR 37160 70 FR 52629 72 FR 29121 

Coho Salmon 

(Oncorhynchus kisutch) 

Central California Coast ESU 

E – 70 FR 37160 64 FR 24049 77 FR 54565 

Coho Salmon 

(Oncorhynchus kisutch) 

Lower Columbia River ESU 

T – 70 FR 37160 81 FR 9251 78 FR 41911 

Coho Salmon 

(Oncorhynchus kisutch) 

Oregon Coast ESU 

T – 73 FR 7816 73 FR 7816 81 FR 90780 

Coho Salmon 

(Oncorhynchus kisutch) 

Southern Oregon and Northern California 

Coasts ESU 

T – 70 FR 37160 64 FR 24049 79 FR 58750 

Eulachon 

(Thaleichthys pacificus) 

Southern DPS 

T – 75 FR 13012 76 FR 65323 9/2017 

Giant Manta Ray 

(Manta birostris) 

T – 82 FR 3694 

(Proposed) -- -- -- --

Green Sturgeon 

(Acipenser medirostris) 

Southern DPS 

T – 71 FR 17757 74 FR 52300 2010 (Outline) 

Gulf Sturgeon 

(Acipenser oxyrinchus desotoi) T – 56 FR 49653 68 FR 13370 09/1995 

Nassau Grouper 

(Epinephelus striatus) T – 81 FR 42268 -- -- -- --

Oceanic Whitetip Shark 

(Carcharhinus longimanus) 

T – 81 FR 96304 

(Proposed) -- -- -- --

Scalloped Hammerhead Shark 

(Sphyrna lewini) 

Central and Southwest Atlantic DPS 

T – 79 FR 38213 -- -- -- --

Scalloped Hammerhead Shark 

(Sphyrna lewini) 

Eastern Atlantic DPS 

E – 79 FR 38213 -- -- -- --

Scalloped Hammerhead Shark 

(Sphyrna lewini) 

Eastern Pacific DPS 

E – 79 FR 38213 -- -- -- --

Scalloped Hammerhead Shark 

(Sphyrna lewini) 

Indo-West Pacific DPS 

T – 79 FR 38213 -- -- -- --

Shortnose Sturgeon 

(Acipenser brevirostrum) E – 32 FR 4001 -- -- 63 FR 69613 

Smalltooth Sawfish 

(Pristis pectinata) 

U.S. portion of range DPS 

E – 68 FR 15674 74 FR 45353 74 FR 3566 

Sockeye Salmon E – 70 FR 37160 58 FR 68543 80 FR 32365 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Species ESA Status Critical Habitat Recovery Plan 

(Oncorhynchus nerka) 

Snake River ESU 

Steelhead Trout 

(Oncorhynchus mykiss) 

California Central Valley DPS 

T – 71 FR 834 70 FR 52487 79 FR 42504 

Steelhead Trout 

(Oncorhynchus mykiss) 

Central California Coast DPS 

T – 71 FR 834 70 FR 52487 81 FR 70666 

Steelhead Trout 

(Oncorhynchus mykiss) 

Lower Columbia River DPS 

T – 71 FR 834 70 FR 52629 78 FR 41911 

Steelhead Trout 

(Oncorhynchus mykiss) 

Middle Columbia River DPS 

T – 71 FR 834 70 FR 52629 74 FR 50165 

Steelhead Trout 

(Oncorhynchus mykiss) 

Northern California DPS 

T – 71 FR 834 70 FR 52487 81 FR 70666 

Steelhead Trout 

(Oncorhynchus mykiss) 

Puget Sound DPS 

T – 72 FR 26722 81 FR 9251 -- --

Steelhead Trout 

(Oncorhynchus mykiss) 

Snake River Basin DPS 

T – 71 FR 834 70 FR 52629 81 FR 74770 

(Draft) 

Steelhead Trout 

(Oncorhynchus mykiss) 

South-Central California Coast DPS 

T – 71 FR 834 70 FR 52487 78 FR 77430 

Steelhead Trout 

(Oncorhynchus mykiss) 

Southern California DPS 

E – 71 FR 834 70 FR 52487 77 FR 1669 

Steelhead Trout 

(Oncorhynchus mykiss) 

Upper Columbia River DPS 

T – 71 FR 834 70 FR 52629 72 FR 57303 

Steelhead Trout 

(Oncorhynchus mykiss) 

Upper Willamette River DPS 

T – 71 FR 834 70 FR 52629 76 FR 52317 

Yelloweye Rockfish 

(Sebastes rubberimus) 

Puget Sound/Georgia Basin DPS 

T – 75 FR 22276 79 FR 68041 and 82 FR 7711 81 FR 54556 

(Draft) 

Marine Invertebrates and Plants 

Acropora globiceps Coral T – 79 FR 53851 -- -- -- --

Acropora jacquelineae Coral T – 79 FR 53851 -- -- -- --

Acropora retusa Coral T – 79 FR 53851 -- -- -- --

Acropora speciosa Coral T – 79 FR 53851 -- -- -- --

Black Abalone 

(Haliotis cracherodii) E – 74 FR 1937 76 FR 66805 -- --

Boulder Star Coral T – 79 FR 53851 -- -- -- --

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Species ESA Status Critical Habitat Recovery Plan 

(Orbicella franksi) 

Elkhorn Coral 

(Acropora palmata) T – 79 FR 53851 73 FR 72210 80 FR 12146 

Euphyllia paradivisa Coral T – 79 FR 53851 -- -- -- --

Isopora crateriformis Coral T – 79 FR 53851 -- -- -- --

Johnson’s Seagrass 

(Halophila johnsonii) T – 63 FR 49035 65 FR 17786 67 FR 62230 

Lobed Star Coral 

(Orbicella annularis) T – 79 FR 53851 -- -- -- --

Mountainous Star Coral 

(Orbicella faveolata) T – 79 FR 53851 -- -- -- --

Rough Cactus Coral 

(Mycetophyllia ferox) T – 79 FR 53851 -- -- -- --

Pillar Coral 

(Dendrogyra cylindrus) T – 79 FR 53851 -- -- -- --

Seriatopora aculeata Coral T – 79 FR 53851 -- -- -- --

Staghorn Coral 

(Acropora cervicornis) T – 79 FR 53851 73 FR 72210 80 FR 12146 

White Abalone 

(Haliotis sorenseni) E – 66 FR 29046 66 FR 29046 

(Not Prudent) 73 FR 62257 

6.1 Species and Designated Critical Habitat Not Likely to be Adversely Affected 

NMFS uses two criteria to identify the ESA-listed or critical habitat that are not likely to be 

adversely affected by the proposed action, as well as the effects of activities that are interrelated 

to or interdependent with the Federal agency’s proposed action. The first criterion is exposure, or 

some reasonable expectation of a co-occurrence, between one or more potential stressors 

associated with the proposed activities and ESA-listed species or designated critical habitat. If 

we conclude that an ESA-listed species or designated critical habitat is not likely to be exposed 

to the proposed activities, we must also conclude that the species or critical habitat is not likely 

to be adversely affected by those activities. 

The second criterion is the probability of a response given exposure. ESA-listed species or 

designated critical habitat that is exposed to a potential stressor but is likely to be unaffected by 

the exposure is also not likely to be adversely affected by the proposed action. We applied these 

criteria to the ESA-listed species in Table 2 and we summarize our results below. 

An action warrants a "may affect, not likely to be adversely affected" finding when its effects are 

wholly beneficial, insignificant or discountable. Beneficial effects have an immediate positive 

effect without any adverse effects to the species or habitat. Beneficial effects are usually 

discussed when the project has a clear link to the ESA-listed species or its specific habitat needs 

and consultation is required because the species may be affected. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Insignificant effects relate to the size or severity of the impact and include those effects that are 

undetectable, not measurable, or so minor that they cannot be meaningfully evaluated. 

Insignificant is the appropriate effect conclusion when plausible effects are going to happen, but 

will not rise to the level of constituting an adverse effect. That means the ESA-listed species may 

be expected to be affected, but not harmed or harassed. 

Discountable effects are those that are extremely unlikely to occur. For an effect to be 

discountable, there must be a plausible adverse effect (i.e., a credible effect that could result from 

the action and that would be an adverse effect if it did impact a listed species), but it is very 

unlikely to occur. 

ESA-Listed Species Not Likely to be Adversely Affected 

• Cetaceans: blue whale, fin whale, sei whale, sperm whale, North Atlantic right whale, 

bowhead whale, false killer whale Main Hawaiian Islands Insular DPS, humpback whale 

Central America DPS, humpback whale Mexico DPS, humpback whale Western North 

Pacific DPS, killer whale Southern Resident DPS 

• Pinnipeds: Hawaiian monk seal, Guadalupe fur seal 

• Pacific Salmonids: 

 Chinook salmon ESUs: California coastal, Central Valley spring-run, Lower 

Columbia River, Puget Sound, Sacramento River winter-run, Snake River fallrun, Snake River spring/ summer-run, Upper Columbia River spring-run, Upper 

Willamette River 

 Coho salmon ESUs: Central California coast, Oregon coast, Lower Columbia 

River, Southern Oregon & Northern California coasts 

 Chum salmon ESUs: Columbia River, Hood Canal summer-run 

 Sockeye salmon ESU: Snake River 

 Steelhead trout DPSs: Central California coast, California Central Valley, Lower 

Columbia River, Middle Columbia River, Northern California, Snake River Basin 

Puget Sound, South-Central California coast, Southern California, Upper 

Columbia River, Upper Willamette River 

• Rockfish (Sebastes sp.): yelloweye rockfish, bocaccio 

• Eulachon Southern DPS 

• White abalone and black abalone 

• Corals: boulder star, lobed star, mountainous star, elkhorn, staghorn, pillar, rough cactus, 

Acropora globiceps, Acropora jacquelineae, Acropora retusa, Acropora speciose, 

Euphyllia paradivisa, Isopora crateriformis, Seriatopora aculeate 

• Johnsons’s seagrass 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Proposed Species Not Likely to be Adversely Affected 

• Bryde’s whale Gulf of Mexico subspecies 

• Oceanic whitetip shark 

• Giant manta ray 

Designated Critical Habitat Not Likely to be Adversely Affected 

• Sea Turtles: green North Atlantic DPS, hawksbill, leatherback, loggerhead Northwest 

Atlantic DPS 

• Cetaceans: North Atlantic right whale, killer whale 

• Fish species: smalltooth sawfish U.S. range, green sturgeon Southern DPS, Gulf sturgeon 

• Hawaiian monk seal 

• Black abalone 

• Corals: elkhorn, staghorn 

• Johnson’s seagrass 

Proposed Critical Habitat Not Likely to be Adversely Affected 

• False killer whale Main Hawaiian Islands Insular DPS 

The rationale for reaching the determination of “not likely to adversely affect” for each of these 

species and/or their designated critical habitat is discussed below. 

6.1.1 ESA-listed and Proposed Cetacean Species 

ESA-listed cetaceans that could potentially occur within the action area include the following: 

blue whale, fin whale, sei whale, sperm whale, North Atlantic right whale, bowhead whale, false 

killer whale Main Hawaiian Islands Insular DPS, humpback whale Central America DPS, 

humpback whale Mexico DPS, humpback whale Western North Pacific DPS, and killer whale 

Southern Resident DPS. In addition, one large whale species that could potentially occur within 

the action area has been proposed for ESA-listing: Bryde’s whale Gulf of Mexico subspecies. 

While it is possible that these cetacean species could be subject to harassment and/or harm from 

sea turtle research vessels or entanglement in turtle capture netting gear, the likelihood of this 

occurring is so low that we consider these effects discountable. To date, there have been no 

reported interactions or take (i.e., vessel strike, capture/entanglement in gear, or harassment) of 

cetaceans by sea turtle researchers permitted by the Permits Division. In addition to the small 

spatial overlap, mitigation measures are in place to prevent interactions and adverse effects from 

occurring. In the event that marine mammals are encountered during permitted research 

activities, as a condition of their permit, researchers must follow the NMFS Marine Mammal 

Approach and Viewing Guidelines applicable to the particular NMFS region with jurisdiction 

over the study area. Additionally, all nets must be closely attended and continuously monitored. 

Netting cannot be initiated if marine mammals are within the vicinity (100-foot radius) of the 

planned netting area, and nets must be pulled if marine mammals enter the research area and 

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remain there after nets have been deployed. Additional mitigation measures implemented by 

researchers include the use of fishing gear that complies with the Harbor Porpoise Take 

Reduction Plan and the Atlantic Large Whale Take Reduction Plan, and the use of nets outfitted 

with acoustic pingers to deter marine mammal interactions. In the event any research vessel is 

within range to be detected by a cetacean, the cetacean is expected to have either no response, or 

to respond with minor adjustments to their behavior, which will be temporary. These behavioral 

adjustments are expected to have negligible impacts on ESA-listed cetacean species and will not 

rise to the level of take. 

Given the extremely low likelihood of interaction between sea turtle research activities and ESAlisted or proposed cetaceans, and the mitigation measures in place as a condition of research 

permits issued under section 10, and the negligible impacts of any behavioral responses of 

cetaceans that are encountered, we determine that the proposed action is not likely to adversely 

affect blue whales, fin whales, sei whales, sperm whales, North Atlantic right whales, bowhead 

whales, false killer whales Main Hawaiian Islands Insular DPS, humpback whales Central 

America DPS, humpback whales Mexico DPS, humpback whales Western North Pacific DPS, 

and killer whales Southern Resident DPS. 

6.1.2 Cetacean Designated and Proposed Critical Habitat 

Designated critical habitat for two cetaceans can potentially overlap with the proposed research 

activities: North Atlantic right whale and southern resident DPS killer whale. Proposed critical 

habitat for the false killer whale Main Hawaiian Islands Insular DPS can also potentially overlap 

with the proposed research activities. 

Critical habitat was initially designated for the North Atlantic right whale in 1994 and replaced 

by NMFS with a new designation in January 2016. The new critical habitat designation includes 

Unit 1 in the Gulf of Maine (GOM) and Georges Bank region and Unit 2 off the Southeast U.S. 

coast. The physical and biological features essential to the conservation of the North Atlantic 

right whale found in these areas include a combination of the following biological and physical 

oceanographic features: 1) the physical oceanographic conditions and structures of the GOM and 

Georges Bank region that combine to distribute and aggregate C. finmarchicus for right whale 

foraging, namely prevailing currents and circulation patterns, bathymetric features (basins, 

banks, and channels), oceanic fronts, density gradients, and temperature regimes; 2) low flow 

velocities in Jordan, Wilkinson, and Georges Basins that allow diapausing C. finmarchicus to 

aggregate passively below the convective layer to that copepods are retained in the basins; 3) late 

stage C. finmarchicus in dense aggregations in the GOM and Georges Bank region; and 4) 

diapausing C. finmarchicus in aggregations in the GOM and Georges Bank region. The essential 

physical and biological feature for right whale calving habitat include: 1) calm sea surface 

conditions of Force 4 or less on the Beaufort Wind Scale; 2) sea surface temperatures from a 

minimum of 7 degrees Celsius and never more than 17 degrees Celsius; 3) water depths of 6 to 

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28 meters, where these features simultaneously co-occur over contiguous areas of at least 231 

nm2 of ocean waters during the months of November through April. 

On November 29, 2006, NMFS designated critical habitat for the Southern Resident killer whale 

(71 FR 69054). The critical habitat consists of approximately 6,630 km2 in three areas: the 

Summer Core Area in Haro Strait and waters around the San Juan Islands; Puget Sound; and the 

Strait of Juan de Fuca. It provides the following physical and biological features essential to the 

conservation of Southern Resident killer whales: water quality to support growth and 

development; prey species of sufficient quantity, quality and availability to support individual 

growth, reproduction and development, as well as overall population growth; and inter-area 

passage conditions to allow for migration, resting, and foraging. 

On November 3, 2017, NMFS published a proposed rule for the false killer whale Main 

Hawaiian Islands Insular DPS critical habitat (82 FR 51186). The rule proposes to designate 

approximately 49,701 km2 (19,184 miles squared) of marine habitat from the 45-meter depth 

contour to the 3200-meter depth contour around the main Hawaiian Islands from Niihau east to 

Hawaii. Specific biological and physical features essential for the conservation of this DPS 

include the following: (1) Island-associated marine habitat that supports all life stages, including 

a wide range of depths for false killer whales to travel, forage, and move freely around and 

between the main Hawaiian Islands, (2) Prey species (i.e., large pelagic fish and squid) of 

sufficient quantity, quality, and availability to support individual growth, reproduction, and 

development, as well as overall population growth, (3) Waters free of pollutants of a type and 

amount harmful to false killer whales, (4) Habitat free of anthropogenic noise that would 

significantly impair the value of the habitat for false killer whales’ use or occupancy. 

While the proposed research activities would directly overlap with some of these essential 

features, very few if any, effects are possible. The proposed activities would not significantly 

alter the physical or oceanographic conditions within the action area, as only minor changes in 

water flow, current and noise level would be expected from vessel traffic, and no changes in 

ocean bathymetry would occur. The capture gears used by turtle researchers will not collect C. 

finmarchius, an important food source of North Atlantic right whales. While some research 

activities may temporarily disturb C. finmarchius aggregations, these disturbances will be 

minimal in time and space. Similarly, the effect of sea turtle research gear on killer whale or 

false killer whale prey quantity, quality and availability is expected to be insignificant. Finally, 

the proposed activities would in no way alter the sea state, temperature, water quality or water 

depth, and so effects to these features are deemed discountable. 

Given the biological and physical features used to designate critical habitat, we determine that 

the proposed action would not destroy or adversely modify either the North Atlantic right whale 

or southern resident killer whale designated critical habitat. We also determine that the proposed 

action would not destroy or adversely modify the proposed critical habitat for false killer whale 

Main Hawaiian Islands Insular DPS. 

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6.1.3 Sea Turtle Designated Critical Habitat 

Designated critical habitat for the following turtle species can potentially overlap with the 

proposed research activities: North Atlantic DPS green, hawksbill, leatherback, and Northwest 

Atlantic DPS loggerhead. In 1998, NMFS designated critical habitat for the North Atlantic green 

sea turtle to include the coastal waters surrounding Culebra Island, Puerto Rico, and the 

hawksbill sea turtle to include the coastal waters surrounding Mona and Monito Islands, Puerto 

Rico (63 FR 46693). Designated critical habitat for green turtles including the waters 

surrounding the island of Culebra from the mean high water line seaward to three nautical miles. 

These waters include Culebra’s outlying Keys including Cayo Norte, Cayo Ballena, Cayos 

Geniqui, Isla Culebrita, Arrecife Culebrita, Cayo de Luis Pena, Las Hermanas, El Mono, Cayo 

Lobo, Cayo Lobito, Cayo Botijuela, Alcarraza, Los Gemelos, and Piedra Steven. Sea grasses are 

a principal dietary component of juvenile and adult green turtles. The Culebra Archipelago is 

important green sea turtle development and feeding habitat that includes sea grasses such as 

Thalassia testudium. The coral reefs and other topographic features within these waters provide 

green turtles with shelter during inter-foraging periods. 

On September 2, 1998, NMFS established critical habitat for hawksbill sea turtles around Mona 

and Monito Islands, Puerto Rico from the mean high water line seaward to three nautical miles 

(63 FR 46693). Aspects of these areas that are important for hawksbill sea turtle survival and 

recovery include important natal development habitat, refuge from predation, shelter between 

foraging periods, and food for hawksbill sea turtle prey. 

Critical habitat was designated on July 10, 2014 for the Northwest Atlantic DPS of loggerhead 

sea turtle and includes 38 occupied marine areas in the Atlantic Ocean and Gulf of Mexico. 

These areas contain one or a combination of habitat types: nearshore reproductive habitat, 

foraging habitat, winter area, breeding areas, constricted migratory corridors, and/or Sargassum 

habitat. The physical and biological features (formerly referred to as primary constituent 

elements in the original designation) essential to the conservation of the Northwest Atlantic DPS 

of Loggerhead Sea Turtles found in nearshore reproductive habitat are (1) nearshore waters 

directly off the highest density nesting beaches and their adjacent beaches as identified in 50 

CFR 17.95(c) to 1.6 km (1 mile) offshore; (2) waters sufficiently free of obstructions or artificial 

lighting to allow transit through the surf zone and outward toward open water; and (3) waters 

with minimal man-made structures that could promote predators (i.e., nearshore predator 

concentration caused by submerged and emergent offshore structures), disrupt wave patterns 

necessary for orientation, and/ or create excessive longshore currents. The essential physical and 

biological features found in loggerhead migratory habitat are (1) constricted continental shelf 

area relative to nearby continental shelf waters that concentrate migratory pathways; and (2) 

passage conditions to allow for migration to and from nesting, breeding, and/or foraging areas. 

The essential physical and biological features found in loggerhead breeding habitat are (1) high 

densities of reproductive male and female loggerheads; (2) proximity to primary Florida 

migratory corridor; and (3) proximity to Florida nesting grounds. 

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On March 23, 1979, leatherback critical habitat was identified adjacent to Sandy Point, St. Croix, 

Virgin Islands from the 183 meter isobath to mean high tide level between 17° 42’12” N and 

65°50’00” W (44 FR 17710). This habitat is essential for nesting, which has been increasingly 

threatened since 1979, when tourism increased significantly, bringing nesting habitat and people 

into close and frequent proximity. The designated critical habitat is within the Sandy Point 

National Wildlife Refuge. On January 20, 2012, NMFS issued a final rule to designate additional 

critical habitat for the leatherback sea turtle (50 CFR 226). This designation includes 

approximately 43,798 square kilometers stretching along the California coast from Point Arena 

to Point Arguello east of the 3,000 m depth contour; and 64,760 square kilometers stretching 

from Cape Flattery, Washington to Cape Blanco, Oregon east of the 2,000 meters depth contour. 

The designated areas comprise approximately 108,558 square kilometers of marine habitat and 

include waters from the ocean surface down to a maximum depth of 80 meters. They were 

designated specifically because of the occurrence of prey species, primarily scyphomedusae of 

the order Semaeostomeae (i.e., jellyfish), of sufficient condition, distribution, diversity, 

abundance and density necessary to support individual as well as population growth, 

reproduction, and development of leatherbacks. 

While the proposed sea turtle research activities would directly overlap with the essential 

features of sea turtle critical habitat, very few if any, effects are possible. The temporary 

operation of a vessel and gear (e.g., stationary nets and trawl) to catch sea turtles is expected to 

result in little to no alteration of the identified essential features of sea turtle critical habitat, 

which include access to habitat, water chemistry, live bottom habitat, and availability of prey 

species. Mitigation measures as a condition of research permit would prevent setting or dragging 

nets over live bottom. The proposed activities would have no anticipated impact on migratory 

pathways or habitat features essential for sea turtle shelter (i.e., coral reefs, ledges and other 

structure), nor would they significantly alter the physical or oceanographic conditions within the 

action area. Only minor changes in water flow and current would be expected from research 

vessel traffic and capture gear. Because research vessel activity and use of capture gear is shortterm and temporary (i.e., not a permanent structure), the proposed research activities would not 

prevent turtles from accessing marine habitat and nesting beaches. Due to the mesh sizes and 

gear configurations used to capture sea turtles, the effect of research gear on turtle prey items 

identified as essential features of critical habitat (e.g., sea grasses, jellyfish) is also expected to be 

insignificant. 

Given the biological and physical features used to designate critical habitat, we determine that 

the proposed action would not destroy or adversely modify the designated critical habitat of the 

North Atlantic DPS green, hawksbill, leatherback, or Northwest Atlantic DPS loggerhead. 

6.1.4 ESA-listed Pinniped Species 

Two species of ESA-listed pinnipeds that could potentially occur within the action area are the 

Hawaiian monk seal and Guadalupe fur seal. While it is possible that these species could be 

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subject to harassment and/or harm from sea turtle research vessels or entanglement in turtle 

capture netting gear, the likelihood of this occurring is so low that we consider these effects 

discountable. To date, there have been no reported interactions or take (i.e., vessel strike, 

capture/entanglement in gear, or harassment) of pinnipeds by sea turtle researchers permitted by 

the Permits Division. In addition to the small spatial overlap, mitigation measures are in place to 

prevent interactions and adverse effects from occurring. In the event that marine mammals are 

encountered during permitted research activities, as a condition of their permit, researchers must 

follow the NMFS Marine Mammal Approach and Viewing Guidelines applicable to the 

particular NMFS region with jurisdiction over the study area. Additionally, all nets must be 

closely attended and continuously monitored. Netting cannot be initiated if marine mammals are 

within the vicinity (100-foot radius) of the planned netting area, and nets must be pulled if 

marine mammals enter the research area and remain there after nets have been deployed. In the 

event any research vessel is within range to be detected by a Guadalupe fur seal or Hawaiian 

monk seal the individual is expected to have either no response, or to respond with minor 

adjustments to their behavior, which will be temporary. These behavioral adjustments are 

expected to have negligible impacts on individual seals and will not rise to the level of take. 

Given the extremely low likelihood of interaction between sea turtle research activities and ESAlisted pinnipeds, and the mitigation measures in place as a condition of research permits issued 

under section 10, and the negligible behavioral response of ESA-listed seals if they were to be 

encountered, we determine that the proposed action is not likely to adversely affect Hawaiian 

monk seals or Guadalupe fur seals. 

6.1.5 Pinniped Designated Critical Habitat 

Hawaiian monk seal critical habitat was originally designated on April 30, 1986 (51 FR 16047) 

and was extended on May 26, 1988 (53 FR 18988). It includes all beach areas, sand spits, and 

islets (including all beach crest vegetation to its deepest extent inland), lagoon waters, inner reef 

waters, and ocean waters out to a depth of 37 meters around the northwestern Hawaiian Islands 

breeding atolls and islands. On September 21, 2015, NMFS published a final rule to revise 

designated critical habitat for Hawaiian monk seals (80 FR 50925), extending the current 

designation in the northwestern Hawaiian Islands out to the 200 m depth contour (including Kure 

Atoll, Midway Islands, Pearl and Hermes Reef, Lisianski Island, Laysan Island, Maro Reef, 

Gardner Pinnacles, French Frigate Shoals, Necker Island, and Nihoa Island). It also designated 

six new areas in the main Hawaiian Islands (i.e., terrestrial and marine habitat from 5 m inland 

from the shoreline extending seaward to the 200 m depth contour around Kaula, Niihau, Kauai, 

Oahu, Maui, Nui, and Hawaii). The physical and biological features identified for these areas 

also include adequate prey quality and quantity for juvenile and adult monk seal foraging. 

While the proposed sea turtle research activities could directly overlap with the essential features 

of Hawaiian monk seal critical habitat, very few if any, effects are possible. The temporary 

operation of vessels and gear (e.g., stationary nets and trawl) to catch sea turtles would not 

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significantly alter the physical or oceanographic conditions within the action area. Only minor 

changes in water flow and current would be expected from research vessel traffic and capture 

gear. Any effects of these activities on the identified essential features of Hawaiian monk seal 

critical habitat would be insignificant. Because research vessel activity and use of capture gear is 

short-term and temporary (i.e., not a permanent structure and in place for several hours or 

overnight at most), the proposed research activities would not prevent monk seals from accessing 

marine habitat or haul out behavior. While certain types of turtle research gear (e.g., tangle nets) 

could potentially capture Hawaiian monk seal prey, the expected frequency of this occurring is 

extremely low. As such, the effect of bycatch in sea turtle research gear on the quality and 

quantity of Hawaiian monk seal prey is also expected to be insignificant. 

Given the biological and physical features used to designate critical habitat, we determine that 

the proposed action would not destroy or adversely modify the designated critical habitat of the 

Hawaiian monk seal. 

6.1.6 ESA-listed and Proposed Fish Species 

There are 27 ESA-listed Pacific salmonid species (i.e., ESUs and DPSs) that could potentially 

occur within the action area (see above for list). Three other ESA-listed fish species that could 

potentially occur within the action area are the yelloweye rockfish, bocaccio, and the Southern 

DPS of eulachon. While it is possible that any of these fish species could be subject to 

harassment and/or harm from sea turtle research vessels or entanglement in turtle capture netting 

gear, the likelihood of this occurring is so low that we consider these effects discountable. To 

date, there have been no reported interactions or take (i.e., vessel strike, capture/entanglement in 

gear, or harassment) of any of these fish species by sea turtle researchers permitted by the 

Permits Division. The relative abundance of these species in the Action Area is low, and, given 

the small amount of spatiotemporal overlap, these fish populations are not likely to be affected 

by turtle research activities. These species are generally not susceptible to impacts from vessel 

transit, and are unlikely to become entangled in turtle research gear due to their small size 

relative to net mesh sizes and gear configurations used to capture sea turtles. 

In addition to these ESA-listed species, there are two species proposed for ESA-listing that could 

potentially occur within the action area: Oceanic whitetip shark and giant manta ray. Similar to 

the species above, the relative abundance of these species in the Action Area is low, and, given 

anticipated the small amount of spatiotemporal overlap, these fish populations are not likely to 

be affected by turtle research activities. While it is possible that large pelagic fish species could 

be subject to harassment and/or harm from sea turtle research vessels or entanglement in turtle 

capture netting gear, the likelihood of this occurring is so low that we consider these effects 

discountable. 

Given the extremely low likelihood of interaction between sea turtle research activities and these 

ESA-listed or proposed fish species, we determine that the proposed action is not likely to 

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adversely affect any ESA-listed Pacific salmonids, yelloweye rockfish, bocaccio, Southern DPS 

of eulachon, oceanic whitetip shark, or giant manta ray. 

6.1.7 Fish Species Designated Critical Habitat 

Designated critical habitat for the following ESA-listed fish species can potentially overlap with 

the proposed research activities: smalltooth sawfish U.S. range, green sturgeon Southern DPS, 

and Gulf sturgeon. 

Critical habitat for smalltooth sawfish was designated in 2009 and includes two major units: 

Charlotte Harbor (221,459 acres) and Ten Thousand Islands/Everglades (619,013 acres). These 

two units include essential sawfish nursery areas. Within the nursery areas, two features were 

identified as essential to the conservation of the species: red mangroves (Rhizophora mangle), 

and euryhaline habitats with water depths less than or equal to 0.9 meters. 

Critical habitat was designated for Southern DPS of green sturgeon on October 9, 2009, and 

includes marine, coastal bay, estuarine, and freshwater areas (74 FR 52300) . Only the marine 

portion of designated Southern DPS of green sturgeon critical habitat occurs with the action area 

and thus may be affected by the proposed action. Critical habitat within marine waters includes 

areas within the 60 fathom (110 m [361ft]) isobath from Monterey Bay to the U.S.-Canada 

border. Many coastal bays and estuaries are designated as critical habitat, including: San 

Francisco Estuary and Humboldt Bay in California; Coos, Winchester, Yaquina, and Nehalem 

bays in Oregon; Willapa Bay and Grays Harbor in Washington; and the lower Columbia River 

estuary from the mouth to river km 74 to the Bonneville Dam. Physical and biological features 

considered in the designation of the marine areas of Southern DPS of green sturgeon critical 

habitat include (1) a migratory pathway necessary for the safe and timely passage of Southern 

DPS fish within marine and between estuarine and marine habitats, (2) nearshore marine waters 

with adequate dissolved oxygen (DO) levels and acceptably low levels of contaminants (e.g., 

pesticides, organochlorines, elevated levels of heavy metals) that may disrupt the normal 

behavior, growth, and viability of sub-adult and adult green sturgeon, and (3) abundant prey 

items for sub-adults and adults, which may include benthic invertebrates and fishes (74 FR 

52300). 

Critical Habitat for gulf sturgeon was established in 2003 68 FR 13370) and consists of 14 

geographic units encompassing 2,783 river kilometers as well as 6,042 square kilometers of 

estuarine and marine habitat. Primary constituent elements for the conservation of Gulf Sturgeon 

are abundant food items, riverine spawning sites with substrates suitable for egg deposition and 

development, riverine aggregation areas, a flow regime necessary for normal behavior, growth, 

and survival, water and sediment quality necessary for normal behavior, growth, and viability of 

all life stages, and safe and unobstructed migratory pathways. As with green sturgeon, only the 

marine portion of designated gulf sturgeon critical habitat occurs with the action area and thus 

may be affected by the proposed action. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

While the proposed sea turtle research activities could directly overlap with the essential features 

of designated sawfish and sturgeon critical habitat, very few if any, effects are possible. The 

temporary operation of vessels and gear (e.g., stationary nets and trawl) to catch sea turtles 

would not significantly alter the physical or oceanographic conditions within the action area. 

Only minor changes in water flow and current would be expected from research vessel traffic 

and capture gear. Any effects of these activities on the identified essential features of sawfish and 

sturgeon critical habitat are expected to be insignificant. It is also unlikely that turtle research 

gear will interact with sturgeon prey items. The freshwater and riverine areas that are included in 

the critical habitat designations for gulf sturgeon and green sturgeon do not overlap with the 

proposed action area and therefore were not further considered in this analysis. 

Given the biological and physical features used to designate critical habitat, we determine that 

the proposed action would not destroy or adversely modify the designated critical habitat of 

smalltooth sawfish U.S. range, green sturgeon Southern DPS, or Gulf sturgeon. 

6.1.8 ESA-listed Abalone Species 

Two species of ESA-listed abalone that could potentially occur within the action area off the 

west coast are the white abalone and black abalone. These invertebrate species inhabit very 

specific, narrowly defined habitats primarily within the intertidal and subtidal zones. White 

abalone are found in open low and high relief rock or boulder habitat that is interspersed with 

sand channels, usually at depths of between 80 and 100 feet. Black abalone can typically be 

found in areas of moderate to high surf, wedged into crevices, cracks, and holes of intertidal and 

shallow subtidal rocks, where they are fairly concealed. The abundance of these two species in 

the Action Area is extremely low. Considering the small amount of anticipated spatiotemporal 

overlap between turtle research activities and ESA-listed abalone, the likelihood of impacts to 

white or black abalone from the proposed action is so low as to be discountable. Therefore, we 

determine that the proposed action is not likely to adversely affect either white or black abalone. 

6.1.9 Abalone Designated Critical Habitat 

NMFS designated critical habitat for the black abalone on October 27, 2011 (76 FR 66805). This 

designation includes approximately 360 square kilometers of rocky intertidal and subtidal habitat 

within five segments of the California coast between the Del Mar Landing Ecological Reserve to 

the Palos Verdes Peninsula, as well as on the Farallon Islands, Año Nuevo Island, San Miguel 

Island, Santa Rosa Island, Santa Cruz Island, Anacapa Island, Santa Barbara Island, and Santa 

Catalina Island. This designation includes rocky intertidal and subtidal habitats from the mean 

higher high water line to a depth of about six meters (relative to the mean lower low water line), 

as well as the coastal marine waters encompassed by these areas. While the proposed sea turtle 

research activities could directly overlap with the essential features of black abalone designated 

critical habitat, very few if any, effects are possible. The temporary operation of vessels and gear 

(e.g., stationary nets and trawl) to catch sea turtles would not significantly alter the physical or 

oceanographic conditions within the action area. Only minor changes in water flow and current 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

would be expected from research vessel traffic and capture gear. Any effects of these activities 

on the identified essential features of black abalone critical habitat are expected to be 

insignificant. 

Given the biological and physical features used to designate critical habitat, we determine that 

the proposed action would not destroy or adversely modify black abalone designated critical 

habitat. 

6.1.10 ESA-listed Coral Species 

Fourteen species of ESA-listed coral could potentially occur within the action area. However, as 

a condition of any research permit authorized under the Program, no gear may be set, anchored 

on, or pulled across coral or hard/live bottom habitats. In addition, researchers must take all 

practicable steps including the use of charts, GIS, sonar, fish finders, or other electronic devices 

to determine characteristics and suitability of bottom habitat prior to using gear to identify coral 

communities, and live/hard bottom habitats and avoid setting gear in such areas. If research gear 

is lost, diligent efforts would be made to recover the lost gear to avoid further damage to benthic 

habitat and impacts related to “ghost fishing.” 

Given the permit conditions and mitigation measures (provided in detail in Appendix C) that 

would be in place as part of the Program, we determine that the proposed action is not likely to 

adversely affect any of the following ESA-listed coral species: boulder star, lobed star, 

mountainous star, elkhorn, staghorn, pillar, rough cactus, Acropora globiceps, Acropora 

jacquelineae, Acropora retusa, Acropora speciose, Euphyllia paradivisa, Isopora crateriformis, 

and Seriatopora aculeate. 

6.1.11 Coral Species Designated Critical Habitat 

Critical habitat units for elkhorn and staghorn coral were designated in 2008 and include Florida 

(portions of Southeastern Florida and the Florida Keys), Puerto Rico, St. Thomas/St. John, and 

St. Croix. The Florida unit comprises approximately 1,329 square miles of marine habitat; Puerto 

Rico approximately 1,383 square miles; St. Thomas/St. John approximately 121 square miles; 

and St. Croix approximately 126 square miles. Thus, the total area covered by the designation is 

approximately 2,959 square miles. Within the geographic area occupied by a listed species, 

critical habitat consists of specific areas on which are found those physical or biological features 

essential to the conservation of the species. The feature essential to the conservation of acroporid 

corals is substrate of suitable quality and availability in water depths from the mean high water 

line to 30 meters to allow for successful sexual and asexual reproduction. Successful sexual and 

asexual reproduction includes flourishing larval settlement, recruitment, and reattachment of 

coral fragments (73 FR 72210). “Substrate of suitable quality and availability” means 

consolidated hard bottom or dead coral skeletons free from fleshy macroalgae or turf algae and 

sediment cover. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Sea turtle research activities as part of the proposed action are not likely to affect the essential 

physical and biological features of designated critical habitat identified for these coral species. 

As discussed above, the use of research gear in coral habitat would be considered a violation of 

the permit conditions specified in Appendix C. The proposed activities would have no 

anticipated impact on the physical or oceanographic conditions within the action area. Only 

minor changes in water flow and current would be expected from research vessel traffic through 

areas that contain ESA-listed coral species. 

Given the permit conditions and mitigation measures that would be in place as part of the 

Program, we determine that the proposed action would not destroy or adversely modify elkhorn 

or staghorn coral designated critical habitat. 

6.1.12 Johnson’s Seagrass 

Johnson's Seagrass was listed as threatened on September 14, 1998. Johnson’s seagrass has been 

found only along an approximately 200-kilometer stretch of coastline in southeastern Florida 

between Sebastian Inlet and north Biscayne Bay. While sea turtle research activities considered 

for this action may overlap with areas where Johnson’s seagrass occurs, the Permits Division has 

placed a condition on research permits such that research will not be allowed to be “conducted 

over, on, or immediately adjacent to Johnson’s seagrass or in Johnson’s seagrass critical habitat.” 

Additional seagrass mitigation measures include setting anchors by hand, setting anchors when 

water visibility is acceptable, and diligent efforts to recover gear that may be lost to avoid further 

damage to seagrass habitat and impacts related to “ghost fishing.” Routine vessel traffic has been 

shown to result in scaring of some seagrass species. However, since researchers are directed to 

avoid conducting research in Johnson seagrass critical habitat, we expect minimal vessel traffic 

in these areas and propeller damage is discountable. 

Given the permit conditions and mitigation measures (provided in detail in Appendix C) that 

would be in place as part of the Program, we determine that the proposed action is not likely to 

adversely affect Johnson’s seagrass. 

6.1.13 Johnson’s Seagrass Designated Critical Habitat 

Ten areas within the geographic range of Johnson's seagrass were designated as critical habitat 

for Johnson's seagrass on April 5, 2000. These ten areas and their approximate acreage (in 

parentheses) include: a portion of the Indian River Lagoon, north of the Sebastian Inlet Channel 

(5.7); a portion of the Indian River Lagoon, south of the Sebastian Inlet Channel (2.0); a portion 

of the Indian River Lagoon near the Fort Pierce Inlet (4.3); a portion of the Indian River Lagoon, 

north of the St. Lucie Inlet (2770); a portion of Hobe Sound (900); a site on the south side of 

Jupiter Inlet (4.3); a site in central Lake Worth Lagoon (15.0); a site in Lake Worth Lagoon, 

Boynton Beach (95.5); a site in Lake Wyman, Boca Raton (20.0); and a portion of Biscayne Bay 

(18,757). These designated areas account for approximately 22,574 acres or 9,139 hectares. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Sea turtle research activities as part of the proposed action are not expected to overlap with 

Johnson’s seagrass designated critical habitat since, as discussed above, this would be considered 

a violation of the permit conditions specified in Appendix C. Given the permit conditions and 

mitigation measures that would be in place as part of the Program, we determine that the 

proposed action would not destroy or adversely modify Johnson’s seagrass designated critical 

habitat. 

6.2 Species Likely to be Adversely Affected 

This opinion examines the status of each species that would be affected by the proposed action. 

The status is determined by the level of risk that the ESA-listed species face, based on 

parameters considered in documents such as recovery plans, status reviews, and listing decisions. 

The species status section helps to inform the description of the species’ current “reproduction, 

numbers, or distribution” as described in 50 C.F.R. 402.02. More detailed information on the 

status and trends of these ESA-listed species, and their biology and ecology can be found in the 

listing regulations and critical habitat designations published in the Federal Register, status 

reviews, recovery plans, and on NMFS Web site: 

http://www.nmfs.noaa.gov/pr/species/esa/listed.htm. No critical habitat is likely to be adversely 

affected as a result of the Program. The ESA-listed species that are likely to be adversely 

affected are listed below: 

Species Likely to be Adversely Affected 

• Green sea turtle DPSs: North Atlantic, South Atlantic, East Indian-West Pacific, Central 

West Pacific, Southwest Pacific, Central South Pacific, Central North Pacific, and East 

Pacific 

• Hawksbill sea turtle 

• Kemp’s ridley sea turtle 

• Leatherback sea turtle 

• Loggerhead sea turtle DPSs: Northwest Atlantic, Northeast Atlantic, North Pacific, and 

South Pacific 

• Olive ridley sea turtle populations: Mexico’s Pacific coast, all other breeding populations 

• Atlantic salmon Gulf of Maine DPS 

• Smalltooth sawfish U.S. portion of range DPS 

• Atlantic sturgeon DPSs: Gulf of Maine, New York Bight, Chesapeake Bay, Carolina, and 

South Atlantic 

• Shortnose sturgeon 

• Green sturgeon Southern DPS 

79 
• Gulf sturgeon 

• Nassau grouper 

• Scalloped hammerhead DPSs: Eastern Pacific, Central and Southwest Atlantic, and IndoWest Pacific 

NMFS has released its ESA Biennial Report to Congress (NMFS 2017c). In it, sea turtles in 

NMFS’ jurisdiction were summarized with abundance trends, and recovery priority numbers 

(Table 3). 

Table 3. ESA-listed sea turtle species abundance trends, and recovery priority numbers 

(through September 20, 2016). 

ESA-listed Species and 

Distinct Population 

Segment(s) 

Trend for 2017 Recovery Priority 

Number1 

New Proposed Recovery 

Priority Number2 

8 

10 

12 

12 

17 

15 

6 

1 

Atlantic: 10 

Pacific: 16 

Global: 3 

8 

22 

10 

15 

Green sea turtle 

North Atlantic Increasing 5 

South Atlantic Mixed3 5 

Central West Pacific Unknown 3 

Central South Pacific Unknown 3 

Central North Pacific Increasing 7 

East Pacific Mixed3 5 

Hawksbill sea turtle Mixed3 3 

Kemp’s ridley sea turtle Unknown 5 

Leatherback sea turtle 

Atlantic: Stable 

Pacific: Decreasing 

Global: Mixed3 

Atlantic: 5 

Pacific: 3 

Global: 1 

Loggerhead sea turtle 

Northwest Atlantic Ocean Stable 5 

North Pacific Ocean Stable 3 

Olive ridley sea turtle 

Breeding colony populations 

of Pacific coast Mexico Mixed3 5 

Rangewide Mixed3 5 

1 Recovery Priority Numbers designated according to guidelines published by NMFS on June 15, 1990 (55 FR 

24296). 2 Draft Revised Recovery Priority Guidelines published on May 31, 2017 (82 FR 24944). 3 Mixed = status 

varying by population location. 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

6.2.1 Green Sea Turtle 

The green sea turtle is globally distributed and commonly inhabits nearshore and inshore waters, 

occurring throughout tropical, subtropical and, to a lesser extent, temperate waters (Figure 7). 

Figure 7. Map depicting range and distinct population segment boundaries for green 

turtles. 

The green sea turtle is the largest of the hardshell marine turtles, growing to a weight of 350 

pounds (159 kilograms) and a SCL of greater than 3.3 feet (1 meter) (Figure 8). The species was 

listed under the ESA on July 28, 1978. The species was separated into two listing designations: 

endangered for breeding populations in Florida and the Pacific coast of Mexico and threatened in 

all other areas throughout its range. 

81 

(right). 

Figure 8. Green sea turtle. Photos: Mark Sullivan, NOAA(left), Andy Bruckner, NOAA 

On April 6, 2016, NMFS listed eleven distinct population segments (DPSs) of green sea turtles 

as threatened or endangered under the ESA (Table 4). Eight DPSs are listed as threatened: 

Central North Pacific, East Indian-West Pacific, East Pacific, North Atlantic, North Indian, 
 

 

 

 

 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

South Atlantic, Southwest Indian, and Southwest Pacific. Three DPSs are listed as endangered: 

Central South Pacific, Central West Pacific, and Mediterranean. 

Table 4. Summary of green sea turtle listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Chelonia 

mydas 

Green 

Turtle 

North Atlantic 

(4 subpopulations) Threatened 2015 

81 FR 20057 

04/06/2016 

43 FR 32800 

07/28/1978 

FR N/A 

1991 

63 FR 46693 

Puerto Rico 

1998 

Chelonia 

mydas 

Green 

Turtle South Atlantic Threatened 2015 

81 FR 20057 

04/06/2016 

43 FR 32800 

07/28/1978 

N/A None 

Designated 

Chelonia 

mydas 

Green 

Turtle 

East IndianWest Pacific Threatened 2015 

81 FR 20057 

04/06/2016 

43 FR 32800 

07/28/1978 

N/A None 

Designated 

Chelonia 

mydas 

Green 

Turtle 

Central West 

Pacific Endangered 2015 

81 FR 20057 

04/06/2016 

43 FR 32800 

07/28/1978 

N/A None 

Designated 

Chelonia 

mydas 

Green 

Turtle 

Southwest 

Pacific Threatened 2015 

81 FR 20057 

04/06/2016 

43 FR 32800 

07/28/1978 

N/A None 

Designated 

Chelonia 

mydas 

Green 

Turtle 

Central South 

Pacific Endangered 2015 

81 FR 20057 

04/06/2016 

43 FR 32800 

07/28/1978 

N/A None 

Designated 

Chelonia 

mydas 

Green 

Turtle 

Central North 

Pacific Threatened 2015 

81 FR 20057 

04/06/2016 

43 FR 32800 

07/28/1978 

N/A None 

Designated 

Chelonia 

mydas 

Green 

Turtle 

East 

Pacific Threatened 2015 

81 FR 20057 

04/06/2016 

43 FR 32800 

07/28/1978 

63 FR 28359 

1998 

None 

Designated 

The DPSs considered in this biological opinion for which take could be authorized are: the North 

Atlantic, South Atlantic, Central West Pacific, Southwest Pacific, Central South Pacific, Central 

North Pacific, and East Pacific DPSs. The East Indian-West Pacific and Southwest Pacific DPSs 

of green are also included, despite being a foreign water population because these DPSs could be 

caught on the high seas. 

We used information available in the 2007 five-year review (NMFS and USFWS 2007a) and 

2015 Status Review (Seminoff et al. 2015) to summarize the life history, population dynamics 

and status of the species, as follows. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Life History 

Age at first reproduction for females is twenty to forty years. Green sea turtles lay an average of 

three nests per season with an average of 100 eggs per nest. The remigration interval (i.e., return 

to natal beaches) is two to five years. Nesting occurs primarily on beaches with intact dune 

structure, native vegetation and appropriate incubation temperatures during summer months. 

After emerging from the nest, hatchlings swim to offshore areas and go through a post-hatchling 

pelagic stage where they are believed to live for several years. During this life stage, green sea 

turtles feed close to the surface on a variety of marine algae and other life associated with drift 

lines and debris. Adult turtles exhibit site fidelity and migrate hundreds to thousands of 

kilometers from nesting beaches to foraging areas. Green sea turtles spend the majority of their 

lives in coastal foraging grounds, which include open coastlines and protected bays and lagoons. 

Adult green turtles feed primarily on seagrasses and algae, although they also eat jellyfish, 

sponges and other invertebrate prey. 

Population Dynamics 

The following is a discussion of the species’ population and its variance over time. This section 

includes population growth rate, genetic diversity, and distribution as it relates to the green sea 

turtle. 

Worldwide, nesting data at 464 sites indicate that 563,826 to 564,464 females nest each year 

(Seminoff et al. 2015). Table 5 shows by DPS the number of nesting females, nesting sites and 

the percentage of nesting females at the largest nesting site. 

Table 5. Green sea turtle nesting abundance in each distinct population segment 

(Seminoff et al. 2015). 

Distinct Population 

Segment 

Abundance 

Estimate 

(nesting 

females) 

Number of 

Nesting Sites Largest Nesting Site 

Percentage at 

largest nesting 

site 

North Atlantic 167,424 73 Tortuguero, Costa Rica 79% 

South Atlantic 63,332 51 Poilão, Guinea-Bissau 46% 

East Indian-West Pacific 77,009 58 Wellesley Group, Australia 32% 

Central West Pacific 6,518 51 Federated States of 

Micronesia 22% 

Southwest Pacific 83,058 12 Northern Great Barrier Reef, 

Australia 38% 

Central South Pacific 2,677 59 Scilly Atoll, French Polynesia 36% 

Central North Pacific 3,846 12 East Island, French Frigate 

Shoals, Hawaii 96% 

East Pacific 20,062 39 Colola, Mexico 58% 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Population Growth Rate 

Many nesting sites worldwide suffer from a lack of consistent, standardized monitoring, making 

it difficult to characterize population growth rates for a DPS. Available information on the 

population growth rates and trends for each of the distinct population segments is presented 

below. 

6.2.1.1 North Atlantic Distinct Population Segment 

Compared to other DPSs, the North Atlantic DPS exhibits the highest nester abundance, with 

approximately 167,424 females at seventy-three nesting sites and available data indicate an 

increasing trend in nesting. The largest nesting site in the North Atlantic DPS is in Tortuguero, 

Costa Rica, which hosts seventy-nine percent of nesting females for the DPS (Seminoff et al. 

2015). 

There are no reliable estimates of population growth rate for the DPS as a whole, but estimates 

have been developed at a localized level. Modeling by Chaloupka et al. (2008a) using data sets 

of 25 years or more show the Florida nesting stock at the Archie Carr National Wildlife Refuge 

growing at an annual rate of 13.9 percent, and the Tortuguero, Costa Rica, population growing at 

4.9 percent. 

6.2.1.2 South Atlantic Distinct Population Segment 

The South Atlantic DPS has fifty-one nesting sites, with an estimated nester abundance of 

63,332. The largest nesting site is at Poilão, Guinea-Bissau, which hosts forty-six percent of 

nesting females for the DPS (Seminoff et al. 2015). 

Of the fifty-one nesting sites, many have insufficient data to determine population growth rates 

or trends. Of the nesting sites where data are available, such as Ascension Island, Suriname, 

Brazil, Venezuela, Equatorial Guinea, and Guinea-Bissau, there is evidence that population 

abundance is increasing. 

6.2.1.3 East Indian-West Pacific Distinct Population Segment 

There are fifty-eight nesting sites for the East Indian-West Pacific DPS, with a total nester 

abundance estimated at 77,009. The largest nesting site is the Wellesley Group, three islands in 

the Gulf of Carpentaria off northern Australia. This group hosts thirty-two percent of the nesting 

females for the DPS (Seminoff et al. 2015). 

There are no estimates of population growth. There is variation in the nesting abundance trends 

across nesting sites, with some showing increase while others are decreasing. Broadly, there is a 

decrease in nesting females throughout the DPS, with the exception of Malaysia and the 

Philippines showing an increase, attributed to successful conservation efforts. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

6.2.1.4 Central West Pacific Distinct Population Segment 

There are fifty-one nesting sites in the Central West Pacific DPS, with an estimated 6,518 

nesting females. The largest nesting site is in the Federated States of Micronesia, which hosts 

twenty-two percent of the nesting females for the DPS (Seminoff et al. 2015). 

There are no estimates of population growth rates. Long-term nesting data is lacking for many of 

the nesting sites in the Central West Pacific DPS, making it difficult to assess population trends. 

The only site which as long-term data available, Chichijima, Japan, shows a positive trend in 

population growth. 

6.2.1.5 Southwest Pacific Distinct Population Segment 

Nesting sites for the Southwest Pacific Ocean DPS are widely distributed throughout the region. 

With proximate nesting sites grouped, there are twelve nesting sites in the Southwest Pacific 

DPS, with an estimated 83,058 nesting females. The largest nesting site is at the northern Great 

Barrier Reef, Australia, which hosts thirty-eight percent of the nesting females for the DPS 

(Seminoff et al. 2015). 

There are no estimates of population growth rates. Only two nesting sites in the Southwest 

Pacific DPS have more than fifteen years of data: Raine Island and Heron Island, both in the 

northern Great Barrier Reef. Both sites show a slight increasing population trend. 

6.2.1.6 Central South Pacific Distinct Population Segment 

Nesting abundance information for the Central South Pacific DPS is limited, but is considered to 

be at low levels and spread out over a large geographic area. There are fifty-nine known nesting 

sites (twenty-two are unquantified), with an estimated 2,677 nesting females. The largest nesting 

site is at Scilly Atoll in French Polynesia, which hosts thirty-six percent of the nesting females 

for the DPS (Seminoff et al. 2015). 

There are no estimates of population growth. The DPS suffers from a lack of consistent, 

systematic nesting monitoring, with no nesting site having even five years of continuous data. 

What data are available indicate steep declines at Scilly Atoll due to illegal harvest, with some 

smaller nesting sites (e.g., Rose Atoll) showing signs of stability. 

6.2.1.7 Central North Pacific Distinct Population Segment 

There are thirteen known nesting sites for the Central North Pacific DPS, with an estimated 

3,846 nesting females. The DPS is very thoroughly monitored, and it is believed there is little 

chance that there are undocumented nesting sites. The largest nesting site is at French Frigate 

Shoals, Hawaii, which hosts ninety-six percent of the nesting females for the DPS (Seminoff et 

al. 2015). 

Nesting surveys have been conducted since 1973 for green turtles in the Central North Pacific 

DPS. Nesting abundance at East Island, French Frigate Shoals, increases at 4.8 percent annually. 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

6.2.1.8 East Pacific Distinct Population Segment 

There are thirty-nine nesting sites for the East Pacific DPS, with an estimated 20,062 nesting 

females. The largest nesting site is at Colola, Mexico, which hosts fifty-eight percent of the 

nesting females for the DPS (Seminoff et al. 2015). 

There are no estimates of population growth. Only one nesting site in the East Pacific DPS at 

Colola, Mexico, has sufficient long-term data to determine population trends. Data analysis 

indicates that the population there is increasing and is likely to continue to do so. 

Genetic Diversity 

Globally, the green turtle is divided into eleven distinct population segments; available 

information on the genetic diversity for each of the distinct population segments is presented 

below. 

6.2.1.9 North Atlantic Distinct Population Segment 

The North Atlantic DPS has a globally unique haplotype, which was a factor in defining the 

discreteness of the population for the DPS. Evidence from mitochondrial DNA studies indicates 

that there are at least 4 independent nesting subpopulations in Florida, Cuba, Mexico and Costa 

Rica (Seminoff et al. 2015). More recent genetic analysis indicates that designating a new 

western Gulf of Mexico management unit might be appropriate (Shamblin et al. 2016). 

6.2.1.10 South Atlantic Distinct Population Segment 

The South Atlantic DPS is characterized as having shallow structuring, and dominated by a 

common shared haplotype. Individuals from nesting sites in Brazil, Ascension Island, and 

western Africa have a shared haplotype found in high frequencies. Green turtles from rookeries 

in the eastern Caribbean however, are dominated by a different haplotype (Seminoff et al. 2015). 

6.2.1.11 East Indian-West Pacific Distinct Population Segment 

Genetic studies have been conducted on over twenty-two of fifty-eight rookeries in the East 

Indian-West Pacific DPS, revealing a complex population structure. Sixteen regional genetic 

stocks have been identified, with a few common and widespread haplotypes throughout the 

region. Rare or unique haplotypes are present at most rookeries (Seminoff et al. 2015). 

6.2.1.12 Central West Pacific Distinct Population Segment 

The Central West Pacific DPS is made up of insular rookeries separated by broad geographic 

distances. Rookeries that are more than 1,000 kilometers apart are significantly differentiated, 

while rookeries 500 kilometers apart are not (Seminoff et al. 2015). Mitochondrial DNA 

analyses suggest that there are at least seven independent stocks in the region (Dutton et al. 

2014). 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

6.2.1.13 Southwest Pacific Distinct Population Segment 

Of the sampled rookeries in the Southwest Pacific DPS, genetic testing shows significant 

population sub-structuring. Four regional genetic stocks have been identified (Dethmers et al. 

2006; Jensen 2010). The DPS is characterized as having high genetic diversity due to a variety of 

highly divergent lines found at nesting sites. 

6.2.1.14 Central South Pacific Distinct Population Segment 

There is very limited information available for the Central South Pacific DPS. Mitochondrial 

DNA studies indicate at least two genetic stocks in the DPS: American Samoa and French 

Polynesia. Overall, there is a moderate level of diversity for the DPS, and the presence of unique 

haplotypes (Seminoff et al. 2015). 

6.2.1.15 Central North Pacific Distinct Population Segment 

The majority of nesting for the Central North Pacific DPS is centered at one site on French 

Frigate Shoals, and there is little diversity in nesting areas. Overall, the Central North Pacific 

DPS has a relatively low level of genetic diversity and stock sub-structuring (Seminoff et al. 

2015). 

6.2.1.16 East Pacific Distinct Population Segment 

Rare and unique haplotypes are present in the East Pacific DPS. Genetic sampling has identified 

four regional stocks in the Eastern Pacific DPS: Revillagigedos Archipelago, Mexico, 

Michoacán, Mexico, Central America (Costa Rica), and the Galápagos Islands, Ecuador 

(Seminoff et al. 2015). 

Distribution 

The green sea turtle occupies the coastal waters of over 140 countries worldwide; nesting occurs 

in more than eighty countries. The green sea turtle is distributed in tropical, subtropical, and to a 

lesser extent, temperate waters (Figure 9). 

87 

Figure 9. Map of all Chelonia mydas nesting sites indicating delineation of distinct 

population segments (Seminoff et al. 2015). 
 

 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

6.2.1.17 North Atlantic Distinct Population Segment 

Green turtles from the North Atlantic DPS range from the boundary of South and Central 

America (7.5°N, 77°W) in the south, throughout the Caribbean, the Gulf of Mexico, and the U.S. 

Atlantic coast to New Brunswick, Canada (48°N, 77°W) in the north. The range of the DPS then 

extends due east along latitudes 48°N and 19°N to the western coasts of Europe and Africa 

Figure 9). Nesting occurs primarily in Costa Rica, Mexico, Florida and Cuba (Figure 10). 

Figure 10. Close up of nesting distribution of green turtles in the western North Atlantic 

distinct population segment (water body labeled ‘1’). Size of circles indicates estimated 

nester abundance. Locations marked with an ‘x’ indicate sites lacking abundance 

information (Seminoff et al. 2015). 

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6.2.1.18 South Atlantic Distinct Population Segment 

Nesting for the green turtle South Atlantic DPS occurs on both sides of the Atlantic Ocean, along 

the western coast of Africa, Ascension Island, the U.S. Virgin Islands in the Caribbean and 

eastern South America, from Brazil north to the Caribbean (Figure 7). Juveniles and adults can 

be found on feeding grounds in the Caribbean and the nearshore waters of Brazil, Uruguay and 

Argentina. In the east, South Atlantic DPS green turtles can be found on foraging grounds off the 

coast of west Africa, from Equatorial Guinea, Gabon, Congo, Angola and Principe Island (Figure 

11). 

Figure 11. Nesting distribution of green turtles in the South Atlantic distinct population 

segment (water body labeled ‘3’). Size of circles indicates estimated nester abundance. 

Locations marked with an ‘x’ indicate sites lacking abundance information (Seminoff et 

al. 2015). 

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6.2.1.19 East Indian-West Pacific Distinct Population Segment 

The East Indian-West Pacific DPS green turtle is found in the Indian Ocean from southeast Asia 

through western Australia (Figure 7). The East Indian-West Pacific DPS comprises nesting sites 

in Northern Australia, Indonesia, Malaysia, Peninsular Malaysia and the Philippine Turtle 

Islands. The DPS is spread throughout the eastern Indian Ocean, east of Sri Lanka, south to 

western and northern Australia, Indonesia, Malaysia, and Taiwan, and north to Japan (Figure 12). 

Figure 12. Nesting distribution of green turtles in the East Indian-West Pacific distinct 

population segment (water body labeled ‘6’). Size of circles indicates estimated nester 

abundance. Locations marked with an ‘x’ indicate sites lacking abundance information 

(Seminoff et al. 2015). 

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6.2.1.20 Central West Pacific Distinct Population Segment 

The Central West Pacific DPS is composed of nesting assemblages in the Federated States of 

Micronesia, the Japanese islands of Chichijima and Hahajima, the Marshall Islands, and Palau 

(Figure 7). Green turtles in this DPS are found throughout the western Pacific Ocean, in 

Indonesia, the Philippines, the Marshall Islands and Papua New Guinea (Figure 13). 

Figure 13. Nesting distribution of green turtles in the Central West Pacific distinct 

population segment (water body labeled ‘7’). Size of circles indicates estimated nester 

abundance. Locations marked with an ‘x’ indicate sites lacking abundance information 

(Seminoff et al. 2015). 

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6.2.1.21 Southwest Pacific Distinct Population Segment 

The Southwest Pacific DPS green turtle is found in the Pacific Ocean near eastern Australia and 

northern New Zealand (Figure 7). The Southwest Pacific DPS extends off the eastern coast of 

Australia, south of Papua New Guinea and goes east to encompass Vanuatu and New Caledonia. 

Major nesting sites for the DPS include the Great Barrier Reef, eastern Torres Strait and the 

northern Great Barrier Reef. Nesting also occurs in New Caledonia, Vanuatu and the Coral Sea 

Islands (Figure 14). 

Figure 14. Nesting distribution of green turtles in the Southwest Pacific distinct 

population segment (water body labeled ‘8’). Size of circles indicates estimated nester 

abundance. Locations marked with an ‘x’ indicate sites lacking abundance information 

(Seminoff et al. 2015). 

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6.2.1.22 Central South Pacific Distinct Population Segment 

The Central South Pacific DPS extends from north from northern New Zealand to Fiji, Tuvalu, 

and Kiribati and east to include French Polynesia (Figure 7). Nesting occurs sporadically 

throughout the geographic distribution of the population, with isolated locations having relatively 

low to moderate nesting activity (Figure 15). 

Figure 15. Nesting distribution of green turtles in the Central South Pacific distinct 

population segment (water body labeled ‘9’). Size of circles indicates estimated nester 

abundance. Locations marked with an ‘x’ indicate sites lacking abundance information 

(Seminoff et al. 2015). 

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6.2.1.23 Central North Pacific Distinct Population Segment 

Green turtles in the Central North Pacific DPS are found in the Hawaiian Archipelago and 

Johnston Atoll (Figure 7). The major nesting site for the DPS is at East Island, French Frigate 

Shoals, in the Northwestern Hawaiian Islands; lesser nesting sites are found throughout the 

Northwestern Hawaiian Islands and the Main Hawaiian Islands (Figure 16). 

Figure 16. Nesting distribution of green turtles in the Central North Pacific distinct 

population segment (water body labeled ‘10’). Size of circles indicates estimated nester 

abundance (Seminoff et al. 2015). 

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6.2.1.24 East Pacific 

Green turtles in the East Pacific DPS are found from the California/Oregon border south to 

central Chile (Figure 7). Major nesting sites occur at Michoacán, Mexico, and the Galá3pagos 

Islands, Ecuador. Smaller nesting sites are found on the Pacific coast of Costa Rica, and in the 

Revillagigedos Archipelago, Mexico. Scattered nesting occurs in Columbia, Ecuador, Guatemala 

and Peru (Seminoff et al. 2015). 

Figure 17. Nesting distribution of green turtles in the East Pacific distinct population 

segment (water body labeled ‘11’). Size of circles indicates estimated nester abundance. 

Locations marked with an ‘x’ indicate sites lacking abundance information (Seminoff et 

al. 2015). 

Status 

Once abundant in tropical and subtropical waters, green sea turtles worldwide exist at a fraction 

of their historical abundance, as a result of over-exploitation. Globally, egg harvest, the harvest 

of females on nesting beaches and directed hunting of turtles in foraging areas remain the three 

greatest threats to their recovery. In addition, bycatch in drift-net, long-line, set-net, pound-net 

and trawl fisheries kill thousands of green sea turtles annually. Increasing coastal development 

(including beach erosion and re-nourishment, construction and artificial lighting) threatens 

nesting success and hatchling survival. On a regional scale, the different DPSs experience these 

threats as well, to varying degrees. Differing levels of abundance combined with different 

intensities of threats and effectiveness of regional regulatory mechanisms make each DPS 

uniquely susceptible to future perturbations. 

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6.2.1.25 North Atlantic Distinct Population Segment 

Historically, green turtles in the North Atlantic DPS were hunted for food, which was the 

principle cause of the population’s decline. Apparent increases in nester abundance for the North 

Atlantic DPS in recent years are encouraging but must be viewed cautiously, as the datasets 

represent a fraction of a green sea turtle generation, up to 50 years. While the threats of pollution, 

habitat loss through coastal development, beachfront lighting, and fisheries bycatch continue, the 

North Atlantic DPS appears to be somewhat resilient to future perturbations. 

6.2.1.26 South Atlantic Distinct Population Segment 

Though there is some evidence that the South Atlantic DPS is increasing, there is a considerable 

amount of uncertainty over the impacts of threats to the South Atlantic DPS. The DPS is 

threatened by habitat degradation at nesting beaches, mortality from fisheries bycatch remains a 

primary concern. 

6.2.1.27 East Indian-West Pacific Distinct Population Segment 

The East Indian-West Pacific DPS is relatively large, though it has been reduced from historic 

levels due to overutilization for commercial and subsistence purposes. Green turtles and their 

eggs are still harvested for consumption in some areas. Other current threats to the DPS include 

mortality from incidental bycatch, and predation by feral pigs, dogs and foxes. 

6.2.1.28 Central West Pacific Distinct Population Segment 

The Central West Pacific DPS is impacted by incidental bycatch in fishing gear, predation of 

eggs by ghost crabs and rats, and directed harvest eggs and nesting females for human 

consumption. Historically, intentional harvest of eggs from nesting beaches was one of the 

principal causes for decline, and this practice continues today in many locations. The Central 

West Pacific DPS has a small number of nesting females and a widespread geographic range. 

These factors, coupled with the threats facing the DPS and the unknown status of many nesting 

sites makes the DPS vulnerable to future perturbations. 

6.2.1.29 Southwest Pacific Distinct Population Segment 

Green turtle populations in the Southwest Pacific DPS declined due to intense harvest in the last 

century. The Southwest Pacific DPS is currently under threat from incidental bycatch in fishing 

gear, although conservation programs in Australia, New Caledonia and Vanuatu are in place to 

mitigate the impacts. Although the directed commercial harvest of eggs and nesting females is 

prohibited in Australia, harvest occurs in the neighboring countries of Fiji, New Caledonia, 

Papua New Guinea and Indonesia. Boat strike, bycatch in shark control programs, increases in 

sea surface temperatures due to climate change all threaten the DPSs. Populations at the two 

largest nesting beaches in the DPS are stable or increasing, but uncertainty about population 

trends in other parts of the DPS still warrant concern. 

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6.2.1.30 Central South Pacific Distinct Population Segment 

Historically, the Central South Pacific DPS declined due to harvest of eggs and females for 

human consumption or for their shells, a practice that still continues throughout the region. 

Incidental bycatch in commercial and artisanal fishing gear, lack of regulatory mechanisms and 

climate change are significant threats to the long-term viability of the DPS. 

6.2.1.31 Central North Pacific Distinct Population Segment 

Green turtles in the Hawaiian Archipelago were subjected to hunting pressure for subsistence 

and commercial trade, which was largely responsible for the decline in the region. Though the 

practice has been banned, there are still anecdotal reports of harvest. Incidental bycatch in fishing 

gear, ingestion of marine debris, and the loss of nesting habitat due to sea level rise are current 

threats to the population. Although these threats persist, the increase in annual nesting 

abundance, continuous scientific monitoring, legal enforcement and conservation programs are 

all factors that favor the resiliency of the DPS. 

6.2.1.32 East Pacific Distinct Population Segment 

The population decline for the East Pacific DPS was primarily caused by commercial harvest of 

green turtles for subsistence and other uses (e.g., sea turtle oil as a cold remedy). Conservation 

laws are in place in several countries across the range of the DPS, but enforcement is 

inconsistent, limiting effectiveness. Incidental bycatch in commercial fishing gear, continued 

harvest, coastal development and beachfront lighting are all continuing threats for the DPS. The 

observed increases in nesting abundance for the largest nesting aggregation in the region 

(Michocán, Mexico), a stable trend at Galápagos, and record high numbers at sites in Costa Rica 

suggest that the population is resilient, particularly in Mexico. 

Designated Critical Habitat 

6.2.1.33 North Atlantic Distinct Population Segment 

On September 2, 1998, NMFS designated critical habitat for green sea turtles, which include 

coastal waters surrounding Culebra Island, Puerto Rico (Figure 18). Seagrass beds surrounding 

Culebra provide important foraging resources for juvenile, subadult and adult green sea turtles. 

Additionally, coral reefs surrounding the island provide resting shelter and protection from 

predators. This area provides important developmental habitat for the species. Activities that may 

affect the critical habitat include beach renourishment, dredge and fill activities, coastal 

construction, and freshwater discharge. Due to its location, this critical habitat would be 

accessible by individuals of the North Atlantic DPS. The only designated critical habitat for 

green sea turtles is in Culebra Island, Puerto Rico. 

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Figure 18. Map depicting green turtle designated critical habitat in Culebra Island, Puerto 

Rico. 

Recovery Goals 

See the 1998 and 1991 recovery plans for the Pacific, East Pacific and Atlantic populations of 

green turtles for complete down-listing/delisting criteria for recovery goals for the species 

(NMFS and USFWS 1991; NMFS and USFWS 1998b). Broadly, recovery plan goals emphasize 

the need to protect and manage nesting and marine habitat, protect and manage populations on 

nesting beaches and in the marine environment, increase public education, and promote 

international cooperation on sea turtle conservation topics. 

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6.2.2 Hawksbill Sea Turtle 

The hawksbill turtle has a circumglobal distribution throughout tropical and, to a lesser extent, 

subtropical oceans (Figure 19). 

Figure 19. Map identifying the range of the endangered hawksbill sea turtle. 

The hawksbill sea turtle has a sharp, curved, beak-like mouth and a “tortoiseshell” pattern on its 

carapace, with radiating streaks of brown, black, and amber (Figure 20). 

Figure 20. Hawksbill sea turtle. Photos: Tom Moore, NOAA (left), Jordan Wilkerson 

(right). 

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The species was first listed under the Endangered Species Conservation Act and listed as 

endangered under the ESA since 1973 (Table 6). 

Table 6. Summary of hawksbill sea turtle listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Eretmochelys 

imbricata 

Hawksbill 

Turtle 

None 

Designated Endangered 2013 35 FR 8491 6/2/1970 

57 FR 38818 

Atlantic 

1992 

63 FR 46693 

Puerto Rico 

1998 

Eretmochelys 

imbricata 

Hawksbill 

Turtle 

None 

Designated Endangered 2013 35 FR 8491 6/2/1970 

63 FR 28359 

Pacific 

1998 

None 

Designated 

We used information available in the 2007 and 2013 five-year reviews (NMFS and USFWS 

2007b; NMFS and USFWS 2013a) to summarize the life history, population dynamics and status 

of the species, as follows. 

Life History 

Hawksbill sea turtles reach sexual maturity at twenty to forty years of age. Females return to 

their natal beaches every two to five years to nest and nest an average of three to five times per 

season. Clutch sizes are large (up to 250 eggs). Sex determination is temperature dependent, with 

warmer incubation producing more females. Hatchlings migrate to and remain in pelagic habitats 

until they reach approximately twenty two to twenty five centimeters in SCL. As juveniles, they 

take up residency in coastal waters to forage and grow. As adults, hawksbills use their sharp 

beak-like mouths to feed on sponges and corals. Hawksbill sea turtles are highly migratory and 

use a wide range of habitats during their lifetimes (Musick and Limpus 1997; Plotkin 2003). 

Satellite tagged turtles have shown significant variation in movement and migration patterns. 

Distance traveled between nesting and foraging locations ranges from a few hundred to a few 

thousand kilometers (Horrocks et al. 2001; Miller et al. 1998). 

Population Dynamics 

The following is a discussion of the species’ population and its variance over time. This section 

includes population growth rate, genetic diversity, and distribution as it relates to the hawksbill 

sea turtle. 

Surveys at eighty eight nesting sites worldwide indicate that 22,004 to 29,035 females nest 

annually (NMFS and USFWS 2013a). In general, hawksbills are doing better in the Atlantic and 

Indian Ocean than in the Pacific Ocean, where despite greater overall abundance, a greater 

proportion of the nesting sites are declining. 

From 1980 to 2003, the number of nests at three primary nesting beaches (Rancho Nuevo, 

Tepehuajes, and Playa Dos) increased fifteen percent annually (Heppell et al. 2005); however, 

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due to recent declines in nest counts, decreased survival at other life stages, and updated 

population modeling, this rate is not expected to continue (NMFS and USFWS 2013a). 

Populations are distinguished generally by ocean basin and more specifically by nesting location. 

Our understanding of population structure is relatively poor. Genetic analysis of hawksbill sea 

turtles foraging off the Cape Verde Islands identified three closely-related haplotypes in a large 

majority of individuals sampled that did not match those of any known nesting population in the 

western Atlantic, where the vast majority of nesting has been documented (McClellan et al. 

2010; Monzón-Argüello et al. 2010). Hawksbills in the Caribbean seem to have dispersed into 

separate populations (rookeries) after a bottleneck roughly 100,000 to 300,000 years ago (Leroux 

et al. 2012). 

The hawksbill has a circumglobal distribution throughout tropical and, to a lesser extent, 

subtropical waters of the Atlantic, Indian, and Pacific Oceans. In their oceanic phase, juvenile 

hawksbills can be found in Sargassum mats; post-oceanic hawksbills may occupy a range of 

habitats that include coral reefs or other hard-bottom habitats, sea grass, algal beds, mangrove 

bays and creeks (Bjorndal and Bolten 2010; Musick and Limpus 1997). 

Status 

Long-term data on the hawksbill sea turtle indicate that sixty-three sites have declined over the 

past twenty to one hundred years (historic trends are unknown for the remaining twenty-five 

sites). Recently, twenty-eight sites (sixty-eight percent) have experienced nesting declines, ten 

have experienced increases, three have remained stable, and forty-seven have unknown trends. 

The greatest threats to hawksbill sea turtles are overharvesting of turtles and eggs, degradation of 

nesting habitat, and fisheries interactions. Adult hawksbills are harvested for their meat and 

carapace, which is sold as tortoiseshell. Eggs are taken at high levels, especially in southeast 

Asia where collection approaches one hundred percent in some areas. In addition, lights on or 

adjacent to nesting beaches are often fatal to emerging hatchlings and alters the behavior of 

nesting adults. The species’ resilience to additional perturbation is low. 

Designated Critical Habitat 

On September 2, 1998, NMFS established critical habitat for hawksbill sea turtles around Mona 

and Monito Islands, Puerto Rico (Figure 21). Aspects of these areas that are important for 

hawksbill sea turtle survival and recovery include important natal development habitat, refuge 

from predation, shelter between foraging periods, and food for hawksbill sea turtle prey. 

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Figure 21. Map depicting hawksbill sea turtle critical habitat; the coastal waters 

surrounding Mona and Monito Islands, Puerto Rico. 

Recovery Goals 

See the 1992 Recovery Plan for the U.S. Caribbean, Atlantic and Gulf of Mexico (NMFS and 

USFWS 1993) and the 1998 Recovery Plan for the U.S. Pacific populations (NMFS and USFWS 

1998c) of hawksbill sea turtles, for complete down listing/delisting criteria for each of their 

respective recovery goals. The following items were the top recovery actions identified to 

support in the Recovery Plans: 

1. Identify important nesting beaches 

2. Ensure long-term protection and management of important nesting beaches 

3. Protect and manage nesting habitat; prevent the degradation of nesting habitat caused 

by seawalls, revetments, sand bags, other erosion-control measures, jetties and 

breakwaters 

4. Identify important marine habitats; protect and manage populations in marine habitat 

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5. Protect and manage marine habitat; prevent the degradation or destruction of 

important [marine] habitats caused by upland and coastal erosion 

6. Prevent the degradation of reef habitat caused by sewage and other pollutants 

7. Monitor nesting activity on important nesting beaches with standardized index 

surveys 

8. Evaluate nest success and implement appropriate nest-protection on important nesting 

beaches 

9. Ensure that law-enforcement activities prevent the illegal exploitation and harassment 

of sea turtles and increase law-enforcement efforts to reduce illegal exploitation 

10. Determine nesting beach origins for juveniles and subadult populations 

6.2.3 Kemp’s Ridley Sea Turtle 

The Kemp’s ridley turtle is considered to be the most endangered sea turtle, internationally 

(Groombridge 1982; Zwinenberg 1977). Its range extends from the Gulf of Mexico to the 

Atlantic coast, with nesting beaches limited to a few sites in Mexico and Texas (Figure 22). 

Figure 22. Map identifying the range of the Kemp’s ridley sea turtle. 

Kemp’s ridley sea turtles the smallest of all sea turtle species, with a nearly circular top shell and 

a pale yellowish bottom shell (Figure 23). 

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Figure 23. Kemp’s ridley sea turtle. Photos: National Oceanic and Atmospheric 

Administration (left), National Park Service (right). 

The species was first listed under the Endangered Species Conservation Act and listed as 

endangered under the ESA since 1970 (Table 7). 

Table 7. Summary of Kemp’s ridley sea turtle listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery Plan Critical 

Habitat 

Lepidochelys 

kempii 

Kemp’s 

Ridley 

Turtle 

None 

Designated Endangered 2015 35 FR 18319 12/02/1970 

75 FR 12496 

U.S. Caribbean, 

Atlantic, and Gulf of 

Mexico 

2011 

None 

Designated 

We used information available in the revised recovery plan (NMFS and USFWS 2011) and the 

2015 five-year review (NMFS and USFWS 2015) to summarize the life history, population 

dynamics and status of the species, as follows. 

Life History 

Females mature at twelve years of age. The average remigration is two years. Nesting occurs 

from April to July in large arribadas, primarily at Rancho Nuevo, Mexico. Females lay an 

average of 2.5 clutches per season. The annual average clutch size is ninety-seven to one 

hundred eggs per nest. The nesting location may be particularly important because hatchlings can 

more easily migrate to foraging grounds in deeper oceanic waters, where they remain for 

approximately two years before returning to nearshore coastal habitats. Juvenile Kemp’s ridley 

sea turtles use these nearshore coastal habitats from April through November, but move towards 

more suitable overwintering habitat in deeper offshore waters (or more southern waters along the 

Atlantic coast) as water temperature drops. Adult habitat largely consists of sandy and muddy 

areas in shallow, nearshore waters less than 120 feet (37 meters) deep, although they can also be 

found in deeper offshore waters. As adults, Kemp’s ridleys forage on swimming crabs, fish, 

jellyfish, mollusks, and tunicates (NMFS and USFWS 2011). 

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Population Dynamics 

The following is a discussion of the species’ population and its variance over time. This section 

includes: abundance, population growth rate, genetic diversity, and spatial distribution as it 

relates to the Kemp’s ridley sea turtle. 

Of the sea turtles species in the world, the Kemp's ridley has declined to the lowest population 

level. Nesting aggregations at a single location (Rancho Nuevo, Mexico) were estimated at 

40,000 females in 1947. By the mid-1980s, the population had declined to an estimated 300 

nesting females. In 2014, there were an estimated 10,987 nests and 519,000 hatchlings released 

from three primary nesting beaches in Mexico (NMFS and USFWS 2015). The number of nests 

in Padre Island, Texas has increased over the past two decades, with one nest observed in 1985, 

four in 1995, fifty in 2005, 197 in 2009, and 119 in 2014 (NMFS and USFWS 2015). 

From 1980 to 2003, the number of nests at three primary nesting beaches (Rancho Nuevo, 

Tepehuajes, and Playa Dos) increased fifteen percent annually (Heppell et al. 2005); however, 

due to recent declines in nest counts, decreased survival at other life stages, and updated 

population modeling, this rate is not expected to continue (NMFS and USFWS 2015). 

Genetic variability in Kemp’s ridley turtles is considered to be high, as measured by 

heterozygosis at microsatellite loci (NMFS and USFWS 2011). Additional analysis of the 

mitochondrial DNA taken from samples of Kemp’s ridley turtles at Padre Island, Texas, showed 

six distinct haplotypes, with one found at both Padre Island and Rancho Nuevo (Dutton et al. 

2006). 

The Kemp's ridley occurs from the Gulf of Mexico and along the Atlantic coast of the United 

States (TEWG 2000). Kemp’s ridley sea turtles have occasionally been found in the 

Mediterranean Sea, which may be due to migration expansion or increased hatchling production 

(Tomás and Raga 2008). The vast majority of individuals stem from breeding beaches at Rancho 

Nuevo on the Gulf of Mexico coast of Mexico. During spring and summer, juvenile Kemp’s 

ridleys occur in the shallow coastal waters of the northern Gulf of Mexico from south Texas to 

north Florida. In the fall, most Kemp’s ridleys migrate to deeper or more southern, warmer 

waters and remain there through the winter (Schmid 1998). As adults, many turtles remain in the 

Gulf of Mexico, with only occasional occurrence in the Atlantic Ocean (NMFS and USFWS 

2011). 

Designated Critical Habitat 

No critical habitat has been designated for Kemp’s ridley sea turtles. 

Recovery Goals 

See the 2011 Final Bi-National (U.S. and Mexico) Revised Recovery Plan for Kemp’s ridley sea 

turtles for complete down listing/delisting criteria for each of their respective recovery goals 

(NMFS and USFWS 2011). The following items were identified as priorities to recover Kemp’s 

ridley sea turtles: 

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1. Protect and manage nesting and marine habitats.

2. Protect and manage populations on the nesting beaches and in the marine

environment.

3. Maintain a stranding network.

4. Manage captive stocks.

5. Sustain education and partnership programs.

6. Maintain, promote awareness of and expand U.S. and Mexican laws.

7. Implement international agreements.

8. Enforce laws.

6.2.4 Leatherback Sea Turtle 

The leatherback sea turtle is unique among sea turtles for its large size, wide distribution (due to 

thermoregulatory systems and behavior), and lack of a hard, bony carapace. It ranges from 

tropical to subpolar latitudes, worldwide (Figure 24). 

Figure 24. Map identifying the range of the leatherback sea turtle with the seven 

subpopulations and nesting sites. Adapted from (Wallace et al. 2010a). 

Leatherbacks are the largest living turtle, reaching lengths of six feet long, and weighing up to 

one ton. Leatherback sea turtles have a distinct black leathery skin covering their carapace with 

pinkish white skin on their belly (Figure 25). 

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Figure 25. Leatherback sea turtle adult and hatchling. Photos: R. Tapilatu (left), N. Pilcher 

(right). 

The species was first listed under the Endangered Species Conservation Act and listed as 

endangered under the ESA since 1970 (Table 8). 

Table 8. Summary of leatherback sea turtle listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Dermochelys 

coriacea 

Leatherback 

Turtle 

None 

Designated Endangered 2013 35 FR 8491 

6/2/1970 

FR N/A 

Atlantic 

1992 

44 FR 17710 

U.S. Virgin 

Islands 

1979 

Dermochelys 

coriacea 

Leatherback 

Turtle 

None 

Designated Endangered 2013 35 FR 8491 6/2/1970 

63 FR 28359 

Pacific 

1998 

77 FR 4170 

Pacific 

2012 

We used information available in the 2013 five-year review (NMFS and USFWS 2013b) and the 

critical habitat designations to summarize the life history, population dynamics and status of the 

species, as follows. 

Life History 

Age at maturity has been difficult to ascertain, with estimates ranging from five to twenty-nine 

years (Avens et al. 2009; Spotila et al. 1996). Females lay up to seven clutches per season, with 

more than sixty-five eggs per clutch and eggs weighing greater than eighty grams (Reina et al. 

2002; Wallace et al. 2007). The number of leatherback hatchlings that make it out of the nest on 

to the beach (i.e., emergent success) is approximately fifty percent worldwide (Eckert et al. 

2012). Females nest every one to seven years. Natal homing, at least within an ocean basin, 

results in reproductive isolation between five broad geographic regions: eastern and western 

Pacific, eastern and western Atlantic, and Indian Ocean. Leatherback sea turtles migrate long, 

transoceanic distances between their tropical nesting beaches and the highly productive 

temperate waters where they forage, primarily on jellyfish and tunicates. These gelatinous prey 

are relatively nutrient-poor, such that leatherbacks must consume large quantities to support their 

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body weight. Leatherbacks weigh about thirty-three percent more on their foraging grounds than 

at nesting, indicating that they probably catabolize fat reserves to fuel migration and subsequent 

reproduction (James et al. 2005; Wallace et al. 2006). Sea turtles must meet an energy threshold 

before returning to nesting beaches. Therefore, their remigration intervals (the time between 

nesting) are dependent upon foraging success and duration (Hays 2000; Price et al. 2004). 

Population Dynamics 

The following is a discussion of the species’ population and its variance over time. This section 

includes abundance, population growth rate, genetic diversity, and spatial distribution as it 

relates to the leatherback sea turtle. 

Leatherbacks are globally distributed, with nesting beaches in the Pacific, Atlantic, and Indian 

oceans. Detailed population structure is unknown, but is likely dependent upon nesting beach 

location. Based on estimates calculated from nest count data, there are between 34,000 and 

94,000 adult leatherbacks in the North Atlantic (TEWG 2007). In contrast, leatherback 

populations in the Pacific are much lower. Overall, Pacific populations have declined from an 

estimated 81,000 individuals to less than 3,000 total adults and subadults (Spotila et al. 2000). 

Deriving abundance estimates from nest counts divided by average clutch frequency from 

(NMFS and USFWS 2013b) give as West Pacific subpopulation estimate of 562 nesting females. 

Population abundance in the Indian Ocean is difficult to assess due to lack of data and 

inconsistent reporting. Available data from southern Mozambique show that approximately ten 

females nest per year from 1994 to 2004, and about 296 nests per year counted in South Africa 

(NMFS and USFWS 2013b). 

Population growth rates for leatherback sea turtles vary by ocean basin. Counts of leatherbacks at 

nesting beaches in the western Pacific indicate that the subpopulation has been declining at a rate 

of almost six percent per year since 1984 (Tapilatu et al. 2013). Leatherback subpopulations in 

the Atlantic Ocean, however, are showing signs of improvement. Nesting females in South 

Africa are increasing at an annual rate of four to 5.6 percent, and from nine to thirteen percent in 

Florida and the U.S. Virgin Islands (TEWG 2007), believed to be a result of conservation efforts. 

Analyses of mitochondrial DNA from leatherback sea turtles indicates a low level of genetic 

diversity, pointing to possible difficulties in the future if current population declines continue 

(Dutton et al. 1999). Further analysis of samples taken from individuals from rookeries in the 

Atlantic and Indian oceans suggest that each of the rookeries represent demographically 

independent populations (NMFS and USFWS 2013b). 

Leatherback sea turtles are distributed in oceans throughout the world. Leatherbacks occur 

throughout marine waters, from nearshore habitats to oceanic environments (Shoop and Kenney 

1992). Movements are largely dependent upon reproductive and feeding cycles and the 

oceanographic features that concentrate prey, such as frontal systems, eddy features, current 

boundaries, and coastal retention areas (Benson et al. 2011). 

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Status 

The leatherback sea turtle is an endangered species whose once large nesting populations have 

experienced steep declines in recent decades. The primary threats to leatherback sea turtles 

include fisheries bycatch, harvest of nesting females, and egg harvesting. Because of these 

threats, once large rookeries are now functionally extinct, and there have been range-wide 

reductions in population abundance. Other threats include loss of nesting habitat due to 

development, tourism, and sand extraction. Lights on or adjacent to nesting beaches alter nesting 

adult behavior and are often fatal to emerging hatchlings as they are drawn to light sources and 

away from the sea. Plastic ingestion is common in leatherbacks and can block gastrointestinal 

tracts leading to death. Climate change may alter sex ratios (as temperature determines hatchling 

sex), range (through expansion of foraging habitat), and habitat (through the loss of nesting 

beaches, because of sea-level rise. The species’ resilience to additional perturbation is low. 

Designated Critical Habitat 

On March 23, 1979, leatherback critical habitat was identified adjacent to Sandy Point, St. Croix, 

Virgin Islands from the 183 meter isobath to mean high tide level between 17° 42’12” N and 

65°50’00” W (Figure 26). This habitat is essential for nesting, which has been increasingly 

threatened since 1979, when tourism increased significantly, bringing nesting habitat and people 

into close and frequent proximity. The designated critical habitat is within the Sandy Point 

National Wildlife Refuge. Leatherback nesting increased at an annual rate of thirteen percent 

from 1994 to 2001; this rate has slowed according to nesting data from 2001 to 2010 (NMFS and 

USFWS 2013b). 

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Figure 26. Map depicting leatherback sea turtle designated critical habitat in the United 

States Virgin Islands. 

January 20, 2012, NMFS issued a final rule to designate additional critical habitat for the 

leatherback sea turtle. This designation includes approximately 43,798 square kilometers 

stretching along the California coast from Point Arena to Point Arguello east of the 3000 m 

depth contour; and 64,760 square kilometers stretching from Cape Flattery, Washington to Cape 

Blanco, Oregon east of the 2,000 meters depth contour (Figure 27). The designated areas 

comprise approximately 108,558 square kilometers of marine habitat and include waters from 

the ocean surface down to a maximum depth of 80 meters. They were designated specifically 

because of the occurrence of prey species, primarily scyphomedusae of the order 

Semaeostomeae (i.e., jellyfish), of sufficient condition, distribution, diversity, abundance and 

density necessary to support individual as well as population growth, reproduction, and 

development of leatherbacks. 

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Figure 27. Map depicting leatherback sea turtle designated critical habitat along the 

United States Pacific coast. 

Recovery Goals 

See the U.S. Pacific (NMFS and USFWS 1998a) and U.S. Caribbean, Gulf of Mexico and 

Atlantic Recovery Plans (NMFS and USFWS 1992) for leatherback sea turtles for complete 

down listing/delisting criteria for each of their respective recovery goals. The following items 

were the top five recovery actions identified to support in the Leatherback Five Year Action 

Plan: 

1) Reduce fisheries interactions 

2) Improve nesting beach protection and increase reproductive output 

3) International cooperation 

4) Monitoring and research 

5) Public engagement 

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6.2.5 Loggerhead Sea Turtle 

Loggerhead sea turtles are circumglobal, and are found in the temperate and tropical regions of 

the Indian, Pacific and Atlantic Oceans (Figure 28). 

Figure 28. Map identifying the range and distinct population segment boundaries of the 

loggerhead sea turtle. 

The loggerhead sea turtle is distinguished from other turtles by its large head and powerful jaws 

(Figure 29). 

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Figure 29. Loggerhead sea turtle. Photos: National Oceanic and Atmospheric 

Administration (left), Marco Giuliano, Fondazione Cetacea (right). 

The species was first listed as threatened under the Endangered Species Act in 1978. On 

September 22, 2011, the NMFS designated nine DPSs of loggerhead sea turtles: South Atlantic 

Ocean and Southwest Indian Ocean as threatened as well as Mediterranean Sea, North Indian 

Ocean, North Pacific Ocean, Northeast Atlantic Ocean, Northwest Atlantic Ocean, South Pacific 

Ocean, and Southeast Indo-Pacific Ocean as endangered (Table 9). Recent ocean-basin scale 

genetic analysis supports this conclusion, with additional differentiation apparent based upon 

nesting beaches (Shamblin et al. 2014). 

Table 9. Summary of loggerhead sea turtle listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan Critical Habitat 

Caretta 

caretta 

Loggerhead 

Turtle 

Northwest 

Atlantic Ocean Threatened 2009 

76 FR 58868 

09/22/2011 

43 FR 32800 

07/28/1978 

74 FR 2995 

2008 

79 FR 39856 

Atlantic/GOM 

2014 

Caretta 

caretta 

Loggerhead 

Turtle 

Northeast 

Atlantic Ocean Endangered 2009 

76 FR 58868 

09/22/2011 

43 FR 32800 

07/28/1978 

N/A None 

Designated 

Caretta 

caretta 

Loggerhead 

Turtle 

North Pacific 

Ocean Endangered 2009 

76 FR 58868 

09/22/2011 

43 FR 32800 

07/28/1978 

63 FR 28359 

1998 

None 

Designated 

Caretta 

caretta 

Loggerhead 

Turtle 

South Pacific 

Ocean Endangered 2009 

76 FR 58868 

09/22/2011 

43 FR 32800 

07/28/1978 

N/A None 

Designated 

The DPSs considered in this biological opinion for which take could be authorized are: the North 

Pacific Ocean and Northwest Atlantic Ocean DPSs. The Northeast Atlantic Ocean DPS and 

South Pacific Ocean DPS of loggerhead are also included, despite being a foreign water 

population because the DPS could be caught on the high seas. Animals cannot be visually 

distinguished by DPS. 

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We used information available in the 2009 status review (Conant et al. 2009) and the final listing 

rule (76 FR 58868) to summarize the life history, population dynamics and status of the species, 

as follows. 

Life History 

Mean age at first reproduction for female loggerhead sea turtles is 30 years (SD = 5). Females 

lay an average of three clutches per season. The annual average clutch size is 112 eggs per nest. 

The average remigration interval is 2.7 years. Nesting occurs on beaches, where warm, humid 

sand temperatures incubate the eggs. Temperature determines the sex of the turtle during the 

middle of the incubation period. Turtles spend the post-hatchling stage in pelagic waters. The 

juvenile stage is spent first in the oceanic zone and later in the neritic zone (i.e., coastal waters). 

Coastal waters provide important foraging habitat, inter-nesting habitat, and migratory habitat for 

adult loggerheads. 

Population Dynamics 

The following is a discussion of the species’ population and its variance over time. This section 

includes abundance, population growth rate, genetic diversity, and spatial distribution as it 

relates to the loggerhead sea turtle. 

There is general agreement that the number of nesting females provides a useful index of the 

species’ population size and stability at this life stage, even though there are doubts about the 

ability to estimate the overall population size (Bjorndal et al. 2005). Adult nesting females often 

account for less than one percent of total population numbers. The global abundance of nesting 

female loggerhead turtles is estimated at 43,320 to 44,560 (Spotila 2004). Abundance estimates 

for the loggerhead sea turtle DPSs and recovery units (prior to the designation of DPSs) are 

found in Table 10. 

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Table 10. Loggerhead sea turtle abundance estimates for distinct population segments 

and recovery units. 

Distinct Population Segment Abundance Estimate Citations 

Northwest Atlantic Ocean 53,000 to 92,000 nests annually (NMFS SEFSC 2009) 

Northeast Atlantic Ocean 12,000 nests annually (Lino et al. 2010; Marco et al. 2010) 

North Pacific Ocean 2,300 nesting females annually; 

43,320 to 44,560 individuals 

(Matsuzawa 2011; Seminoff et al. 

2014) 

South Pacific Ocean 200 nesting females annually (Wabnitz and Andréfouët 2008) 

Northern Recovery Unit 5,215 nests, on average; 1989 to 2008 (NMFS and USFWS 2008) 

Peninsular Florida Recovery Unit >10,000 nesting females annually (Ehrhart et al. 2003) 

Greater Caribbean Recovery Unit 903 to 2,700 nests annually (Ehrhart et al. 2003; NMFS and 

USFWS 2008; Zurita et al. 2003) 

Dry Tortugas Recovery Unit 246 nests annually (NMFS and USFWS 2007c) 

Gulf of Mexico Recovery Unit 100 to 999 nesting females annually (NMFS SEFSC 2009) 

Population Growth Rate 

Available information on the population growth rates and trends for each of the distinct 

population segments is presented below. 

6.2.5.1 Northwest Atlantic Ocean Distinct Population Segment 

Using a stage/age demographic model, the adult female population size of the DPS is estimated 

at 20,000 to 40,000 females, and 53,000 to 92,000 nests annually (NMFS SEFSC 2009). 

The Peninsular Florida Recovery Unit hosts more than 10,000 females nesting annually, which 

constitutes eighty-seven percent of all nesting effort in the DPS (Ehrhart et al. 2003). Nest counts 

taken at index beaches in Peninsular Florida show a significant decline in loggerhead nesting 

from 1989 to 2006, most likely attributed to mortality of oceanic-stage loggerheads caused by 

fisheries bycatch (Witherington et al. 2009). Loggerhead nesting on the Archie Carr National 

Wildlife Refuge (representing individuals of the Peninsular Florida subpopulation) has fluctuated 

over the past few decades. There was an average of 9,300 nests throughout the 1980s, with the 

number of nests increasing into the 1990s until it reached an all-time high in 1998, with 17,629 

nests. From that point, the number of loggerhead nests at the Refuge have declined steeply to a 

low of 6,405 in 2007, increasing again to 15,539, still a lower number of nests than in 1998 

(Bagley et al. 2013). 

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The Northern Recovery Unit, from North Carolina to northeastern Florida, and is the second 

largest nesting aggregation in the DPS, with an average of 5,215 nests from 1989 to 2008, and 

approximately 1,272 nesting females(NMFS and USFWS 2008). For the Northern recovery unit, 

nest counts at loggerhead nesting beaches in North Carolina, South Carolina and Georgia 

declined at 1.9 percent annually from 1983 to 2005 (NMFS and USFWS 2007c). 

The Gulf of Mexico Recovery Unit has between one hundred to 999 nesting females annually, 

and a mean of 910 nests per year. The nesting subpopulation in the Florida panhandle has 

exhibited a significant declining trend from 1995 to 2005 (Conant et al. 2009; NMFS and 

USFWS 2007c). Recent model estimates predict an overall population decline of 17 percent for 

the St. Joseph Peninsula, Florida subpopulation of the Northern Gulf of Mexico recovery unit 

(Lamont et al. 2014). 

The Greater Caribbean Recovery Unit encompasses nesting subpopulations in Mexico to French 

Guiana, the Bahamas, and the Lesser and Greater Antilles. The majority of nesting for this 

recovery unit occurs on the Yucatán peninsula, in Quintana Roo, Mexico, with 903 to 2,331 

nests annually (Zurita et al. 2003). Other significant nesting sites are found throughout the 

Caribbean, and including Cuba, with approximately 250 to 300 nests annually (Ehrhart et al. 

2003) and over one hundred nests annually in Cay Sal in the Bahamas (NMFS and USFWS 

2008). 

The population growth rate for each of the four of the recovery units for the Northwest Atlantic 

DPS (Peninsular Florida, Northern, Northern Gulf of Mexico, and Greater Caribbean) all exhibit 

negative growth rates (Conant et al. 2009). 

6.2.5.2 Northeast Atlantic Ocean Distinct Population Segment 

Loggerheads of the Northeast Atlantic Ocean DPS nest on the islands of the Cape Verde 

Archipelago, off the coast of western Africa. Boavista Island hosts the largest nesting 

aggregation, with over 10,000 nests annually, making it the third largest loggerhead nesting 

population in the world (Marco et al. 2010). Annually, about 1,000 nests were observed in 2009 

at Sal island, and the islands of Maio and Sao Nicolau support about 500 nests each (Lino et al. 

2010; Marco et al. 2010). Limited nesting occurs on beaches along the coast of Morocco and 

Senegal (Fretey 2001). 

There was not sufficient time series nesting data to calculate population growth rates for the 

Northeast Atlantic Ocean DPS in the 2009 status review (Conant et al. 2009). 

6.2.5.3 North Pacific Ocean Distinct Population Segment 

The North Pacific Ocean DPS has a nesting population of about 2,300 nesting females 

(Matsuzawa 2011). Loggerhead abundance on foraging grounds off the Pacific Coast of the Baja 

California Peninsula, Mexico, was estimated to be 43,226 individuals (Seminoff et al. 2014). 

Overall, Gilman (2009) estimated that the number of loggerheads nesting in the Pacific has 

declined by eighty percent in the past twenty years. There was a steep (fifty to ninety percent) 

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decline in the annual nesting population in Japan during the last half of the twentieth century 

(Kamezaki et al. 2003). Since then, nesting has gradually increased, but is still considered to be 

depressed compared to historical numbers, and the population growth rate is negative (-0.032) 

(Conant et al. 2009). 

6.2.5.4 South Pacific Ocean Distinct Population Segment 

The South Pacific Ocean DPS has a nesting population of approximately 200 females annually 

(Wabnitz and Andréfouët 2008). 

Overall, Gilman (2009) estimated that the number of loggerheads nesting in the Pacific has 

declined by eighty percent in the past twenty years. Eastern Australia supported one of the major 

global loggerhead nesting assemblages until recently (Limpus 1985). For many years, the nesting 

population at Queensland was in decline; there were approximately 3,500 females in the 1976 

and 1977 nesting season, and less than 500 in 1999, representing an 86 percent reduction in the 

size of the annual nesting population in twenty-three years (Limpus and Reimer 1994; Limpus 

1985; Limpus and Limpus 2003). From 2000 to 2009, there has been an increasing number of 

females nesting. Despite that increase, the arithmetic mean of the log negative population growth 

rate calculated for various nesting beaches in eastern Australia range from -0.013 to -0.075 

(Conant et al. 2009). Population modeling focusing on a nesting beach in Queensland, Australia 

indicates that the loss of only a few hundred adult and sub-adult females would lead to the 

extinction of the population in eastern Australia in less than one hundred years (Heppell et al. 

1996). 

Genetic Diversity 

There are nine loggerhead DPSs, which are geographically separated and genetically isolated, as 

indicated by genetic, tagging, and telemetry data. Our understanding of the genetic diversity and 

population structure of the different loggerhead DPSs is being refined as more studies examine 

samples from a broader range of specimens using longer mitochondrial DNA sequences. 

6.2.5.5 Northwest Atlantic Ocean Distinct Population Segment 

Based on genetic analysis of nesting subpopulations, the Northwest Atlantic Ocean DPS is 

further divided into five recovery units: Northern, Peninsular Florida, Dry Tortugas, Northern 

Gulf of Mexico, and Greater Caribbean (Conant et al. 2009). A more recent analysis using 

expanded mitochondrial DNA sequences revealed that rookeries from the Gulf and Atlantic 

coasts of Florida are genetically distinct, and that rookeries from Mexico’s Caribbean coast 

express high haplotype diversity (Shamblin et al. 2014). Furthermore, the results suggest that the 

Northwest Atlantic Ocean DPS should be considered as ten management units: (1) South 

Carolina and Georgia, (2) central eastern Florida, (3) southeastern Florida, (4) Cay Sal, Bahamas, 

(5) Dry Tortugas, Florida, (6) southwestern Cuba, (7) Quintana Roo, Mexico, (8) southwestern 

Florida, (9) central western Florida, and (10) northwestern Florida (Shamblin et al. 2012). 

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6.2.5.6 Northeast Atlantic Ocean Distinct Population Segment 

The Cape Verde Archipelago hosts the highest concentration of Northeast Atlantic Ocean DPS 

nesting, with most nesting occurring on Boa Vista Island. Mitochondrial DNA analysis of 

nesting females on Boa Vista Island reveals that the Cape Verde nesting assemblage is 

genetically distinct from other rookeries, and more similar to Northwest Atlantic Ocean 

rookeries than those in the nearby Mediterranean (Conant et al. 2009; Monzón-Argüello et al. 

2009). 

6.2.5.7 North Pacific Ocean Distinct Population Segment 

Recent mitochondrial DNA analysis using longer sequences has revealed a more complex 

population sub-structure for the North Pacific Ocean DPS. Previously, five haplotypes were 

present, and now, nine haplotypes have been identified in the North Pacific Ocean DPS. This 

evidence supports the designation of three management units in the North Pacific Ocean DPS: 1) 

the Ryukyu management unit (Okinawa, Okinoerabu, and Amami), 2) Yakushima Island 

management unit and 3) Mainland management unit (Bousou, Enshu-nada, Shikoku, Kii and 

Eastern Kyushu) (Matsuzawa et al. 2016). Genetic analysis of loggerheads captured on the 

feeding grounds of Sanriku, Japan, found only haplotypes present in Japanese rookeries 

(Nishizawa et al. 2014). 

6.2.5.8 South Pacific Ocean Distinct Population Segment 

South Pacific Ocean DPS loggerheads possess three haplotypes, including one dominant 

haplotype not found elsewhere (Conant et al. 2009). 

Distribution 

Loggerheads are circumglobal, occurring throughout the temperate and tropical regions of the 

Atlantic, Pacific, and Indian oceans, returning to their natal region for mating and nesting. Adults 

and sub-adults occupy nearshore habitat. While in their oceanic phase, loggerheads undergo long 

migrations using ocean currents. Individuals from multiple nesting colonies can be found on a 

single feeding ground. 

6.2.5.9 Northwest Atlantic Ocean Distinct Population Segment 

Loggerhead hatchlings from the western Atlantic disperse widely, most likely using the Gulf 

Stream to drift throughout the Atlantic Ocean. Mitochondrial DNA evidence demonstrates that 

juvenile loggerheads from southern Florida nesting beaches comprise the vast majority (71 to 88 

percent) of individuals found in foraging grounds throughout the western and eastern Atlantic: 

Nicaragua, Panama, Azores and Madiera, Canary Islands and Adalusia, Gulf of Mexico and 

Brazil (Masuda 2010). 

6.2.5.10 Northeast Atlantic Ocean Distinct Population Segment 

Loggerheads from the eastern Atlantic can migrate west to feeding grounds. Individuals from the 

Cape Verde nesting beaches can be found in foraging aggregations in Nicaragua (4 percent), 

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Panama (3.8 percent), Azores and Madiera (7.2 percent), Canary Islands and Andalusia (6.2 

percent), Gulf of Mexico (2.0 percent), the southern Atlantic coast of Florida (2.5 percent), and 

Brazil (1.0 percent) (Masuda 2010). Juvenile loggerheads from Cape Verde are thought to drift 

predominantly westward using the southern branch of the North Atlantic gyre (Monzón-Argüello 

et al. 2012). 

6.2.5.11 North Pacific Ocean Distinct Population Segment 

Hatchlings from Japanese nesting beaches use the North Pacific Subtropical Gyre and the 

Kurishio Extension to migrate to foraging grounds. Two major juvenile foraging areas have been 

identified in the North Pacific Basin: Central North Pacific and off of Mexico’s Baja California 

Peninsula. Both of these feeding grounds are frequented by individuals from Japanese nesting 

beaches (Abecassis et al. 2013; Seminoff et al. 2014). 

6.2.5.12 South Pacific Ocean Distinct Population Segment 

Loggerheads hatched on beaches in the southwest Pacific range widely in the southern portion of 

the basin, with individuals from nesting beaches in western Australia found as far east as 

Peruvian coast foraging areas (Boyle et al. 2009). Loggerheads from Australia and New 

Caledonia do not appear to go north of the equator. Loggerhead sea turtles are also present in the 

waters offshore northern Chile and Peru, where they comprise the majority of sea turtle bycatch 

in commercial fisheries (Alfaro-Shigueto et al. 2011; Donoso and Dutton 2010). 

Status 

Once abundant in tropical and subtropical waters, loggerhead sea turtles worldwide exist at a 

fraction of their historical abundance, as a result of over-exploitation. Globally, egg harvest, the 

harvest of females on nesting beaches and directed hunting of turtles in foraging areas remain the 

greatest threats to their recovery. In addition, bycatch in drift-net, long-line, set-net, pound-net 

and trawl fisheries kill thousands of loggerhead sea turtles annually. Increasing coastal 

development (including beach erosion and re-nourishment, construction and artificial lighting) 

threatens nesting success and hatchling survival. On a regional scale, the different DPSs 

experience these threats as well, to varying degrees. Differing levels of abundance combined 

with different intensities of threats and effectiveness of regional regulatory mechanisms make 

each DPS uniquely susceptible to future perturbations. 

6.2.5.13 Northwest Atlantic Ocean Distinct Population Segment 

Due to declines in nest counts at index beaches in the United States and Mexico, and continued 

mortality of juveniles and adults from fishery bycatch, the Northwest Atlantic Ocean DPS is at 

risk and likely to decline in the foreseeable future (Conant et al. 2009). 

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6.2.5.14 Northeast Atlantic Ocean Distinct Population Segment 

Due to the on-going harvest of females, low hatchling and emergence success, and mortality of 

juveniles and adults from fishing bycatch, the Northeast Atlantic Ocean DPS is predicted to have 

a high likelihood of decline (Conant et al. 2009). 

6.2.5.15 North Pacific Ocean Distinct Population Segment 

Neritic juveniles and adults in the North Pacific Ocean DPS are at risk of mortality from coastal 

fisheries in Japan and Baja California, Mexico. Habitat degradation in the form of coastal 

development and armoring pose a threat to nesting females. Based on these threats and the 

relatively small population size, the Biological Review Team concluded that the North Pacific 

Ocean DPS is currently at risk of extinction (Conant et al. 2009). 

6.2.5.16 South Pacific Ocean Distinct Population Segment 

Based on nest count data from the past thirty years, and mortality of juveniles and adults from 

fishery bycatch, the South Pacific Ocean DPS is at risk, and is likely to decline in the foreseeable 

future (Conant et al. 2009; Limpus 2008). 

Designated Critical Habitat 

6.2.5.17 Northwest Atlantic Ocean Distinct Population Segment 

NMFS has designated critical habitat for the Northwest Atlantic Ocean DPS loggerhead sea 

turtles. On July 10, 2014, NMFS and FWS designated critical habitat for the Northwest Atlantic 

Ocean DPS loggerhead sea turtles along the U.S. Atlantic and Gulf of Mexico coasts from North 

Carolina to Mississippi. These areas contain one or a combination of nearshore reproductive 

habitat, winter area, breeding areas, and migratory corridors. The critical habitat is categorized 

into 38 occupied marine areas and 685 miles of nesting beaches (Figure 30). 

The physical or biological features and primary constituent elements identified for the different 

habitat types include waters adjacent to high density nesting beaches, waters with minimal 

obstructions and manmade structures, high densities of reproductive males and females, 

appropriate passage conditions for migration, conditions that support sargassum habitat, 

available prey, and sufficient water depth and proximity to currents to ensure offshore transport 

of post-hatchlings. 

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Figure 30. Map depicting loggerhead turtle designated critical habitat. 

Recovery Goals 

See the 2008 Final Recovery Plan (NMFS and USFWS 2008) for the Northwest Atlantic 

Population of Loggerheads for complete down listing/delisting criteria for each of the following 

recovery objectives. 

1. Ensure that the number of nests in each recovery unit is increasing and that this 

increase corresponds to an increase in the number of nesting females. 

2. Ensure the in-water abundance of juveniles in both neritic and oceanic habitats is 

increasing and is increasing at a greater rate than strandings of similar age classes. 

3. Manage sufficient nesting beach habitat to ensure successful nesting. 

4. Manage sufficient feeding, migratory and inter-nesting marine habitats to ensure 

successful growth and reproduction. 

5. Eliminate legal harvest. 

6. Implement scientifically based nest management plans. 

7. Minimize nest predation. 

8. Recognize and respond to mass/unusual mortality or disease events appropriately. 

9. Develop and implement local, state, Federal and international legislation to ensure 

long-term protection of loggerheads and their terrestrial and marine habitats. 

10. Minimize bycatch in domestic and international commercial and artisanal fisheries. 

11. Minimize trophic changes from fishery harvest and habitat alteration. 

12. Minimize marine debris ingestion and entanglement. 

13. Minimize vessel strike mortality. 

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6.2.6 Olive Ridley Sea Turtle 

The olive ridley sea turtle is a small, mainly pelagic, sea turtle with a circumtropical distribution 

(Figure 31). 

Figure 31. Map identifying the range of the olive ridley sea turtle. 

Olive ridley sea turtles are olive or grayish-green in color, with a heart-shaped carapace (Figure 

32). 

Figure 32. Olive ridley sea turtle. Photo: Reuven Walder (left), Michael Jensen (right). 

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The species was listed under the ESA on July 28, 1978. The species was separated into two 

listing designations: endangered for breeding populations on the Pacific coast of Mexico, and 

threatened wherever found except where listed as endangered (i.e., in all other areas throughout 

its range) (Table 11). 

Table 11. Summary of olive ridley sea turtle listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Lepidochelys 

olivacea 

Olive 

Ridley 

Turtle 

Mexico’s Pacific 

coast breeding 

population 

Endangered 2014 43 FR 32800 

7/28/1978 

63 FR 28359 

U.S. Pacific 

1998 

None 

Designated 

Lepidochelys 

olivacea 

Olive 

Ridley 

Turtle 

All other 

populations Threatened 2014 43 FR 32800 

7/28/1978 

63 FR 28359 

U.S. Pacific 

1998 

None 

Designated 

We used information available in the 2014 five-year review (NMFS and USFWS 2014) to 

summarize the life history, population dynamics and status of the threatened olive ridley sea 

turtle, as follows. 

Life History 

Olive ridley females mature at ten to eighteen years of age. They lay an average of two clutches 

per season (three to six months in duration). The annual average clutch size is one hundred to 

110 eggs per nest. Olive ridleys commonly nest in successive years. Females nest in solitary or in 

arribadas, large aggregations coming ashore at the same time and location. As adults, olive 

ridleys forage on crustaceans, fish, mollusks, and tunicates, primarily in pelagic habitats. 

Population Dynamics 

The following is a discussion of the species’ population and its variance over time. This section 

includes: abundance, population growth rate, genetic diversity, and spatial distribution as it 

relates to the endangered range-wide population of the olive ridley sea turtle. 

6.2.6.1 Mexico’s Pacific Coast Breeding Population 

Olive ridley sea turtles are thought to be the most abundant species of sea turtle. Shipboard 

transects along the Mexico and Central American coasts between 1992 and 2006 indicate an 

estimated 1.39 million adults. There are six primary arribada nesting beaches in Mexico, the 

largest being La Escobilla, with about one million nesting females annually. There are several 

monitored nesting beaches where solitary nesting occurs. At Nuevo Vallarta, about 4,900 nests 

are laid annually. 

Based on the number of olive ridleys nesting in Mexico, populations appear to be increasing in 

one location (La Escobilla: from 50,000 nests in 1988 to more than one million in 2000), 

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decreasing at Chacahua, and stable at all others. At-sea estimates of olive ridleys off of Mexico 

and Central America also support an increasing population trend. 

6.2.6.2 All Other Populations 

Globally, olive ridley sea turtles can be found in tropical and subtropical waters in the Atlantic, 

Pacific and Indian Oceans. The range of the endangered Pacific coast breeding population 

extends as far south as Peru and up to California. Olive ridley sea turtles of the Pacific coast 

breeding colonies nest on arribada beaches at Mismaloya, Ixtapilla and La Escobilla, Mexico. 

Solitary nesting takes place all along the Pacific coast of Mexico. 

Olive ridley sea turtles are thought to be the most abundant species of sea turtle, and can be 

found in the Atlantic, Indian and Pacific Oceans. There is no global estimate of olive ridley 

abundance, and we rely on nest counts and nesting females to estimate abundance in each of the 

ocean basins, described below. However, Eguchi et al. (2007) estimated a weighted average of 

the yearly abundance estimates as 1.39 million (confidence interval: 1.15 to 1.62 million). 

In the Western Atlantic, two arribada nesting beaches occur in Suriname and French Guiana. The 

Cayenne Peninsula in French Guiana hosts about 2,000 nests annually, while the Galibi Nature 

Reserve in Suriname had 335 nests in 1995. Solitary nesting also occurs elsewhere in Suriname, 

Guyana and French Guiana, although no abundance estimates are available. In Sergipe, Brazil, 

solitary nesting amounted to about 2,600 nests in 2002 and 2003. 

In the Eastern Atlantic, there are no arribada nesting beaches, but solitary nesting occurs in 

several countries along the western coast of Africa, from Gambia to Angola. For many countries, 

there are no abundance estimates available. For beaches with data available (Angola, the 

Republic of Congo, the Democratic Republic of Congo, Equatorial Guinea and Guinea Bissau), 

nest counts are low, with most monitoring taking place for only a few years. The most abundant 

nesting beaches are Orango National Park in Guinea Bissau, which had between 170 and 620 

nests from 1992 to 1994; and the Republic of Congo, which had between 300 and 600 nests 

annually from 2003 to 2010 (NMFS and USFWS 2014). 

In the Indian Ocean, three arribada nesting beaches are found in India, amounting to 150,000-

200,000 nesting females annually. Solitary nesting also occurs elsewhere in the region, in eastern 

Africa, Oman, India, Pakistan, and other southeast Asian countries; for many, there are no 

estimates available. The largest recorded solitary nesting beach is in Myanmar, when in 1999, 

700 nests were counted (NMFS and USFWS 2014). 

There are no known arribada nesting beaches in the western Pacific Ocean; however, some 

solitary nesting occurs in Australia, Brunei, Malaysia, Indonesia and Vietnam. Data are lacking 

for many sites. Terengganu, Malaysia had ten nests in 1998 and 1999. Alas Purwo, Indonesia, 

had 230 nests annually from 1993 to 1998. 

In the eastern Pacific Ocean (excluding breeding populations in Mexico), there are arribada 

nesting beaches in Nicaragua, Costa Rica and Panama. La Flor, Nicaragua had 521,440 effective 

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nesting females in 2008 and 2009; Chacocente, Nicaragua had 27,947 nesting females over the 

same period (Gago et al. 2012). Two other arribada nesting beaches are in Nicaragua, Masachapa 

and Pochomil, but there are no abundance estimates available. Costa Rica hosts two major 

arribada nesting beaches; Ostional has between 3,564 and 476,550 turtles per arribada, and 

Nancite has between 256 and 41,149 turtles per arribada. Panama has one arribada nesting beach, 

with 8,768 turtles annually. 

There are several solitary nesting beaches in the East Pacific Ocean (excluding breeding 

populations in Mexico); however no abundance estimates are available for beaches in El 

Salvador, Honduras, Nicaragua, Costa Rica, Panama, Columbia and Ecuador. On Hawaii Beach 

in Guatemala, 1,004 females were recorded in 2005 (NMFS and USFWS 2014). 

Population Growth 

Population growth rate and trend information for the threatened population of olive ridley sea 

turtles is difficult to discern, owing to its range over a large geographic area, and a lack of 

consistent monitoring data in all nesting areas. Below, we present the any known population 

trend information for olive ridley sea turtles by ocean basin (NMFS and USFWS 2014). 

Nesting at arribada beaches in French Guiana appears to be increasing, while in Suriname, 

nesting has declined by more than ninety percent since 1968. Solitary nesting also occurs 

elsewhere in Suriname, Guyana and French Guiana; no trend data are available. Solitary nesting 

in Brazil appears to be increasing, with one hundred nests recorded in 1989 to 1990, to 2,606 in 

2002 to 2003. 

In the Eastern Atlantic, trend data is not available for most solitary nesting beaches. Nest counts 

in the Republic of Congo decreased from 600 nests in 2003 and 2004 to less than 300 in 2009 

and 2010. 

The three arribada nesting beaches in India: Gahirmatha, Rushikulya, and Devi River are 

considered stable over three generations. There is no trend data available for several solitary 

nesting beaches in the Indian Ocean. However, even for the few beaches with short-term 

monitoring, the nest counts are believed to represent a decline from earlier years. 

There are no arribada nesting beaches in the Western Pacific Ocean. Data are lacking or 

inconsistent for many solitary nesting beaches in the Western Pacific, so it is not possible to 

assess population trends for these sites. Nest counts at Alas Purwo, Indonesia, appear to be 

increasing, the nest count at Terengganu, Malaysia, is thought to be a decline from previous 

years. 

Population trends at Nicaraguan arribada nesting beaches are unknown or stable (La Flor). 

Ostional, Costa Rica arribada nesting beach is increasing, while trends Nancite, Costa Rica, and 

Isla Cañas, Panama, nesting beaches are declining. For most solitary nesting beaches in the East 

Pacific Ocean, population trends are unknown, except for Hawaii Beach, Guatemala, which is 

decreasing. 

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Genetic Diversity 

Genetic studies have identified four main lineages for the olive ridley: east India, Indo-Western 

Pacific, Atlantic, and the eastern Pacific. In the eastern Pacific, rookeries on the Pacific Coasts of 

Costa Rica and Mexico were not genetically distinct, and fine-scale population structure was not 

found when solitary and arribada nesting beaches were examined. There was no population 

subdivision among olive ridleys along the east India coastline. Low levels of genetic diversity 

among Atlantic French New Guinea and eastern Pacific Baja California nesting sites are 

attributed to a population collapse caused by past overharvest (NMFS and USFWS 2014). 

Distribution 

Globally, olive ridley sea turtles can be found in tropical and subtropical waters in the Atlantic, 

Pacific and Indian Oceans. Major nesting arribada beaches are found in Nicaragua, Costa Rica, 

Panama, India and Suriname. The range of the endangered Pacific coast breeding population 

extends as far south as Peru and up to California. Olive ridley sea turtles of the Pacific coast 

breeding colonies nest on arribada beaches at Mismaloya, Ixtapilla and La Escobilla, Mexico. 

Solitary nesting takes place all along the Pacific coast of Mexico. 

Status 

6.2.6.3 Mexico’s Pacific Coast Breeding Population 

In the first half of the twentieth century, there was an estimated ten million olive ridleys nesting 

on the Pacific coast of Mexico. Olive ridleys became targeted in a fishery in Mexico and 

Ecuador, which severely depleted the population; there was an estimated one million olive 

ridleys by 1969. Olive ridley breeding populations on the Pacific coast of Mexico were listed as 

endangered in response to this severe population decline. Legal harvest of olive ridleys has been 

prohibited, although illegal harvest still occurs. The population is threatened by incidental 

capture in fisheries, exposure to pollutants and climate change. In spite of the severe population 

decline, the olive ridley breeding populations on the Pacific coast of Mexico appear to be 

resilient, evidenced by the increasing population. 

6.2.6.4 All Other Populations 

It is likely that solitary nesting locations once hosted large arribadas; since the 1960s, 

populations have experienced declines in abundance of fifty to eighty percent. Many populations 

continue to decline. Olive ridley sea turtles continue to be harvested as eggs and adults, legally in 

some areas, and illegally in others. Incidental capture in fisheries is also a major threat. The olive 

ridley sea turtle is the most abundant sea turtle in the world; however, several populations are 

declining as a result of continued harvest and fisheries bycatch. The large population size of the 

range-wide population, however, allows some resilience to future perturbation. 

Designated Critical Habitat 

No critical habitat has been designated for olive ridley sea turtles. 

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Recovery Goals 

There has not been a Recovery Plan prepared specifically for olive ridley sea turtles of the 

breeding populations of the Pacific coast of Mexico. The 1998 Recovery Plan was prepared for 

olive ridleys found in the U.S. Pacific. Olive ridley sea turtles found in the Pacific could 

originate from the Pacific coast of Mexico or from another nesting population. As such, the 

recovery goals in the 1998 Recovery Plan for the U.S. Pacific olive ridley sea turtle can apply to 

both listed populations. See the 1998 Recovery Plan for the U.S. Pacific olive ridley sea turtles 

for complete down listing/delisting criteria for their recovery goals. The following items were the 

recovery criteria identified to consider delisting: 

1. All regional stocks that use U.S. waters have been identified to source beaches based 

on reasonable geographic parameters 

2. Foraging populations are statistically significantly increasing at several key foraging 

grounds within each stock region 

3. All females estimated to nest annually at source beaches are either stable or 

increasing for over ten years 

4. Management plan based on maintaining sustained populations for turtles is in effect 

5. International agreements in place to protect shared stocks 

6.2.7 Gulf of Maine Atlantic Salmon 

The Atlantic salmon is an anadromous fish, occupying freshwater streams in North America 

(Figure 33). Adult Atlantic salmon are silver-blue with dark spots. They average 8-12 pounds but 

can get as large as 30 pounds. 

Figure 33. Atlantic salmon. Photo: William Hartley, United States Fish and Wildlife 

Service (left), Betty Holmes, NOAA Northeast Fisheries Science Center (right). 

There are three Atlantic salmon DPSs in the United States: Long Island Sound, Central New 

England, and the GOM (Fay et al. 2006a). The GOM DPS Atlantic salmon are found in 

watersheds throughout Maine (Figure 34). 

127 
Figure 34. Map identifying the range of Gulf of Maine Atlantic salmon. 

The GOM DPS was first listed as endangered by the U. S. Fish and Wildlife Service and NMFS 

on November 17, 2000 (Table 12). The listing was refined by the Services on June 19, 2009, to 

include all anadromous Atlantic salmon whose freshwater range occurs in the watersheds from 

the Androscoggin River northward along the Maine coast to the Dennys River, and wherever 

these fish occur in the estuarine and marine environment. 

Table 12. Summary of Atlantic salmon listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Salmo 

salar 

Atlantic 

salmon 

Gulf of 

Maine Endangered 2006 74 FR 29344 

06/19/2009 

70 FR 75473 

2005 

Draft Plan 

2016 

74 FR29300 

Maine 

Turtle Research Programmatic Biological Opinion FPR-2017-9230 

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We used information available in the 2006 status review (Fay et al. 2006a) and recent scientific 

publications to summarize the life history, population dynamics and status of the species, as 

follows. 

Life History 

Atlantic salmon have a complex life history that ranges from territorial rearing in rivers to 

extensive feeding migrations on the high seas. Most adult Atlantic salmon ascend the rivers of 

New England beginning in the spring, continuing into the fall with the peak occurring in June. 

Adult Atlantic salmon typically spawn around early November and eggs hatch in late March or 

April. Preferred spawning habitat is a gravel substrate with adequate water circulation to keep 

the buried eggs well oxygenated. Juveniles spend about two years feeding in freshwater until 

they weigh approximately two ounces and are six inches in length. Smoltification (the 

physiological and behavioral changes required for the transition to saltwater) usually occurs at 

age two for GOM DPS Atlantic salmon. GOM DPS Atlantic salmon migrate more than 4,000 

kilometers in the open ocean to reach feeding areas in the Davis Strait between Labrador and 

Greenland. The majority of GOM DPS Atlantic salmon (about ninety percent) spend two winters 

at sea before reaching maturity and returning to their natal rivers, with the remainder spending 

one or three winters at sea. At maturity, GOM DPS Atlantic salmon typically weigh between 

eight to fifteen pounds and average thirty inches in length. Atlantic salmon are iteroparous (i.e., 

capable of spawning more than once). 

Population Dynamics 

GOM DPS Atlantic salmon can be found in at least eight rivers in Maine: Dennys River, East 

Machias River, Machias River, Pleasant River, Narraguagus River, Ducktrap River, Sheepscot 

River, Cove Brook, Penobscot River, Androscoggin River and the Kennebec River. The GOM 

DPS Atlantic salmon is genetically distinct from other Atlantic salmon populations in Canada, 

and can be further delineated into stocks: Downeast Coastal stock which includes the Dennys, 

East Machias, Machias, Pleasant and Narraguagus Rivers; Penobscot Bay stock; and the 

Merrymeeting Bay (Sheepscot) stock. The hatchery supplementation programs for the Penobscot 

and Merrymeeting Bays stocks use river-specific broodstock (USASAC 2016). The conservation 

hatchery program plays a significant role in the persistence of GOM DPS Atlantic salmon. Adult 

returns of GOM DPS Atlantic salmon captured in six Maine rivers from 1997 to 2004 ranged 

from 567 to 1,402. These counts include both wild and hatchery origin fish. Each year, the 

majority (ninety-two to ninety-eight percent) of adult returns were found in the Penobscot River; 

the Narraguagus River supported between 0.8 to 4.1 percent of adult returns during those years 

(Fay et al. 2006a). In 2015, four million juvenile salmon (eggs, fry, parr and smolts) and 4,271 

adults were stocked in the Connecticut, Merrimack, Saco, Penobscot and five other coastal rivers 

in Maine (USASAC 2016). The total number of adult returns to U.S. rivers in 2015 was 921, the 

majority (eighty percent) of which were of hatchery origin. The fact that so few of the returning 

adults are naturally-reared is concerning to managers; the reliance on hatcheries can pose risks 

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such as artificial selection, inbreeding depression and outbreeding depression (Fay et al. 2006a). 

There is no population growth rate available for GOM DPS Atlantic salmon. However, the 

consensus is that the DPS exhibits a continuing declining trend (NOAA 2016). 

Status 

Historically, Atlantic salmon occupied U.S. rivers throughout New England, with an estimated 

300,000 to 500,000 adults returning annually (Fay et al. 2006a). Of the three DPSs found in the 

United States, native salmon in the Long Island Sound and Central New England DPSs were 

extirpated in the 1800s. Several rivers within these DPSs are presently stocked with GOM DPS 

salmon. The GOM DPS Atlantic salmon was listed as endangered in response to population 

decline caused by many factors, including overexploitation, degradation of water quality and 

damming of rivers, all of which remain persistent threats (Fay et al. 2006a). Coastal development 

poses a threat as well, as artificial light can disrupt and delay fry dispersal (Riley et al. 2013). 

Climate change may cause changes in prey availability and thermal niches, further threatening 

Atlantic salmon populations (Mills et al. 2013). Even with current conservation efforts, returns of 

adult Atlantic salmon to the GOM DPS rivers remain extremely low, with an estimated 

extinction risk of nineteen to seventy-five percent in the next one hundred years (Fay et al. 

2006a). Estimated Atlantic salmon returns to U.S. rivers from 2005 to 2015 range from a low in 

2014 of 450 to a high in 2011 of 4,178 (USASAC 2016). Based on the information above, the 

species would likely have a low resilience to additional perturbations. 

Designated Critical Habitat 

NMFS and the USFWS designated critical habitat for the GOM DPS on June 19, 2009, which 

identified essential physical and biological features of Atlantic salmon spawning and rearing 

sites and migration routes. These include freshwater and estuary migratory sites free from 

physical and biological barriers that can delay or prevent spawning migrations or smolt 

emigration, and freshwater and estuary migration sites with abundant, diverse native fish 

communities to serve as a protective buffer against predation. The action area for this opinion 

does not overlap with designated critical habitat for the GOM DPS of Atlantic salmon. 

Recovery Goals 

See the 2016 Draft Recovery Plan for the GOM DPS Atlantic Salmon (USFWS and NMFS 

2016), for complete down listing/delisting criteria for each of their respective recovery goals. 

Recovery actions identified in the Draft Recovery Plan include the following: 

1) Enhance connectivity between ocean and freshwater habitats important for recovery 

2) Maintain the genetic diversity of Atlantic salmon populations over time 

3) Increase adult spawners through the conservation hatchery program 

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4) Increase Atlantic salmon survival through increased ecosystem understanding and 

identification of spatial and temporal constraints to salmon marine productivity to 

inform and support management actions that improve survival 

5) Consult with all involved Tribes on a government-to-government basis 

6) Collaborate with partners and engage interested parties in recovery efforts 

6.2.8 Smalltooth Sawfish, U.S. Portion of Range 

The smalltooth sawfish (Pristis pectinata) is a tropical marine and estuarine elasmobranch. 

Although they are rays, sawfish physically resemble sharks, with only the trunk and especially 

the head ventrally flattened. Smalltooth sawfish are characterized by their “saw,” a long, narrow, 

flattened rostral blade with a series of transverse teeth along either edge (NMFS 2009c) (Figure 

35). 

Figure 35. Smalltooth sawfish. Photo: Florida Museum of Natural History (left), R. Dean 

Grubbs (right). 

Although this species is reported to have a circumtropical distribution, NMFS identified 

smalltooth sawfish from the southeast United States as a DPS. Within the U.S., smalltooth 

sawfish have been captured in estuarine and coastal waters from New York southward through 

Texas, although peninsular Florida has historically been the region of the United States with the 

largest number of recorded captures (NMFS 2010c) (Figure 36). 

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Figure 36. Smalltooth sawfish range and designated critical habitat. 

The U.S. DPS of smalltooth sawfish was listed as endangered under the ESA effective May 1, 

2003 (Table 13). 

Table 13. Summary of smalltooth sawfish listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Pristis 

pectinata 

Sawfish, 

smalltooth 

U.S. portion 

of range Endangered 2010 68 FR 15674 

04/01/2003 

74 FR 3566 

2009 

74 FR 45353 

Florida 

Life History 

Smalltooth sawfish size at sexual maturity has been reported as 360 centimeters total length (TL) 

by Simpfendorfer (2005). Carlson and Simpfendorfer (2015) estimated that sexual maturity for 

females occurs between 7 and 11 years of age. As in all elasmobranchs, smalltooth sawfish are 

viviparous; fertilization is internal. The gestation period for smalltooth sawfish is estimated at 

five months based on data from the largetooth sawfish (Thorson 1976). Females move into 

shallow estuarine and nearshore nursery areas to give birth to live young between November and 

July, with peak parturition occurring between April and May (Poulakis et al. 2011). Litter sizes 

range between 10 and 20 individuals (Bigalow and Schroeder 1953; Carlson and Simpfendorfer 

2015; Simpfendorfer 2005). 

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Neonate smalltooth sawfish are born measuring 67 to 81 centimeters TL and spend the majority 

of their time in the shallow nearshore edges of sand and mud banks (Poulakis et al. 2011; 

Simpfendorfer et al. 2010). Once individuals reach 100 to 140 centimeters TL they begin to 

expand their foraging range. Capture data suggests smalltooth sawfish in this size class may 

move throughout rivers and estuaries within a salinity range of 18 and 30 (practical salinity 

units). Individuals in this size class also appear to have the highest affinity to mangrove habitat 

(Simpfendorfer et al. 2011). Juvenile sawfish spend the first 2 to 3 years of their lives in the 

shallow waters provided in the lower reaches of rivers, estuaries, and coastal bays 

(Simpfendorfer et al. 2008; Simpfendorfer et al. 2011). As smalltooth sawfish approach 250 

centimeters TL they become less sensitive to salinity changes and begin to move out of the 

protected shallow-water embayments and into the shorelines of barrier islands (Poulakis et al. 

2011). Adult sawfish typically occur in more open-water, marine habitats (Poulakis and Seitz 

2004). 

Population Dynamics 

The abundance of smalltooth sawfish in U.S. waters has decreased dramatically over the past 

century. Efforts are currently underway to provide better estimates of smalltooth sawfish 

abundance (NMFS 2014b). Current abundance estimates are based on encounter data, genetic 

sampling, and geographic extent. Carlson and Simpfendorfer (2015) used encounter densities to 

estimate the female population size to be 600. Chapman et al. (2011) analyzed genetic data from 

tissue samples (fin clips) to estimate the effective genetic population size as 250 to 350 adults 

(95 percent confidence interval from 142 to 955). Simpfendorfer (2002) estimated that the U.S. 

population may number less than five percent of historic levels based on the contraction of the 

species’ range. 

The abundance of juveniles encountered in recent studies (Poulakis et al. 2014; Seitz and 

Poulakis 2002; Simpfendorfer and Wiley 2004) suggests that the smalltooth sawfish population 

remains reproductively viable. The overall abundance appears to be stable (Wiley and 

Simpfendorfer 2010). Data analyzed from the Everglades portion of the smalltooth sawfish range 

suggests that the population growth rate for that region may be around five percent per year 

(Carlson and Osborne 2012; Carlson et al. 2007). Intrinsic rates of growth (λ) for smalltooth 

sawfish have been estimated at 1.08 to 1.14 per year and 1.237 to 1.150 per year by 

Simpfendorfer (2000) and Carlson and Simpfendorfer (2015) respectively. However, these 

intrinsic rates are uncertain due to the lack of long-term abundance data. 

Chapman et al. (2011) investigated the genetic diversity within the smalltooth sawfish 

population. The study reported that the remnant population exhibits high genetic diversity (allelic 

richness, alleles per locus, heterozygosity) and that inbreeding is rare. The study also suggested 

that the protected population will likely retain greater than 90 percent of its current genetic 

diversity over the next century. 

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Recent capture and encounter data suggest that the current distribution is focused primarily to 

south and southwest Florida from Charlotte Harbor through the Dry Tortugas (Poulakis and Seitz 

2004; Seitz and Poulakis 2002). Water temperatures (no lower than 16 to 18 degrees Celsius) and 

the availability of appropriate coastal habitat (shallow, euryhaline waters and red mangroves) are 

the major environmental constraints limiting the distribution of smalltooth sawfish (Bigalow and 

Schroeder 1953). 

Status 

The decline in the abundance of smalltooth sawfish has been attributed to fishing (primarily 

commercial and recreational bycatch), habitat modification (including changes to freshwater 

flow regimes as a result of climate change), and life history characteristics (i.e., slow-growing, 

relatively late-maturing, and long-lived species) (NMFS 2009c; Simpfendorfer et al. 2011). 

These factors continue to threaten the smalltooth sawfish population. Recent records indicate 

there is a resident reproducing population of smalltooth sawfish in south and southwest Florida 

from Charlotte Harbor through the Dry Tortugas, which is also the last U.S. stronghold for the 

species (Poulakis and Seitz 2004; Seitz and Poulakis 2002; Simpfendorfer and Wiley 2004). 

Recent information indicates the smalltooth sawfish population is likely stable or increasing 

(Carlson and Osborne 2012; Carlson and Simpfendorfer 2015). While the overall abundance 

appears to be stable, low intrinsic rates of population increase suggest that the species is 

particularly vulnerable to rapid population declines (NMFS 2010c). 

Designated Critical Habitat 

Critical habitat for smalltooth sawfish was designated in 2009 and includes two major units: 

Charlotte Harbor (221,459 acres) and Ten Thousand Islands/Everglades (619,013 acres) (Figure 

36). These two units include essential sawfish nursery areas. Within the nursery areas, two 

features were identified as essential to the conservation of the species: red mangroves 

(Rhizophora mangle), and euryhaline habitats with water depths less than or equal to 0.9 meters. 

The action area for this biological opinion overlaps with smalltooth sawfish designated critical 

habitat. Based on our analysis above (see Section 6.1), we determine that the proposed action is 

not likely to adversely affect smalltooth sawfish designated critical habitat. 

Recovery Goals 

The 2009 Smalltooth Sawfish Recovery Plan (NMFS 2009c) contains complete 

downlisting/delisting criteria for each of the three following recovery goals: 

1. Minimize human interactions and associated injury and mortality. 

Specific criteria include: a) educational programs, b) handling and release guidelines, 

c) injury and mortality regulations, and d) other State and/or Federal measures (not 

including those provided under the ESA. 

2. Protect and/or restore smalltooth sawfish habitats. 

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Specific criteria include: a) protection of existing mangrove shoreline habitat, b) 

assurance of availability and accessibility of both mangrove and non-mangrove 

habitat sufficient to support subpopulations of juvenile sawfish, c) appropriate 

freshwater flow regimes, and d) identification and protection of habitat areas utilized 

by adult smalltooth sawfish. 

3. Ensure smalltooth sawfish abundance increases substantially and the species 

reoccupies areas from which it had been previously extirpated. 

Specific criteria include: a) annual increases in the relative abundance of juvenile 

smalltooth sawfish, b) annual increases in the relative abundance of adult smalltooth 

sawfish, and c) verified records of adult smalltooth sawfish in outer regions of the 

species range. 

6.2.9 Atlantic Sturgeon 

Sturgeon are among the most primitive of the bony fishes. The Atlantic sturgeon is a long-lived 

(approximately 60 years), late maturing, iteroparous, estuarine dependent species (ASSRT 2007; 

Dadswell 2006). Atlantic sturgeon are anadromous, spawning in freshwater but spending most of 

their subadult and adult life in the marine environment. They can grow to approximately 14 feet 

long and can weigh up to 800 pounds. Atlantic sturgeon are bluish-black or olive brown dorsally 

(on their back) with paler sides, a white belly, and have five major rows of dermal "scutes” 

(Figure 37). 

Figure 37. Atlantic sturgeon. Photo: Robert Michelson (left), NOAA (right). 

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Turtle Research Programmatic Biological Opinion FPR-2017-9230 

Five DPSs of Atlantic sturgeon were listed under the ESA in 2012 (Table 14). The GOM DPS is 

listed as threatened while the New York Bight, Chesapeake Bay, Carolina, and South Atlantic 

DPSs are listed as endangered (Figure 38). 

Figure 38. Range and boundaries of the five Atlantic sturgeon Distinct Population 

Segments. 

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Table 14. Summary of Atlantic sturgeon listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan Critical Habitat 

Acipenser 

oxyrinchus 

oxyrinchus 

Atlantic 

sturgeon Gulf of Maine Threatened 2007 77 FR 5880 02/06/2012 N/A 

82 FR 39160 

Gulf of Maine 

2017 

Acipenser 

oxyrinchus 

oxyrinchus 

Atlantic 

sturgeon 

New York 

Bight Endangered 2007 77 FR 5880 02/06/2012 N/A 

82 FR 39160 

New York Bight 

2017 

Acipenser 

oxyrinchus 

oxyrinchus 

Atlantic 

sturgeon 

Chesapeake 

Bay Endangered 2007 77 FR 5880 02/06/2012 N/A 

82 FR 39160 

Chesapeake Bay 

2017 

Acipenser 

oxyrinchus 

oxyrinchus 

Atlantic 

sturgeon Carolina Endangered 2007 77 FR 5914 02/06/2012 N/A 

82 FR 39160 

Carolina 

2017 

Acipenser 

oxyrinchus 

oxyrinchus 

Atlantic 

sturgeon 

South 

Atlantic Endangered 2007 77 FR 5914 02/06/2012 N/A 

82 FR 39160 

South Atlantic 

2017 

This section provides general information on the Atlantic sturgeon coast-wide population, 

including information about the species life history, population dynamics, and status. The 

subsections that follow provide information and characteristics particular to each of the five 

listed DPSs of Atlantic sturgeon. 

Life History 

The general life history pattern of Atlantic sturgeon is that of a long lived, late maturing, 

iteroparous, anadromous species. Atlantic sturgeon spawn in freshwater, but spend most of their 

subadult and adult life in the marine environment. 

Traditionally, it was believed that spawning within all populations occurred during the spring 

and early summer months. More recent studies, however, suggest that spawning occurs from late 

summer to early autumn in two tributaries of the Chesapeake Bay (James River and York River, 

Virginia) and in the Altamaha River, Georgia (Balazik et al. 2012; Hager et al. 2014). 

Sturgeon eggs are highly adhesive and are deposited on the bottom substrate, usually on hard 

surfaces (e.g., cobble) (Smith and Clugston 1997). Hatching occurs approximately 94 to 140 

hours after egg deposition, and larvae assume a demersal existence (Smith et al. 1980). The 

yolksac larval stage is completed in about 8 to 12 days, during which time the larvae move 

downstream to rearing grounds over a 6 to 12-day period (Kynard and Horgan 2002). During the 

first half of their migration downstream, movement is limited to nighttime. During the day, 

larvae use benthic structure (e.g., gravel matrix) as refugia (Kynard and Horgan 2002). During 

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the latter half of migration when larvae are more fully developed, movement to rearing grounds 

occurs both day and night. The larvae grow rapidly and are 4” to 5 1/2" long at a month old 

(MSPO 1993). At this size, the young sturgeon bear teeth and have sharp, closely spaced spinetipped scutes. As growth continues, they lose their teeth, the scutes separate and lose their 

sharpness. 

Juvenile Atlantic sturgeon continue to move downstream into brackish waters, and eventually 

become residents in estuarine waters. Juvenile Atlantic sturgeon are resident within their natal 

estuaries for two to six years, depending on their natal river of origin, after which they emigrate 

as subadults to coastal waters (Dovel 1983) or to other estuaries seasonally (Waldman et al. 

2013). Atlantic sturgeon undertake long marine migrations and utilize habitats up and down the 

East Coast for rearing, feeding, and migrating (Bain 1997; Dovel 1983; Stevenson 1997). 

Migratory subadults and adults are normally located in shallow (10-50m) nearshore areas 

dominated by gravel and sand substrate (Stein et al. 2004a). Tagging and genetic data indicate 

that subadult and adult Atlantic sturgeon may travel widely once they emigrate from rivers 

(Bartron 2007; Wirgin et al. 2015). Once in marine waters, subadults undergo rapid growth 

(Dovel 1983; Stevenson 1997). Despite extensive mixing in coastal waters, Atlantic sturgeon 

display high site fidelity to their natal streams. 

Atlantic sturgeon have been aged to 60 years (Mangin 1964), but this should be taken as an 

approximation because the age validation studies conducted to date show ages cannot be reliably 

estimated after 15-20 years (Stevenson and Secor 2000). Vital parameters of sturgeon 

populations generally show clinal variation with faster growth, earlier age at maturation, and 

shorter life span in more southern systems. Spawning intervals range from one to five years for 

male Atlantic sturgeon (Collins et al. 2000; Smith 1985) and three to five years for females 

(Schueller and Peterson 2010; Stevenson and Secor 2000). Fecundity of Atlantic sturgeon is 

correlated with age and body size, ranging from approximately 400,000 to 8 million eggs 

(Dadswell 2006; Smith et al. 1982; Van Eenennaam and Doroshov 1998). The average age at 

which 50 percent of Atlantic sturgeon maximum lifetime egg production is achieved is estimated 

to be 29 years, approximately 3-10 times longer than for most other bony fish species (Boreman 

1997). 

Atlantic sturgeon feed on molluscs, polychaeta worms, gastropods, shrimps, pea crabs, decapods, 

amphipods, isopods, and small fishes in the marine environment (Collins et al. 2006; Guilbard et 

al. 2007; Savoy 2007). The sturgeon "roots" in the sand or mud with its snout, like a pig, to 

dislodge worms and molluscs that it sucks into its protrusible mouth, along with considerable 

amounts of mud. The Atlantic sturgeon has a stomach with very thick, muscular walls that 

resemble the gizzard of a bird. This gizzard enables it to grind such food items as molluscs and 

gastropods (MSPO 1993). 

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Population Dynamics 

The Atlantic sturgeon’s historic range included major estuarine and riverine systems that 

spanned from Hamilton Inlet on the coast of Labrador, Canada, to the Saint Johns River in 

Florida (ASSRT 2007; Smith and Clugston 1997). Atlantic sturgeon have been documented as 

far south as Bermuda and Venezuela (Lee et al. 1980). Historically, Atlantic sturgeon were 

present in approximately 38 rivers in the United States from St. Croix, Maine, to the Saint Johns 

River, Florida, of which 35 rivers have been confirmed to have had historic spawning 

populations. Atlantic sturgeon are currently present in 36 rivers, and spawning occurs in at least 

21 of these (ASSRT 2007). Other estuaries along the U.S. Atlantic Coast formed by rivers that 

do not support Atlantic sturgeon spawning populations may still be important as rearing habitats. 

Atlantic sturgeon throughout their range exhibit ecological separation during spawning that has 

resulted in multiple, genetically distinct, interbreeding population segments. Studies have 

consistently found populations to be genetically diverse and indicate that there are between seven 

and ten populations that can be statistically differentiated (Grunwald et al. 2008; King et al. 

2001; Waldman et al. 2002; Wirgin et al. 2007). However, there is some disagreement among 

studies, and results do not include samples from all rivers inhabited by Atlantic sturgeon. Recent 

studies conducted indicate that genetically distinct populations of spring and fall-run Atlantic 

sturgeon can exist within a given river system (Balazik et al. 2017; Balazik and Musick 2015; 

Farrae et al. 2017). 

Status 

In 2012, NMFS listed the New York Bight and Chesapeake Bay DPSs as endangered and the 

GOM DPS as threatened based on low population sizes and the level of continuing threats such 

as degraded water quality, habitat impacts from dredging, bycatch in state and federally managed 

fisheries, and vessel strikes. Historically, each of these DPSs likely supported more than 10,000 

spawning adults (ASSRT 2007; MSPO 1993; Secor and Niklitschek 2002). The best available 

data indicate that current numbers of spawning adults for each DPS are one to two orders of 

magnitude smaller than historical levels (ASSRT 2007; Kahnle et al. 2007). The Carolina and 

South Atlantic DPSs were estimated to have declined to less than three and six percent of their 

historical population sizes, respectively (ASSRT 2007). Both of these DPSs were listed as 

endangered in 2012 due to a combination of habitat curtailment and alteration, bycatch in 

commercial fisheries, and inadequacy of regulatory mechanisms in ameliorating these impacts 

and threats. The largest estimated adult Atlantic sturgeon populations are currently found in the 

Hudson (3,000), Altamaha (1,325), Delaware (1,305), Kennebec (865), Savannah (745), and 

James (705). Published estimates of Atlantic sturgeon juvenile abundance are available in the 

following river systems: 4,314 age 1 fish in the Hudson in 1995 (Peterson et al. 2000); 3,656 age 

0-1 fish in the Delaware in 2014(Hale et al. 2016); between 1,072 to 2,033 age 1-2 fish on 

average from 2004-2007 in the Altamaha - (Schueller and Peterson 2010); and 154 age 1 fish in 

2010 in the Satilla (Fritts et al. 2016). 

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Designated Critical Habitat 

NMFS designated critical habitat for each ESA-listed DPS of Atlantic sturgeon in August of 

2017. Physical and biological features determined to be essential for Atlantic sturgeon 

reproduction and recruitment include (1) suitable hard bottom substrate in low salinity waters for 

settlement of fertilized eggs, refuge, growth, and development of early life stages, (2) transitional 

salinity zones for juvenile foraging and physiological development, (3) water of appropriate 

depth and absent physical barriers to passage, (4) unimpeded movement of adults to and from 

spawning sites, and (5) water quality conditions that support spawning, survival, growth, 

development, and recruitment. The action area for this opinion does not overlap with areas 

proposed as critical habitat for any of the five Atlantic sturgeon DPSs. 

6.2.9.1 Gulf of Maine Atlantic Sturgeon 

The GOM DPS of Atlantic sturgeon was listed as threatened on February 6, 2012. The GOM 

DPS historically supported at least four spawning subpopulations; however, today it is suspected 

that only two extant subpopulations exist (Penobscot and Kennebec) (ASSRT 2007). The 

Kennebec River is the primary spawning and nursery area for GOM Atlantic sturgeon. Ripe 

female Atlantic sturgeon with enlarged, fully mature eggs ready to be fertilized have been found 

in the Kennebec River from mid-July through early August (MSPO 1993). Prior to any 

commercial fishing, the Kennebec supported approximately 10,000 to 15,000 spawning adults 

(ASSRT 2007; MSPO 1993). The construction of the Edwards Dam in 1837 was believed to 

have caused the commercial sturgeon catch to decline over 50 percent (MSPO 1993). Severe 

pollution in the river from the 1930’s through the early 1970’s is also believed to have been a 

major factor in the continued decline of the sturgeon population in the Kennebec. In 2007, the 

Atlantic Sturgeon Status Review Team (ASSRT) concluded that, due to stressors related to poor 

water quality, dredging, and commercial bycatch, there was a moderate risk (i.e., greater than 50 

percent chance) of the Kennebec subpopulation of Atlantic sturgeon becoming endangered 

within the next 20 years. 

It was speculated that the Penobscot subpopulation was extirpated until a fisherman captured an 

adult Atlantic sturgeon in 2005, and a gill net survey directed toward Atlantic sturgeon captured 

seven in 2006 (ASSRT 2007). The ASSRT concluded that the Penobscot subpopulation also had 

a moderate risk of becoming endangered due to its potentially small size (likely less than 300 

spawning adults), increased dredging projects, and poor water quality (ASSRT 2007). Within the 

Penobscot, substrate has been severely degraded by upstream mills, and water quality has been 

negatively affected by the presence of coal deposits and mercury hot spots. The potential for 

commercial bycatch was also viewed as a moderate threat to this subpopulation due to its small 

size. 

6.2.9.2 New York Bight Atlantic Sturgeon 

The New York Bight DPS was listed as endangered under the ESA on February 6, 2012. The 

New York Bight, ranging from Cape Cod to the Delmarva Peninsula, historically supported four 

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or more spawning subpopulations, but currently this DPS only supports two known spawning 

subpopulations: Delaware and Hudson River. The Delaware River once supported the largest 

spawning subpopulation of Atlantic sturgeon in the United States, with 3,200 metric tons of 

landings in 1888 (ASSRT 2007; Secor and Niklitschek 2002; Secor and Waldman 1999). 

Population estimates based on juvenile mark and recapture studies and commercial logbook data, 

indicate that the Delaware subpopulation has continued to decline rapidly since 1990. Based on 

genetic analyses, the majority of subadults captured in the Delaware Bay are thought to be of 

Hudson River origin (ASSRT 2007). However, a more recent study by Hale et al. (2016) 

suggests that a spawning population of Atlantic Sturgeon exists in the Delaware River and that 

some level of early juvenile recruitment is continuing to persist despite current depressed 

population levels. They estimated that 3,656 (95 percent confidence interval from 1,935 to 

33,041) juveniles (ages 0 to 1) used the Delaware River estuary as a nursery in 2014. These 

findings suggest that the Delaware River spawning subpopulation contributes more to the New 

York Bight DPS than was formerly considered. 

The ASSRT found that the Delaware River subpopulation had a moderately high risk (greater 

than 50 percent chance) of becoming endangered in the next 20 years, due to the loss of adults 

from ship strikes. Other stressors contributing to this conclusion that were ranked as moderate 

risk were dredging, water quality, and commercial bycatch (ASSRT 2007). Dredging in the 

upper portions of the river near Philadelphia were considered detrimental to successful Atlantic 

sturgeon spawning as this is suspected to be the historical spawning grounds of Atlantic 

sturgeon. Though dredging restrictions are in place during the spawning season, the continued 

degradation of suspected spawning habitat likely increases the instability of the subpopulation 

and could lead to its endangerment in the foreseeable future (ASSRT 2007). 

The Hudson River currently supports the largest U.S. subpopulation of Atlantic sturgeon 

spawning adults. Historically, it supported an estimated 6,000 to 8,000 spawning females 

(Kahnle et al. 2007; Secor 2002). Long-term surveys indicate that the Hudson River 

subpopulation has been stable and/or slightly increasing since 1995 in abundance (ASSRT 

2007). The ASSRT concluded that the Hudson River subpopulation had a moderate risk (less 

than 50 percent chance) of becoming endangered in the next 20 years due to the threat of 

commercial bycatch (ASSRT 2007). Other stressors, such as water quality, have improved since 

the 1980s and no longer seem to present a significant threat to the Hudson River population 

(ASSRT 2007). 

6.2.9.3 Chesapeake Bay Atlantic Sturgeon 

The Chesapeake Bay DPS was listed as endangered under the ESA on February 6, 2012. 

Historically, Atlantic sturgeon were common throughout the Chesapeake Bay and its tributaries 

(Kahnle et al. 1998, Wharton 1957, Bushnoe et al. 2005). Based on U.S. Fish Commission 

landings data, approximately 20,000 adult female Atlantic sturgeon inhabited the Chesapeake 

Bay and its tributaries prior to development of a commercial fishery in 1890 (Secor 2002). 

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Chesapeake Bay rivers once supported at least six historical spawning subpopulations (ASSRT 

2007), but today reproducing populations are only known to occur in the James and York Rivers. 

However, the presence of telemetry tagged Atlantic sturgeon in freshwater portions of 

Chesapeake Bay tributaries during the summer/fall spawning season (late July to mid-October) 

suggests that spawning may also occur in the Rappahannock, Potomac, Nanticoke, and 

Pocomoke Rivers. 

The James River supports the largest population of Atlantic sturgeon within the DPS. Balazik et 

al. (2012) reported empirical evidence that James River Atlantic sturgeon spawn in the fall, and a 

more recent study indicates that Atlantic sturgeon also spawn in the spring in the James River 

(i.e., dual spawning races) (Balazik and Musick 2015). Genetic analysis of tissue samples 

suggest effective populations in the James River range from around 40 to 100 (O’Leary et al. 

2014). The ASSRT concluded that the James River had a moderately high risk (greater than 50 

percent chance) of becoming endangered in the next 20 years, due to anticipated impacts from 

commercial bycatch. Dredging and ship strikes were also identified as threats (i.e., moderate 

risk) that contribute to the risk of extinction for the James subpopulation of Atlantic sturgeon. 

The York River has a much smaller population, with annual spawning abundance estimates for 

2013 of 75 (Kahn et al. 2014). The effective population size of the York River population ranges 

from 6 to 12 individuals, the smallest effective population size for any Atlantic sturgeon 

subpopulation along the Atlantic Coast. The total York River adult Atlantic sturgeon abundance 

is estimated at 289 individuals. The highest ranked stressor for the York River was commercial 

bycatch, which received a moderate risk rank (ASSRT 2007). 

6.2.9.4 Carolina Atlantic Sturgeon 

The Carolina DPS was listed as endangered under the ESA on February 6, 2012. The Carolina 

DPS ranges from the Albemarle Sound to the Santee-Cooper River and consists of seven extant 

subpopulations; one subpopulation (Sampit) is believed to be extirpated. The current abundance 

of these subpopulations is likely less than 3 percent of their historical abundance based on 1890s 

commercial landings data (ASSRT 2007; Secor and Niklitschek 2002). 

Water quality issues represented either a moderate or moderately high risk for most 

subpopulations within this DPS (ASSRT 2007). The Pamlico Sound suffers from eutrophication 

and experiences periodically low DO events and major fish kill events, mainly in the Neuse 

Estuary of the Sound. The Cape Fear River is a blackwater river; however, the low DO 

concentrations in this river can also be attributed to eutrophication. Water quality is also a 

problem in Winyah Bay, where portions of the Bay have high concentrations of dioxins that can 

adversely affect sturgeon development (Chambers et al. 2012). Commercial bycatch was a 

concern for all of the subpopulations examined by the ASSRT. The Cape Fear and SanteeCooper rivers were found to have a moderately high risk (greater than 50 percent) of becoming 

endangered within the next 20 years due to impeded habitat from dams. The Cape Fear and 

Santee-Cooper are the most impeded rivers along the range of the species, where dams are 

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located in the lower coastal plain and impede between 62 to 66 percent of the habitat available 

between the fall line and mouth of the river (ASSRT 2007). The ASSRT concluded that the 

limited habitat in which sturgeon could spawn and utilize for nursery habitat in these rivers likely 

leads to the instability of these subpopulations and to the entire DPS being at risk of 

endangerment. 

6.2.9.5 South Atlantic Sturgeon 

The South Atlantic DPS was listed as endangered under the ESA on February 6, 2012. This DPS 

historically supported eight spawning subpopulations but currently supports five extant spawning 

subpopulations (ASSRT 2007). The Altamaha and ACE Basin subpopulations support the largest 

number of spawning adults. The current abundance of these subpopulations are suspected to be 

less than six percent of their historical abundance, extrapolated from the 1890s commercial 

landings (ASSRT 2007; Secor and Niklitschek 2002). Peterson et al. (2008) reported that 

approximately 324 and 386 adults per year returned to the Altamaha River in 2004 and 2005, 

respectively. Few captures have been documented in subpopulations other than the Altamaha and 

ACE Basin within this DPS, and these smaller systems are suspected to contain less than one 

percent of their historic abundance (ASSRT 2007). The ASSRT found that the South Atlantic 

DPS of Atlantic sturgeon had a moderate risk (greater than 50 percent) of becoming endangered 

in the next 20 years due primarily to dredging, degraded water quality, and commercial fisheries 

bycatch. 

6.2.10 Shortnose Sturgeon 

The shortnose sturgeon is the smallest of the three sturgeon species that occur in eastern North 

America; they grow up to 4.7 feet (1.4 meters) and weigh up to 50.7 pounds (23 kilograms). It 

has a short, conical snout with four barbells in front of its large underslung mouth. Five rows of 

bony plates (called scutes) occur along its body: one on the back, two on the belly, and one on 

each side. The body coloration is generally olive-yellow to gray or bluish on the back, and 

milky-white to dark yellow on the belly. The peritoneum (body cavity lining) is black (Figure 

39). 

Figure 39. Shortnose sturgeon. Photo: Nancy Haley, NOAA (left), University of Maine 

(right). 

Shortnose sturgeon were initially listed as endangered on March 11, 1967 under the Endangered 

Species Preservation Act of 1966. In 1994, the species was listed as endangered throughout its 

range under the ESA (Table 15). Critical habitat has not been designated for shortnose sturgeon. 

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Shortnose sturgeon occur along the Atlantic Coast of North America, from the St. John River in 

Canada to the St. Johns River in Florida (Figure 40). 

Table 15. Summary of shortnose sturgeon listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Acipenser 

brevirostrum 

Shortnose 

sturgeon N/A Endangered 2010 32 FR 4001 03/11/1967 

63 FR 69613 

1998 

None 

Designated 

Life History 

The shortnose sturgeon is a relatively slow growing, late maturing, and long-lived fish species. 

The maximum recorded size of shortnose sturgeon was collected from the Saint John River, 

Canada, measuring 143 centimeters TL and weighing 23 kilograms (Dadswell et al. 1984). 

Shortnose sturgeon typically live longer in the northern portion of their range compared to the 

southern portion (Gilbert 1989). The maximum ages reported of female shortnose sturgeon by 

river system include 67 years for the St. John River (New Brunswick), 40 years for the Kennebec 

River, 37 years for the Hudson River, 34 years for the Connecticut River, 20 years for the Pee 

Dee River, and ten years for the Altamaha River (Dadswell et al. 1984; Gilbert 1989). Female 

shortnose sturgeon generally outlive and outgrow males, which seldom exceed 30 years of age 

(Dadswell et al. 1984; Gilbert 1989). Shortnose sturgeon also exhibit sexually dimorphic growth 

and maturation patterns across latitudes (Dadswell et al. 1984). In the northern parts of its range, 

males reach maturity at 5 to 11 years, while females mature between 7 and 18 years. Shortnose 

sturgeon in southern rivers typically grow faster, mature at younger ages (2 to 5 years for males 

and 4 to 5 for females), but attain smaller maximum sizes than those in the north which grow 

throughout their longer lifespans (Dadswell et al. 1984). 

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Figure 40. Geographic range of shortnose sturgeon. 

Shortnose sturgeon are amphidromous, inhabiting large coastal rivers or nearshore estuaries 

within river systems (Buckley and Kynard 1985; Kieffer and Kynard 1993). They spawn in 

upper, freshwater areas, and feed and overwinter in both fresh and saline habitats. During the 

summer and winter months, adults occur primarily in freshwater tidally influenced river reaches 

(Buckley and Kynard 1985). Older juveniles or subadults tend to move downstream in the fall 

and winter as water temperatures decline and the salt wedge recedes. In the spring and summer, 

they move upstream and feed mostly in freshwater reaches; however, these movements usually 

occur above the saltwater/freshwater river interface (Dadswell et al. 1984; Hall et al. 1991). 

While shortnose sturgeon do not undertake the long marine migrations documented for Atlantic 

sturgeon, telemetry data indicate that shortnose sturgeon do make localized coastal migrations 

(Dionne et al. 2013). Non-spawning movements include rapid, directed post-spawning 

movements to downstream feeding areas in the spring, and localized, wandering movements in 

the summer and winter (Buckley and Kynard 1985; Dadswell et al. 1984). Young-of-the-year 

shortnose sturgeon are believed to move downstream after hatching (Dovel 1983) but remain 

within freshwater habitats. 

Shortnose sturgeon have been found in waters with temperatures as low as 2 to 3oC (Dadswell et 

al. 1984) and as high as 34oC (Heidt and Gilbert 1979). However, temperatures above 28oC are 

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thought to adversely affect shortnose sturgeon (Kynard 1997). Shortnose sturgeon are known to 

occur at a wide range of depths from a minimum depth of 0.6 m up to 30 m (Dadswell 1979; 

Dadswell et al. 1984). Shortnose sturgeon exhibit tolerance to a wide range of salinities from 

freshwater (Taubert 1980) to waters with salinity of 30 parts-per-thousand (Holland and 

Yelverton 1973). Shortnose sturgeon typically occur in the deepest parts of rivers or estuaries 

where suitable oxygen and salinity levels are present (Gilbert 1989). 

Spawning occurs from late winter/early spring (southern rivers) to mid to late spring (northern 

rivers) depending upon location and water temperature. Shortnose sturgeon spawning migrations 

are characterized by rapid, directed and often extensive upstream movement (NMFS 1998). 

Mature males will spawn every other year or annually depending on the river they inhabit 

(Dadswell 1979; NMFS 1998). Age at first spawning for females is around five years postmaturation, with spawning occurring approximately every three to five years (Dadswell 1979). 

Shortnose sturgeon are believed to spawn at discrete sites within their natal river (Kieffer and 

Kynard 1996), typically at the farthest upstream reach of the river, if access is not obstructed by 

dams (NMFS 1998). Spawning occurs over channel habitats containing gravel, rubble, or rockcobble substrates (Dadswell 1979; NMFS 1998). Additional environmental conditions associated 

with spawning activity include decreasing river discharge following the peak spring freshet, 

water temperatures ranging from 6.5 to 18oC, and bottom water velocities of 0.4 to 0.8 m/sec 

(Dadswell 1979; Hall et al. 1991; Kieffer and Kynard 1996; NMFS 1998). 

Estimates of annual egg production for shortnose sturgeon are difficult to calculate and are likely 

to vary greatly in this species because females do not spawn every year. Fecundity estimates that 

have been made range from 27,000 to 208,000 eggs/female, with a mean of 11,568 eggs/kg body 

weight (Dadswell et al. 1984). At hatching, shortnose sturgeon are 7 to 11 mm long and resemble 

tadpoles (Buckley and Kynard 1981). In 9 to 12 days, the yolk sac is absorbed and the sturgeon 

develops into larvae which are about 15 mm TL (Buckley and Kynard 1981). Sturgeon larvae are 

believed to begin downstream migrations at about 20 mm TL. 

Shortnose sturgeon are benthic omnivores that feed on crustaceans, insect larvae, worms, 

mollusks (Collins et al. 2008; Moser and Ross 1995; Savoy and Benway 2004), oligochaete 

worms (Dadswell 1979) and off plant surfaces (Dadswell et al. 1984). Subadults feed 

indiscriminately, consuming aquatic insects, isopods, and amphipods along with large amounts 

of mud, stones, and plant material (Bain 1997; Dadswell 1979). 

Population Dynamics 

Historically, shortnose sturgeon are believed to have inhabited nearly all major rivers and 

estuaries along the entire east coast of North America. NMFS’s Shortnose Sturgeon Recovery 

Plan identifies 19 populations based on the fish’s strong fidelity to natal rivers and the premise 

that populations in adjacent river systems did not interbreed with any regularity (NMFS 1998). 

Both mtDNA and nDNA analyses indicate effective (with spawning) coastal migrations are 

occurring between adjacent rivers in some areas, particularly within the GOM and the Southeast 

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(King et al. 2014). The currently available genetic information suggests that shortnose sturgeon 

can be separated into smaller groupings that form regional clusters across their geographic range 

(SSSRT 2010). Both regional population and metapopulation structures may exist according to 

genetic analyses and dispersal and migration patterns (King et al. 2014; Wirgin et al. 2010). The 

Shortnose Sturgeon Status Review Team (SSSRT) concluded shortnose sturgeon across their 

geographic range include five genetically distinct groupings each of which have geographic 

ecological adaptations: 1) GOM; 2) Connecticut and Housatonic Rivers; 3) Hudson River; 4) 

Delaware River and Chesapeake Bay; and 5) Southeast (SSSRT 2010). Two additional 

geographically separate populations occur behind dams in the Connecticut River (above the 

Holyoke Dam) and in Lake Marion on the Santee-Cooper River system in South Carolina (above 

the Wilson and Pinopolis Dams). Although these populations are geographically isolated, genetic 

analyses suggest individual shortnose sturgeon move between some of these populations each 

generation (Quattro et al. 2002; Wirgin et al. 2005; Wirgin et al. 2010). The SSSRT 

recommended that each riverine population be considered as a separate management/recovery 

unit (SSSRT 2010). The distribution of shortnose sturgeon is disjointed across their range, with 

northern populations separated from southern populations by a distance of about 400 kilometers 

near their geographic center in Virginia. 

Status 

The 2010 SSSRT conducted a three-step risk assessment for shortnose sturgeon at a riverine 

scale: (1) assess population health, (2) populate a “matrix of stressors” by ranking threats, and 

(3) review assessment by comparing population health scores to stressor scores. The Hudson 

River had the highest estimated adult abundance (30,000 to 61,000), followed by the Delaware 

(12,000), Kennebec Complex (9,000), and Altamaha (6,000) (SSSRT 2010). The SSSRT found 

evidence of an increasing abundance trend for the Kennebec Complex and ACE Basin 

populations; a stable trend for the Merrimack, Connecticut, Hudson, Delaware, Winyah Bay 

Complex, Cooper, Savannah, Ogeechee, and Altamaha populations; and a declining trend only 

for the Cape Fear population (all other populations had an unknown trend) (SSSRT 2010). 

The SSSRT summarized continuing threats to the species in each of the 29 identified populations 

(SSSRT 2010). Dams represent a major threat to seven shortnose sturgeon populations and a 

moderate threat to seven additional populations. Dredging represents a major threat to one 

shortnose sturgeon population (Savannah River), a moderately high threat to three populations, 

and a moderate threat to seven populations. Fisheries bycatch represents a major threat to one 

shortnose sturgeon population (Lakes Marion and Moultrie in Santee-Cooper Reservoir System), 

a moderately high threat to four populations, and a moderate threat to ten populations (SSSRT 

2010). Water quality represents a major threat to one shortnose sturgeon population (Potomac 

River), a moderately high threat to six populations, a moderate threat to 13 populations, and a 

moderately low threat to one population. Specific sources of water quality degradation affecting 

shortnose sturgeon include coal tar, wastewater treatment plants, fish hatcheries, industrial waste, 

pulp mills, sewage outflows, industrial farms, water withdrawals, and non-point sources. 

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Impingement/entrainment at power plants and treatment plants was rated as a moderate threat to 

two shortnose sturgeon populations (Delaware and Potomac). 

The SSSRT examined the relationship between population health scores and associated 

stressors/threats for each shortnose sturgeon riverine population and concluded the following: 1) 

despite relatively high stressor scores, the Hudson and Kennebec River populations appear 

relatively healthy; 2) shortnose sturgeon in the Savannah River appear moderately healthy, but 

their status is perilous; 3) shortnose in the ACE system are of moderate health with low stress 

and may be most able to recover (SSSRT 2010). Climate warming has the potential to reduce 

abundance or eliminate shortnose sturgeon in many rivers, particularly in the South (Kynard et 

al. 2016). 

The SSSRT reported results of an age-structured population model using the RAMAS software 

(Akçakaya and Root 2007) to estimate shortnose sturgeon extinction probabilities for three river 

systems: Hudson, Cooper, and Altamaha. The estimated probability of extinction was zero for all 

three populations under the default assumptions, despite the long (100-year) horizon and the 

relatively high year-to-year variability in fertility and survival rates. The estimated probability of 

a 50 percent decline was relatively high (Hudson 0.65, Cooper 0.32, Altamaha 0.73), whereas the 

probability of an 80 percent decline was low (Hudson 0.09, Cooper 0.01, Altamaha 0.23) 

(SSSRT 2010). The largest shortnose sturgeon adult populations are found in the Northeastern 

rivers: Hudson 56,708 adults (Bain et al. 2007); Delaware 12,047 (ERC 2006); and Saint Johns 

greater than 18,000 adults (Dadswell 1979). Shortnose sturgeon populations in southern rivers 

are considerably smaller by comparison. 

Designated Critical Habitat 

No critical habitat has been designated for the shortnose sturgeon. 

Recovery Goals 

The Shortnose Sturgeon Recovery Plan was developed in 1998. The long-term recovery 

objective, as stated in the Plan, is to recover all 19 discrete populations to levels of abundance at 

which they no longer require protection under the ESA (NMFS 1998). To achieve and preserve 

minimum population sizes for each population segment, essential habitats must be identified and 

maintained, and mortality must be monitored and minimized. Accordingly, other key recovery 

tasks discussed in the Plan are to define essential habitat characteristics, assess mortality factors, 

and protect shortnose sturgeon through applicable federal and state regulations. 

6.2.11 Green Sturgeon, Southern Distinct Population Segment 

Green sturgeon are long-lived, late-maturing, iteroparous, anadromous species that spawn 

infrequently in natal streams, and spend substantial portions of their lives in marine waters. 

Although they are members of the class of bony fishes, the skeleton of sturgeons is composed 

mostly of cartilage. Sturgeon have five rows of characteristic bony plates on their body (called 

scutes). Green sturgeon have an olive green to dark green back, a yellowish green-white belly, 

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and a white stripe beneath the lateral scutes (Adams et al. 2002) (Figure 41). Green sturgeon 

occur in the nearshore Eastern Pacific Ocean from Alaska to Mexico (Moyle 2002). 

Figure 41. Adult green sturgeon. Photo: Thomas Dunklin. 

NMFS has identified two DPSs of green sturgeon; northern and southern (Israel et al. 2009). In 

2006, NMFS determined that the southern DPS green sturgeon (Figure 42) warranted listing as a 

threatened species under the ESA (71 FR 17757) (Table 16). 

Table 16. Summary of green sturgeon listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA 

Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Acipenser 

medirostris 

Green 

sturgeon Southern Threatened 2015 71 FR 17757 04/07/2006 

Recovery 

Plan Outline 

2010 

74 FR 52300 

Pacific 

2009 

Life history 

Green sturgeon reach sexual maturity at approximately fifteen years of age (Van Eenennaam et 

al. 2006), and may spawn every three to five years throughout their long lives (Tracy 1990). 

Southern DPS green sturgeon spawn in cool (14 to 17 degrees Celsius), deep, turbulent areas 

with clean, hard substrates. Six discrete spawning sites have been identified in the upper 

Sacramento River between Gianella Bridge (RK 320.6) and the Keswick dam (RK 486) 

(Poytress et al. 2013). Spawning has also been confirmed in the Feather River near the 

Thermalito Afterbay Outlet (RK 95) (Seesholtz et al. 2015). Adult diet includes shrimp, 

mollusks, amphipods, and even small fish (Houston 1988; Moyle et al. 1992). Juveniles in the 

Sacramento River delta feed on opossum shrimp, Neomysis mercedis, and Corophium 

amphipods (Radtke 1966). 

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Figure 42. Geographic range (within the contiguous US) and designated critical habitat 

for green sturgeon, southern distinct population segment. 

In preparation for spawning, adult Southern DPS green sturgeon enter San Francisco Bay 

between mid-February and early-May, and migrate rapidly (on the order of a few weeks) up the 

Sacramento River (Heublein et al. 2009). Spawning occurs from April through early July, with 

peaks of activity that depend on a variety of factors including water temperature and water flow 

rates (Poytress et al. 2009; Poytress et al. 2010). Post-spawn fish typically congregate and hold 

for several months in a few deep pools in the upper mainstream Sacramento River near spawning 

sites and migrate back downstream when river flows increase in fall. They re-enter the ocean 

during the winter months (November through January) and begin their marine migration north 

along the coast (California Fish Tracking Consortium database). 

Green sturgeon larvae are different from all other sturgeon because of the absence of a distinct 

swim-up or post-hatching stage. Larvae grow fast; young fish grow to 74 mm 45 days after 

hatching (Deng 2000). Larvae and juveniles migrate downstream toward the Sacramento-San 

Joaquin Delta/Estuary, where they rear for one to four years before migrating out to the Pacific 

Ocean as subadults (Nakamoto et al. 1995). Once at sea, subadults and adults occupy coastal 

waters to a depth of 110 m from Baja California, Mexico to the Bering Sea, Alaska (Erickson 

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and Hightower 2007). Seasonal migrations are known to occur. Fish congregate in coastal bays 

and estuaries of Washington, Oregon, and California during summer and fall. In winter and 

spring, similar aggregations can be found from Vancouver Island to Hecate Strait, British 

Columbia, Canada (Lindley et al. 2008). 

Population Dynamics 

Israel et al. (2009) detailed genetic analysis of 20 collections of green sturgeon samples and 10 

microsatellite loci and examined DPS composition in different estuaries along the US west coast. 

The study upholds the Northern and Southern DPS determination of spawning rivers. Telemetry 

studies and unpublished data also confirm the DPS structure (Lindley et al. 2011; Lindley et al. 

2008). Individuals from the threatened Southern DPS and the non-listed Northern DPS regularly 

co-occur in non-natal estuaries including the Columbia River estuary, Willapa Bay, and Grays 

Harbor. Schreier et al. (2016) found that majority of green sturgeon sampled from 2010-2012 in 

the Columbia River estuary and Willapa Bay were assigned to the Southern DPS, while green 

sturgeon from Grays Harbor were assigned nearly even proportions between the two DPSs. The 

authors suggest that the Columbia River may serve as alternative spawning habitat for green 

sturgeon as climate change occurs. 

Based on survey data from 2010-14, the total number of adults in the Southern DPS population is 

estimated to be 1,348 (95 percent confidence interval ± 524) (Mora 2015; NMFS 2015c). The 

spawning population of the Southern DPS in the Sacramento River congregates in a limited area 

of the river compared to potentially available habitat (NMFS 2015c). This is concerning given 

that a catastrophic or targeted poaching event affecting just a few holding areas could affect a 

significant portion of the adult population. 

Status 

Attempts to evaluate the status of southern DPS green sturgeon have been met with limited 

success due to the lack of reliable long-term data. The final rule listing Southern DPS green 

sturgeon indicates that the principle factor for the decline in the DPS is the reduction of 

spawning to a limited area in the Sacramento River caused primarily by impoundments, but they 

also face threats from water temperature, water flow, and commercial and recreational bycatch. 

Many of the principle factors considered when listing Southern DPS green sturgeon as 

threatened in 2006 are relatively unchanged. Recent studies confirm that the spawning area 

utilized by Southern DPS green sturgeon is small (NMFS 2015c). Confirmation of spawning in 

the Feather River is encouraging and the decommissioning of the Red Bluff Diversion Dam and 

breach of Shanghai Bench makes spawning conditions more favorable, although Southern DPS 

green sturgeon still encounter impassible barriers in the Sacramento, Feather and other rivers that 

limit their spawning range (NMFS 2015c). Entrainment as well as stranding in flood diversions 

during high water events also negatively affect Southern DPS green sturgeon. The prohibition of 

retention in commercial and recreational fisheries has eliminated a known threat and likely had a 

very positive effect on the overall population, although recruitment indices are not presently 

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available. Climate change has the potential to impact Southern DPS green sturgeon in the future, 

but it is unclear how changing oceanic, nearshore and river conditions will affect the population 

overall (NMFS 2015c). The recovery potential for Southern DPS green sturgeon is considered 

moderate to high; however, certain life history characteristics (e.g., long-lived, delayed maturity) 

indicate recovery could take many decades, even under the best circumstances (NMFS 2010a). 

Designated Critical Habitat 

Critical habitat was designated for Southern DPS green sturgeon on October 9, 2009, and 

includes marine, coastal bay, estuarine, and freshwater areas. The action area for this biological 

opinion overlaps with Southern DPS green sturgeon designated critical habitat. Based on our 

analysis above (Section 6.1), we determine that the proposed action is not likely to adversely 

affect Southern DPS green sturgeon designated critical habitat. 

Recovery Goals 

The final recovery plan for Southern DPS green sturgeon has not been released. According to the 

recovery outline, key recovery needs and implementation measures identified include additional 

spawning and egg/larval habitat as well as additional research and monitoring (NMFS 2010a). 

6.2.12 Gulf Sturgeon 

The Gulf sturgeon was listed as threatened on September 30, 1991 (Table 17). NMFS and the 

USFWS jointly manage Gulf sturgeon under the ESA. NMFS is responsible for consultations on 

actions affecting Gulf sturgeon and their critical habitat in marine habitats. USFWS is 

responsible for Gulf sturgeon consultations in riverine habitats. In estuarine habitats, 

responsibility is divided based on the action agency involved: USFWS consults with the 

Department of Transportation, the USEPA, the U.S. Coast Guard, and the Federal Emergency 

Management Agency; NMFS consults with the Department of Defense, U.S. Army Corps of 

Engineers, the Bureau of Ocean Energy Management, and any other federal agencies not 

specifically mentioned at 50 CFR 226.214. In 2009, NMFS and USFWS conducted a 5-year 

review and found Gulf sturgeon continued to meet the definition of a threatened species 

(USFWS and NMFS 2009). 

The current range of the Gulf sturgeon extends from Lake Pontchartrain in Louisiana east to the 

Suwannee river system in Florida (Figure 43). Within that range, seven major rivers are known 

to support reproducing populations: Pearl, Pascagoula, Escambia, Yellow, Choctawhatchee, 

Apalachicola, and Suwannee (USFWS and NMFS 2009). 

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Figure 43. Geographic range and designated critical habitat of the Gulf sturgeon. 

Gulf sturgeon are benthic fusiform fish with an extended snout, vertical mouth, five rows of 

scutes (bony plates surrounding the body), four barbels (slender, whisker-like feelers anterior to 

the mouth used for touch and taste), and a heterocercal (upper lobe is longer than lower) caudal 

fin. Adults range from 6 to 8 feet in length and weigh up to 200 pounds; females grow larger 

than males (USFWS and NMFS 2009). 

Table 17. Summary of Gulf sturgeon listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA 

Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Acipenser 

oxyrinchus 

desotoi 

Gulf 

sturgeon None Threatened 2009 56 FR 49653 09/30/1991 

FR N/A 

1995 

68 FR 13370 

Gulf of Mexico 

2003 

Life history 

Gulf sturgeon are long-lived, with some individuals reaching at least 42 years in age. Surveys in 

the Suwannee River suggest that a more common maximum age may be around 25 years (Sulak 

and Clugston 1999). Age at sexual maturity for females ranges from 8 to 17 years, and for males 

from 7 to 21 years (Huff 1975). In general, gulf sturgeon spawn up-river in spring, spend winter 

months in near-shore marine environments, and utilize pre- and post-spawn staging and nursery 

areas in the lower rivers and estuaries (Heise et al. 2005; Heise et al. 2004). There is some 

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evidence of autumn spawning in the Suwannee River, however there is uncertainty as to whether 

this spawning is due to environmental conditions or represents a genetically distinct population 

(Randall and Sulak 2012). Gulf sturgeon spawn at intervals ranging from 3 to 5 years for females 

and 1 to 5 years for males (Fox et al. 2000; Smith 1985). The spring migration to up-river 

spawning sites begins in mid-February and continues through May. Fertilization is external; 

females deposit their eggs in the upper reaches of and show preference for hard, clean substrate 

(e.g., bedrock covered in gravel and small cobble). 

Upon hatching from their eggs, gulf sturgeon larvae spend the first few days of life sheltered in 

interstitial spaces at the spawning site (Kynard and Parker 2004). At the onset of feeding, age-0 

gulf sturgeon disperse and are often found on shallow sandbars and rippled sand shoals (less than 

4 meters depth) (Sulak and Clugston 1998). Young-of-the-year spend 6 to 10 months slowing 

working their way downstream feeding on aquatic insects (e.g., mayflies and caddisflies), worms 

(oligochaetes), and bivalve mollusks, and arrive in estuaries and river mouths by mid-winter 

(Sulak and Clugston 1999) where they will spend their next 6 years developing. After spawning, 

adult gulf sturgeon migrate downstream to summer resting and holding areas in the mid to lower 

reaches of the rivers where they may hold until November (Wooley and Crateau 1985). While in 

freshwater adults lose a substantial amount of their weight, but regain it upon entering the 

estuaries. Sub adult and non-spawning adults also spend late spring through fall in these holding 

areas (Foster and Clugston 1997). By early December all adult and sub-adult gulf sturgeon return 

to the marine environment to forage on benthic (bottom dwelling) invertebrates along the 

shallow nearshore (2 to 4 meters depth), barrier island passes, and in unknown off-shore 

locations in the gulf (Carr et al. 1996; Fox et al. 2002; Huff 1975; Ross et al. 2009). Juvenile gulf 

sturgeon overwinter in estuaries, river mouths, and bays; juveniles do not enter the 

nearshore/offshore marine environments until around age 6 (Sulak and Clugston 1999). Gulf 

sturgeon show a high degree of river-specific fidelity (Rudd et al. 2014). Adult and sub-adult 

gulf sturgeon fast while in freshwater environments and are almost entirely dependent on the 

estuarine/marine environment for food (Gu et al. 2001; Wooley and Crateau 1985). Some 

juveniles (ages 1 to 6) will also fast in the freshwater summer holding areas, but the majority 

feed year round in the estuaries, river mouths, and bays (Sulak et al. 2009). 

Population Dynamics 

Currently, seven rivers are known to support reproducing populations of Gulf sturgeon. The most 

recent abundance estimates were reported in the 5-Year Status Review conducted in 2009 

(USFWS and NMFS 2009). The largest estimated populations of Gulf sturgeon are found in the 

Suwannee (14,000), the Choctawhatchee (3,314), and the Yellow (911) rivers (USFWS and 

NMFS 2009). The most recent population estimates for the other four rivers with known 

reproducing populations are all below 500. 

Gulf sturgeon abundance trends are typically assessed on a riverine basis. In general, gulf 

sturgeon populations in the eastern portion of the range appear to be stable or slightly increasing, 

while populations in the western portion are associated with lower abundances and higher 

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uncertainty (USFWS and NMFS 2009). Pine and Martell (2009) reported that, due to low 

recapture rates and sparse data, the population viability of gulf sturgeon is currently uncertain. 

When grouped by genetic relatedness, five regional or river-specific stocks emerge: (1) Lake 

Pontchartrain and Pearl River; (2) Pascagoula River; (3) Escambia, Blackwater and Yellow 

Rivers; (4) Choctawhatchee River; and (5) Apalachicola, Ochlocknee and Suwanee Rivers (Rudd 

et al. 2014; Stabile et al. 1996). Gene flow is low in Gulf sturgeon stocks, with each stock 

exchanging less than one mature female per generation (Waldman and Wirgin 1998). 

Status 

The decline in the abundance of gulf sturgeon has been attributed to targeted fisheries in the late 

19th and early 20th centuries, habitat loss associated with dams and sills, habitat degradation 

associated with dredging, de-snagging, and contamination by pesticides, heavy metals, and other 

industrial contaminants, and certain life history characteristics (e.g., slow growth and late 

maturation) (56 FR 49653). Effects of climate change (warmer water, sea level rise and higher 

salinity levels) could lead to accelerated changes in habitats utilized by Gulf sturgeon. The rate 

that climate change and corollary impacts are occurring may outpace the ability of the Gulf 

sturgeon to adapt given its limited geographic distribution and low dispersal rate. In general, gulf 

sturgeon populations in the eastern portion of the range appear to be stable or slightly increasing, 

while populations in the western portion are associated with lower abundances and higher 

uncertainty (USFWS and NMFS 2009). 

Designated Critical Habitat 

Designated critical habitat for gulf sturgeon was established in 2003 and consists of 14 

geographic units encompassing 2,783 river kilometers as well as 6,042 square kilometers of 

estuarine and marine habitat. Primary constituent elements for the conservation of Gulf Sturgeon 

are abundant food items, riverine spawning sites with substrates suitable for egg deposition and 

development, riverine aggregation areas, a flow regime necessary for normal behavior, growth, 

and survival, water and sediment quality necessary for normal behavior, growth, and viability of 

all life stages, and safe and unobstructed migratory pathways. 

Recovery Goals 

The 1995 Recovery Plan outlined three recovery objectives: (1) to prevent further reduction of 

existing wild populations of Gulf sturgeon within the range of the subspecies; (2) to establish 

population levels that would allow delisting of the Gulf sturgeon by management units 

(management units could be delisted by 2023 if required criteria are met); (3) to establish, 

following delisting, a self-sustaining population that could withstand directed fishing pressure 

within management units (USFWS and GSMFC 1995). The most recent Gulf sturgeon 5-year 

review recommended that criteria be developed in a revised recovery plan (USFWS and NMFS 

2009). 

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6.2.13 Nassau Grouper 

Adult Nassau grouper are large (up to 0.45 meters or 1.5 feet), have distinctive black and white 

stripes, and are generally found in shallow reef habitats (Figure 44). 

Figure 44. Nassau grouper. Photo: C. Dahlgren 

The Nassau grouper is a large, long-lived, slow growing fish species primarily occupying 

nearshore waters throughout the Caribbean, south Florida, Bermuda, and the Bahamas (Figure 

45). The Nassau grouper was listed as threatened on June 29, 2016 (Table 18). 

Figure 45. Map identifying the range of the Nassau grouper. From NMFS Biological 

Report (NMFS 2013). 

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Table 18. Summary of Nassau grouper listing and recovery plan information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA 

Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Epinephelus 

striatus 

Nassau 

grouper 

None Threatened 2013 81 FR 42268 

06/29/2016 N/A None 

Designated 

We used information available in the 2013 status review (NMFS 2013b) and recent scientific 

publications to summarize the life history, population dynamics and status of the species, as 

follows. 

Life History 

Nassau groupers spawn once a year in spawning aggregations, ranging in size from a few dozen 

to thousands of fish spawning at once. Nassau groupers move in groups towards the spawning 

aggregation sites parallel to the coast or along the shelf edge. Spawning runs occur from late fall 

through winter (i.e., a month or two before spawning is likely). Sea surface temperature is 

thought to be a key factor in the timing of spawning, with spawning occurring at temperatures 

around 25 degrees Celsius. Spawning aggregation sites are located near significant 

geomorphological features, such as reef projections (as close as 50 meters to shore) and close to 

a drop-off into deep water over a wide depth range (six to sixty meters). Sites are usually several 

hundred meters in diameter, with soft corals, sponges, stony coral outcrops, and sandy 

depressions. Nassau groupers stay on the spawning site for up to three months, spawning at the 

full moon or between the new and full moons. Spawning occurs within twenty minutes of sunset 

over the course of several days. Historically, there have been an estimated fifty known spawning 

aggregation sites in insular areas throughout the Caribbean; many of these aggregations no 

longer form. Current spawning locations are found in Mexico, Bahamas, Belize, Cayman 

Islands, the Dominican Republic, Cuba, Puerto Rico and the U.S. Virgin Islands. 

Fertilized eggs are transported offshore by ocean currents. Thirty-five to forty days after 

hatching, larvae recruit from oceanic environments to demersal habitats (at a size of about 32 

millimeters total length). Juveniles inhabit macroalgae, coral clumps, and seagrass beds, and are 

relatively solitary. As they grow they occupy progressively deeper areas and offshore reefs, and 

can be found in schools of up to forty individuals. When not spawning, adults are most 

commonly found in waters less than one hundred meters deep. Nassau grouper diet changes with 

age. Juveniles eat plankton, pteropods, amphipods, and copepods. Adults are unspecialized 

piscivores, bottom-dwelling ambush suction predators (NMFS 2013b). 

Male and female Nassau groupers reach sexual maturity at lengths between 40 and 45 

centimeters standard length, at about four to five years old. It is thought that sexual maturity is 

more determined by size, rather than age. Otolith studies indicate that the minimum age at 

maturity is between four and eight years; most groupers have spawned by age seven (Bush et al. 

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2006). Nassau grouper is a long-lived species with maximum longevity estimated up to 29 years 

(Bush et al. 1996). 

Population Dynamics 

The following is a discussion of the species’ population and its variance over time. This section 

includes abundance, population growth rate, genetic diversity, and spatial distribution as it 

relates to the Nassau grouper. 

There is no range-wide abundance estimate available for Nassau grouper. The species is 

characterized as having patchy abundance due largely to differences in habitat availability or 

quality, and differences in fishing pressure in different locations. Although abundance has been 

reduced compared to historical levels, spawning still occurs and abundance is increasing in some 

locations, such as the Cayman Islands and Bermuda. 

There is no population growth rate available for Nassau grouper. Available information from 

observations of spawning aggregations has shown steep declines (Aguilar-Perera 2006; Claro 

and Lindeman 2003; Sala et al. 2001); however, some aggregation sites are comparatively robust 

and show signs of increase (Vo et al. 2014; Whaylen et al. 2004). 

Early genetic analyses indicated high gene flow throughout the geographic range of Nassau 

grouper, but were unable to determine the relative contributions of populations (Hateley 2005; 

Hinegardner and Rosen 1972). A recent study on Nassau grouper genetic variation found strong 

genetic differentiation across Caribbean subpopulations, likely due to barriers created by ocean 

currents and larval distribution (Jackson et al. 2014). While this study indicated some instances 

of genetic differentiation, the results do not indicate a high degree of population structuring 

across the range. Bernard et al. (2016) found that genetic diversity across temporal collections at 

the U.S. Virgin Islands spawning aggregation was relatively high; no marked differences were 

found between the U.S. Virgin Islands and Cayman spawning aggregations. These results 

suggest that external recruitment is an important driver of the U.S. Virgin Islands Nassau grouper 

population recovery and that, despite an apparent genetic bottleneck, the genetic diversity of the 

U.S. Virgin Islands Nassau grouper has not been severely compromised (Bernard et al. 2016). 

Nassau grouper is distributed throughout the Caribbean, south to the northern coast of South 

America (Figure 45). Current Nassau grouper distribution is considered equivalent to its 

historical range, although abundance has been severely depleted. 

Status 

Nassau grouper possess life history characteristics that increase vulnerability to harvest, 

including slow growth to a large size, late maturation, formation of large spawning aggregations, 

and occurrence in shallow water. Two different aspects of fishing affect Nassau grouper 

populations: fishing effort throughout the non-spawning months and fishing effort directed at 

spawning aggregations or migratory access to spawning aggregations. Since grouper species 

were historically reported collectively in landings data (i.e., “groupers”), it is not possible to 

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know how many Nassau grouper were harvested, or to estimate historic abundance based on 

fishery dependent data. Few formal stock assessments have been conducted for the Nassau 

grouper. One recent published assessment conducted in the Bahamas indicates fishing mortality 

needs to be reduced from the 1998 to 2001 levels, otherwise the stocks are likely to be 

overexploited relative to biological reference points (Cheung et al. 2013). 

Lacking information from stock assessments or population estimates, changes in Nassau grouper 

spawning aggregations have been used as a proxy for population status. Historically, tens of 

thousands of Nassau grouper spawned at aggregation sites throughout the Caribbean. That these 

large spawning aggregations occurred in predictable locations at regular times made the species 

susceptible to over-fishing, and was a primary cause of its decline. At some sites, spawning 

aggregations have decreased by over 80 percent in the last 25 years (e.g., Belize), or have 

disappeared entirely (e.g., Mexico) (Aguilar-Perera 2006; Sala et al. 2001). Nassau grouper 

spawning aggregations within U.S. Virgin Island waters were overfished until their 

disappearance in the 1970s and 1980s. 

The most serious ongoing threats to Nassau grouper are fishing at spawning aggregations and 

inadequate law enforcement. Many Caribbean countries have banned or restricted Nassau 

grouper harvest, and it is believed that current areas of higher abundance are correlated with 

effective regulations. In some locations, spawning aggregations are increasing. In the early 

2000s, Nassau grouper were found gathering at Grammanik Bank, a mesophotic coral reef 

adjacent to one of the previously extinct U.S. Virgin Islands aggregation sites. Although harvest 

has decreased due to management measures, Nassau grouper populations remain vulnerable to 

unregulated harvest. 

Since Nassau grouper are dependent upon coral reefs at various points in their life history, loss of 

coral reef habitat due to climate change represents a potential threat to this species. However, the 

overall impact of climate change on Nassau grouper populations is still largely unknown at this 

time. Recent studies suggest that the highly invasive Pacific red lionfish (Pterois volitans) may 

also pose a threat to Nassau grouper through direct competition for food and shelter (Cheung et 

al. 2013; O'Farrell et al. 2014; Raymond et al. 2015). 

Designated Critical Habitat 

No critical habitat has been designated for the Nassau grouper. 

Recovery Goals 

NMFS has not prepared a recovery plan for the Nassau grouper. 

6.2.14 Scalloped Hammerhead 

This section provides general information on the scalloped hammerhead shark species, including 

information about the species’ life history, population dynamics, and status. The subsections that 

follow provide information and characteristics particular to each of the three listed DPSs of 

scalloped hammerhead considered in this opinion. 

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Hammerhead sharks are recognized by their laterally expanded head that resembles a hammer, 

hence the common name “hammerhead.” The scalloped hammerhead shark is distinguished from 

other hammerheads by a noticeable indentation on the center and front portion of the head, along 

with two more indentations on each side of this central indentation, giving the head a “scalloped” 

appearance. It has a broadly arched mouth and the back of the head is slightly swept backward 

(Figure 46). 

Figure 46. Scalloped hammerhead shark. Photo: NOAA (left), Brian Skerry, National 

Geographic (right). 

Scalloped hammerheads are moderately large coastal pelagic sharks found worldwide in coastal 

warm temperate and tropical seas in the Atlantic, Pacific and Indian Oceans between 46°N and 

36°S (Miller et al. 2014) (Figure 47). Four scalloped hammerhead shark DPSs were listed in July 

2014: Eastern Pacific DPS and Eastern Atlantic DPS (entirely foreign) were listed as endangered 

and the Central and Southwest Atlantic DPS and Indo-West Pacific DPS were listed as 

threatened (Table 19). 

Table 19. Summary of scalloped hammerhead shark listing and recovery plan 

information. 

Species Common 

Name 

Distinct 

Population 

Segment 

ESA Status 

Recent 

Review 

Year 

Listing Recovery 

Plan 

Critical 

Habitat 

Sphyrna 

lewini 

Scalloped 

Hammerhead 

shark 

Eastern 

Pacific Endangered N/A 79 FR 38213 

07/03/2014 N/A None 

Designated 

Sphyrna 

lewini 

Scalloped 

Hammerhead 

shark 

Central & 

Southwest 

Atlantic 

Threatened N/A 79 FR 38213 

07/03/2014 N/A None 

Designated 

Sphyrna 

lewini 

Scalloped 

Hammerhead 

shark 

Indo-West 

Pacific Threatened N/A 79 FR 38213 

07/03/2014 N/A None 

Designated 

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Figure 47. Map depicting the distinct population segments for the scalloped hammerhead 

shark. 

Life History 

The scalloped hammerhead shark gives birth to live young (i.e., “viviparous”), with a gestation 

period of 9 to 12 months (Branstetter 1987; Stevens and Lyle 1989) which may be followed by a 

one-year resting period (Liu and Chen 1999). Females attain maturity around 6.5 to 8 feet (2.0 to 

2.5 meters) TL, while males reach maturity at smaller sizes (range 4 to 6.5 feet [1.3 to 2.0 

meters] TL). The age at maturity differs by region. For example, in the Gulf of Mexico, 

Branstetter (1987) estimated that females mature at about 15 years of age and males at around 

nine to ten years of age. In northeastern Taiwan, Chen et al. (1990) calculated age at maturity to 

be 4 years for females and 3.8 years for males. On the east coast of South Africa, age at sexual 

maturity for females was estimated at 11 years (Dudley and Simpfendorfer 2006). Parturition, 

however, does not appear to vary by region and may be partially seasonal (Harry et al. 2011), 

with neonates present year round but with abundance peaking during the spring and summer 

months (Adams and Paperno 2007; Duncan and Holland 2006; Harry et al. 2011; Noriega et al. 

2011). Females move inshore to birth, with litter sizes anywhere between one and 41 live pups. 

Off the coast of northeastern Australia, Noriega et al. (2011) found a positive correlation 

between litter size and female shark length for scalloped hammerheads, as did White et al. 

(2008) in Indonesian waters. However, off the northeastern coast of Brazil, Hazin et al. (2001) 

found no such relationship. Size at birth is estimated between one and two feet (0.3 to 0.6 

meters) TL. 

Scalloped hammerheads are found over continental shelves and the shelves surrounding islands, 

as well as adjacent deep waters, but is seldom found in waters cooler than 22 degrees Celsius 

(Compagno 1984; Schulze-Haugen and Kohler 2003). They range from the intertidal and surface 

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to depths of up to 450-512 meters (Klimley 1993), with occasional dives to even deeper waters 

(Jorgensen et al. 2009). Scalloped hammerheads have also been documented entering enclosed 

bays and estuaries (Compagno 1984). Neonates and juveniles inhabit nearshore nursery habitats 

for up to one year or more as these areas provide valuable refuge from predation (Duncan and 

Holland 2006). Scalloped hammerheads are high trophic level, opportunistic predators whose 

diet includes crustaceans, fish and cephalopods. 

Population Dynamics 

Scalloped hammerhead sharks are highly mobile and partly migratory and are likely the most 

abundant of the hammerhead species (Maguire 2006); however the risk of local depletions is of 

concern. Scalloped hammerhead sharks have a life history that is susceptible to overharvesting, 

and according to the most recent stock assessment the Northwestern Atlantic and Gulf of Mexico 

stock has declined to a relatively low level of abundance in recent years (Hayes et al. 2009). 

Populations in other parts of the world are assumed to have suffered similar declines, however 

data to conduct stock assessments on those populations are currently lacking. 

Based on information related to genetic variation among populations, behavior and physical 

factors, and differences in international regulatory mechanisms, the scalloped hammerhead 

Extinction Risk Analysis team identified six DPSs: Northwest Atlantic and Gulf of Mexico; 

Central and Southwest Atlantic; Eastern Atlantic; Indo-West Pacific; Central Pacific; and 

Eastern Pacific (Miller et al. 2014). 

Status 

Based on a combination of fisheries dependent and fisheries independent data, it is estimated that 

hammerhead shark populations have experienced drastic population declines, in excess of 90 

percent, in several parts of their global range (Gallagher et al. 2014). The primary factors 

responsible for the decline of the ESA-listed scalloped hammerhead DPSs are overutilization, 

due to both catch and bycatch of these sharks in fisheries, and inadequate regulatory mechanisms 

for protecting these sharks, with illegal fishing identified as a significant problem (Miller et al. 

2014). More details on the status of each DPS are provided in the DPS subsections below. 

Designated Critical Habitat 

No critical habitat has been designated for the scalloped hammerhead shark. 

Recovery Goals 

NMFS has not prepared a recovery plan for the scalloped hammerhead shark. 

6.2.14.1 Eastern Pacific Distinct Population Segment 

Historical estimates of effective population size (or the number of breeding individuals in the 

population) in the eastern Pacific range from 34,995 to 43,551 individuals (Nance et al. 2011). 

Using 15 microsatellite loci and mitochondrial DNA (mtDNA) from eastern Pacific tissue 

samples, Nance et al. (2011) discovered that the current effective population size is significantly 

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smaller (one to three orders of magnitude) than the historical effective population size, indicating 

that scalloped hammerheads in the eastern Pacific experienced a bottleneck and suffered 

significant declines. While current abundance data for this DPS are sparse, local and regional 

population declines have been indicated from recent fishery dependent data. Using fishing 

mortality estimates calculated from 1997 and 1998 catches, the INP (2006) estimated that the 

scalloped hammerhead shark population in the Gulf of Tehuantepac (Mexico) is decreasing by 

six percent per year. In Michoacán, hammerheads represent 70 percent of the catch, with fishing 

effort concentrated in breeding areas and directed towards juveniles and pregnant females 

(CITES 2012). In Costa Rica, shark catches reported by artisanal and longline fisheries have 

shown a dramatic decline (~ 50 percent) after reaching a maximum of 5,000 tons in 2000 

(SINAC 2012). Available data on relative abundance of pelagic sharks in general in the Costa 

Rica exclusive economic zone (EEZ) suggest sharp declines (approximately 58 percent) between 

1991 and 2002 (Arauz et al. 2004). Evidence of heavy fishing pressure by industrial/commercial 

and artisanal fisheries, high at-vessel fishing mortality, limited regulatory mechanisms and poor 

enforcement indicate that the Eastern Pacific DPS is currently at or near a level of abundance and 

productivity that places its current and future persistence in question (Miller et al. 2014). 

6.2.14.2 Central and Southwest Atlantic Distinct Population Segment 

While scalloped hammerhead sharks in the northwest Atlantic may currently be in a rebuilding 

phase, populations found further south in the Atlantic could still be in danger of decline (Miller 

et al. 2014). Historical landings data indicate that large numbers of hammerhead sharks were 

removed by longliners off the coast of Brazil in the late 20th century (Amorim et al. 1998). 

Although abundance estimates and quality catch data are unavailable for this DPS, the evidence 

of heavy fishing pressure on this species off the coast of Brazil, Central America, and the 

Caribbean, with documented large numbers of juvenile and neonate landings, suggests this DPS 

is likely approaching a level of abundance and productivity that places its current and future 

persistence in question (Miller et al. 2014). Overutilization by industrial/commercial fisheries 

combined with high at-vessel fishing mortality were ranked by the Extinction Risk Analysis 

team as the greatest risks to the persistence of this DPS. Overutilization by artisanal fisheries, 

lack of adequate regulatory mechanisms, illegal, unreported and unregulated fishing, and the 

schooling behavior of the species were ranked as moderate risks. 

6.2.14.3 Indo-West Pacific Distinct Population Segment 

The Indo-West Pacific DPS range covers a very large area and abundance estimates for this 

entire DPS are unavailable. However, documented trends in abundance in particular areas 

suggest significant depletions of local populations. Data collected from East Lombok, Indonesia, 

suggest potential population declines as the proportion of scalloped hammerheads in the Tanjung 

Luar artisanal longline fishery catch decreased from 15 percent to 2 percent from 2001 to 2011 

(FAO 2013). Scalloped hammerhead sharks off the coast of South Africa are also thought to be 

experiencing similar decreases in population size. Analyses of fishery-independent data from 

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beach protection programs have revealed drastic declines in catch rates since the early 1950s. 

From 1952-1972, Ferretti et al. (2010) estimated a decline of 99.3 percent in scalloped 

hammerhead catch rates off Main Beach in South Africa, and a decline of 86 percent from 1961-

1972 off Brighton Beach, South Africa. Estimates of the decline in hammerhead abundance in 

Australia’s northwest marine region, based on analysis of catch-per-unit-effort data from 1996-

2005, range from 58-76 percent (Heupel and McAuley 2007). Data from protective shark 

meshing programs off beaches in New South Wales and Queensland also suggest significant 

declines in hammerhead populations off the east coast of Australia. Over a 35 year period, the 

number of hammerheads caught per year in beach protection nets has decreased by more than 90 

percent, from over 300 individuals in 1973 to less than 30 in 2008 (Reid and Krogh 1992). 

Similarly, data from the Queensland shark control program indicates a 63 percent decline in 

scalloped hammerhead shark abundance between 2005 and 2010 (QPIF 2011). 

Evidence of heavy fishing pressure by industrial, commercial and artisanal fisheries, reports of 

significant illegal, unreported, unregulated fishing, especially off the coast of Australia, and high 

at-vessel mortality rates have likely led to overutilization of the Indo-West Pacific DPS. Coupled 

with inadequate regulatory measures, especially in the Western Indian Ocean and Indonesian 

waters, and habitat degradation, the present and future threats facing this DPS indicate it is 

approaching a level of abundance and productivity that places its current and future persistence 

in question (Miller et al. 2014). 

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7 ENVIRONMENTAL BASELINE 

The “environmental baseline” includes the past and present impacts of all Federal, state, or 

private actions and other human activities in the action area, the anticipated impacts of all 

proposed Federal projects in the action area that have already undergone formal or early section 

7 consultation, and the impact of state or private actions which are contemporaneous with the 

consultation in process (50 C.F.R. §402.02). We focus our discussion of the environmental 

baseline on threats to all ESA-listed species in those areas where sea turtle research primarily 

occurs, with a particular emphasis on threats affecting ESA-listed sea turtles. 

7.1 Global Climate Change 

Global annually averaged surface air temperature has increased by about 1.8 degrees Fahrenheit 

(1.0 degrees Celsius) over the last 115 years (1901 to 2016). This period is now the warmest in 

the history of modern civilization. The last few years have also seen record-breaking, climaterelated weather extremes, and the last three years have been the warmest years on record for the 

globe. These trends are expected to continue over climate timescales (Wuebbles et al. 2017). It is 

extremely likely that human activities, especially emissions of greenhouse gases, are the 

dominant cause of the observed warming since the mid-20th century. For the warming over the 

last century, there is no convincing alternative explanation supported by the extent of the 

observational evidence (Wuebbles et al. 2017). 

In addition to warming, many other aspects of global climate are changing, primarily in response 

to human activities. Thousands of studies conducted by researchers around the world have 

documented changes in surface, atmospheric, and oceanic temperatures; melting glaciers; 

diminishing snow cover; shrinking sea ice; rising sea levels; ocean acidification; and increasing 

atmospheric water vapor. For example, global average sea level has risen by about 7 to 8 inches 

since 1900, with almost half (about 3 inches) of that rise occurring since 1993. Human-caused 

climate change has made a substantial contribution to this rise since 1900, contributing to a rate 

of rise that is greater than during any preceding century in at least 2,800 years (Wuebbles et al. 

2017). Global sea level rise has already affected the United States; the incidence of daily tidal 

flooding is accelerating in more than 25 Atlantic and Gulf Coast cities. Global average sea levels 

are expected to continue to rise by at least several inches in the next 15 years and by 1 to 4 feet 

by 2100. A rise of as much as 8 feet by 2100 cannot be ruled out. Sea level rise will be higher 

than the global average on the East and Gulf Coasts of the United States (Wuebbles et al. 2017). 

The magnitude of climate change beyond the next few decades will depend primarily on the 

amount of greenhouse gases (especially carbon dioxide) emitted globally. Without major 

reductions in emissions, the increase in annual average global temperature relative to 

preindustrial times could reach 9 degrees Fahrenheit (5 degrees Celsius) or more by the end of 

this century. With significant reductions in emissions, the increase in annual average global 

temperature could be limited to 3.6 degrees Fahrenheit (2 degrees Celsius) or less (Wuebbles et 

al. 2017). The global atmospheric carbon dioxide concentration has now passed 400 parts per 

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million, a level that last occurred about 3 million years ago, when both global average 

temperature and sea level were significantly higher than today. Continued growth in carbon 

dioxide emissions over this century and beyond would lead to an atmospheric concentration not 

experienced in tens to hundreds of millions of years. There is broad consensus that the further 

and the faster the Earth system is pushed towards warming, the greater the risk of unanticipated 

changes and impacts, some of which are potentially large and irreversible (Wuebbles et al. 

2017). The observed increase in carbon emissions over the past 15 to 20 years has been 

consistent with higher emissions pathways. In 2014 and 2015, emission growth rates slowed as 

economic growth became less carbon-intensive. Even if this slowing trend continues, however, it 

is not yet at a rate that would limit global average temperature change to well below 3.6 degrees 

Fahrenheit (2 degrees Celsius) above preindustrial levels (Wuebbles et al. 2017). 

Climate change is projected to have substantial direct and indirect effects on individuals, 

populations, species, and the community structure and function of marine, coastal, and terrestrial 

ecosystems in the near future (IPCC 2007; IPCC 2013; McCarty 2001). Direct effects of climate 

change include increases in atmospheric temperatures, decreases in sea ice, and changes in sea 

surface temperatures, ocean acidity, patterns of precipitation, and sea level. Indirect effects of 

climate change include altered reproductive seasons/locations, shifts in migration patterns, 

reduced distribution and abundance of prey, and changes in the abundance of competitors and/or 

predators. Climate change will likely have its most pronounced effects on vulnerable species 

whose populations are already in tenuous positions (Williams et al. 2008). Increasing 

atmospheric temperatures have already contributed to changes in the quality of freshwater, 

coastal, and marine ecosystems and to the decline of endangered and threatened species 

populations (Karl 2009; Mantua et al. 1997). 

Sea turtles occupy a wide range of terrestrial and marine habitats, and many aspects of their life 

history have been demonstrated to be closely tied to climatic variables such as ambient 

temperature and storminess (Hawkes et al. 2009). Sea turtles have temperature-dependent sex 

determination, and many populations produce highly female-biased offspring sex ratios, a skew 

likely to increase further with global warming (Patrício et al. 2017). In addition to altering sex 

ratios, increased temperatures in sea turtle nests can result in reduced incubation times 

(producing smaller hatchling), reduced clutch size, and reduced nesting success due to exceeded 

thermal tolerances (Azanza-Ricardo et al. 2017; Fuentes et al. 2010; Fuentes et al. 2011; Fuentes 

et al. 2009). 

Other climatic aspects, such as extreme weather events, precipitation, ocean acidification and sea 

level rise also have potential to affect marine turtle populations. Changes in global climatic 

patterns will likely have profound effects on the coastlines of every continent, thus directly 

impacting sea turtle nesting habitat (Wilkinson and Souter 2008). In some areas, increases in sea 

level alone may be sufficient to inundate turtle nests and reduce hatching success by creating 

hypoxic conditions within inundated eggs (Caut et al. 2009; Pike et al. 2015). Flatter beaches, 

preferred by smaller sea turtle species, would likely be inundated sooner than would steeper 

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beaches preferred by larger species (Hawkes et al. 2014). Relatively small increases in sea level 

can result in the loss of a large proportion of nesting beaches in some locations. For example, a 

study in the northwestern Hawaiian Islands predicted that up to 40 percent of green turtle nesting 

beaches could be flooded with 0.9 m of sea level rise (Baker et al. 2006). The loss of nesting 

beaches would have catastrophic effects on sea turtle populations globally if they are unable to 

colonize new beaches that form, or if the newly formed beaches do not provide the habitat 

attributes (sand depth, temperature regimes, refuge) necessary for egg survival. 

Changing patterns of coastal erosion and sand accretion, combined with an anticipated increase 

in the number and severity of extreme weather events, may further exacerbate the effects of sea 

level rise on turtle nesting beaches (Wilkinson and Souter 2008). Extreme weather events may 

directly harm sea turtles, causing “mass” strandings and mortality (Poloczanska et al. 2009). 

Studies examining the spatio-temporal coincidence of marine turtle nesting with hurricanes, 

cyclones and storms suggest that cyclical loss of nesting beaches, decreased hatching success and 

hatchling emergence success could occur with greater frequency in the future due to global 

climate change (Hawkes et al. 2009). 

Global climate change may affect the ESA-listed fish species and DPSs considered in this 

opinion. Thermal changes of just a few degrees Celsius can substantially alter fish protein 

metabolism (McCarthy and Houlihan 1997), response to aquatic contaminants (Reid 1997), 

reproductive performance (Van Der Kraak and Pankhurst 1997), smolt development 

(McCormick et al. 1997), species distribution limits (McCarthy and Houlihan 1997), and 

community structure of fish populations (Schindler 2001). Apart from direct changes to 

anadromous fish survival, increased water temperatures may alter habitat, including the 

availability of prey (ISAB 2007). 

Shortnose and Atlantic sturgeon are tolerant to water temperatures up to approximately 28° C; 

these temperatures are experienced naturally in some areas of rivers during the summer months. 

If temperature rises beyond thermal limits for extended periods, habitat could be lost; this could 

be the case if southern habitats warm, resulting in range loss (Lassalle et al. 2010). As water 

temperatures increase, juvenile sturgeon may experience elevated mortality due to lack of cooler 

water refuges. The Atlantic salmon GOM DPS may be particularly vulnerable to elevated water 

temperature regimes since Maine is near the southern extent species’ range in North America 

(Fay et al. 2006b). Rising temperatures could also exacerbate existing water quality problems 

associated with DO and temperature. 

Salinity plays an important role in the movement and distribution of some nearshore and 

estuarine fish species (Simpfendorfer et al. 2011). Rising sea levels associated with climate 

change will likely shift the salt wedge upstream in affected rivers. Given the importance of 

salinity, changes in freshwater flow regimes into estuaries as a result of climate change will 

affect fish populations by potentially changing their distributions. Anadromous fish species (e.g., 

sturgeon and salmon) spawn in fresh water reaches of rivers because early life stages have little 

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to no tolerance for salinity. If the salt wedge moves further upstream, sturgeon spawning and 

rearing habitat could be restricted. In river systems with dams or natural falls that are impassable 

by sturgeon, the extent that spawning or rearing may be shifted upstream to compensate for the 

shift in the movement of the salt wedge would be limited. Simpfendorfer et al. (2011) found that 

juvenile smalltooth sawfish moved farther inland into estuary reaches within their preferred 

salinity range. Sea level rise will also likely impact important sawfish mangrove habitats as 

sediment surface elevations for mangroves will not keep pace with conservative projected rates 

sea level rise (Gilman et al. 2008). 

Changes in precipitation patterns are anticipated as a result of global climate change. The 

increased rainfall predicted in some areas may increase runoff and scour spawning areas, and 

flooding events could cause temporary water quality issues. Increased extremes in river flow 

(i.e., periods of flooding and low flow) can alternatively disrupt and fill in spawning habitat that 

sturgeon and salmon rely upon (ISAB 2007). In some areas, longer and more frequent droughts 

are predicted, in combination with increased water withdrawal for human use, may cause loss of 

habitat including loss of access to spawning habitat. Drought conditions in the spring may also 

expose eggs and larvae in rearing habitats. If a river becomes too shallow or flows become 

intermittent, anadromous fish may become susceptible to strandings or habitat restrictions. Low 

flow and drought conditions are also expected to cause additional water quality issues. Any of 

the conditions associated with climate change are likely to disrupt river ecology, causing shifts in 

community structure and the type and abundance of prey. Additionally, cues for spawning 

migration and spawning could occur earlier in the season, which might affect prey availability in 

rearing habitat. Overall, it is likely that global climate change would increase pressures on the 

survival and recovery of ESA-listed sturgeon and salmon populations considered in this opinion. 

Nassau grouper are found in a wide range of temperatures but spawning occurs within a narrow 

temperature range around 25 degrees Celsius. If sea surface temperatures rise, the geographic 

range of the species may shift in response to such changes. Changes in reproductive output or 

seasonal timing are also possible with unknown consequences for population abundance. One of 

the other potential effects of climate change on Nassau grouper is the loss of structural habitat in 

coral reef ecosystems (Munday et al. 2008). Increased sea surface temperatures have been 

responsible for coral loss through bleaching and disease, and bioerosion may reduce three 

dimensional structure in affected areas (Alvarez-Filip et al. 2009), reducing adult habitat for 

Nassau grouper (Coleman and Koenig 2010; Rogers and Beets 2001). 

7.2 Habitat Degradation 

The modification and destruction of habitat remains one of the primary threats to many 

threatened and endangered species. In this section we summarize the impacts of habitat 

degradation on the ESA-listed species within the action area. This section is divided into two 

subsections: (1) the effects of anthropogenic stressors (e.g., development, erosion control, 

lighting, and pollution) on sea turtle terrestrial nesting habitat, and (2) the effects of general 

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anthropogenic stressors (e.g., land-use changes, run-off, and population increase) on aquatic 

habitats used by turtles and fish species considered in this opinion. The effects of human 

activities on aquatic habitats located within the action area is further discussed subsequent 

sections addressing the following threats: marine debris, pollutants, oil spills, sound, power 

plants, dredging, and hydromodification. 

7.2.1 Terrestrial Habitat 

Destruction and modification of sea turtle nesting habitat is occurring worldwide. The main 

anthropogenic threats impacting nesting habitat include coastal development/construction, 

placement of erosion control structures and other barriers to nesting, beachfront lighting, 

vehicular and pedestrian traffic, sand extraction, beach erosion, beach sand placement, beach 

pollution, removal of native vegetation, and planting of non-native vegetation. Development near 

coastal areas continues and is a major problem as more and more people are moving to or 

visiting coastal areas. Development impacts may include the construction of roads, highways, 

public infrastructure, hotels, condominiums, houses, harbors, and nearshore shoreline 

stabilization structures (e.g., groins, jetties, breakwaters). Such development can deter or 

interfere with sea turtle nesting, affect nest success, and degrade nesting habitat. 

Nesting habitat is threatened by rigid shoreline protection or “coastal armoring” such as sea 

walls, rock revetments, and sandbag installations. Many miles of once productive nesting beach 

have been permanently lost to this type of shoreline protection. Beach armoring (e.g., bulkheads, 

seawalls, soil retaining walls, rock revetments, sandbags, and geotextile tubes) can impede a 

turtle's access to upper regions of the beach/dune system, thereby limiting the amount of 

available nesting habitat (Mazaris et al. 2009). At many ocean inlets along the U.S. Atlantic 

coast jetties have been constructed perpendicular to the shore to keep transported sand from 

closing the inlet channel. Witherington et al. (2005) found a significant negative relationship 

between loggerhead nesting density and distance from the nearest of 17 ocean inlets on the 

Atlantic coast of Florida. The effect of inlets in lowering nesting density was observed both 

updrift and downdrift of the inlets, leading researchers to propose that beach instability from 

both erosion and accretion may discourage loggerhead nesting. 

Numerous beaches in the southeastern U.S. are eroding due to both natural (e.g., storms, sea 

level changes, waves, shoreline geology) and anthropogenic (e.g., construction of armoring 

structures, groins, and jetties; coastal development; inlet dredging) factors. Such shoreline 

erosion leads to a loss of nesting habitat for sea turtles. Beach nourishment is a commonly used 

engineering solution to offset the loss of sandy beaches due to erosion. Although beach 

nourishment provides more sand, the quality of that sand, and hence the nesting beach, is 

typically less suitable than pre-existing natural beaches. Characteristics are engineered beaches 

via nourishment include (1) increased beach compaction, which can decrease nesting success, 

alter nest-chamber geometry, and alter nest concealment, and (2) escarpments, which can block 

turtles from reaching nesting areas (Ackerman 1980; Mann 1978; Mortimer 1990). For eggs and 

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hatchlings, nourishment can decrease survivorship and affect development by altering beach 

characteristics such as sand compaction, gaseous environment, hydric environment, contaminant 

levels, nutrient availability, and thermal environment (Grain et al. 1995). In addition, nests can 

be covered with excess sand if nourishment is implemented in areas with incubating eggs. Sand 

mining (i.e., the removal of beach sand for upland construction) can also seriously reduce or 

degrade sea turtle nesting habitat and interfere with hatchling movement to sea (NMFS 2003). 

Erosion of nesting beaches can occur as a result of coastal development when native dune 

vegetation, which enhances beach stability and acts as an integral buffer zone between land and 

sea, is degraded or destroyed. This in turn often leaves insufficient nesting opportunities above 

the high tide line, and nests may be washed out. Hawksbill turtles prefer to nest under vegetation 

and are, therefore, particularly affected by beachfront development and the associated clearing of 

dune vegetation (Mortimer and Donnelly 2007). Non-native vegetation has invaded many coastal 

areas and often out competes native species. Non-native vegetation is usually less-stabilizing and 

can lead to increased erosion and degradation of suitable nesting habitat. Exotic vegetation may 

also form impenetrable root mats that can prevent proper nest cavity excavation, invade and 

desiccate eggs, or trap hatchlings. 

The presence of lights on or adjacent to nesting beaches alters the behavior of nesting adults and 

is often fatal to emerging hatchlings as they are attracted to light sources and drawn away from 

the sea (Witherington 1992). Artificial lighting may deter adult female turtles from emerging 

from the ocean to nest and can disorient emerging hatchlings away from the ocean. Hatchlings 

have a tendency to orient toward the brightest direction, which on natural, undeveloped beaches 

is commonly toward the broad open horizon of the sea. However, on developed beaches, the 

brightest direction is often away from the ocean and toward lighted structures. Hatchlings unable 

to find the ocean, or delayed in reaching it, are likely to incur higher mortality risk from 

dehydration, exhaustion, or predation. Hatchlings lured into lighted parking lots or toward 

streetlights can get crushed by passing vehicles. 

Coastal development brings large numbers of people into close contact with sea turtle nesting 

areas. Human debris, beach equipment, and ruts lefts by vehicles may interfere with turtle 

hatchling’s progress towards the ocean (Conant et al. 2009). Trash left on the beach may attract 

terrestrial and avian predators to sea turtle nesting sites. Vehicle traffic on nesting beaches can 

also contribute to sand compaction, which hinders nest construction and hatchling emergence, 

and erosion, especially during high tides or on narrow beaches where driving is concentrated on 

the high beach and foredune. 

7.2.2 Aquatic Habitat 

Many stream, riparian, and coastal areas within the action area have been degraded by the effects 

of land and water use associated with urbanization, road construction, forest management, 

agriculture, mining, transportation, water development, and other human activities. Development 

activities contribute to a variety of interrelated factors that lead to the decline of ESA-listed fish 

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species considered in this opinion. These include reduced in-channel and off-channel habitat, 

restricted lateral channel movement, increased flow velocities, increased erosion, decreased 

cover, reduced prey sources, increased contaminants, increased water temperatures, degraded 

water quality, and decreased water quantity. 

Urbanization and increased human population density within a watershed result in changes in 

stream habitat, water chemistry, and the biota (plants and animals) that live there. In many cases, 

these changes negatively impact species, particularly those with small population sizes like the 

ESA-listed species within the action area. The most obvious effect of urbanization is the loss of 

natural vegetation, which results in an increase in impervious cover and dramatic changes to the 

natural hydrology of urban and suburban streams (O'Driscoll et al. 2010). Urbanization generally 

results in land clearing, soil compaction, modification and/or loss of riparian buffers, and 

modifications to natural drainage features. The increased impervious cover in urban areas leads 

to increased volumes of runoff, increased peak flows and flow duration, and greater stream 

velocity during storm events (Bledsoe and Watson 2001; Booth et al. 1995). Runoff from urban 

areas also contains chemical pollutants from vehicles and roads, industrial sources, and 

residential sources (Connor et al. 2003). Urban runoff is typically warmer than receiving waters 

and can significantly increase temperatures, particularly in smaller streams (O'Driscoll et al. 

2010). Municipal wastewater treatment plants replace septic systems, resulting in point 

discharges of nutrients and other contaminants not removed in the processing (Booth et al. 1995). 

Municipalities with combined sewer/stormwater overflows or older treatment systems may 

directly discharge untreated sewage following heavy rainstorms. Urban and suburban nonpoint 

and point source discharges affect water quality and quantity in basin surface waters (O'Driscoll 

et al. 2010). Dikes and levees constructed to protect infrastructure and agriculture have isolated 

floodplains from their river channels and restricted fish access (Bayley 1995). The many miles of 

roads and rail lines that parallel streams within the action area have degraded stream bank 

conditions and decreased floodplain connectivity by adding fill to floodplains (O'Driscoll et al. 

2010). Culvert and bridge stream crossings have similar effects and create additional problems 

for fish when they act as physical or hydraulic barriers that prevent fish access to spawning or 

rearing habitat, or contribute to adverse stream morphological changes upstream and downstream 

of the crossing itself. 

Modification and loss of smalltooth sawfish habitat, especially nursery habitat, is a contributing 

factor in the decline of the species. Activities such as agricultural and urban development, 

commercial activities, dredge-and-fill operations, boating, erosion, and diversions of freshwater 

runoff contribute to these losses (SAFMC 1998). In Florida, coastal development often involves 

the removal of mangroves and the armoring of shorelines through seawall construction. Changes 

to the natural freshwater flows into estuarine and marine waters through construction of canals 

and other water control devices have had other impacts including: altered temperatures, salinity, 

and nutrient regimes; reduced both wetlands and submerged aquatic vegetation; and degraded 

vast areas of coastal habitat utilized by smalltooth sawfish (Gilmore 1995; Reddering 1988; 

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Whitfield and Bruton 1989). Juvenile sawfish may be particularly susceptible to habitat 

modification and loss due to their affinity for shallow, estuarine nursery habitats. While habitat 

modification is not the primary reason for the decline of smalltooth sawfish abundance, it is a 

contributing factor and almost certainly hampers species recovery. 

7.3 Marine Debris 

Marine debris is a significant concern for ESA-listed species and sea turtles in particular. The 

initial developmental stages of all turtle species are spent in the open sea. During this time both 

the juvenile turtles and their buoyant food are drawn by advection into fronts (convergences, 

rips, driftlines). The same process accumulates large volumes of marine debris, such as plastics 

and lost fishing gear, in ocean gyres (Carr 1987). An estimated four to twelve million metric tons 

of plastic enter the oceans annually (Jambeck et al. 2015). It is thought that sea turtles eat plastic 

because it closely resembles jellyfish, a common natural prey item (Schuyler 2014). 

Ingestion of plastic debris can block the digestive tract which can cause turtle mortality as well 

as sub-lethal effects including dietary dilution, reduced fitness, and absorption of toxic 

compounds (Laist et al. 1999; Lutcavage et al. 1997). Santos et al. (2015) found that a 

surprisingly small amount of plastic debris was sufficient to block the digestive tract and cause 

death. They reported that 10.7 percent of green turtles in Brazilian waters were killed by plastic 

ingestion, while 39.4 percent had ingested enough plastic to have killed them. These results 

suggest that debris ingestion is a potentially important source of turtle mortality, one that may be 

masked by other causes of death. Gulko and Eckert (2003) estimated that between one-third and 

one-half of all sea turtles ingest plastic at some point in their lives. A more recent study by 

Schuyler et al. (2015) estimates that 52 percent of sea turtles globally have ingested plastic 

debris. Schuyler et al. (2016) synthesized the factors influencing debris ingestion by turtles into a 

global risk model, taking into account the area where turtles are likely to live, their life history 

stage, the distribution of debris, the time scale, and the distance from stranding location. They 

found that oceanic life stage turtles are at the highest risk of debris ingestion. Base on this model, 

olive ridley turtles are the most at-risk species; green, loggerhead, and leatherback turtles were 

also found to be at a high and increasing risk from plastic ingestion (Schuyler 2014). The regions 

of highest risk to global turtle populations are off the east coasts of the U.S., Australia, and South 

Africa; the east Indian Ocean, and Southeast Asia. 

In addition to ingestion risks, sea turtles can also become entangled in marine debris such as 

fishing nets, monofilament line, and fish-aggregating devices (FADs) (Laist et al. 1999; 

Lutcavage et al. 1997; NRC 1990). An estimated 640,000 tons of fishing gear is lost, abandoned, 

or discarded at sea each year throughout the world’s oceans (Macfadyen et al. 2009). These 

“ghost nets” drift in the ocean and can fish unattended for decades (ghost fishing), killing huge 

numbers of marine animals. Turtles, in particular, are affected by ghostnets due to their tendency 

to use floating objects for shelter and as foraging stations (Dagorn et al. 2013; Kiessling 2003). 

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7.4 Pollutants 

Coastal habitats are often in close proximity to major sources of pollutants and heavy metals, 

which make their way into the marine environment from industrial, domestic and agricultural 

sources. Persistent organic pollutants (POPs) are organic compounds that are resistant to 

environmental degradation through chemical, biological, and photolytic processes. These 

contaminants bioaccumulate through the food chain and can result in lethal and sublethal effects 

on marine organisms. 

A variety of heavy metals have been found in sea turtles tissues in levels that increase with turtle 

size. These include arsenic, barium, cadmium, chromium, copper, iron, lead, manganese, 

mercury, nickel, selenium, silver, and zinc, (Barbieri 2009; Fujihara et al. 2003; GarcíaFernández et al. 2009; Godley et al. 1999; Storelli et al. 2008). Cadmium has been found in 

leatherbacks at the highest concentration compared to any other marine vertebrate (Gordon et al. 

1998). Newly emerged hatchlings have higher concentrations than are present when laid, 

suggesting that metals may be accumulated during incubation from surrounding sands (Sahoo et 

al. 1996). Arsenic has been found to be very high in green turtle eggs (Van de Merwe et al. 

2009). Sea turtle tissues have been found to contain organochlorines, including chlorobiphenyl, 

chlordane, lindane, endrin, endosulfan, dieldrin, perfluorooctane sulfonate, perfluorooctanoic 

acid, DDT, and PCB (Alava et al. 2006; Gardner et al. 2003; Keller et al. 2005; Oros et al. 2009; 

Storelli et al. 2007). PCB concentrations are reportedly equivalent to those in some marine 

mammals, with liver and adipose levels of at least one congener being exceptionally high 

(Davenport et al. 1990; Oros et al. 2009). Levels of PCBs found in green sea turtle eggs are 

considered far higher than what is fit for human consumption (Van de Merwe et al. 2009). 

Several studies have reported correlations between organochlorine concentration level and 

indicators of sea turtle health or fitness. Organochlorines have the potential to suppress the 

immune system of loggerhead sea turtles and may affect metabolic regulation (Keller et al. 2006; 

Oros et al. 2009). Accumulation of these contaminants can also lead to deficiencies in endocrine, 

developmental and reproductive health (Storelli et al. 2007). Females from sexual maturity 

through reproductive life should have lower levels of contaminants than males because 

contaminants are shared with progeny through egg formation. Balazs (1991) suggested that 

environmental contaminants are a possible factor contributing to the development of the viral 

disease FP in sea turtles by reducing immune function. Day et al. (2007) investigated mercury 

toxicity in loggerhead sea turtles by examining trends between blood mercury concentrations and 

various health parameters. They concluded that subtle negative impacts of mercury on sea turtle 

immune function are possible at concentrations observed in the wild. Keller et al. (2004) 

investigated the possible health effects of organochlorine contaminants, such as polychlorinated 

biphenyls (PCBs) and pesticides on loggerhead sea turtles. Although concentrations were 

relatively low compared with other species, they found significant correlations between 

organochlorine contaminants levels and health indicators for a wide variety of biologic functions, 

including immunity and homeostasis of proteins, carbohydrates, and ions. 

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The life histories of sturgeon species (i.e., long lifespan, extended residence in estuarine habitats, 

benthic foraging) predispose them to long-term, repeated exposure to environmental 

contamination and potential bioaccumulation of heavy metals and other toxicants (Dadswell 

1979). Shortnose sturgeon collected from the Delaware and Kennebec Rivers had total toxicity 

equivalent concentrations of polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans, 

PCBs, DDE, aluminum, cadmium, and copper all above adverse effect concentration levels 

reported in the literature (Brundage III 2008). Dioxin and furans were detected in ovarian tissue 

from shortnose sturgeon caught in the Sampit River/Winyah Bay system (South Carolina). 

Heavy metals and organochlorine compounds accumulate in sturgeon tissue, but their long-term 

effects are not well studied (Ruelle and Keenlyne 1993). High levels of contaminants, including 

chlorinated hydrocarbons, in several other fish species are associated with reproductive 

impairment (Billsson 1998; Cameron et al. 1992; Giesy et al. 1986; Hammerschmidt et al. 2002), 

reduced survival of larval fish (McCauley et al. 2015; Willford et al. 1981), delayed maturity and 

posterior malformations (Billsson 1998). Pesticide exposure in fish may affect anti-predator and 

homing behavior, reproductive function, physiological maturity, swimming speed, and distance 

(Beauvais et al. 2000; Scholz et al. 2000; Waring and Moore 2004). Sensitivity to environmental 

contaminants also varies by life stage. Early life stages of fish appear to be more susceptible to 

environmental and pollutant stress than older life stages. (Rosenthal and Alderdice 1976). Early 

life stage Atlantic and shortnose sturgeon are vulnerable to PCB and Tetrachlorodibenzo-pdioxin (TCDD) toxicities of less than 0.1 parts per billion (Chambers et al. 2012). Increased 

doses of PCBs and TCDD have been correlated with reduced physical development of Atlantic 

sturgeon larvae, including reductions in head size, body size, eye development and the quantity 

of yolk reserves (Chambers et al. 2012). Juvenile shortnose sturgeon raised for 28 days in North 

Carolina’s Roanoke River had a 9 percent survival rate compared to a 64 percent survival rate at 

non-riverine control sites (Cope et al. 2011). The reduced survival rate could not be correlated 

with contaminants, but significant quantities of retene, a paper mill by-product with dioxin-like 

effects on early life stage fish, were detected in the river (Cope et al. 2011). 

Dwyer et al. (2005) compared the relative sensitivities of common surrogate species used in 

contaminant studies to 17 ESA-listed species including Atlantic sturgeons. The study examined 

96-hour acute water exposures using early life stages where mortality is an endpoint. Chemicals 

tested were carbaryl, copper, 4-nonphenol, pentachlorophenal and permethrin. Of the ESA-listed 

species, Atlantic sturgeon were ranked the most sensitive species tested for four of the five 

chemicals (Atlantic and shortnose sturgeon were found to be equally sensitive to permethrin). 

Additionally, a study examining the effects of coal tar, a byproduct of the process of destructive 

distillation of bituminous coal, indicated that components of coal tar are toxic to shortnose 

sturgeon embryos and larvae in whole sediment flow-through and coal tar elutriate static renewal 

(Kocan et al. 1993). 

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7.5 Oil Spills 

Oil pollution has been a significant concern in the Gulf of Mexico for several decades due to the 

large amount of extraction and refining activity in the region. Routine discharges into the 

northern Gulf of Mexico (not including oil spills) include roughly 88,200 barrels of petroleum 

per year from municipal and industrial wastewater treatment plants and roughly 19,250 barrels 

from produced water discharged overboard during oil and gas operations (MMS 2007; USN 

2008). These sources amount to over 100,000 barrels of petroleum discharged into the northern 

Gulf of Mexico annually. Although this is only 10 percent of the amount discharged in a major 

oil spill, such as the Exxon Valdez spill (roughly 1 million barrels), this represents a significant 

and “unseen” threat to Gulf of Mexico wildlife and habitats. Generally, accidental oil spills may 

amount to less than 24,000 barrels of oil discharged annually in the northern Gulf of Mexico, 

making non-spilled oil normally one of the leading sources of oil discharge into the Gulf of 

Mexico, although incidents such as the 2010 Deepwater Horizon incident are exceptional (MMS 

2007). The other major source from year to year is oil naturally seeping into the northern Gulf of 

Mexico. Although exact figures are unknown, natural seepage is estimated at between 120,000 

and 980,000 barrels of oil annually (MacDonald et al. 1993; MMS 2007). 

Although non-spilled oil is the primary contributor to oil introduced into the Gulf of Mexico, 

concern over accidental oil spills is well-founded (Campagna et al. 2011). From 2006 to 2015, 

U.S. outer continental shelf oil production averaged approximately 0.5 billion barrels per year 

(Anderson et al. 2012). It is estimated that 3.2 million tons of oil is released into the environment 

annually with 10 percent attributed to natural seepage, and the rest as a result of oil and gas 

activities (Epstein and Selber 2002). Even if a small fraction of the annual oil and gas extraction 

is released into the marine environment, major, concentrated releases can result in significant 

environmental impacts. Oil released into the marine environment contains aromatic organic 

chemicals known to be toxic to a variety of marine life; these chemicals tend to dissolve into the 

air to a greater or lesser extent, depending on oil type and composition (Yender et al. 2002). 

Several oil spills have affected the northern Gulf of Mexico over the past few years, largely due 

to hurricanes. The impacts of Hurricane Ivan in 2004 on the Gulf Coast included pipeline 

damage causing 16,000 barrels of oil to be released and roughly 4,500 barrels of petroleum 

products from other sources (USN 2008). The next year, Hurricane Katrina caused widespread 

damage to onshore oil storage facilities, releasing 191,000 barrels of oil (LHR 2010). Another 

4,530 barrels of oil were released from 70 other smaller spills associated with hurricane damage. 

Shortly thereafter, Hurricane Rita damaged offshore facilities resulting in 8,429 barrels of oil 

released (USN 2008). 

Major oil spills have impacted the Gulf of Mexico for decades (NMFS 2010b). Until 2010, the 

largest oil spill in North America (Ixtoc oil spill) occurred in the Bay of Campeche (1979), when 

a well “blew out,” allowing oil to flow into the marine environment for nine months, releasing 

2.8-7.5 million barrels of oil. Oil from this release eventually reached the Texas coast, including 

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the Kemp’s ridley sea turtle nesting beach at Rancho Nuevo, where 9,000 hatchlings were 

airlifted and released offshore (NOAA 2010). Over 7,600 cubic meters of oiled sand was 

eventually removed from Texas beaches, and 200 gallons of oil were removed from the area 

around Rancho Nuevo (NOAA 2010). Eight dead and five live sea turtles were recovered during 

the oil spill event; although causes of deaths were not determined, oiling was suspected to play a 

part (NOAA 2010). Also in 1979, the oil tanker Burmah Agate collided with another vessel near 

Galveston, Texas, causing an oil spill and fire that ultimately released 65,000 barrels of oil into 

estuaries, beachfronts, and marshland along the northern and central Texas coastline (NMFS 

2010b). Clean up of these areas was not attempted due to the environmental damage such efforts 

would have caused. Another 195,000 barrels of oil are estimated to have been burned in a multimonth-long fire aboard the Burmah Agate (NMFS 2010b). The tanker Alvenus grounded in 1984 

near Cameron, Louisiana, spilling 65,500 barrels of oil, which spread west along the shoreline to 

Galveston (NMFS 2010b). One oiled sea turtle was recovered and released (NOAA 2010). In 

1990, the oil tanker Megaborg experienced an accident near Galveston during the lightering 

process and released 127,500 barrels of oil, most of which burned off in the ensuing fire (NMFS 

2010b). 

On April 20 2010, a fire and explosion occurred aboard the semisubmersible drilling platform 

Deepwater Horizon roughly 80 kilometers southeast of the Mississippi Delta. The platform had 

17,500 barrels of fuel aboard, which likely burned, escaped, or sank with the platform. However, 

once the platform sank, the riser pipe connecting the platform to the wellhead on the seafloor 

broke in multiple locations, initiating an uncontrolled release of oil from the exploratory well. 

Over the next three months, oil was released into the Gulf of Mexico, resulting in oiled regions 

of Texas, Louisiana, Mississippi, Alabama, and Florida and widespread oil slicks throughout the 

northern Gulf of Mexico that closed more than one-third of the US Gulf of Mexico Exclusive 

Economic Zone to fishing due to contamination concerns. Apart from the widespread surface 

slick, massive undersea oil plumes formed, possibly through the widespread use of dispersants 

and reports of tarballs washing ashore throughout the region were common. Although estimates 

vary, roughly 4.1 million barrels of oil were released directly into the Gulf of Mexico (USDOI 

2012). During surveys in offshore oiled areas, 1,050 sea turtles were seen and half of these were 

captured. Of the 520 sea turtles captured, 394 showed signs of being oiled (Witherington et al. 

2012). A large majority of these were juveniles, mostly green (311) and Kemp’s ridley sea turtles 

(451). An additional 78 adult or subadult loggerheads were observed (Witherington et al. 2012). 

Captures of sea turtles along the Louisiana’s Chandeleur Islands in association with emergency 

sand berm construction resulted in 185 loggerheads, eight Kemp’s ridley, and a single green sea 

turtle being captured and relocated (Dickerson and Bargo 2012). In addition, 274 nests along the 

Florida panhandle were relocated that ultimately produced 14,700 hatchlings, but also had 

roughly 2 percent mortality associated with the translocation (MacPherson et al. 2012). Females 

that laid these nests continued to forage in the area, which was exposed to the footprint of the oil 

spill (Hart et al. 2014). Large areas of Sargassum were affected, with some heavily oiled or 

dispersant-coated Sargassum sinking and other areas accumulating oil where sea turtles could 

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inhale, ingest, or contact it (Powers et al. 2013; USDOI 2012). Of 574 sea turtles observed in 

these Sargassum areas, 464 were oiled (USDOI 2012). 

Use of dispersants can increase oil dispersion, raising the levels of toxic constituents in the water 

column, but speeding chemical degradation overall (Yender et al. 2002). Although the effects of 

dispersant chemicals on sea turtles is unknown, testing on other organisms have found currently 

used dispersants to be less toxic than those used in the past (NOAA 2010). It is possible that 

dispersants can interfere with surfactants in the lungs (surfactants prevent the small spaces in the 

lungs from adhering together due to surface tension, facilitating large surface areas for gas 

exchange), as well as interfere with digestion, excretion, and salt gland function (NOAA 2010). 

The most toxic chemicals associated with oil can enter marine food chains and bioaccumulate in 

invertebrates such as crabs and shrimp to a small degree (prey of some sea turtles) (Law and 

Hellou 1999), but generally do not bioaccumulate or biomagnify in finfish (Meador et al. 1995; 

Varanasi et al. 1989; Yender et al. 2002). Sea turtles are known to ingest and attempt to ingest tar 

balls, which can block their digestive systems, impairing foraging or digestion and potentially 

causing death (NOAA 2010), ultimately reducing growth, reproductive success, as well as 

increasing mortality and predation risk (Fraser 2014). Tarballs were found in the digestive tracts 

of 63 percent of post hatchling loggerheads in 1993 following an oil spill and 20 percent of the 

same species and age class in 1997 (Fraser 2014). Oil exposure can also cause acute damage on 

direct exposure to oil, including skin, eye, and respiratory irritation, reduced respiration, burns to 

mucous membranes such as the mouth and eyes, diarrhea, gastrointestinal ulcers and bleeding, 

poor digestion, anemia, reduced immune response, damage to kidneys or liver, cessation of salt 

gland function, reproductive failure, and death (NOAA 2010; Vargo et al. 1986). Nearshore 

spills or large offshore spills can oil beaches on which sea turtles lay their eggs, causing birth 

defects or mortality in the nests (NOAA 2010). 

Oil can also cause indirect effects to sea turtles through impacts to habitat and prey organisms. 

Seagrass beds may be particularly susceptible to oiling as oil contacts grass blades and sticks to 

them, hampering photosynthesis and gas exchange (Wolfe et al. 1988)s. If spill cleanup is 

attempted, mechanical damage to seagrass can result in further injury and long-term scarring. 

Loss of seagrass due to oiling would be important to green sea turtles, as this is a significant 

component of their diets (NOAA 2010). The loss of invertebrate communities due to oiling or oil 

toxicity would also decrease prey availability for hawksbill, Kemp’s ridley, and loggerhead sea 

turtles (NOAA 2010). Furthermore, Kemp’s ridley and loggerhead sea turtles, which commonly 

forage on crustaceans and mollusks, may ingest large amounts of oil due oil adhering to the 

shells of these prey and the tendency for these organisms to bioaccumulate the toxins found in oil 

(NOAA 2010). It is suspected that oil adversely affected the symbiotic bacteria in the gut of 

herbivorous marine iguanas when the Galápagos Islands experienced an oil spill, contributing to 

a more than 60 percent decline in local populations the following year. The potential exists for 

green sea turtles to experience similar impacts, as they also harbor symbiotic bacteria to aid in 

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their digestion of plant material (NOAA 2010). Dispersants are believed to be as toxic to marine 

organisms as oil itself. 

7.6 Vessel Strikes 

Nearshore marine habitats occupied by ESA-listed species often feature both heavy commercial 

and recreational vessel traffic. Vessel strikes represent a recognized threat to several taxa of large 

air breathing marine vertebrates, including sea turtles. Many recovered turtles display injuries 

that appear to result from interactions with vessels and their associated propulsion systems 

(Work et al. 2010). Impact from a boat hull or outboard motor, or cuts from a propeller can kill 

or severely injure turtles. Turtles may use auditory cues to react to approaching vessels rather 

than visual cues, making them more susceptible to strike as vessel speed increases (Hazel et al. 

2007). Results from a study by Hazel et al. (2007) suggest that green turtles cannot consistently 

avoid being struck by vessels moving at relatively moderate speeds (i.e., greater than four 

kilometers per hour). Vessel strikes have been identified as one of the important mortality factors 

in several near shore turtle habitats worldwide (Denkinger et al. 2013). However, available 

information is sparse regarding the overall magnitude of this threat or the impact on sea turtle 

populations globally. 

High levels of vessel traffic in nearshore areas along the U.S. Atlantic and Gulf of Mexico coasts 

result in frequent injury and mortality of sea turtles. From 1997 to 2005, nearly 15 percent of all 

stranded loggerheads in this region were documented as having sustained some type of propeller 

or collision injury, although it is not known what proportion of these injuries were sustained 

ante-mortem versus post mortem. In one study from Virginia, Barco et al. (2016) found that all 

15 dead loggerhead turtles encountered with signs of acute vessel interaction were apparently 

normal and healthy prior to human-induced mortality. For example, the incidence of propeller 

wounds of stranded turtles from the U.S. Atlantic and Gulf of Mexico doubled from about ten 

percent in the late 1980s to about 20 percent in 2004. Singel et al. (2007) reported a tripling of 

boat strike injuries in Florida from the 1980’s to 2005. Over this time period, in Florida alone 

over 4,000 (~500 live; ~3500 dead) sea turtle strandings were documented with propeller 

wounds, which represents 30 percent of all sea turtle strandings for the state (Singel et al. 2007). 

These studies suggest that the threat of vessel strikes to sea turtles may be increasing over time 

as vessel traffic continues to increase in the southeastern U.S. and throughout the world. 

Vessel strikes were identified as a source of mortality for green sea turtles in Hawaii waters, 

although reported incidence rates among stranded turtles are not as high as in the southeastern 

United States. Chaloupka et al. (2008b) reported that 2.5 percent of green turtles found dead on 

Hawaiian beaches between 1982 and 2003 had been killed by boat strike. Vessel strikes have 

also been reported as a potentially important threat to sea turtle populations by researches in 

other parts of the world including the Canary Islands (Orós et al. 2005), Italy (Casale et al. 

2010), and the Galápagos Islands (Denkinger et al. 2013; Parra et al. 2011). 

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Sturgeon are also susceptible to vessel strikes due to their large size and frequent use of coastal 

waterways with heavy commercial vessel traffic. The factors relevant to determining the risk to 

sturgeon from vessel strikes are currently unknown, but are likely related to size and speed of the 

vessels, navigational clearance (i.e., depth of water and draft of the vessel) in the area where the 

vessel is operating, and the behavior of sturgeon in the area (e.g., foraging, migrating, etc.). The 

ASSRT determined Atlantic sturgeon in the Delaware River are at a moderately high risk of 

extinction because of ship strikes, and sturgeon in the James River are at a moderate risk from 

ship strikes (ASSRT 2007). Balazik et al. (2012) estimated up to 80 sturgeon were killed 

between 2007 and 2010 in these two river systems. Brown and Murphy (2010) examined 28 dead 

Atlantic sturgeon from the Delaware River from 2005 through 2008 and found that fifty percent 

of the mortalities resulted from apparent vessel strikes, and 71 percent of these (10 out of 14) had 

injuries consistent with being struck by a large vessel. Eight of the fourteen vessel-struck 

sturgeon were adult-sized fish which, given the time of year the fish were observed, were likely 

migrating through the river to or from the spawning grounds. Ship strikes may also be 

threatening Atlantic sturgeon populations in the Hudson River where large ships move from the 

river mouth to ports upstream through narrow shipping channels. The channels are dredged to 

the approximate depth of the ships, usually leaving less than six feet of clearance between the 

bottom of ships and the river bottom. Any aquatic life along the bottom is at risk of being sucked 

up through the large propellers of these ships. 

Large Atlantic sturgeon are most often killed by ship strikes because their size means they are 

unable to pass through the ship’s propellers without making contact. Shortnose sturgeon may not 

be as susceptible due to their smaller size in comparison to Atlantic sturgeon. There has been 

only one confirmed incidence of a ship strike on a shortnose sturgeon in the Kennebec River, and 

two suspected ship strike mortalities in the Delaware River (SSSRT 2010). Green sturgeon and 

smalltooth sawfish may also been susceptible to ship strikes but there is no available information 

on this threat to these species. 

7.7 Anthropogenic Sound 

As anthropogenic noise continues to rise throughout the world’s oceans, there is growing 

concern about the impact of sound on sea turtles. There are limited data on the hearing abilities 

of sea turtles, their uses of sounds, and their vulnerability to sound exposure. The functional 

morphology of the sea turtle ear is poorly understood and debated. Some evidence suggests that 

sea turtles are able to detect (Bartol and Ketten 2006; Bartol et al. 1999; Martin et al. 2012; 

Ridgway et al. 1969) and behaviorally respond to acoustic stimuli (DeRuiter and Doukara 2012; 

McCauley et al. 2000; Moein et al. 1995; O'Hara and Wilcox 1990). Sea turtles may use sound 

for navigation, locating prey, avoiding predators, and general environmental awareness (Dow 

Piniak et al. 2012). Anthropogenic sound within the action area includes explosions, seismic 

airguns/oil and gas exploration, pile driving, active sonar, offshore wind farms, shipping noise, 

and continuous sound sources. 

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To evaluate the possible vulnerability of sea turtles to sound, it is necessary to extrapolate from 

other animal groups. Some scientists believe using data from marine mammals is the best 

surrogate, however others find that unsatisfactory and are inclined to use data from fish (Popper 

et al. 2014). The rationale is that the hearing range for sea turtles is more closely related to fish 

than that of any marine mammal, and the functioning of the basilar papilla in the turtle ear is 

dissimilar to the functioning of the cochlea in mammals (Popper et al. 2014). Morphological 

examinations of green and loggerhead sea turtles (Lenhardt et al. 1985; Ridgway et al. 1969; 

Wever 1978) describe the sea turtle ear as reptilian with a few underwater modifications, 

supporting the assessment that the sea turtle ear is more similar to that of a fish than a mammal. 

Ridgway et al. (1969) collected the first measurements of sea turtle hearing sensitivity by using 

both aerial and vibrational sound stimuli to collect measurements of the cochlear response 

potential of three juvenile green sea turtles. Turtles responded to aerial stimuli between 100 and 

1000 Hertz (Hz) and vibrational stimuli between 30 and 700 Hz, with maximum sensitivity 

between 300 and 500 Hz for both stimuli with a rapid decline in sensitivity in lower and higher 

frequencies. They found 2000 Hz was the upper limit for observation of cochlear potentials 

without injury and suggested the practical hearing range of the green turtle did not exceed 1000 

Hz. 

More recent measurements of sea turtle hearing have been made using auditory evoked 

potentials (AEPs). This is an electrical response of the central auditory nervous system after 

stimulation by sound detectable by the ear, and can be recorded using electrodes. Bartol et al. 

(1999) measured the hearing of thirty-five juvenile loggerhead sea turtles, by collecting short 

latency AEPs (auditory brainstem responses, or ABRs), recorded in response to two types of 

vibrational stimuli: 1) low-frequency clicks and 2) tone bursts delivered directly to the 

tympanum using a mechanical vibrator. They measured a mean threshold in response to click 

stimuli of -10.8 decibels (dB) re: 1 gram root mean squared (rsm) ± 2.3 dB standard deviation 

(SD), and a hearing range from tone bursts from 250 Hz to 750 Hz. The most sensitive threshold 

was the lowest frequency tested, 250 Hz, with a mean threshold of -23.3 dB re: 1g rms ± 2.3 dB 

SD. Bartol and Ketten (2006) measured ABRs in two juvenile and six sub-adult green sea turtles, 

and two juvenile Kemp’s ridley sea turtle’s ears partially submerged using an aerial tonal stimuli. 

Sub-adult Pacific green turtles responded to stimuli between 100 and 500 Hz, with maximum 

sensitivity between 200 and 400 Hz, while juvenile Atlantic greens responded to stimuli between 

100 and 800 Hz, with maximum sensitivity between 600 and 700 Hz. Kemp’s ridleys responded 

stimuli between 100 and 500 Hz with maximum sensitivity between 100 and 200 Hz. 

Wendy Dow Piniak et al. (2012) developed techniques to measure fully submerged underwater 

sea turtle hearing and recorded AEPs underwater and in air in five juvenile green sea turtles. 

Green sea turtle AEP signals exhibited a frequency-doubling signature similar to that seen in 

fish. Juvenile green sea turtles responded to stimuli between 50 and 1600 Hz in water and 50 and 

800 Hz in air, with ranges of maximum sensitivity between 50 and 400 Hz in water and 300 and 

400 Hz in air. In both media, sensitivity decreased sharply after 400 Hz. Martin et al. (2012) used 

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similar underwater methodologies to record AEPs in one adult loggerhead and recorded 

responses to frequencies between 100 and 1131 Hz with greatest sensitivity between 200 and 400 

Hz. Both studies using this newly developed methodology found that green and loggerhead sea 

turtles responded to a broader and higher range of frequency sensitivity than previously reported 

by Bartol et al. (1999), Bartol and Ketten (2006), and Ridgway et al. (1969) in air and at the 

water’s surface. 

Leatherback sea turtles are morphologically and physiologically unique among the sea turtle 

species. Dow Piniak et al. (2012) found leatherback sea turtle hatchlings are able to detect 

sounds underwater and in air, responding to stimuli between 50 and 1200 Hz in water and 50 and 

1600 Hz in air with maximum sensitivity between 100 and 400 Hz in water (84 dB re: 1 micro 

Pascal-rms at 300 Hz) and 50 and 400 Hz in air (62 dB re: 20 micro Pascal-rms at 300 Hz). 

Hearing sensitivity in both media declined considerably above 400 Hz. 

Explosions 

In-water explosions (e.g., TNT) produce a spherical shock wave with a large oscillating gas 

bubble which radiates sound. Some explosives have an instantaneous pressure rise-time followed 

by exponential decay, while the rise time for some may be longer, with a slower decay of the 

pulse (Urick 1983). The rise time is important because it affects the frequency signature of the 

explosion, with longer rise times having higher frequencies. Knowledge gaps inhibit the use of 

biological (fish kill) models to predict the risk to fish and other animals from the pressure wave 

generated by an explosion. Explosions are described by metrics such as amplitude, energy and 

time-space characteristics of the pressure wave (Popper et al. 2014). Explosions may result in not 

only sea turtle death (Klima et al. 1988), but acoustic annoyance, physical discomfort to soft 

tissue areas, and injurious effects (e.g., gastrointestinal injury, carapace damage) (Viada et al. 

2008). 

Seismic Airguns/Oil and Gas Exploration 

Offshore seismic surveys involve the use of high energy sound sources operated in the water 

column to probe below the seafloor. Most seismic sources involve the rapid release of 

compressed air to produce an impulsive signal. The signal is directed downward to the seabed, 

and reflected upwards again. The returned signal is received and processed to give profiles of the 

seafloor. This technique is essential for oil and gas exploration and development. Airguns are 

used as an acoustic source for seismic exploration. They produce an air bubble from a 

compressed air supply; the air bubble first expands rapidly, but has a slower rise time to peak 

pressure than with explosions. The sound impulse generated by a single airgun is omnidirectional 

with frequencies typically 20 to 50 Hz with declining energy at frequencies above 200 Hz. A 

study of ambient sound in the North Atlantic (Nieukirk et al. 2004) showed that airgun activity 

contributes significantly to ocean sound sound levels and can appear to be more continuous than 

impulsive sounds because of the reverberation from the surface and seabed. 

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McCauley et al. (2000) conducted trials with caged sea turtles and an approaching-departing 

single air gun to gauge behavioral responses of green and loggerhead sea turtles. Their findings 

showed behavioral responses to an approaching air gun array at 166 dB re: 1 micro Pascal rms 

and avoidance around 175 dB re: 1 micro Pascal rms. From measurements of a seismic vessel 

operating 3D air gun arrays in 100 to 120 meters water depth this corresponds to behavioral 

changes at around 2 kilometers and avoidance around 1 kilometer. Sea turtle habitats mostly 

occur in shallower water, often less than 20 meters deep. The propagation of an air gun array in 

such water depths may be vastly different than that for the array measured in 120 meter water 

depth. One would generally expect that sound propagation in water less than 20 meters deep 

would be significantly worse, that is the signal would not carry as far. But under some 

circumstances dictated by the seabed properties, this may not be so. Avoidance behavior and 

physiological responses from airgun exposure may affect the natural behaviors of sea turtles 

(McCauley et al. 2000). 

Oil and gas exploration and extraction presently occurs in many important sea turtle nesting and 

foraging habitats and generates high-intensity, low-frequency, impulsive sounds within the 

leatherback hearing range. In a report prepared for the International Association of Oil and Gas 

Producers Exploration and Production Sound and Marine Life Joint Industry Project, leatherback 

sea turtles are shown to be present in eleven of the thirteen oil and gas industry offshore interest 

areas (Thorson et al. 2005). The explosive removal methods of offshore structures in the marine 

environment can impact sea turtles, as discussed above. Even with protective measures in place, 

there have been observations of sea turtles affected by explosive platform removals (Viada et al. 

2008). 

Pile Driving 

Pile driving is commonly used for the construction of foundations for a large number of 

structures including bridges, buildings, retaining walls, harbor facilities, offshore wind turbines, 

and offshore structures for the oil and gas industry. It always involves multiple strikes over an 

extended period of time, with an average strike interval of 1.0 to 1.5 seconds. Pile driving can 

generate sounds into the water column if the pile is driven in water or on land near water. The 

impulsive sounds generated by impact pile driving are characterized by a relatively rapid rise 

time to a maximal pressure value followed by a decay period that may include a period of 

diminishing, oscillating maximal and minimal pressures (Illingworth and Rodkin 2001; 

Illingworth and Rodkin 2007; Reyff 2012). Peak levels resulting from impact pile driving vary 

substantially and depend on numerous factors such as pile type and diameter, hammer size, and 

substrate. The predominant energy in pile impact impulses is at frequencies below approximately 

2000 Hz with most occurring below 1000 Hz (Laughlin 2006; Reyff 2008; Reyff 2012). 

Impact pile driving occurs over small spatial and temporal scales and produces high-intensity, 

low-frequency, impulsive sounds with high peak pressures that can be detected by sea turtles 

(Dow Piniak et al. 2012). Peak sound pressure levels are useful for characterizing pile driving 

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strikes, but do not account for the total energy of the sound. Vibratory pile driving produces a 

continuous sound with peak pressures lower than those observed in impulses generated by 

impact pile driving (Popper et al. 2014). 

Active Sonar 

Active sonar and echo sounders are in operation throughout the world’s oceans as well as in 

freshwater lakes and rivers. The primary sonar characteristics that vary with application are the 

frequency band, signal type (pulsed or continuous), rate of repetition, and source level. They can 

be roughly divided into three categories depending on their primary frequency of operation; low 

frequency for 1 kHz and less, mid frequency for 1 to 10 kHz, and high frequency for 10 kHz and 

greater. Low, and possibly mid, frequency sonars are most relevant to fishes and sea turtles 

because of the low frequency hearing ranges of these animals. Sonar usually operates with duty 

cycles below 10 to 20 percent and with generally brief durations. However, multipath 

propagation can often be substantial for many of these systems, effectively prolonging the sonar 

sounds well beyond their nominal durations. Low frequency systems are designed for long-range 

detection (Popper et al. 2014). For example, the U.S. Navy SURTASS Low Frequency Active 

system is described by Friedman (2006) as a vertical line array of 18 elements operating between 

100 and 500 Hz. Signals projected include combinations of swept frequency and tones pulses, 

totaling up to 100 seconds in length with individual signals of the order of 10 seconds. The 

interval between transmissions varies between 6 and 15 minutes. Naval sonar also occurs 

intermittently (although while active, the sound is continuous), and often in designated areas or 

ranges. However many of these areas/ranges provide habitat for sea turtles. 

While leatherback hatchlings appear to be capable of detecting low-frequency sonar (less than 

1000 Hz), frequencies for the peak sound pressure level for mid-frequency sonar (2000 to 8000 

Hz) appear out the range of sea turtle hearing sensitivity (Dow Piniak et al. 2012). However, 

Dow Piniak et al. (2012) did not expose leatherbacks to the high sound pressure levels of midfrequency sonar, and is possible that turtles are able to detect these higher frequencies at 

increased sound pressure levels. 

Offshore Wind Farms 

The construction of offshore wind farms generates high-intensity sounds (pile driving). In this 

case, the spatial and temporal scales of pile driving could be quite large, as offshore wind farms 

can span tens of kilometers and require many months to install. However once in place, turbines 

generate continuous, moderate levels of low frequency sound that can be detected by leatherback 

sea turtles. Depending on environmental variables (wind speed) and turbine type, leatherbacks 

are unlikely to be able to detect these sounds at large distances away from the source, however 

wind farms could disrupt leatherback behavior or habitat use depending on their placement (Dow 

Piniak et al. 2012). 

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Continuous Sound Sources 

The most common and best-studied continuous sounds in the oceans are those produced by ships 

as well as smaller vessels. However, continuous sounds are also produced by other sources, such 

as vibratory pile drivers and vessels dredging for aggregates (Robinson et al. 2011). In addition, 

over long distances, emissions from seismic surveys or impact pile driving may appear to be 

continuous as a result of multipath effects. 

Shipping noise is a combination of the relatively continuous sound generated by large ocean 

tankers and more intermittent sounds generated by local inshore boat traffic. The frequency and 

sound pressure level of individual vessels varies widely by overall size, and engine and propeller 

size and configuration. The low-frequency sound created by commercial shipping can be heard 

in every ocean of the world and can be detected by leatherback sea turtles. Areas of high use by 

commercial vessels (e.g., inshore ports and shipping lanes), and those used by recreational 

vessels (e.g., nearshore waters and inshore ports) overlap with sea turtle reproductive and 

foraging habitat at many locations. 

The sounds of vessels are predominately low frequency (i.e., below 1 kilohertz) from onboard 

machinery, hydrodynamic flow around the hull, and from propeller cavitation, which is typically 

the dominant source of sound (Ross 1987; Ross 1993). Estimated source levels can range from 

less than 150 dB to over 190 dB (re 1 mico Pascal-rms at 1 meter) for the largest commercial 

vessels (Arveson and Vendittis 2000; Hildebrand 2009; McKenna et al. 2012; Richardson et al. 

1995). Low frequency sounds from larger vessels can travel hundreds of kilometers and can 

increase ambient noise levels over large areas of the ocean, interfering with sound 

communication in species using the same frequency range (see Southall (2005)). Samuel et al. 

(2005) recorded levels of up to 113 dB re: 1 micro Pascal (200 to 700 Hz) for small, recreational 

boats during high-use seasons in juvenile loggerhead, green and Kemp’s ridley sea turtle habitat 

in the Peconic Bay Estuary system in Long Island, New York. While these levels may not 

directly damage hearing, they may mask important auditory cues. Tens of thousands of large 

commercial vessels are typically underway at any point in time, concentrated in high-traffic sea 

lanes and ports, presenting an effectively continuous noise source in many parts of the ocean. 

The number of large commercial ships has doubled between 1965 and 2003 to nearly 100,000. 

Shipping industry analysts have forecast that the volume of cargo shipped will again double or 

triple by 2025, with an expected attendant increase in the amount of ambient noise entering the 

ocean from commercial shipping (NRC 2003). In much of the northern hemisphere, shipping 

noise is the dominant source of underwater noise below 300 Hz (Ross 1987; Ross 1993). Vessel 

operations have increased over time and as a result have increased low-frequency ambient noise 

levels in some areas (Andrew et al. 2002; Curtis et al. 1999; McDonald et al. 2006; NRC 2003). 

One of the most serious implications of this increase in shipping noise is the impact it may have 

in masking sounds of biological importance. 

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7.8 Disease 

Fibropapillomatosis is a neoplastic disease that can negatively impact ESA-listed sea turtle 

populations. FP has long been present in sea turtle populations with the earliest recorded mention 

from the late 1800s in the Florida Keys (Hargrove et al. 2016). FP has been reported in every 

species of marine turtle but is of greatest concern in green turtles, the only known species where 

this disease has reached a panzootic status (Williams Jr et al. 1994). Historical data indicate that 

the disease rose in prevalence most noticeably in the 1980s. Prevalence rates as high as 45 to 50 

percent have been reported within some local green turtle populations (Hargrove et al. 2016; 

Jones et al. 2015). FP primarily affects medium-sized immature turtles in coastal foraging 

pastures. 

FP is characterized by both internal and external tumorous growths, which can range in size from 

very small to extremely large. Large tumors can interfere with feeding and essential behaviors, 

and tumors on the eyes can cause permanent blindness (Foley et al. 2005). Renan de Deus Santos 

et al. (2017) assessed stress responses (corticosterone, glucose, lactate, and hematocrit) to 

capture and handling in green sea turtles with different FP severity levels. Their findings suggest 

that moderate FP severity may affect a turtle’s ability to adequately feed themselves (as 

evidenced by poor body condition), and advanced-stage FP severity may result in an impaired 

corticosterone response. While FP can result in reduced individual fitness and survival, 

documented mortality rates in Australia and Hawaii are low. The mortality impact of FP is not 

currently exceeding population growth rates in some intensively monitored populations (e.g., 

Florida and Hawaii in the U.S., and the Southern Great Barrier Reef stock in Queensland, 

Australia) as evidenced by increasing nesting trends despite the incidence of FP in immature 

foraging populations (Hargrove et al. 2016). Recovery from FP through natural processes has 

been documented in cases where the affliction is not too severe. Despite some conflicting 

conclusions, the overwhelming consensus among turtle researchers is that, at present, FP does 

not significantly impact the overall survival of sea turtle populations (Hargrove et al. 2016). 

However, FP cannot be discounted as a potential threat to sea turtle populations (particularly 

green turtles) as the distribution, prevalence rate, severity, and environmental co-factors 

associated with the disease have the capacity to change over time (Jones et al. 2015). 

Environmental factors likely play a role in the development of FP. Most sites with a high 

frequency of FP tumors are areas with some degree of water quality degradation resulting from 

altered watersheds (Hargrove et al. 2016). Chemical contaminants which can affect sea turtle 

immune systems may be part of a multifactorial problem that leads to FP (Herbst 1994). An 

increased concentration of arginine in the diet of green turtles as a result of invasive macroalgae 

blooms has also been linked to an increasing prevalence of the disease (Van Houtan et al. 2010). 

Water temperature may also be a factor in lesion development and growth rate as warmer water 

temperatures during summer have been shown to promote lesion growth in some regions (Jones 

et al. 2015). Natural biotoxins have also been implicated as a co-factor involved in FP 

development. Despite there being a strong positive correlation between the prevalence of FP in 

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green turtle populations and areas with degraded water quality, it is difficult to identify one 

specific causal contaminant or a combination of such working synergistically to lead to FP 

formation. 

Expression of FP differs across ocean basins and to some degree within basins (Hargrove et al. 

2016). Turtles in the Southeast U.S., Caribbean, Brazil, and Australia rarely have oral tumors, 

whereas such tumors are common and often severe in Hawaiian turtles. Internal tumors (on vital 

organs) have been found in turtles from the Atlantic and Hawaii, but are only rarely reported in 

Australia. Liver tumors appear to be common in Florida, but are not reported from Hawaii 

(Hargrove et al. 2016). 

Fish diseases and parasitic organisms occur naturally in the water. Many fish species are highly 

susceptible to parasites and disease, particularly during early life stages. Native fish have coevolved with such organisms and individuals can often carry diseases and parasites at less than 

lethal levels. While disease organisms commonly occur among wild fish populations, under 

favorable environmental conditions these organisms are not expected to cause populationthreatening epizootics. However, outbreaks may occur when stress from disease and parasites is 

compounded by other stressors such as diminished water quality, flows, and crowding (Guillen 

2003; Spence and Hughes 1996). At higher than normal water temperatures fish species may 

become stressed and lose their resistance to diseases (Spence and Hughes 1996). Consequently, 

diseased fish become more susceptible to predation and are less able to perform essential 

functions, such as feeding, swimming, and defending territories (McCullough 1999). The 

introduction of non-indigenous fish pathogens to wild fish populations through aquaculture 

operations also represents a threat to some fish populations. The aquarium industry is another 

possible source for transfer of non-indigenous pathogens or non-indigenous species from one 

geographic area to another, primarily through release of aquaria fish into public waters. 

Salmonids are susceptible to numerous bacterial, viral, and fungal diseases. The more common 

bacterial diseases in New England waters include furunculosis, bacterial kidney disease, enteric 

redmouth disease, coldwater disease, and vibriosis (Egusa and Kothekar 1992; Olafesen and 

Roberts 1993; USFWS and Gaston 1988). Furunculosis, which is particularly widespread, can be 

a significant source of mortality in wild Atlantic salmon populations if river water temperatures 

become unusually high for extended periods (USFWS and Gaston 1988). Whirling disease is a 

parasitic infection caused by the microscopic parasite Myxobolus cerebrali. Infected fish 

continually swim in circular motions and eventually expire from exhaustion. The disease occurs 

both in the wild salmonids and in hatcheries. Saprolegnia is a fungal disease of Atlantic salmon 

and is primarily found in adult males. It invades the epidermis and is associated with the 

presence of high levels of androsteroids (Olafesen and Roberts 1993; USFWS and Gaston 1988). 

In 1996, the first occurrence of the infectious salmon anemia (ISA) virus in North America was 

found in an aquaculture facility in New Brunswick, Canada (Fay et al. 2006b). The first outbreak 

of ISA in the United States was reported in 2001 in an aquaculture facility in Cobscook Bay, 

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Maine. Approximately 925,000 fish were removed from aquaculture pens throughout the Bay 

that year, and eventually all cultured salmon in the Bay had to be removed (Fay et al. 2006b). 

While captive fish have the highest risk for transmission and outbreaks of diseases such as ISA, 

wild fish that must pass near aquaculture facilities are at risk of encountering both parasites and 

pathogens from hatchery operations. Although substantial progress has been made in recent 

years to reduce the risks to wild fish posed by aquaculture, this remains a potential threat. 

There are over 30 identified parasites of Atlantic salmon including external parasites such as gill 

maggot, freshwater louse, and leech, and internal parasites such as trematodes (flukes), cestodes 

(tapeworms), acanthocephalans (spiny-headed worms) and nematodes (round worms) (Hoffman 

1999; Scott and Scott 1988). Several species of sea lice, a marine ectoparasite found in Atlantic 

and Pacific coastal waters, can cause deadly infestations of farm-grown salmon and may also 

affect wild salmon. 

There have been very few incidences of disease in wild populations of sturgeon species and most 

disease related mortality has been documented in captive rearing facilities (SSSRT 2010). While 

some disease organisms have been identified from wild Atlantic sturgeon, they are unlikely to 

threaten the survival of the wild populations (ASSRT 2007). Parasites, including flatworms and 

roundworms, have been documented in Atlantic sturgeon but are not considered a threat to 

populations of this species. Thirteen taxa of parasites have been identified in shortnose sturgeon 

including four coelenterates, two nematodes, three leeches, one arthropod, and the sea lamprey. 

The degree of parasite infestation is believed to be quite low and, in general, shortnose sturgeon 

do not appear to be harmed by these parasites (SSSRT 2010). Parasites are known to occur in 

both wild-caught and cultivated Nassau grouper, predominantly in the viscera and gonads. These 

include encysted larval tapeworms, nematode, isopods, and trematodes (Manter 1947; Thompson 

and Munro 1978). However, the impact of parasites on populations of Nassau grouper is largely 

unknown. 

There are no studies indicating that diseases or parasitism represent a threat factor for 

populations of green sturgeon or Gulf sturgeon (USFWS and NMFS 2009). There is also no 

information to indicate that disease is a factor affecting populations of scalloped hammerhead 

(Miller et al. 2014) or smalltooth sawfish (NMFS 2010c). Like most sharks, scalloped 

hammerheads likely carry a range of external parasites including leeches and copepods but there 

are no studies suggesting parasites are negatively affecting the fitness or survival of this species 

(Miller et al. 2014). 

7.9 Industrial and Power Generating Plants 

Industrial and power generating plants (e.g., hydro, steam, coal, nuclear) located within the 

action area can adversely affect ESA-listed species including sturgeon, salmon, sawfish and sea 

turtles. Stressors caused by these operations include impingement and entrainment, thermal 

discharges, chemical discharges, and the indirect effect of prey reduction. Impingement occurs 

when organisms are trapped against cooling water intake screens, racks, or removal equipment 

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by the force of moving water. Adult, juvenile, and larval sturgeon are known to be killed or 

injured due to impingement on cooling water intake screens (Dadswell et al. 1984; Hoff and 

Klauda 1979). Sea turtles entering coastal or inshore areas can also be affected by impingement 

in such systems. There is limited information on power plant impingement rates for sea turtles. 

Based on long-term monitoring data for the past 40 years, an average of 415 sea turtles were 

captured per year near the nuclear power plant in St. Lucie, Florida. Operation of this power 

plant has resulted in about seven turtle mortalities per year over this time period, mostly 

loggerheads and greens (NMFS 2016a). Entrainment occurs when marine organisms enter the 

intake water flow and pass through the cooling water intake structure and into a cooling water 

system. While sea turtles and adult sturgeon, salmon and sawfish are too large to be entrained, 

early life stages of ESA-listed fish species (e.g., eggs and larvae) are potentially susceptible to 

power plant entrainment. 

Some power plants use “once-through-cooling” technology that withdraws large volumes of 

water from adjacent oceans, bays and rivers, pumps the water through the plant to cool the 

reactors, and then discharges the heated water back to rivers. There are approximately 550 

“once-through-cooling” power plants currently operating in the U.S. (Turner-Tomaszewicz and 

Seminoff 2012). Cooling water discharge can alter habitat around the outflow pipe. Some discharges 

have been measured as high as 46 degrees Celsius (Hester and Doyle 2011). This can potentially 

present both advantages (e.g., provide thermal refuge from cold water temperatures that may stun sea 

turtles and allow for unseasonal growth of marine plants that green sea turtles may forage upon) and 

disadvantages (e.g., alter normal ecological processes that sea turtles and fish rely upon and result in 

individuals depending on unnatural conditions that can be problematic if a plant is decommissioned 

or goes offline) for ESA-listed species. Sturgeon experience lower survival when water 

temperatures exceed 28 degrees Celsius (Niklitschek and Secor 2005). Increases in water 

temperature have also been shown to increase the susceptibility of sturgeon to hypoxia (Secor 

and Niklitschek 2001). Simpfendorfer and Wiley (2004) reported the occurrence of smalltooth 

sawfish in the warm water outfalls of power stations in Florida during the coldest time of year. 

They postulate that this potentially represents the use by sawfish of power plant outfall areas as 

thermal refugia; alternatively, sawfish may become trapped in the warm water outflow as 

surrounding temperatures decline below their tolerance level (Simpfendorfer and Wiley 2004). 

Chemical discharges from cooling water intake structure may include radionuclides such as 

tritium, strontium, nickel, and cesium. Chlorine, lithium hydroxide, boron, and total suspended 

solids may also be discharged from cooling water intake structures. 

Recent regulations have been implemented by the U.S. Environmental Protection Agency 

(USEPA) to reduce the risk of jeopardizing the continued existence of federally-listed species 

due to the impact of impingement and entrainment of cool water intakes at industrial facilities. 

Specifically, the USEPA promulgated a Clean Water Act section 316(b) regulation on August 

15, 2014, establishing standards for cooling water intake structures (79 FR 48300-439 2015) and 

mandating the best technology available to reduce impingement and entrainment of aquatic 

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organisms. As the rule is implemented it will include a number of provisions designed to reduce 

and monitor the take of ESA-listed species at the cooling water intakes. 

7.10 Dredging 

Riverine, nearshore, and offshore coastal areas are often dredged to support commercial 

shipping, recreational boating, construction of infrastructure, and marine mining. Dredging in 

spawning and nursery grounds modifies habitat quality, and limits the extent of available habitat 

in some rivers where anadromous fish habitat has already been impacted by the presence of 

dams. Dredging and filling operations impact important habitat features of Atlantic sturgeon as 

they disturb benthic fauna, eliminate deep holes, and alter rock substrates (Smith and Clugston 

1997). Dredging operations may also pose risks to anadromous fish species by destroying or 

adversely modifying benthic feeding areas, disrupting spawning migrations, and filling spawning 

habitat with resuspended fine sediments. As benthic omnivores, sturgeon are particularly 

sensitive to modifications of the benthos that affect the quality, quantity and availability of prey 

species. Nellis et al. (2007) documented that dredge spoil drifted 12 kilometers downstream over 

a ten-year period in the Saint Lawrence River, and that those spoils have significantly less 

macrobenthic biomass compared to control sites. Hatin et al. (2007) reported avoidance behavior 

by Atlantic sturgeon during dredging operations and McQuinn and Nellis (2007) found that 

Atlantic sturgeon were substrate dependent and avoided dredge spoil dumping grounds. Indirect 

effects of dredging related to water quality include changes in DO and salinity gradients in and 

around dredged channels (Campbell and Goodman 2004; Jenkins et al. 1993; Secor and 

Niklitschek 2001). Adult shortnose sturgeon can tolerate at least short periods of low DO and 

high salinities, but juveniles are less tolerant of these conditions in laboratory studies. Collins et 

al. (2000) concluded harbor modifications in the lower Savannah River have altered 

hydrographic conditions for juvenile sturgeon by extending high salinities and low DO upriver. 

In addition to indirect impacts, hydraulic dredging can directly harm sturgeon and sea turtles by 

lethally entraining fish up through the dredge drag-arms and impeller pumps. Large marine 

animals that are entrained in hydraulic dredges rarely survive the encounter. Hopper dredges, in 

particular, are capable of moving relatively quickly compared to turtles and fish which can be 

overtaken and entrained by the suction draghead of the advancing dredge. A total of 609 

incidental takes (lethal or sublethal interactions) of sea turtles have been documented from 

hopper dredging activities in the southeastern U.S. from 1980 through 2006 (Dickerson et al. 

2007). Dickerson (2006) reported 15 Atlantic sturgeon taken in dredging activities conducted by 

the United States Corps of Engineers from 1990 to 2010, most captured by hopper dredge. 

Notably, these reports include only those trips when an observer was on board to document 

capture. Atlantic sturgeon have also been taken in both hydraulic pipeline and bucket-and-barge 

operations in the Cape Fear River, North Carolina (Moser and Ross 1995), and by mechanical 

dredges in the Delaware River (Hastings 1983). 

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Reductions in entrainment rates for sea turtles have been achieved through gear modifications, 

operational changes, time-area restrictions, and the capture and relocation of turtles away from 

dredge sites (Dickerson et al. 2007). Dickerson et al. (2007) studied the effectiveness of turtle 

relocation trawling in reducing the incidental take of sea turtles in hopper dredge operations. 

They found that relocation trawling can be an effective management option provided that a 

substantial amount of trawling effort is conducted either at the onset of dredging or early in the 

project. 

7.11 Hydromodification 

Hydromodification is generally defined as a change in natural channel form, watershed 

hydrologic processes and runoff characteristics (i.e., interception, infiltration, overland flow, 

interflow and groundwater flow) associated with alterations in stream and rivers flows and 

sediment transport due to anthropogenic activities. Such changes often result in negative impacts 

to water quality, quantity, and aquatic habitats. 

7.11.1 Dams 

Dams are used to impound water for water resource projects such as hydropower generation, 

irrigation, navigation, flood control, industrial and municipal water supply, and recreation. Dams 

can also have profound effects on anadromous fish species by fragmenting populations, 

impeding access to spawning and foraging habitat, and altering natural river hydrology and 

geomorphology, water temperature regimes, and sediment and debris transport processes 

(Pejchar and Warner 2001; Wheaton et al. 2004). The loss of historic habitat can ultimately 

affect anadromous fish in two ways: 1) it forces fish to spawn in sub-optimal habitats that can 

lead to reduced reproductive success and lower recruitment, and 2) it reduces the carrying 

capacity (physically) of these species and affects the overall health of the ecosystem (Patrick 

2005). Physical injury and direct mortality occurs as fish pass through turbines, bypasses, and 

spillways. Other effects of passage through dam structures may include disorientation, stress, 

delay in passage, exposure to high concentrations of dissolved gases, elevated water 

temperatures, and increased vulnerability to predation. Activities associated with dam 

maintenance, such as dredging and minor excavations along the shore, release silt and other fine 

river sediments that can be deposited in nearby spawning habitat. Dams can also reduce habitat 

diversity by forming a series of homogeneous reservoirs; these changes generally favor different 

predators, competitors and prey, than were historically present in the ecosystem (Auer 1996). 

The suitability of riverine habitat for sturgeon and salmon spawning and rearing depends on 

annual fluctuations in water flow, which can be greatly altered or reduced by the presence and 

operation of dams (Cooke and Leach 2004; Jager et al. 2001). Effects on spawning and rearing 

may be most dramatic in hydropower facilities that operate in peaking mode (Auer 1996; Secor 

and Niklitschek 2002). Daily peaking operations store water above the dam when demand is low 

and release water for electricity generation when demand is high, creating substantial daily 

fluctuations in flow and temperature regimes. Kieffer and Kynard (2012) reported extreme flow 

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fluctuations for hydroelectric power generation on the Connecticut River affected access to 

shortnose sturgeon spawning habitat, possibly deterred spawning, and left rearing shoals either 

completely scoured during high flows or dry and exposed during low flows. 

Obstructed fish passage and degraded habitat caused by dams is considered the greatest 

impediment to self-sustaining anadromous fish populations in Maine (NRC 2004). GOM DPS 

Atlantic salmon are not well adapted to the artificially created and maintained impoundments 

resulting from dam construction (NRC 2004). Other aquatic species that thrive in impounded 

riverine habitat have proliferated and significantly altered the prey resources available to salmon, 

as well as the abundance and species composition of salmon competitors and predators. The 

National Inventory of Dams Program lists 639 dams (over four feet high) in Maine, over half of 

which are located within the range of the GOM DPS (USACOE National Inventory of Dams 

Program, http://nid.usace.army.mil/cm_apex/f?p=838:12). The larger hydroelectric dams and 

storage projects within the GOM DPS are primarily located in the Penobscot, Kennebec, and 

Androscoggin watersheds. With the exception of several of the licensed West Branch Penobscot 

dams, and three unlicensed storage dams on the East Branch Penobscot, all of the larger dams in 

the basin are licensed to operate solely in a “run-of-the-river” mode, which means inflow 

generally equals outflow. GOM DPS salmon habitat is also degraded as a result of bypassed 

reaches of natural river channels that re-route river flows within the Penobscot, Kennebec, and 

Androscoggin watersheds through forebays or penstocks. Many smaller dams still remain on 

smaller rivers and streams within the GOM DPS range. While most small dams do not generate 

hydroelectricity, many continue to impact substantial amounts of Atlantic salmon spawning and 

rearing habitat. 

The detrimental effects of dams on populations of shortnose and Atlantic sturgeon are generally 

well documented (Cooke and Leach 2004; Kynard 1998). Perhaps the largest impact dams have 

on sturgeon is the loss of upriver spawning and rearing habitat. Migrations of sturgeon in rivers 

without barriers are wide-ranging with total distances exceeding 200 kilometers or more, 

depending on the river system (Kynard 1997). Although some rivers have dams constructed at 

the fall line that have not impacted sturgeon spawning, in many other rivers dams have blocked 

sturgeon upriver passage, restricting spawning activities to areas below the impoundment and 

leaving sturgeon vulnerable to perturbations of natural river conditions at different life stages 

(Cooke and Leach 2004; Kynard 1997). Observations of sturgeon spawning immediately below 

dams further suggests that they are unable to reach their preferred spawning habitat upriver. 

Overall, 91 percent of historic Atlantic sturgeon habitat seems to be accessible, but the quality of 

the remaining portions of habitat as spawning and nursery grounds is unknown, therefore 

estimates of percentages of availability do not necessarily equate to functionality (ASSRT 2007). 

Thus, dams may one of the primary causes of the extirpation of sturgeon subpopulations on the 

east coast. 

On the west coast, green sturgeon spawning areas have been lost or significantly altered by 

dams. The final rule listing Southern DPS green sturgeon indicates that the principle factor in the 

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decline of this DPS is the reduction of spawning to a limited area, due largely to impassable 

barriers on the Sacramento River (Keswick Dam) and the Feather River (Oroville Dam) (71 FR 

17757; April 7, 2006). The Southern DPS of green sturgeon are currently concentrated into one 

spawning area outside of their natural habitat in the Sacramento River, making them vulnerable 

to catastrophic extinction (Adams et al. 2007). 

Despite decades of effort, fish passage infrastructure retrofitted at hydroelectric dams has largely 

failed to restore anadromous fish to historical spawning habitat (Brown et al. 2013). While 

improvements to fish passage are often required when hydroelectric dams go through Federal 

Energy Regulatory Commission relicensing, the relicensing process occurs infrequently, with 

some licenses lasting up to 50 years. Over 95 percent of dams on the eastern seaboard are not 

hydroelectric facilities, and are thus not subject to continual relicensing or fish passage 

improvement measures (ASMFC 2008). Sturgeon appear unable to use some fishways (e.g., 

ladders) but have been transported in fish lifts (Kynard 1998). Data on the effects of the fish lift 

at the Holyoke Hydroelectric Project on the Connecticut River suggest that fish lifts that 

successfully attract other anadromous species (i.e., shad, salmon etc.) do a poor job of attracting 

sturgeon: attraction and lifting efficiencies for shortnose sturgeon at the Holyoke Project are 

estimated around 11 percent (ASSRT 2007). 

7.11.2 Water Diversions 

Like many regions throughout the world, the U.S. is experiencing increasing demand for fresh, 

clean water. Population growth and agricultural needs frequently conflict with water availability. 

The twentieth century saw tremendous increases in dam construction, irrigation practices for 

agriculture, recreational use of waterbodies, and the use of waterways for waste disposal, both 

sanitary and industrial. Water use in the western U.S. presents a particular concern because the 

western states are characterized by low precipitation and extended periods of draught. 

The withdrawal of large volumes of water from rivers for multiple uses can have direct and 

indirect impacts on fish species. The amount and extent of water withdrawals or diversions for 

agriculture impacts streams and their inhabitants by reducing water flow/velocity and DO levels, 

which can have negative effects on listed species and their designated critical habitat. Water 

diversions and withdrawals for agricultural irrigation or other purposes can directly impact fish 

populations by constraining available spawning and rearing habitat. Adequate water quantity and 

quality are critical to all salmonid life stages, especially adult migration and spawning, fry 

emergence, and smolt emigration. Low flow events may delay anadromous fish migrations or 

lengthen fish presence in a particular water body until favorable flow conditions permit fish 

migration along the migratory corridor or into the open ocean. Survival of eggs, fry, and 

juveniles are also mediated by streamflow. Water withdrawals may dewater redds thus reducing 

egg survival. Other potential detrimental impacts of water diversions include increases in 

nutrient loading, sediments (from bank erosion), and water temperature. Flow management, in 

combination with the effects of climate change (i.e., droughts), has further decreased the delivery 

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of suspended particulate matter and fine sediment to estuaries. Low river flows may constrain 

conditions necessary for important salmonid refuge habitat (shade, woody debris, overhanging 

vegetation), making fish more vulnerable to predation, elevated temperatures, crowding, and 

disease. 

Juvenile sturgeon and salmon are also susceptible to entrainment through unscreened agricultural 

water-diversion pipes lining levees and riverbanks. Mussen et al. (2014) found that green 

sturgeon, in particular, were not as adept at avoiding entrainment as some other species due to 

their poor ability to detect the flow acceleration and directional changes near the pipe inlet. Data 

on entrainment of Southern DPS green sturgeon is limited. In the final listing rule, the threat 

posed by juvenile entrainment to the continued existence of the Southern DPS was considered to 

be uncertain (71 FR 17757). Although the actual number entrained in water diversions is 

unknown, with over 3,300 water diversions operating in the Sacramento-San Joaquin watershed 

(a large majority of which are unscreened) this represent a potentially major threat to outmigrating juvenile green sturgeon (Mussen et al. 2014). Entrainment risk is further increased 

because the downstream migration of juvenile green sturgeon (May to August) coincides with 

peak agricultural water extraction in this watershed. Green sturgeon entrainment has been 

reported at pumping operations at the state and federal water export facilities in the SacramentoSan Joaquin River Delta. From 1986 through 2001, an estimated 79 green sturgeon have been 

killed annually at these two facilities combined (Adams et al. 2007). 

Water withdrawal may impact Atlantic salmon habitat in the main stem areas of the Penobscot, 

Kennebec, and Androscoggin Rivers. Because of the large size of these watersheds there are a 

variety of consumptive water uses, including municipal water supplies, snow making, mills, golf 

course and agricultural irrigation, and industrial cooling. Depending upon the location of current 

water uses, impacts to Atlantic salmon habitat may be occurring in headwater areas and 

tributaries of these watersheds (Fay et al. 2006b). 

Diversion of freshwater run-off in the southeastern U.S. has contributed to the decline of 

smalltooth sawfish. Construction of a 1,400 mile network of canals, levees, locks, and other 

water control structures that modulate freshwater flow have had profound impacts on 

hydrological regimes in south Florida (Serafy et al. 1997). Sawfish are now either extirpated or 

severely depleted in areas where they were once considered abundant due to the destruction and 

modification of their habitat. 

7.12 Scientific Research and Enhancement Permits 

Information obtained from scientific research is essential for understanding the status of ESAlisted species, obtaining specified critical biological information, and achieving species recovery 

goals. Research on ESA-listed species is granted an exemption to the ESA take prohibitions of 

section 9 through the issuance of section 10(a)(1)(A) permits. Research activities authorized 

through scientific research permits can produce various stressors on wild and captive animals 

resulting from capture, handling, and research procedures. As required by regulation, research 

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conducted under a section 10(a)(1)(A) research permit cannot operate to the disadvantage of the 

species. Scientific research permits issued by NMFS are conditioned with mitigation measures to 

ensure that the impacts of research activities on target and non-target ESA-listed species are as 

minimal as possible. Section 10(a)(1)(A) permits are also issued to research facilities and 

educational display facilities for the captive research and educational display of ESA-listed 

species. 

7.12.1 Sea Turtle Research 

Currently there are 41 Section 10(a)(1)(A) scientific research permits that authorize the study of 

sea turtles. Three of these permits are solely for the receipt and study of sea turtle parts for 

purposes such as cell line development; they do not authorize take of live animals. Thirty permits 

authorize research on live animals in Atlantic waters (including the Gulf of Mexico and 

Caribbean) and eight authorize research in Pacific waters (see Appendix E for locations of active 

sea turtle research permits as of June 30, 2017). Permits for study of wild animals authorize take 

of post-hatchling through adult life stages. On average, from 2007 to 2017 approximately 2,370 

turtle (all species) takes were reported within the program in any given year. This includes an 

annual average of 831 sea turtles taken by capture with subsequent procedures, 157 sea turtles 

taken by conducting procedures only (i.e., capture authorized through different permit), and 

1,382 sea turtles taken only during remote surveys. Both authorized and reported take numbers 

for remote survey methods are expected to decrease significantly as a result of the 2016 NMFS’ 

Interim Guidance on the ESA Term Harass (NMFS 2016c). The most commonly authorized sea 

turtle capture methods in research permits from 2007-2017 were hand and/or dip nets and tangle 

nets (Figure 48). Average annual reported captures over this time frame, by species and capture 

method, are shown in Table 20. Permits 

Figure 48. Frequency of Capture Methods Authorized in Sea Turtle Research Permits 

from June 2007 to May 2017 (N = 43 permits). 

30 

25 

20 

15 

10 

5 

0 

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Mortality is rarely authorized by the Permits Division in sea turtle research permits. Five permits, 

all for research in the Atlantic ocean basin, authorize lethal take between 2007 and 2017. By 

capture gear, the reported mortalities of green and Kemp’s ridley (four combined) over the past 

ten years were turtles captured in pound nets; the one loggerhead reported mortality was from 

trawl gear. In addition to the lethal takes shown in Table 21, there was one other permit (Permit 

No. 15315) that authorized a relatively high number of sea turtle lethal takes to conduct a shortterm study evaluating an experimental tangle net design in North Carolina waters. This permit 

authorized the lethal take of five Kemp’s ridley, 15 green, and five loggerhead sea turtles over 

the 19-month life of the permit. This permit was considered exceptional because it authorized 

methods that did not adhere to the standard mitigation measures and procedures (e.g., night 

sampling and unattended tangle nets) for capture of sea turtles. Two Kemp’s ridleys and two 

green turtles died during this study. 

Table 20. Average annual reported captures by turtle species and capture method from 

2007 to 2017. 

Species 

Sea Turtle Capture Method 

Hand 

or Dip Tangle Seine Cast Pound Trawl Breakaway Hoop 

Encircle 

Strike 

Green 293 302 15 71 8 4 8 20 

Hawksbill 68 12 < 1 12 < 1 < 1 2 0 

Kemp’s ridley 30 21 6 9 7 25 8 23 

Leatherback 1 1 1 1 1 1 3 0 

Loggerhead 110 40 15 31 18 78 28 6 

Olive ridley 0 0 0 0 0 0 0 0 

Most permits authorize a minimum set of standard procedures on all captured sea turtles 

including handling, examination, morphometrics, photography, marking, and skin biopsy. Other 

commonly requested procedures by turtle researchers include transmitter attachments, blood and 

tissue collection, and lavage. Less commonly requested research activities such as laparoscopy, 

imaging, ultrasound and tank-based studies have also been authorized on some permits 

depending on the particular study objectives. No deaths were reported as a result of a research 

procedure or the use of anesthesia, and no serious injuries have been reported during research 

over the last ten years. 

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Table 21. Number of lethal takes authorized and reported, by species, from June 2007 to 

July 2017. 

Species Authorized lethal take over 

duration of permit Reported Mortalities 

Green 6 2 

Hawksbill 3 0 

Kemp’s ridley 6 2 

Leatherback 4 0 

Loggerhead 13 1 

Olive ridley 2 0 

Unidentified/Any species 9 0 

Total 43 5 

7.12.2 Research on Other ESA-listed Species 

In addition to sea turtles, the Permits Division issues section 10(a)(1)(A) permits for research on 

other ESA-listed species considered in this opinion including Atlantic sturgeon, shortnose 

sturgeon and smalltooth sawfish. Since 2006, conservative mitigation measures implemented by 

NMFS through permit conditions (e.g., reduced soak times at warmer temperatures or lower DO 

concentrations, minimal holding or handling time) and additional precautions taken by sturgeon 

researchers have significantly reduced the lethal and sublethal effects of capture in gill, trammel 

and trawl nets on Atlantic and shortnose sturgeon. From 2006 through 2016, researchers reported 

only two shortnose sturgeon killed by capture gear out of 7,019 captured, for a capture mortality 

rate of 0.03 percent. Since they were listed in 2012, the mortality rate associated with Atlantic 

sturgeon capture in scientific research is 0.22 percent (14 killed out of 6,466 captured). In 2017 

the Permits Division implemented a program for the issuance of permits for research and 

enhancement activities on Atlantic sturgeon and shortnose sturgeon. A section 7 programmatic 

consultation biological opinion determined that this action would not likely jeopardize the 

continued existence of ESA-listed species and would not likely result in the destruction or 

adverse modification of critical habitat. In addition to the required mitigation measures designed 

to reduce lethal take and sub-lethal effects on sturgeon, the Program establishes annual limits on 

sturgeon mortality resulting from research activities by subpopulation (i.e., spawning stock) and 

life stage. Relative mortality limits are calculated as a proportion of the estimated population size 

and are based on the relative health of the population. A health index is calculated by NMFS 

based on the best available information on the population including abundance, population 

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trends, known threats, and information on spawning activity. For adults/subadults and juveniles, 

relative annual maximum mortality limits are set at 0.4, 0.6, and 0.8 percent of the estimated 

population size for sturgeon populations with a health index rating of “low,” “medium,” and 

“high,” respectively. For populations where there is insufficient information to calculate a health 

index or there is no estimate of population size, the default maximum mortality limit is 

conservatively established at one fish per year. Maximum annual mortality limits can be 

exceeded in any given year by up to two times (i.e., 2X), as long as the five-year moving average 

is within the established maximum annual mortality limit for that population and life stage. 

There are currently three permits issued for research on smalltooth sawfish. The NMFS Permits 

Division and Interagency Cooperation Division are currently working on a programmatic 

consultation on a program for the issuance of permits for research and enhancement activities on 

the U.S. DPS of smalltooth sawfish. Since their listing in 2003, only one smalltooth sawfish 

mortality has been reported as a result of research authorized under a section 10(a)(1)(A) permit. 

As with turtles and sturgeon, mitigation measures implemented by NMFS through permit 

conditions and additional precautions taken by researchers have significantly reduced the lethal 

and sublethal effects of research activities on smalltooth sawfish. 

With the exception of Atlantic salmon and Gulf sturgeon, scientific research permits for other 

ESA-listed species considered in this opinion are issued by the NMFS regional office with 

jurisdiction over that particular species. The USFWS issues section 10(a)(1)(A) permits for 

Atlantic salmon. For Gulf sturgeon, a special rule promulgated at the time of listing (56 FR 

49658) gives the states permitting authority to allow taking of this species, in accordance with 

applicable state laws, for educational purposes, scientific purposes, and enhancement of 

propagation. 

7.13 Directed Harvest of Sea Turtles 

Sea turtles have been harvested throughout history as both a protein source (for meat or eggs) 

and as raw material in the manufacture of ornaments and artifacts. A threat unique to hawksbill 

turtles is the tortoiseshell trade. Tortoiseshell is made from hawksbill scutes and is used to 

produce products such as sunglasses, bracelets, and boxes that are often sold illegally on the 

black market (Shattuck 2011). In many parts of the world, the customs and traditions associated 

with the harvest, consumption and artistic use of sea turtle products have been passed from 

generation to generation and have developed cultural meaning and significance over time 

(Campbell 2003). 

For many centuries, the harvest of sea turtles and turtle eggs was primarily limited to small-scale, 

artisanal and subsistence fisheries. Although small-scale turtle fisheries still exist today, by the 

mid-20th century directed turtle harvest was dominated by large-scale commercial operations 

with access to global markets (Stringell et al. 2013). From the 1950s to 1970s, commercial 

fisheries in Mexico accounted for about one-half of the global sea turtle harvest, consisting 

mainly of green and olive ridley turtles (Márquez 1990). During the peak of Mexico’s sea turtle 

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exploitation in 1968, it is estimated that the national take was over 380,000 turtles (Cantu and 

Sanchez, 1999 as cited in (Humber et al. 2014). By the late 1960s, the global capture of sea 

turtles had peaked at an estimated 17,000 tons (FAO 2011). Based on Japanese commercial 

import data, between 1970 and 1986 an estimated two million turtles (mostly hawksbills, greens, 

and olive ridleys) were harvested to satisfy the demand for turtle products in Japan alone 

(Milliken and Tokunaga 1987). To maximize efficiency, commercial harvesting effort was often 

concentrated at mass nesting sites or arribadas with high densities of breeding adult turtles. With 

the introduction of mechanized fishing in the 1970s to India’s Orissa coast, an area known to 

support the world’s largest olive ridley arribada, turtle take increased sharply to an estimated 

50,000 adults per breeding season (Tripathy and Choudhury 2007). In Ecuador, during the 

1970s, an estimated 100,000 to 148,000 olive ridley turtles were killed each year for both 

consumption of meat and the expanding turtle leather market (Alava et al. 2005). 

Increased conservation awareness at the international scale has led to greater protection of 

marine turtles in recent decades. The Convention on International Trade in Endangered Species 

(CITES), which went into effect in 1975, helped to reduce demand and promote regional 

cooperation in increasing turtle populations. All six ESA-listed sea turtles are listed in CITES 

Appendix I, which provides the greatest level of protection, including a prohibition on 

commercial trade. Marine turtle species have also been listed on the International Union for 

Conservation of Nature Red List of Threatened Species since 1982 (IUCN 2017). In 1981, 

Ecuador, one of the two largest turtle harvesting nations at the time, banned the export of sea 

turtle products. In 1990, following international pressures, Mexico, the other major turtle 

exporter, closed commercial fisheries and instituted a moratorium on the take of turtles and eggs 

(Senko et al. 2014). 

As of 2014, there were 42 countries and territories that reported sea turtle harvest through legally 

authorized fisheries (Humber et al. 2014). Collectively, an estimated 42,000 turtles are killed 

each year in these countries and territories. Over 80 percent of these are green turtles, followed 

by hawksbills (8.2 percent), loggerheads (2.5 percent), olive ridley (0.6 percent), and leatherback 

(0.1 percent)(Humber et al. 2014). Geographically, the legal take of sea turtles is currently 

concentrated in two regions: the Indo-Pacific region accounts for 63 percent and the wider 

Caribbean region accounts for 35 percent. The countries of Papua New Guinea (36 percent), 

Nicaragua (22 percent) and Australia (16 percent) combined account for almost three-quarters of 

the current legal take of sea turtles (Humber et al. 2014). 

Humber et al. (2014) documented the change in the legal take of sea turtles over the past three 

decades. Just considering the 46 countries that still allow sea turtle directed take (including the 

four with current moratoria), turtle harvest has decreased by more than 60 percent over the past 

three decades. The average number of turtles killed in these fisheries annually has declined 

steadily over time: 116,420 in the 1980s; 68,844 turtles in the 1990s; and 45,387 in the 2000s 

(Humber et al. 2014). One of the major changes in species taken over the past three decades has 

been in the nearly complete cessation of the olive ridley harvest on the Pacific coast of Colombia 

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from nearly 40,000 turtles per year in the early 1980s to fewer than ten turtles per year in the 

1990s and 2000s. While legal directed take of sea turtles has declined significantly, illegal 

harvest may still represent a significant source of sea turtle mortality, one that is more difficult to 

estimate. The scale of global illegal take is likely to be severely underreported due to the inherent 

difficulty in collecting data on such activity (Humber et al. 2014). 

7.14 Fisheries Bycatch 

Bycatch occurs when fisheries interact with living marine resources (e.g., marine mammals, sea 

turtles, non-market fish species, corals, or seabirds) that are not the target species for commercial 

sale. Bycatch represents a global threat to many ESA-listed species. Populations of marine 

megafauna (e.g., turtles, dolphins, sharks) can be particularly sensitive to the detrimental effects 

of bycatch due to life history parameters such as slow growth, late age at maturity, and low 

reproductive rates (Hall et al. 2017). Highly migratory, transboundary species that spend large 

amounts of time in ocean jurisdictions lacking adequate bycatch mitigation measures, monitoring 

or enforcement are often most vulnerable to this threat. 

While mitigation and minimization measures have reduced U.S. fisheries bycatch in recent years, 

large numbers of ESA-listed species are still routinely captured in federal and state commercial 

fisheries targeting other species. Some ESA-listed species also interact with recreational hookand-line fisheries. Fisheries management plans (FMPs) developed for federally regulated 

fisheries with ESA-listed species bycatch are required to undergo section 7 consultation, 

including a NMFS issued biological opinion and an ITS. The ITS includes the anticipated 

amount of take (lethal and nonlethal) and reasonable and prudent measures (RPMs) with specific 

terms and conditions for mitigating and minimizing the adverse effects of the proposed action on 

ESA-listed species and designated critical habitat. Some state-managed fisheries with ESA-listed 

species bycatch have also been the subject of section 7 consultations with NMFS for issuance of 

ESA section 10(a)(1)(B) incidental take permits (ITPs). ITPs are issued based on NMFS 

approval of a state’s Conservation Plan, which includes ESA-listed species mitigation and 

minimization measures. Take levels provided for in an ITS or ITP represent an upper limit of 

authorized take, and do not necessarily reflect the reported amount of take by the fishery in any 

given year. 

7.14.1 Bycatch of Sea Turtles 

In this section, we summarize the best available information on fisheries bycatch of ESA-listed 

sea turtles. First, we provide an overview of the types of fisheries and fishing gears that typically 

interact with sea turtles, and the relative magnitude of this threat to sea turtle populations. Next, 

we discuss the global threat that fisheries bycatch represents to ESA-listed sea turtles captured on 

the high seas and in foreign waters. We then describe the primary federal and state fisheries 

operating within U.S. waters that result in sea turtle bycatch based on information from (1) 

previously issued NMFS biological opinions addressing the effects of fisheries bycatch on 

turtles, (2) bycatch estimates based on observer reported data, and (3) other sources of fisheries 

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bycatch information as available in the published literature and unpublished reports. The 

summary of U.S. commercial fisheries bycatch of sea turtles is organized by major ocean basin 

(Atlantic and Pacific) and by type of fishery (i.e., species targeted, gears used and/or locations 

fished) or FMP within a particular ocean basin. More detailed information on the effects of U.S. 

fisheries bycatch on sea turtles and the specific mitigation measures in place to minimize those 

effects, can be found in the biological opinions referenced below. 

7.14.1.1 Overview 

Bycatch of ESA-listed sea turtles occurs in a diversity of fisheries throughout the broad 

geographic oceanic ranges of these species. Sea turtle bycatch occurs in both large-scale 

commercial fishing operations as well as small-scale, artisanal fisheries throughout the world. 

Fishing gears that are known to interact with sea turtles include trawls, longlines, purse seines, 

gillnets, pound nets, dredges and to a lesser extent, pots and traps (Finkbeiner et al. 2011; 

Lewison et al. 2013). 

Trawl vessels typically pull one or more large funnel-shaped nets through the water where target 

and non-target species are captured in a bag at the end of the net, termed a cod-end. For sea 

turtles, coastal or shallow bottom trawls used to capture shrimp and other coastal fish can result 

in high bycatch levels (Finkbeiner et al. 2011). When sea turtles enter the cod-end they are 

unable to escape, and will die if the duration of a trawl operation exceeds the physiological 

capacity for a sea turtle to remain submerged without surfacing to breathe. 

Gillnets are comprised of vertical panels that are used to form walls of nets of varying lengths 

and mesh sizes. The primary threat to sea turtles is entanglement in the gillnet mesh, which can 

result in injury or death from drowning (Lewison et al. 2013). 

Pound nets are a stationary net gear that work by corralling migrating fish through a series of 

funnels into a holding pen. Turtles may become entangled in a vertically hung leader net, which 

is set perpendicular to shore to divert fish to the mouth of the pound net. In some regions, the 

holding pen is open (i.e., has no roof) and in others, it is enclosed. If turtles enter a pen that is 

enclosed, they are unable to reach the surface to breathe and drown (Lewison et al. 2013). 

Purse seines consist of a wall of netting that is set in a circle around a school of targeted fish. The 

bottom of the net is pulled shut (i.e., “pursed”) to form a bag that is then hauled on board the 

ship. Purse seiners often set nets around natural floating debris and FADs because target fish 

species are attracted to these objects. Turtles can become entangled in the tethered ropes, buoys, 

or floats that are part of the FAD. There is some evidence that the use of FADs in purse seine 

fisheries has resulted in increased sea turtle bycatch (Gilman and Lundin 2010). 

Longlines are a series of hundreds or thousands of hooks that hang off a mainline of variable 

length set at discrete depths to target large pelagic fish species such as tunas and swordfish. 

Much of the longline bycatch of sea turtles occurs when the lines are set shallowly (0 to 100 

meters), a depth range where all sea turtle species dive extensively (Lewison et al. 2013). Sea 

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turtles can be hooked while trying to ingest bait from longline hooks or become entangled when 

their flippers encounter the hooked branch or mainlines. 

Sea turtle bycatch rates (i.e., individuals captured per unit of fishing effort) and mortality rates 

(i.e., individuals killed per number captured) can vary widely both within and across particular 

fisheries due to a combination of factors. These include gear types and gear configurations, 

fishing methods (e.g., depth fished, soak times), fishing locations, fishing seasons, time fished 

(i.e., day versus night), and turtle handling and release techniques used (Lewison et al. 2013; 

Wallace et al. 2010b). Henwood (1987) found a strong positive correlation between shrimp trawl 

tow time and mortality rate of turtles bycaught in commercial shrimp trawlers. Similarly, Murray 

(2009) found that sea turtle mortality rates in sink gillnet gear was largely a function of soak 

time. Differences in bycatch rates among gear deployment practices and gear configurations 

have driven many of the bycatch reduction strategies in longline vessels (Lewison et al. 2013; 

Watson et al. 2005). Shallow-set longlines (less than 50 meters) have been shown to result in 

higher turtle bycatch rates than deeper sets (Beverly et al. 2009; Gilman et al. 2006); 

leatherbacks are caught more often during nighttime longline sets compared to daytime sets; 

increased longline soak times have resulted in higher catches of loggerhead turtles (Gilman et al. 

2006); and switching from J-shaped hooks with squid bait to circle hooks with fish bait resulted 

in significant declines in loggerhead (83 percent) and leatherback (90 percent) bycatch in the 

Hawaii longline swordfish fishery (Gilman et al. 2007). Estimated turtle mortality rates from 

capture in longline gear have also been shown to vary widely (8 percent to over 30 percent) 

depending on numerous factors including hook type used, set depth, and hook location (Casale et 

al. 2008; Chaloupka et al. 2004). 

If mortality is not directly observed during gear retrieval, it may occur after the turtle is released 

due to physiological stress and injury suffered during capture. Entanglement in fishing gear 

and/or plastics can result in severe ulcerative dermatitis, and amputation of flippers (Orós et al. 

2005). Although rates of post-release mortality and serious injury are essential to understanding 

the impact of bycatch on sea turtle populations, it is a major knowledge gap for many fisheries 

that interact with turtles (Lewison et al. 2013). Recent studies indicate that underwater 

entrapment in fishing gear (i.e., trawls and gillnets) followed by rapid decompression when gear 

is brought to the surface may cause gas bubble formation within the blood stream (i.e., 

embolism) and tissues leading to organ injury, impairment, and even post-release mortality in 

some bycaught turtles (Fahlman et al. 2017; Garcia-Parraga et al. 2014). Swimmer et al. (2006) 

used pop-off satellite archival tags to compare post-release mortality and dive behavior of olive 

ridley’s captured with longline gear (n = 9) with those captured by hand at the surface (n = 5). 

No clear differences were found in dive behavior between longline-caught and hand captured 

turtles and the only mortality event recorded was that of a hand captured turtle. The authors 

conclude that olive ridley turtles that are lightly hooked and handled properly survive, and 

generally behave normally following interactions with shallow-set longline gear (Swimmer et al. 

2006). 

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There have been some major advancements in sea turtle bycatch reduction technologies and 

management approaches in the past few decades. Direct gear and fishery modifications such as 

changes to bait type, modifying gear to make it less visible or attractive to sea turtles, making 

gear less likely to cause direct mortality, or changing the way that gear is deployed are all 

examples of bycatch mitigation techniques that have been employed to reduce sea turtle bycatch 

in trawl, passive net, and longline large-scale fisheries (Hall et al. 2017; Lewison et al. 2013). 

Time-area closures have also proven effective at reducing sea turtle bycatch in commercial 

fishing gear (Dunn et al. 2011). Sea turtle bycatch mitigation measures and fisheries regulations 

implemented for particular fisheries are discussed further below. 

In 2003, NMFS developed a National Bycatch Strategy that identified concrete actions necessary 

for reducing bycatch in U.S. fisheries (Benaka and Dobrzynski 2004). This document was 

recently updated and expanded to enhance the effectiveness of existing bycatch reduction 

approaches. The 2016 National Bycatch Reduction Strategy identifies several key objectives 

including: (1) improved monitoring of bycatch and bycatch mortality, (2) conduct research to 

improve bycatch estimates, (3) implement management measures to further reduce the effects of 

bycatch, and (4) more emphasis on enforcement to ensure compliance with bycatch measures 

(NMFS 2016d). The most effective way to monitor sea turtle bycatch is to place trained 

observers aboard fishing vessels. Although observer programs have increased in recent decades, 

many fisheries still lack the level of observer coverage necessary to produce reliable estimates of 

bycatch and associated mortalities needed to assess fishery impacts on ESA-listed species. In 

2007, NMFS established a new regulation (72 FR 43176) to annually review sea turtle 

interactions across fisheries, identify those that require monitoring, and require fishermen to 

accommodate observers if requested. This annual process should help NMFS and the fishing 

industry learn more about sea turtle interactions with fishing operations, continually evaluate 

existing measures to reduce sea turtle takes, and determine whether additional measures to 

address prohibited sea turtle takes may be necessary to avoid exceeding established take limits. 

7.14.1.2 Global Perspective 

Estimating sea turtle interactions and mortality rates associated with commercial fisheries 

globally remains challenging because a relatively small proportion of fisheries worldwide 

adequately monitor bycatch (Long and Schroeder 2004). Wallace et al. (2010b) compiled a 

global database of reported marine turtle bycatch from 1990 to 2008 in gillnet, longline, and 

trawl fisheries. The total reported marine turtle bycatch from the sources used in this study was 

around 85,000 turtles. However, due to the small percentage of fishing effort observed and 

reported (typically less than one percent of total fleets), and to a global lack of bycatch 

information from small-scale fisheries, the authors note that this likely underestimates the true 

total by at least two orders of magnitude. Based on these results, they conclude that bycatch is a 

moderate or high threat for more than three-fourths of all sea turtle regional management units, 

and represents the greatest overall threat to sea turtles globally (Wallace et al. 2010b). Lewison 

et al. (2014) used the same 1990-2008 bycatch database as Wallace et al. 2010 to identify global 

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hotspots of turtle bycatch intensity. High-intensity sea turtle bycatch was most prevalent in three 

regions: the eastern Pacific Ocean, southwest Atlantic Ocean, and Mediterranean Sea (Figure 

49). 

Figure 49. Map of global documented bycatch records of sea turtles from 1990 to 2008, 

across gillnets, longlines, and trawls where bycatch intensity of each record is ranked 

from high (red) to low (blue). Symbol size corresponds to the amount of fishing effort for 

each data record (Lewison et al. 2013). 

Wallace et al. (2011) found differences in the relative impacts of global fisheries bycatch on 

different turtle species, as well as differences by gear types. Loggerheads, olive ridleys, and 

leatherbacks had the highest average bycatch scores, with 80 percent of loggerhead, 75 percent 

of olive ridley, and 50 percent of leatherback regional management units classified as high 

bycatch areas. The average bycatch scores for the other turtle species in this study were 

moderate, and no other species had more than 30 percent of its regional management units scored 

as high bycatch. By gear type, gillnets were identified as the gear of primary concern most 

frequently for leatherbacks, green turtles, and hawksbills; longlines were identified as the gear of 

primary concern for loggerheads; and trawls were identified as the gear of primary concern for 

olive ridleys. Such interspecific differences, in terms of which gears have the highest impacts, 

are likely due to a combination of differences in turtle species’ life histories and habitat use, and 

fishing effort by gear type across the global regions occupied by these species (Lewison et al. 

2013). 

Several studies have reported foreign fisheries as a significant source of mortality for populations 

of leatherback and loggerhead sea turtles. Pelagic longline bycatch has been implicated as a 

proximate cause for regional declines in loggerhead and leatherback populations in the Pacific 

(Lewison et al. 2004b; Spotila et al. 2000). Lewison et al. (2004b) compiled fisheries landings 

data from 40 nations and turtle bycatch data from 13 international observer programs to estimate 

global longline bycatch of loggerhead and leatherback turtles. Based on this study, between 

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60,000 and 250,000 loggerheads and between 9,000 and 60,000 leatherbacks were captured in 

pelagic longline fisheries globally in 2000. High levels of bycatch continue to be reported in 

Pacific Ocean longline and gillnet fisheries operating in ‘hotspot” areas where loggerheads are 

known to congregate (Peckham et al. 2007). The western Pacific and South China Sea longline 

fisheries are dominated by Japan and Taiwan (Long and Schroeder 2004), while the eastern 

Pacific longline effort is primarily from Chile, Ecuador, Costa Rica, and Spanish fleets 

(operating out of Peru), in addition to the United States. Dominant longline fisheries in the 

Atlantic include Brazil, Canada, Japan, Portugal, Spain, Taiwan, United States, Uruguay, and the 

Caribbean (Long and Schroeder 2004). Interactions and mortality with coastal and artisanal 

fisheries in Mexico and the Asian region likely represent the most serious threats to the 

loggerhead North Pacific DPS population (Conant et al. 2009; Peckham et al. 2007). Coastal 

pound net fisheries off Japan may also pose a significant threat to this loggerhead population 

(Conant et al. 2009). 

Commercial fisheries operating in coastal waters near arribadas (i.e., mass nesting areas) can 

result in high numbers of adult olive ridely mortalities. This is evident in the eastern Indian 

Ocean, where thousands of olive ridley carcasses from a large arribada on the Orissa coast have 

washed ashore annually since expansion of the shrimp trawl fishery in the mid-1970s (Wright 

and Mohanty 2006). From 1999 to 2006, over 10,000 olive ridley carcasses per year have been 

documented on the Orissa coast (Wright and Mohanty 2006). Shrimp trawlers off the coast of 

Central America have historically killed tens of thousands of sea turtles annually, most of which 

are olive ridleys (Arauz 1996). Trawl fishing was banned in Costa Rican waters in 2013 as a 

result of litigation over the impacts of bycatch on marine ecosystems (Arias 2013). Based on 

observer program data, an estimated 699,600 olive ridleys (including 92,300 adult females) and 

23,000 green turtles were bycaught in the Costa Rican longline fishery from 1999 to 2010 (Dapp 

et al. 2013). While the large number of olive ridleys caught in this fishery has been associated 

with declines in nesting turtles at nearby arribada beaches, the population level impact of this 

bycatch is difficult to quantify (Dapp et al. 2013). Compared to capture in shrimp trawls, 

mortality rates of olive ridley’s from longline capture are typically low in Costa Rica (Whoriskey 

et al. 2011), and the effects of post-release mortality or reduced fitness are largely unknown. 

Whereas bycatch in large-scale industrial and commercial fisheries (e.g., pelagic longlines and 

shrimp trawlers) has been associated with sea turtle population declines, small-scale, artisanal 

fisheries can also pose a significant threat due to a range of factors. Small-scale fisheries often 

have large fleet sizes, concentrated fishing effort in highly productive coastal waters where many 

sea turtle species occur, and limited control and enforcement measures for mitigating bycatch 

(Ortiz et al. 2016). In addition, many small-scale fisheries are not adequately monitored, making 

it difficult to fully assess the impact these fisheries may have on sea turtle populations. AlfaroShigueto et al. (2011) assessed the impact of bycatch on marine turtles from three small-scale 

fisheries (longline, bottom set nets and driftnet fisheries) out of three Peruvian fishing ports. 

They estimated these fisheries resulted in the annual bycatch of about 5,900 turtles (3,200 

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loggerhead, 2,400 green, 240 olive ridley, and 70 leatherback). Since this study covered only a 

small portion of the nation’s nearshore fishing effort, the authors suggest that the number of 

turtles captured per year in all Peruvian small-scale fisheries is likely to be in the tens of 

thousands. They conclude that the Peruvian small-scale fisheries have the potential to severely 

impact sea turtles populations in the Pacific, especially green, loggerhead and leatherback turtles

(Alfaro-Shigueto et al. 2011). Peru’s small-scale, nearshore gillnet fishery may also exert 

significant pressure on Pacific green sea turtle populations (Lewison et al. 2014; Ortiz et al. 

2016; Wallace et al. 2010b). 

In 1989, the U.S. passed legislation aimed at reducing the impact of global shrimp trawl fisheries 

bycatch on sea turtle populations. Section 609 of Public Law 101-162 prohibits the import of 

shrimp harvested with technology that may adversely affect certain species of sea turtles (16 

U.S.C. 1537). The shrimp import prohibition does not apply if the Department of State certifies 

to Congress that the harvesting nation has a regulatory program and an incidental take rate 

comparable to that of the United States (that is, require and enforce the use of TEDs), or, 

alternatively, that the fishing environment in the harvesting nation does not pose a threat of the 

incidental taking of sea turtles (64 FR 36946). Nations that seek to import shrimp into the U.S. 

must be certified annually. Approximately 40 countries are currently certified to export shrimp to 

the U.S. Although most certifications are done on a national basis, State Department guidelines 

allow for import of individual shipments of TED-harvested shrimp from uncertified countries. 

The State Department and NOAA Fisheries can, if requested, inspect portions of a nation's 

shrimp trawl fleet for adequate use of TEDs. NMFS has provided extensive TED training 

throughout the world to further encourage and promote the use of these effective bycatch 

mitigation devices in foreign shrimp trawl fisheries. 

7.14.1.3 U.S. Fisheries: Atlantic Ocean Basin (including Gulf of Mexico and Caribbean) 

This subsection describes the impact of U.S. commercial fisheries bycatch on sea turtle 

populations within the Atlantic Ocean, Gulf of Mexico, and Caribbean Sea. The primary turtle 

species captured in U.S. fisheries in Atlantic and Gulf of Mexico fisheries is the loggerhead 

(Moore et al. 2009). The southeastern U.S. comprises one of the largest aggregate nesting 

rookeries for loggerhead sea turtles in the world, and the continental shelf provides critical 

ontogenetic habitats for this population. Thus, because a large number of individuals are present 

throughout areas of high fishing activity, loggerheads interact with a greater number of fishing 

fleets and gear types in the Atlantic than other sea turtle species (Moore et al. 2009). 

Southeast Shrimp Trawl Fishery 

The Southeast shrimp trawl fishery in the Atlantic and Gulf of Mexico has historically accounted 

for the overwhelming majority (up to 98 percent) of sea turtle bycatch in U.S. fisheries 

(Finkbeiner et al., 2011). Regulations that went into effect in the early 1990’s require shrimp 

trawlers in the Atlantic and Gulf of Mexico to modify their gear with TEDs designed to allow 

turtles to escape trawl nets and avoid drowning. TEDs consist of metal bars inserted into the 

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neck of a trawl; when a turtle encounters the bars, it is forced out of an opening in the bottom of 

the net while smaller organisms such as shrimp continue through the bars into the bag end of the 

trawl (Lewison et al. 2013). There is an exception allowed to the NMFS TED requirement in the 

Southeast shrimp trawl fishery for skimmer, pusher-head, and wing net (butterfly) trawls. 

Vessels fishing with these types of trawls are currently allowed to use limited tow times in lieu 

of TEDs, as short duration tow times has a similar effect of mitigating turtle bycatch. However, 

due to the difficulty of enforcing limited tow times, in December 2016 NMFS proposed a rule 

(81 FR 91097) to withdraw the tow time requirement and require all skimmer trawl, pusher-head 

trawl, and wing net (butterfly trawl) vessels rigged for fishing to use TEDs (with the exception of 

vessels participating in the Biscayne Bay, Florida wing net fishery). 

Analyses by Epperly and Teas (2002) indicated that, while early versions of TEDs were effective 

for some species, the minimum requirements for the escape opening dimension were too small 

for larger sea turtles, particularly loggerheads and leatherbacks. NMFS implemented revisions to 

the TED regulations in 2003 to address this issue (68 FR 8456, February 21, 2003). The revised 

TED regulations were estimated to reduce shrimp trawl related mortality by 94 percent for 

loggerheads and 97 percent for leatherbacks (NMFS 2014c). Finkbeiner et al. (2011) compared 

sea turtle bycatch estimated before and after the 2003 TED enlargement regulations. In the late 

1990’s, the southeast shrimp trawl fishery resulted in an estimated 340,500 sea turtle interactions 

and 133,400 mortalities. By comparison, by 2007 this fishery resulted in an estimated 69,300 

interactions and 3,700 mortalities (Finkbeiner et al. 2011). The decline in sea turtle bycatch over 

this period can be attributed to a combination of the revised TED regulations and a significant 

decrease in fishing effort. Time-area closures have also been implemented to reduce sea turtle 

bycatch in shrimp trawl fisheries operating in particularly sensitive areas. In 2000, the state of 

Texas implemented a no-take marine protected area along Padre Island within five miles of the 

southern Texas coast from December 1 through July 15 each year to protect nesting Kemp’s 

ridleys from capture in shrimp trawls (Lewison et al. 2003). 

Although mitigation measures have greatly reduced the impact on sea turtle populations, the 

shrimp trawl fishery is still responsible for large numbers of turtle mortalities each year. The 

Gulf of Mexico fleet accounts for a large percentage of the sea turtle bycatch in this fishery. In 

2010, the Gulf of Mexico shrimp trawl fishery had an estimated bycatch mortality of 5,166 

turtles (18 leatherback, 778 loggerhead, 486 green and 3,884 Kemp’s ridley). By comparison, the 

southeast Atlantic fishery had an estimated bycatch mortality of 1,033 turtles (8 leatherback, 673 

loggerhead, 28 green and 324 Kemp’s ridley) in 2010 (NMFS 2014c). 

In 2014, NMFS issued a biological opinion for reinitiation of the section 7 consultation on the 

southeast shrimp trawl fishery (NMFS 2014c). Unlike most other fisheries, conventional 

observer programs are not effective for determining the numbers of sea turtle interactions and 

mortalities in this fishery. As a result, the ITS for this opinion is based on monitoring fishing 

effort and TED compliance rate as a surrogate for monitoring take. The baseline effort levels for 

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this fishery, as established in the ITS, are 132,900 days fished in the Gulf of Mexico and 14,560 

trips in the South Atlantic. The baseline TED compliance level is 88 percent. 

Pelagic Longline Fishery 

The U.S. Atlantic pelagic longline fishery began in the early 1960s. This fishery is currently 

comprised of five distinct fishing sectors: Gulf of Mexico yellowfin tuna fishery; southern 

Atlantic swordfish fishery; Mid-Atlantic and New England swordfish and tuna fishery; U.S. 

Atlantic Distant Water swordfish fishery; and the Caribbean tuna and swordfish fishery. The 

pelagic longline fishery mainly interacts with leatherback sea turtles and pelagic juvenile 

loggerhead sea turtles. The estimated average annual bycatch in this fishery (all geographic areas 

combined) between 1992-2002 was 912 loggerhead interactions (including 7 captured dead) and 

846 leatherback interactions (including 11 captured dead) (NMFS 2004). These mortality 

estimates do not account for post-release mortality, which historically was likely substantial 

(NMFS 2014c). 

NMFS has taken numerous steps to reduce sea turtle bycatch and bycatch mortality in domestic 

longline fisheries. In 2001, NMFS implemented requirements for U.S. flagged vessels with 

pelagic longline gear on board to have line clippers and dipnets to remove gear on incidentally 

captured sea turtles (66 FR 17370). Specific handling and release guidelines designed to 

minimize injury to sea turtles were also implemented. In 2004, NMFS issued a biological 

opinion on reinitiation of a section 7 consultation on the Atlantic pelagic longline fishery (NMFS 

2004). This opinion concluded that the pelagic longline fisheries were likely to jeopardize the 

continued existence of leatherback sea turtles. An RPA was provided to avoid jeopardy that 

included take reduction measures related to fishing gear, bait, disentanglement gear, and training. 

NMFS published a final rule in 2004 to implement management measures to reduce sea turtle 

bycatch and bycatch mortality in the Atlantic pelagic longline fishery (69 FR 40734). These 

measures effectively reduced post-release mortality rates by reducing the number of turtles that 

swallow hooks which engage in the gut or throat, decreasing the number of turtles that are foulhooked, and improving handling and gear removal protocols. Incidental take of sea turtles over 

any three-year period, as specified in the RPA ITS of the 2004 opinion, are as follows: 

• Kemp’s ridley, olive ridley, green, and hawksbill (combined): 105 total, including up to 

18 lethal. 

• Leatherback: 1,764 total, including up to 252 lethal. 

• Loggerhead, Northwest Atlantic DPS: 1,905, including up to 339 lethal. 

Since 2004, bycatch estimates for both loggerheads and leatherbacks in pelagic longline gear 

have been well below the average prior to implementation of gear regulations under the RPA 

(Garrison, Stokes, & Fairfield, 2012). The pelagic longline fishery resulted in an estimated 259 

loggerhead and 268 leatherback sea turtle interactions in 2014 (NMFS, 2015). NMFS is currently 

reviewing a request for reinitiation of section 7 consultation on the pelagic longline fishery based 

on the following: (1) information indicating that the net mortality rate and total mortality 

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estimates for leatherbacks specified in the 2004 RPA were exceeded (although the take level 

specified in the ITS has not been exceeded), (2) changes in information about leatherback and 

loggerhead sea turtle populations, and (3) new information about sea turtle mortality associated 

with pelagic longline fishing gear. 

Federal Shark Fisheries 

In 2012, NMFS issued an updated biological opinion on the federal shark fisheries managed 

under the Consolidated Highly Migratory Species FMP (NMFS 2012c). Gears used to capture 

sharks in these fisheries include bottom longlines, gillnets (drift, strike, and sink nets), and 

commercial and recreational rod-and-reel and handlines. The ITS for this opinion exempted take 

of ESA-listed sea turtle species as follows: 

• Green, North Atlantic DPS: up to 57 captures every three years of which 24 could be 

lethal. 

• Hawksbill: up to 18 captures every three years of which nine could be lethal. 

• Kemp’s ridley: up to 36 captures every three years of which 15 could be lethal. 

• Leatherback: up to 18 captures every three years of which nine could be lethal. 

• Loggerhead, Northwest Atlantic DPS: up to 126 captures every three years of which 78 

could be lethal. 

Scallop Fishery 

Sea turtles overlap seasonally with the Atlantic sea scallop fishery in the Mid-Atlantic region 

from Cape Cod, Massachusetts to southern Virginia when turtles migrate to this area to forage in 

early summer (Murray 2015). Loggerheads account for the large majority of interactions with 

this fishery. An estimated 200 interactions between loggerheads and scallop dredge fishing gear 

occurred on average annually from 2001 to early 2006 (Murray 2011). Subsequent fishing effort 

reductions and gear modifications implemented in this fishery reduced these interactions to less 

than 100 per year from late 2006 to 2008, and to an estimated 22 per year from 2009 to 2014 

(Murray 2015). 

In 2012, NMFS issued a biological opinion on the continued authorization of the Atlantic sea 

scallop FMP (NMFS 2012d). An amended ITS for this opinion was issued in 2015 with the 

following levels of anticipated sea turtle take: 

• Green: annual lethal take of up to two individuals in dredge and trawl gear combined. 

• Kemp’s ridley: annual take of up to three individuals in dredge and trawl gear combined, 

of which up to two takes are anticipated to be lethal. 

• Leatherback: annual lethal take of up to two individuals in dredge and trawl gear 

combined. 

• Loggerhead, Northwest Atlantic DPS: (a) the take of no more than 322 individuals over 

any consecutive two-year period in dredge gear, of which up to 92 may be lethal, and (b) 

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the take of no more than 700 individuals over any consecutive five-year period in trawl 

gear, of which up to 330 may be lethal. 

Federally Managed Gillnet and Trawl Fisheries 

Gillnets and bottom trawls are commonly used gears by many of the commercial fisheries 

operating in the northeastern U.S. Atlantic EEZ from North Carolina through Maine. These 

fisheries are also known to interact with large numbers of sea turtles, particularly loggerheads. 

Following an event in which over 200 sea turtle carcasses washed ashore in an area where large 

mesh gillnetting had been occurring, NMFS published new restrictions for the use of gill nets 

with larger than 8-inch stretched mesh, in the EEZ off of North Carolina and Virginia (67 FR 

71895, December 3, 2002). This rule was in response to a direct need to reduce the impact of this 

fishery on sea turtles. The rule was subsequently modified on April 26, 2006, by requiring the 

use of gillnets with greater than or equal to 7-inch stretched mesh when fished in federal waters 

from the North Carolina/South Carolina border to Chincoteague, Virginia. 

In 2013, NMFS issued a “batched” section 7 biological opinion on the following fisheries: 

Northeast multispecies; monkfish; spiny dogfish; Atlantic bluefish; Northeast skate complex; 

mackerel/squid/butterfish; and summer flounder /scup/black sea bass (NMFS, 2013). Gill net 

gear is used by five of the seven fisheries, and bottom trawl gear is used by six of the seven 

fisheries covered by this opinion. The “batched” FMP opinion includes an ITS (amended March 

10, 2016) that exempts the following take of ESA-listed sea turtles: 

Loggerhead sea turtle Northwest Atlantic DPS: up 1,345 individuals over any consecutive fiveyear period in gillnet gear, of which up to 835 may be lethal; up to 1,020 individuals over any 

consecutive five-year period in trawl gear, of which up to 335 may be lethal; and the annual take 

of up to one individual in trap/pot gear, which may be lethal or non-lethal. 

Leatherback sea turtle: annual observed take of up to four individuals in gillnet gear, of which up 

to three may be lethal; annual observed take of up to four individuals in bottom trawl gear, of 

which up to two may be lethal; and annual observed take of up to four individuals in trap/pot 

gear, which may be lethal or non-lethal 

Kemp’s ridley sea turtle: annual observed take of up to four individuals in gillnet gear, of which 

up to three may be lethal; and the annual observed take of up to three individuals in bottom trawl 

gear, of which up to two may be lethal. 

Green sea turtle: annual observed take of up to four individuals in gillnet gear, of which up to 

three may be lethal; and annual observed take of up to three individuals in bottom trawl gear, of 

which up to two may be lethal. 

Coastal Migratory Pelagics 

Sea turtles occasionally interact with commercial gillnets targeting king mackerel, Spanish 

mackerel, and cobia managed under the coastal migratory pelagics FMP. In 2015, NMFS issued 

a biological opinion on reinitiation of a section 7 consultation on the FMP for coastal migratory 

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pelagics in the Atlantic and Gulf of Mexico (NMFS 2015b). Sea turtle incidental take authorized 

over any three-year period as provided for in the ITS of this opinion is as follows: 

• Green, North Atlantic DPS: 31 total, including up to nine lethal. 

• Hawksbill: one (lethal or non-lethal). 

• Kemp’s ridley: eight total, including up to two lethal. 

• Leatherback: one (lethal or non-lethal). 

• Loggerhead, Northwest Atlantic DPS: 27 total, including up to seven lethal. 

South Atlantic Snapper-Grouper Complex 

The South Atlantic commercial snapper-grouper fishery occurs in the U.S. federal waters from 

North Carolina through Florida. Four fishing methods are used in this fishery: vertical line 

(handline, hydraulic, or electric), longline, black sea bass pots, and powerheads or spears. In 

2006, NMFS issued a biological opinion on the continued authorization of the South Atlantic 

snapper-grouper fishery (NMFS 2006b). Sea turtle incidental take authorized over any three-year 

period as provided for in the ITS of this opinion is as follows: 

• Green: 39 total, including up to 14 lethal. 

• Hawksbill: four total, including up to three lethal. 

• Kemp’s ridley: 19 total, including up to eight lethal. 

• Leatherback: 25 total, including up to 15 lethal. 

• Loggerhead: 202 total, including up to 67 lethal. 

Reef Fish Fisheries 

In 2011, NMFS issued a biological opinion on the continued authorization of the reef fish 

fisheries in the Gulf of Mexico (NMFS 2011b). Fishing gears used in these fisheries that may 

interact with sea turtles include commercial bottom longlines and bandit rigs (a type of vertical 

line gear), and recreational hook-and-line gear. This opinion also addresses the anticipated take 

of sea turtles by these fisheries due to vessel strikes. Sea turtle incidental take authorized over 

any three-year period as provided for in the ITS of this opinion are as follows: 

• Green: 116 total, including up to 75 lethal. 

• Hawksbill: nine total, including up to eight lethal. 

• Kemp’s ridley: 108 total, including up to 41 lethal. 

• Leatherback: 11 (lethal or non-lethal). 

• Loggerhead: 1,044 total, including up to 572 lethal. 

In 2011, NMFS issued a biological opinion on the continued authorization of the reef fish 

fisheries in Puerto Rico and the U.S. Virgin Islands (NMFS 2011a). Fishing gears used in these 

fisheries that may interact with sea turtles include traps and hook-and-line gear. This opinion 

also addresses the anticipated take of sea turtles by these fisheries due to vessel strikes. Sea turtle 

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incidental take authorized over any three-year period as provided for in the ITS of this opinion 

are as follows: 

• Green: 75 (lethal or non-lethal). 

• Hawksbill: 51 total, including up to 48 lethal. 

• Leatherback: 18 (lethal or non-lethal). 

Spiny Lobster Fisheries 

ESA-listed sea turtle distributions overlap with spiny lobster fisheries operating in the Gulf of 

Mexico, South Atlantic, and the Caribbean. However, sea turtle interactions with fishing gear 

used to catch spiny lobster are rare. Based on a 2011 biological opinion (NMFS 2011c), NMFS 

anticipates the following average annual turtle take (lethal or nonlethal) by the U.S. Caribbean 

spiny lobster fishery: four green, four hawksbill, and three leatherback. Similarly, based on a 

2009 biological opinion (NMFS 2009a), NMFS anticipates the following average annual turtle 

take (lethal or nonlethal) by spiny lobster fisheries from North Carolina through Texas: one 

loggerhead, one green, and one hawksbill, leatherback, or Kemp’s ridley in combination. 

Gulf of Mexico Stone Crab Fishery 

In 2009, NMFS issued a biological opinion on the continued authorization of the Gulf of Mexico 

stone crab fishery that occurs off Florida’s west coast (NMFS 2009b). Commercial and 

recreational crab traps and pots authorized in this fishery can adversely affect sea turtles via 

entanglement and forced submergence. Sea turtle incidental take authorized over any three-year 

period as provided for in the ITS of this opinion is as follows: 

• Green: four total, including up to one lethal. 

• Hawksbill: one (lethal or non-lethal). 

• Kemp’s ridley: three total, including up to two lethal. 

• Leatherback: one (lethal or non-lethal). 

• Loggerhead: 16 total, including up to four lethal. 

Fisheries in State Waters 

Various fishing gears (e.g., trawls, pots, pound nets and gillnets) used in state waters from Maine 

through Texas are known to incidentally take sea turtles. However, information on turtle bycatch 

in these coastal, nearshore fisheries is often sparse. State managed fisheries bycatch estimates are 

often based on extremely low observer coverage, and historically sea turtles have not always 

been included in the data collection effort. Thus, these data may provide insights into gear 

interactions that could potentially occur but are often not indicative of the magnitude of the 

overall threat to sea turtles from bycatch in state fisheries. Although the past and current effects 

of state managed fisheries on sea turtles is currently not determinable, NMFS believes that 

ongoing state fishing activities may be responsible for seasonally high levels of observed sea 

turtles strandings in state waters on both the Atlantic and Gulf of Mexico coasts (see Section 

7.15 Sea Turtle Stranding below). 

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In 2002, NMFS issued a biological opinion on sea turtle conservation measures for the Virginia 

pound net fishery in response to a proposed NMFS rule that prohibited pound net leaders 

measuring 12 inches and greater (stretched mesh) and pound net leaders with stringers in the 

Virginia waters of the mainstem Chesapeake Bay and portions of Virginia tributaries from May 8 

to June 30 each year (67 FR 15160; March 29, 2002). Another formal consultation on the 

Virginia pound net fishery was completed in 2004 in response to new information on the effects 

of the fishery and issuance of a proposed rule prohibiting the use of offshore pound net leaders. 

The 2004 opinion included an ITS for the anticipated incidental take of loggerhead (507), 

leatherback (2), Kemp's ridley (103), and green sea turtles (3) in the Virginia pound net fishery 

(no lethal take was authorized). Section 7 consultation on this action was reinitiated in 2017 due 

to (1) recent changes to the fishery through the February 2015 amendments (80 FR 6925) to the 

pound net regulations under the MMPA and ESA (namely the expanded use of modified pound 

net leaders), (2) new information on listed species interactions (i.e., incidental takes) that were 

not considered in the previous 2004 opinion, and (3) new species listings for distinct population 

segments (DPSs) of loggerhead and green sea turtles as well as five DPSs of Atlantic sturgeon. 

In 2013, NMFS issued an incidental take Section 10(a)(1)(B) permit (Permit No. 16230) to the 

state of North Carolina authorizing the take of listed sea turtles incidental to large and small 

mesh gill net fishing. Authorized take in this fishery includes an estimated 165 green sea turtle 

mortalities and 49 Kemp’s ridley mortalities. For hawksbill, leatherback, and loggerhead turtles, 

incidental take was expressed in terms of observed numbers (from observer program data) since 

insufficient observer data existed to model an estimated annual take level for these species. 

7.14.1.4 U.S. Fisheries: Pacific Ocean Basin 

This subsection describes the impact of U.S. commercial fisheries bycatch on sea turtle 

populations within the Pacific Ocean basin, including fisheries operations along the U.S. West 

Coast and the Pacific Islands region. The primary turtle species of concern for U.S. fisheries 

bycatch in the Pacific are leatherbacks and loggerheads, due to their critical conservation status 

(Moore et al. 2009). 

West Coast Longline Fishery 

The west coast longline fishery operates in the north Pacific ocean, mainly from the U.S. EEZ 

west to 140 o W longitude and from the equator to 35 o N (NMFS 2016b). This fishery primarily 

targets bigeye tuna, although other tuna and non-tuna species are also caught and retained. As of 

2016 there was only one boat participating in this fishery, although fishing effort is expected to 

increase in the future (NMFS 2016b). Sea turtle incidental take authorized over a ten-year period 

(starting in 2016) as provided for in the ITS of the 2016 biological opinion (NMFS 2016b) on 

this fishery is as follows: 

• Green, East Pacific DPS and Central North Pacific DPS: one total (lethal or non-lethal). 

• Leatherback: four total, including up to two lethal. 

• Loggerhead, North Pacific DPS: one (lethal or non-lethal). 

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• Olive ridley: six total (lethal or non-lethal). 

Hawaii Pelagic Longline 

Domestic longline fishing around Hawaii consists of two separately managed fisheries: a deepset fishery that primarily targets bigeye tuna and a shallow-set fishery that targets swordfish. 

The shallow-set fishery operates almost entirely north of Hawaii. The deep-set fishery operates 

primarily to the south of Hawaii between the equator and 35° N, although in some years this 

fishery expands northward and overlaps with the shallow-set fishery. 

In 1999, the shallow-set longline fishery targeting swordfish was closed by court order due to 

high levels of sea turtle bycatch. Before the closure took effect, an estimated 417 loggerheads 

and 110 leatherbacks (McCracken 2000) were captured annually (with about 40 percent 

mortality) (Gilman et al. 2007) in Hawaii’s longline fisheries (shallow and deep-set combined). 

Subsequent court orders led to regulations in 2001 prohibiting all Hawaii longline vessels from 

targeting swordfish until 2004. When the shallow-set fishery was reopened in 2004 it was 

restricted to considerably less fishing effort than pre-2001 levels. As a result, the deep-set fishery 

targeting tuna made up an increasingly larger proportion of Hawaii’s longline fishing effort since 

2004. A final rule published in 2004 (69 FR 17329) established a limited shallow-set swordfish 

fishery and required the use of circle hooks with mackerel-type bait, a combination that had 

proven effective at reducing interactions with leatherback and loggerhead turtles in the Atlantic 

longline fishery (Watson et al. 2005). The use of circle hooks with mackerel-type bait reduced 

sea turtle interaction rates by approximately 90 percent for loggerheads and 83 percent for 

leatherbacks compared to the previous period 1994-2002 when the shallow-set fishery was 

operating without these requirements (Gilman et al. 2007). Annual sea turtle bycatch limits (17 

loggerhead or 16 leatherback turtles) were also established for the swordfish fishery as part of 

the 2004 rule. From 2005 through 2014, the Hawaii-based longline fisheries resulted in an 

estimated total of 15 loggerhead and 17 leatherback mortalities in the shallow-set fishery and 16 

loggerhead, 45 leatherback, and 264 olive ridley mortalities in the deep-set fishery (NMFS 

2014a). 

In addition to gear restrictions and bycatch limits, Hawaii longline vessel operators are required 

to take an annual NMFS protected species workshop that instructs fishermen in mitigation, 

handling, and release techniques for sea turtles, seabirds, and marine mammals. Longline 

fishermen must carry and use specific equipment, and follow certain procedures for handling and 

releasing sea turtles, seabirds, and marine mammals that may be caught incidentally. 

In 2012, NMFS issued a biological opinion on the continued operation of the Hawaii shallow-set 

longline fishery (NMFS 2012a). Sea turtle incidental take authorized over a continuous two-year 

calendar period in the ITS of this opinion is as follows: 

• Green: six total, including up to two lethal. 

• Leatherback: 52 total, including up to 12 lethal. 

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• Loggerhead North Pacific DPS: 68 total, including up to 14 lethal. 

• Olive ridley: four total, including up to two lethal. 

In 2014, NMFS issued a biological opinion on the continued operation of the Hawaii deep-set 

longline fishery (NMFS 2014a). Sea turtle incidental take authorized over a three-year period in 

the ITS of this opinion is as follows: 

• Green: nine total, including up to nine lethal. 

• Leatherback: 72 total, including up to 27 lethal. 

• Loggerhead North Pacific DPS: nine total, including up to nine lethal. 

• Olive ridley: 99 total, including up to 96 lethal. 

American Samoa Longline 

The pelagic longline fishery based in American Samoa is a limited access fishery with a 

maximum of 60 vessels under the federal permit program. This fishery targets tunas is the EEZ 

surrounding American Samoa, and has been monitored under a mandatory observer program 

since March 2006. Since the observer program went into effect, annual reported sea turtle 

interactions have ranged from a low of one turtle (in 2007, 2008 and 2012) to a high of 14 turtles 

(in 2011) (NMFS 2007-2017). Observer coverage represents approximately 20 percent of the 

entire fishing effort in this fishery. In 2015, NMFS issued a biological opinion on the continued 

operation of the American Samoa longline fishery (NMFS 2015a). Sea turtle incidental take 

authorized over a three-year period in the ITS of this opinion is as follows: 

• Green: 60 total, including up to 54 lethal. These are divided proportionally by DPS as 

follows: Central South Pacific 50 percent; Southwest Pacific 33 percent; East Pacific 12 

percent; Central West Pacific three percent; and East Indian-West Pacific two percent. 

• Hawksbill: six total, including up to three lethal. 

• Leatherback: 69 total, including up to 49 lethal. 

• Loggerhead, South Pacific DPS: six total, including up to three lethal. 

• Olive ridley: 33 total, including up to 10 lethal. 

West Coast Drift Gillnet Fishery for Highly Migratory Species 

The West coast drift gillnet fishery targets swordfish and thresher sharks in the U.S. EEZ and 

adjacent high seas off the coasts of California, Oregon, and Washington (NMFS 2013a). In 2001, 

NMFS established Pacific Sea Turtle Conservation Areas that prohibit drift gillnet fishing in 

large portions of the historical fishing grounds, either seasonally or conditionally, to protect 

endangered leatherback and loggerhead sea turtle populations (66 FR 44549; August 24, 2001). 

Oregon and Washington state laws currently prohibit landings caught with drift gillnet gear, 

although vessels still fish drift gillnets in federal waters off these states and land their catch in 

California. The drift gillnet fishery can also be closed during El Niño events in order to reduce 

bycatch of loggerhead turtles that move further north on the warm El Niño currents from Mexico 

into U.S. waters (72 FR 31756, June 8, 2007). 

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In 2013, NMFS issued a biological opinion on the continued authorization of the West Coast 

drift gillnet fishery (NMFS 2013a). Sea turtle incidental take authorized over a five-year period 

in the ITS of this opinion is as follows: 

• Green: two total, including up to one lethal. 

• Leatherback: ten total, including up to seven lethal. 

• Loggerhead: seven total, including up to four lethal. 

• Olive ridley: two total, including up to one lethal. 

Pacific Purse Seine Fishery 

The U.S. commercial purse seine fishery operating in the western and central Pacific is managed 

under the authority of the South Pacific Tuna Treaty Act of 1988 (16 U.S.C. Chapter 16C). The 

treaty area, where U.S. and other treaty member nations fish, extends from Palau eastward to the 

Line Islands of Kiribati (approximately 15°N to 15°S and 125°E to 140°W) and includes some of 

the world’s most productive tuna fishing grounds (NMFS 2006a). Although there is potential for 

bycatch mortality or serious injury, based on historical observer reports turtles captured in this 

fishery are generally released alive and healthy (NMFS 2006a). The best available data do not 

indicate that take in the form of mortality is likely to result to any sea turtle species due to 

interactions with the Pacific purse seine fishery. Turtle bycatch in this fishery may result in 

harassment and/or temporary harm. In 2006, NMFS issued a biological opinion for the continued 

authorization of this fishery with an ITS that exempts the following non-lethal take of sea turtles 

annually: 14 green, 14 hawksbill, 11 leatherback, 11 loggerhead, and 11 olive ridley. 

7.14.2 Bycatch of Other ESA-Listed Species 

7.14.2.1 Atlantic and Shortnose Sturgeon 

Atlantic and shortnose sturgeon are taken incidentally in fisheries targeting other species in 

rivers, estuaries, and marine waters throughout their range (ASSRT 2007; Collins et al. 1996). 

Sturgeon are benthic feeders and as a result they are generally captured near the seabed unless 

they are actively migrating (Moser and Ross 1995). Sturgeon are particularly vulnerable to being 

caught in commercial gill nets; therefore, fisheries using this type of gear account for a high 

percentage of sturgeon bycatch and bycatch mortality. Sturgeon have also been documented in 

the following gears: otter trawls, pound nets, fyke/hoop nets, catfish traps, shrimp trawls, and 

recreational hook and line fisheries. 

Estimated rates of Atlantic sturgeon caught as bycatch in federal fisheries are highly variable and 

somewhat imprecise due to small sample sizes of observed trips. An estimated 1,385 individual 

Atlantic sturgeon were killed annually from 1989 to 2000 as a result of bycatch in offshore gill 

net fisheries operating from Maine through North Carolina (Stein et al. 2004b). From 2001-2006 

an estimated 649 Atlantic sturgeon were killed annually in offshore gill net and otter trawl 

fisheries. From 2006 to 2010 an estimated 391 Atlantic sturgeon were killed (out of 3,118 

captured) annually in Northeast federal fisheries (Miller and Shepherd 2011). 

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Several federally regulated fisheries that may encounter Atlantic sturgeon have fishery 

management plans (FMPs) that have undergone section 7 consultation with NMFS. On 

December 16, 2013, NMFS issued a “batched” section 7 biological opinion on the following 

fisheries: Northeast multispecies; monkfish; spiny dogfish; Atlantic bluefish; Northeast skate 

complex; mackerel/squid/butterfish; and summer flounder /scup/black sea bass. The majority (73 

percent) of all Atlantic sturgeon bycatch mortality in New England and Mid-Atlantic waters is 

attributed to the monkfish sink gill net fishery (ASMFC 2007). Observer data from 2001 to 2006 

shows 224 recorded interactions between the monkfish fishery and Atlantic sturgeon, with 99 

interactions resulting in death, a 44 percent mortality rate. For all seven fisheries combined, the 

following take of Atlantic sturgeon was authorized annually: 1,331 trawl interactions of which 

42 may be lethal and 1,229 gill net interactions of which 155 may be lethal. The 2012 NMFS 

biological opinion on the Southeast shrimp trawl fishery exempted the take of Atlantic sturgeon 

as follows: 1,731 total interactions, including 243 captures of which 27 are expected to be lethal 

every three years. In 2012, NMFS provided an updated biological opinion on the Federal shark 

fisheries, including the smoothhound fishery on ESA-listed species. For the federal smoothhound 

fishery and shark fisheries combined, NMFS exempted the take of 321 Atlantic sturgeon over a 

three-year span, with 66 of those takes expected to be lethal. 

Given the high prevalence of gill net and otter trawl use in nearshore coastal and inland fisheries, 

state managed fisheries may have a greater impact on Atlantic and shortnose sturgeon than 

federal fisheries using these same gear types. Commercially important state fisheries that interact 

with sturgeon include those targeting shrimp, Atlantic croaker, weakfish, striped bass, black 

drum, spot, shad, and spiny dogfish. 

7.14.2.2 Gulf Sturgeon 

Direct take of Gulf sturgeon is prohibited in all four states within the current range of the species. 

However, fisheries directed at other species that employ various trawling and entanglement gear 

in areas that gulf sturgeon regularly occupy pose a risk of incidental bycatch. Gulf sturgeon are 

occasionally incidentally captured in state managed shrimp fisheries in bays and sounds along 

the northern Gulf of Mexico. Gulf sturgeon bycatch has also been documented in entanglement 

gear (trammel and gill nets) used to target gar in the Pearl River in southeast Louisiana, where 

(USFWS and NMFS 2009). While state regulations prohibit the taking or possession of gulf 

sturgeon (including roe), there is no available data to determine bycatch capture or mortality 

rates (NMFS 2014c). 

Relocation trawling, associated mostly with the removal of sea turtles to avoid interactions with 

channel dredging and beach nourishment projects, has successfully moved several Gulf sturgeon 

in recent years. These captures in near-shore waters illustrate the relative vulnerability of Gulf 

sturgeon to incidental bycatch in fisheries that use trawls (USFWS and NMFS 2009). 

The Florida “net ban”, approved by voter referendum in November 1994 and implemented in 

July 1995, made unlawful the use of entangling nets (i.e., gill and trammel nets) in Florida state 

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waters. Other forms of nets (i.e., seines, cast nets, and trawls) were restricted, but not totally 

eliminated. Implementation of the net ban in Florida has likely benefited Gulf sturgeon as they 

are residents of near-shore waters during much of their life span. 

Federal fisheries that NMFS authorizes in the Gulf of Mexico have likely had a minor impact on 

Gulf sturgeon. This is because Gulf sturgeon occur in the Gulf of Mexico only during winter 

months and during that time, most migrate alongshore and to barrier island habitats within 

shallower state waters (NMFS 2014c). 

7.14.2.3 Green Sturgeon 

Take of Southern DPS green sturgeon in federal fisheries was prohibited as a result of the ESA 

4(d) protective regulations issued in June of 2010 (75 FR 30714). Green sturgeon are 

occasionally encountered as bycatch in Pacific groundfish fisheries (Al-Humaidhi 2011), 

although the impact of these fisheries on green sturgeon populations is estimated to be small 

(NMFS 2012b). NMFS (2012b) estimates between 86 and 289 Southern DPS green sturgeon are 

annually encountered as bycatch in the state-regulated California halibut bottom trawl fishery. 

Approximately 50 to 250 green sturgeon are encountered annually by recreational anglers in the 

lower Columbia River (NMFS 2015c), of which 86 percent are expected to be Southern DPS 

green sturgeon based on the higher range estimate of Israel et al. (2009). In Washington, 

recreational fisheries outside of the Columbia River may encounter up to 64 Southern DPS green 

sturgeon annually (Kirt Hughes, Washington Dept. of Fish and Wildlife, pers. comm. to NMFS, 

January 30, 2015) cited in (NMFS 2015c). Southern DPS green sturgeon are also captured and 

released by California recreational anglers. Based on self-reported catch card data, an average of 

193 green sturgeon were caught and released annually by California anglers from 2007 to 2013 

(NMFS 2015c). Recreational catch and release can potentially result in indirect effects on green 

sturgeon, including reduced fitness and increased vulnerability to predation. However, the 

magnitude and impact of these effects on Southern DPS green sturgeon are not well studied. 

7.14.2.4 Smalltooth Sawfish 

The primary reason for the decline in smalltooth sawfish abundance has been bycatch in various 

commercial fishing gear, including gill nets, otter trawls, trammel nets, and seines (NMFS 

2010c). The long, toothed rostrum of the smalltooth sawfish causes this species to be particularly 

vulnerable to entanglement in fishing nets. The majority of historical documented landings of 

smalltooth sawfish were from otter trawl fisheries. Total Gulf of Mexico landings dropped 

continually from around five metric tons in 1950 to less than 0.2 metric tons in 1978 (NMFS 

2010c). Data gathered by Louisiana shrimp trawlers from 1945 to 1978 indicate a decline in 

smalltooth sawfish bycatch from a high of 34,900 pounds in 1949 to less than 1,500 pounds in 

most years after 1967 (Simpfendorfer 2002). Anecdotal information collected by NMFS port 

agents indicates that smalltooth sawfish are now taken very rarely in the shrimp trawl fishery. 

Smalltooth sawfish have been captured incidentally in federal shark fisheries using drift gillnets 

and bottom longlines, although interaction rates with these fisheries are relatively low. 

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Smalltooth sawfish are also occasionally captured in recreational hook-and-line fisheries 

targeting shark, red drum, snook, and tarpon (NMFS 2010c). 

The Florida net ban has led to a reduction in the number of smalltooth sawfish incidentally 

captured in nearshore commercial fisheries since 1995. The net ban made unlawful the use of 

entangling nets (i.e., gill and trammel nets) in Florida state waters. Other forms of nets (i.e., 

seines, cast nets, and trawls) were restricted but not completely eliminated. 

7.14.2.5 Nassau Grouper 

Nassau grouper were protected from directed fisheries throughout their U.S. range prior to the 

ESA listing in 2016. In U.S. federal waters, including those federal waters around Puerto Rico 

and the U.S. Virgin Islands take and possession of Nassau grouper have been prohibited since 

1990. Since 1993, a ban on fishing/possessing Nassau grouper was implemented for the state of 

Florida and has since been enacted in all U.S. state waters. The species was fully protected in 

Puerto Rico in 2004 and in the U.S. Virgin Islands in 2006. The 2010 Nassau grouper bycatch 

estimate in U.S. commercial fisheries was 1,044 fish (NMFS 2013c). 

Nassau grouper are also occasionally reported by recreational anglers fishing in Florida and 

Puerto Rico as part of the NMFS Marine Recreational Information Program. Statistical estimates 

of total U.S. recreational catch of Nassau grouper over the past five years (2012 to 2016) range 

from zero to 2,320 fish (NMFS Fisheries Statistics Division, pers. comm. to NMFS OPR, July 

24, 2017). However, these estimates are considered highly imprecise due to the rare event nature 

of Nassau grouper catches in recreational survey data. While the large majority of Nassau 

grouper caught recreationally are reported as released alive, there is little information available to 

estimate recreational fishery post-release mortality rates for this species. 

7.14.2.6 Atlantic Salmon 

Commercial bycatch is not thought to be a major source of mortality for GOM DPS Atlantic 

salmon. Beland (1984 cited in (Fay et al. 2006b) reported that fewer than 100 salmon per year 

were caught incidental to other commercial fisheries in the coastal waters of Maine. A more 

recent study found that bycatch of Maine Atlantic salmon in herring fisheries is not a significant 

mortality source (ICES 2004). Commercial fisheries for white sucker, alewife, and American eel 

conducted in state waters also have the potential to incidentally catch Atlantic salmon. 

Recreational angling occurs for many freshwater fish species throughout the range of the GOM 

DPS Atlantic salmon. As a result, Atlantic salmon can be incidentally caught (and released) by 

anglers targeting other species such as striped bass or trout. Studies on the effects of catch and 

release on trout and salmon have concluded that exhaustive exertion may result in significant 

physiological disturbances including mortality (Brobbel et al. 1996; Graham et al. 1982; Wood et 

al. 1983a). Conditions that contribute to Atlantic salmon post-release mortality include elevated 

water temperatures, exposure of the fish to air after capture, extremely soft water, low oxygen 

levels, low river flow and improper handling (Booth et al. 1995). The potential also exists for 

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anglers to misidentify juvenile Atlantic salmon as brook trout, brown trout, or landlocked 

salmon. A maximum length for landlocked salmon and brown trout (25 inches) has been adopted 

in Maine in an attempt to avoid the accidental harvest of sea-run Atlantic salmon due to 

misidentification. 

7.14.2.7 Scalloped Hammerhead 

Scalloped hammerhead sharks are both targeted and taken as bycatch in many global fisheries 

(e.g., bottom and pelagic longlines, coastal gillnet fisheries, artisanal fisheries). This species is 

highly desired for the shark fin trade because of its fin size and high fin ray count. In the United 

States, scalloped hammerhead sharks are mainly caught as bycatch in longline and coastal gillnet 

fisheries and are known to suffer high post-release mortality rates (76 FR 72891). Many of the 

scalloped hammerhead sharks captured in U.S. fisheries are not from an ESA-listed DPS since 

the only non-foreign listed DPSs are the Central and Southwest Atlantic, Eastern Pacific, and 

Indo-West Pacific. 

The NMFS Pelagic Observer Program reported 100 scalloped hammerhead bycaught in the U.S. 

Atlantic pelagic longline fishery in 2015, including 51 released dead (NMFS 2015d). Another 

126 unidentified hammerhead sharks were also reported captured in this fishery, presumably 

some of which were scalloped hammerheads. In 2014, 138 scalloped hammerheads were caught 

during observed bottom longline trips in the sandbar shark research fishery in the Gulf of Mexico 

and Southern Atlantic (NMFS 2015d). In 2015, seven scalloped hammerheads were caught (five 

of which were released dead) during observed Southeast sink gillnet trips targeting Atlantic 

sharpnose, blacknose, and other shark species (NMFS 2015d). In the Pacific, shark bycatch 

occurs primarily in the Hawaii-based pelagic longline fishery. An observer program has been in 

place since 1995 with targeted coverage of 25 percent in the deep-set sector and 100 percent in 

the shallow-set sector. Observer data from 1995-2006 indicated a very low catch of scalloped 

hammerhead sharks in this fishery (56 individuals on 26,507 sets total, both fishery sectors 

combined) (Miller et al. 2013). Scalloped hammerheads are also occasionally caught in U.S. 

recreational fisheries, although recreational catch estimates are often unreliable due to the rare 

event nature of capture and species identification issues. 

7.15 Sea Turtle Strandings 

As discussed above, bycatch studies are often compromised by limited data, lack of spatial 

coverage, and difficulty estimating the effects of post-capture mortality or reduced fitness 

(Lewison et al. 2004a; Tomás et al. 2008). Supplemental information regarding the effects of 

bycatch and other potential threats on sea turtles can be derived from strandings data (i.e., turtles 

that wash ashore, dead or alive, or are found floating dead or alive, generally in a weakened 

condition). In this section we summarize information obtained from sea turtle strandings 

program reports and published papers based on strandings in U.S. waters and globally. 

Previous studies have used turtle strandings data to evaluate sea turtle health, age, size 

composition, diet, reproductive status, and population trends. The cause of stranding (i.e., 

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bycatch, ship strikes, biotoxins, and disease) can sometimes be inferred from stranded turtles, 

although it is often recorded as “unknown” because there is no clear indicator (i.e., lesions, 

tumors, fishing gear) on the carcass or because the carcass is too decomposed to determine. 

Fishery interactions, in particular, can be difficult to assess in stranded turtles as some fishing 

gears leave little or no evidence on the body (either in the form of attached gear or specific 

injuries), while others cannot always be attributed with certainty to a particular fishery. In 

addition, bycaught turtles that are released alive may be more susceptible to other mortality 

factors (e.g., ship strikes, disease) due to increased stress and/or injuries suffered during capture. 

The relationship between unobserved turtle mortality at sea and observed strandings is not wellstudied (Hart et al. 2006). Because carcasses decompose while entrained in currents and eddies, 

the number of recorded sea turtle strandings likely represents a minimum estimate of mortality 

(Epperly et al. 1996). Epperly et al. (1996) compared estimates of sea turtle mortalities from 

North Carolina’s winter trawl fishery in 1991-1992 to the number of turtles stranded on beaches 

adjacent to the fishing grounds. They found that the number of dead turtle strandings accounted 

for only 7 to 13 percent of the estimated fishery-induced mortalities. They attributed this 

discrepancy to offshore bottom currents, which normally transport lifeless turtles away from the 

beach during the winter. 

Although inferences from reported strandings may be subject to a number of caveats, when 

considered over wide spatio-temporal extents and in conjunction with other data sources, 

strandings data can offer useful insights into turtle distributions, life histories, and vulnerability 

to various sources of mortality (Tomás et al. 2008). While the cause of a turtle stranding is not 

always determinable, strandings data have been used by researchers to indicate the relative 

impacts of various anthropogenic and natural stressors on turtle populations. 

Long-term time series strandings data from several studies suggest that anthropogenic factors, 

particularly fisheries, are responsible for a relatively large proportion of mortalities in many sea 

turtle populations globally. Casale et al. (2010) used stranding data to investigate mortality 

factors in loggerhead turtles stranded in the waters around Italy from 1980-2008. They found that 

mortalities due to anthropogenic factors, primarily from bycatch, were two to three times as 

prevalent as natural mortalities in stranded loggerheads. In addition to bycatch in longlines and 

trawls, entanglement in ghost-gear or other debris and boat strikes were identified as important 

anthropogenic sources of mortality in this study. 

Orós et al. (2016) analyzed the causes of stranding of 1,860 loggerhead turtles admitted to a 

rehabilitation center on Gran Canaria Island, Spain from 1998 to 2014. Entanglement in fishing 

gear and/or plastics accounted for 64 percent of the strandings with a known cause (20 percent 

were recorded as “unknown” cause), followed by ingestion of hooks and monofilament lines (15 

percent), infectious disease (7 percent), and boat strike (7 percent). The cause of mortality could 

not be determined for 70 percent of the 226 loggerheads that were dead when admitted to the 

rehabilitation center; 12 percent died from entanglement, 9 percent from trauma, and 6 percent 

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from ingestion of hooks (Orós et al. 2016). This study also reported a decrease in the number of 

annual strandings attributed to crude oil after 2006, presumably linked to the designation of the 

Canary Islands as a Particularly Sensitive Sea Area in 2005 by the International Maritime 

Organization (Camacho et al. 2013). 

Panagopoulos et al. (2003) used strandings data from 1992 to 2000 to evaluate causes of sea 

turtle mortality in the waters around mainland Greece and the Greek Islands. A total of 1,080 

turtle strandings were reported, of which nearly 93 percent were loggerheads. About 80 percent 

of turtles that were recovered with injuries showed signs of incidental capture in fishing gear. Of 

these, 46 percent were injured due to hook ingestion and/or entanglement; the remaining 34 

percent were intentionally hit on the head, presumably after incidental capture in fishing gear 

(Panagopoulos et al. 2003). 

Tomás et al. (2008) analyzed sea turtle strandings (n = 619) over a 14 year period (1993 to 2006) 

from the Mediterranean Sea near Valencia in eastern Spain. Loggerhead turtles accounted for 98 

percent of recorded strandings. Interactions with longline fisheries accounted for 43.5 percent of 

observed stranding for which a likely cause was identified. 

Strandings data have also been used to document the relative impact of disease in sea turtles, 

particularly the tumor forming disease FP (see section 7.6 for more details on this disease). 

Elevated mortality rates dues to the combination of disease and fisheries bycatch can be 

particularly impactful on turtle populations. Chaloupka et al. (2008b) investigated cause-specific 

temporal and spatial trends in sea turtle strandings in the Hawaiian Archipelago over a 22-year 

period (1982–2003). Green turtles comprised 97 percent of the 3,861 strandings recorded over 

this period. Fibropapillomatosis was the most common known cause of the green turtle 

strandings in this study (28 percent), followed by hook-and-line fishing gear-induced trauma (7 

percent), gill net fishing gear-induced trauma (5 percent), boat strike (2.5 percent), and shark 

attack (2.7 percent) (Chaloupka et al. 2008b). Miscellaneous causes comprised 5.4 percent of 

strandings whereas 49 percent of green turtle strandings could not be attributed to any known 

cause. Estimated mortality rates (i.e., conditional probability) were 88 percent for FP, 69 percent 

for gill net gear and 52 percent for hook-and-line gear. 

Poli et al. (2014) analyzed sea turtle strandings on the coast of Paraíba State, Northeastern Brazil, 

from August 2009 to July 2010. A total of 124 strandings were recorded in this period, 85 

percent of which were green turtles and 12 percent hawksbill. The presence of external tumors, 

suggestive of FP, was found in nearly one-third of the strandings in this study. Twenty 

individuals had synthetic anthropogenic debris in the gastrointestinal tract. Other traces of human 

interactions were observed in 43 individuals, such as injuries caused by entanglement in fishing 

lines or nets, collisions with vessels, direct contact with oil spills and lesions caused by sharp or 

spiked objects (Poli et al. 2014). 

Sea turtle mass stranding events have also been documented in the literature. Alava et al. (2005) 

studied the olive ridely mass mortality events that occurred in Ecuador in 1999. From August 

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through September of that year a total of 1,113 turtles were stranded (99 percent were olive 

ridleys). The cause of this stranding event was not clear. The majority of dead turtles in the mass 

stranding events did not exhibit discernable injuries or other external damage that might have 

suggested prior interactions with fisheries. Other possible alternative explanations for the 

strandings put forward by the authors include thermal stress or hypothermia due to the presence 

of cold currents such as the Humboldt Current and the presence of an epizootic event or outbreak 

(e.g., bacteria or virus) that affected migratory olive ridleys in waters off Ecuador. 

7.15.1 Sea Turtle Stranding and Salvage Network 

The Sea Turtle Stranding and Salvage Network (STSSN) was established in the southeastern 

United States and Gulf of Mexico in 1980, in Hawaii in 1982, and in the NMFS Southwest 

Region through the California Marine Mammal Stranding Network in 1983 in response to sea 

turtles washing up on beaches or floating in the water, dead or in need of assistance. The STSSN 

is organized through a structure that consists of Atlantic, west Pacific, and east Pacific 

coordinators, and there is a coordinator for each state. The network consists of trained 

volunteers, municipal, state and federal employees and their designated agents who operate 

under the direction of the state and national coordinators. Network participants document marine 

turtle strandings and incidental captures, including any fishing gear or other marine debris 

associated with the stranded turtle, in their respective states and enter that data into a central 

database. 

Based on data collected by NOAA, in the Atlantic and Gulf of Mexico between 2005 and 2015, 

3,928 in-water stranded sea turtles were reported to the STSSN (NMFS 2016e). The species 

composition of these events was 1,641 loggerheads, 1,659 green turtles, 47 leatherbacks, 80 

hawksbills, 390 Kemp's ridleys and 111 unidentified species. The term “in-water stranded sea 

turtles” can be described as any animal encountered that is cold stunned, sick, injured, entangled 

or dead. In the Hawaiian Islands, 972 in-water strandings were reported between 2005 and 2015. 

The species composition of these events was 913 greens, one leatherback, 47 hawksbills, six 

olive ridleys and one unknown turtle species. 

Leatherbacks, green turtles, loggerheads, and olive ridleys off the United States west coast face 

anthropogenic and natural threats that can result in both live and dead strandings. However, 

reported turtle strandings off the West Coast are significantly less common compared to 

strandings off the Atlantic and Gulf of Mexico coasts or Hawaii. In Oregon and Washington, 41 

in-water strandings were reported between 2005 and 2015: 14 greens, one leatherback, four olive 

ridleys and one unknown species. In California, 60 sea turtles have been reported through the 

STSSN from 2005 to 2015: four loggerheads, 45 greens, five leatherbacks, four olive ridleys and 

two unknown species (NMFS 2016e). About 350 turtle strandings along the entire west coast 

were reported to NMFS between 1958 and 2009 (LeRoux 2012). The causes of these strandings 

included illness-related, marine debris (entanglement and ingestion), boat collisions, fisheries 

interactions, and power plant entrainments. Approximately one-third of the stranding incidents 

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involved the capture and release of live turtles, the majority of which were stranded due to power 

plant entrainment. The remaining two-thirds involved either live animals that were transported to 

rehabilitation facilities and died or animals found dead; in many cases the direct cause of death 

was not determined (LeRoux 2012). 

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8 EFFECTS OF THE ACTION 

Section 7 regulations define “effects of the action” as the direct and indirect effects of an action 

on the species or critical habitat, together with the effects of other activities that are interrelated 

or interdependent with that action, that will be added to the environmental baseline (50 C.F.R. 

§402.02). This effects section is organized following the stressor, mitigation, exposure, response, 

risk assessment framework. 

The jeopardy analysis relies upon the regulatory definition of “to jeopardize the continued 

existence of a listed species,” which is “to engage in an action that would be expected, directly or 

indirectly, to appreciably reduce the likelihood of both the survival and recovery of a listed 

species in the wild by reducing the reproduction, numbers, or distribution of that species” (50 

C.F.R. §402.02). Therefore, the jeopardy analysis considers both survival and recovery of the 

species. 

The destruction and adverse modification analysis considers whether the action produces “a 

direct or indirect alteration that appreciably diminished the value of critical habitat for the 

conservation of a listed species. Such alterations may include, but are not limited to, those that 

alter the physical or biological features essential to the conservation of a species or that preclude 

or significantly delay development of such features” (50 C.F.R. 402.02). 

8.1 Stressors Associated with the Proposed Action 

The following research activities that would be authorized under the Program create stressors 

that could pose a risk to ESA-listed sea turtles: 

1) Research vessel operations create stressors of vessel presence, sounds, and potential 

vessel/propeller strikes. 

2) Aerial surveys using manned or unmanned aircraft create stressors of aircraft presence and 

sounds. 

3) Underwater tracking of sea turtles by ROVs and AUVs, create stressors of vehicle 

presence, sound, and potential collision with vehicle body or attachments (e.g., tethers). 

4) Acoustic surveys involving sonar transducers used to detect sea turtles, create stressors of 

introducing man-made sounds into the environment. 

5) Capture of sea turtles is a stressor that may result from any of the following authorized 

methods: hand capture, dip net, cast (or throw) net, breakaway hoop net, encircle (or 

strike) net, entanglement (or gill) net, pound net, seine net, or trawl. 

6) Recapture of sea turtles using any of the capture methods identified above. 

7) Holding, handling, and transport of sea turtles for procedures, measurements and 

monitoring vital parameters. 

8) Morphometric measuring and weighing sea turtles and the monitoring of vital parameters. 

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9) Turtle shell marking using paint or shell etching. 

11) Oral and ophthalmic examinations that may employ fluorescein staining or use of a slit 

lamp. 

12) Piercing skin for attachment of a flipper tag and injection of PIT tag under sea turtle skin. 

13) Injection of oxytetracycline for aging studies. 

14) Biological sampling including: epibiota collection, swabs, skin biopsy, scute scraping, 

blood sampling, tear collection, soft tissue biopsy, and urine/fecal collection. 

15) Gastric lavage procedure that involves orally inserting plastic tubing into the turtle’s 

esophagus and pumping of water to discharge stomach contents. 

16) Insertion of a laparoscope/laparoscopic biopsy instrument through small surgical incision 

and use of a trocar to penetrate the body cavity and insert a cannula for passage of the 

endoscope; sampling internal organs and tissues as part of a laparoscopic procedure, and 

the use of local or general anesthetization depending on the procedure being performed. 

17) Fecal collection that may involve using a lubricated, gloved finger, or by fecal loops, 

swabs, or cloacal lavage using a rubber catheter. 

18) Attachment of suction-cups to turtle shell and attachment of turtle tags using an adhesive 

such as epoxy, marine putty, resin, fiberglass strips, neoprene, or silicone. 

19) Drilling the turtle carapace for attachment of acoustic tags. 

20) Insertion of a stomach pill transmitter into turtle’s esophagus. 

21) Non-invasive imaging techniques including X-rays, CT, MRI, and ultrasound. 

The following potential stressors associated with activities authorized under the Program could 

pose a risk to ESA-listed non-target species (i.e., Atlantic salmon, smalltooth sawfish, Atlantic 

sturgeon, shortnose sturgeon, green sturgeon, Gulf sturgeon, Nassau grouper, and scalloped 

hammerhead) are: 

1) Interactions between research vessels and non-target fish species including effects of 

vessel sounds, physical presence, and potential vessel/propeller strikes 

2) Incidental capture of non-target species in entanglement (or gill) nets, pound nets, seine 

nets, or trawl nets 

3) Incidental recapture of non-target species in any of the capture methods above 

8.2 Mitigation to Minimize or Avoid Exposure 

As a condition of their permit, researchers will be required to follow specific protocols to avoid, 

minimize, and mitigate the unintended detrimental effects that may result from research activities 

such as capture, handling, or performing various invasive procedures. Specific permit conditions 

to mitigate adverse effects on both target and non-target ESA-listed species are described for 

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each research activity in Section 3.4 above, with more details provided in Appendix C. In 

addition to standard protocols, a permit condition will require each researcher to consider 

additional precautionary measures that can be taken to further minimize impacts on individual 

sea turtles. 

Mitigation to minimize or avoid exposure of ESA-listed species to adverse effects is a core 

principle of the Permits Division’s mission to “protect and conserve marine mammals and 

threatened and endangered species by providing special exceptions for take, import, and export 

that maximize recovery value and minimize individual and cumulative impacts as directed under 

ESA section 10(a)(1)(A) and its regulations” (NMFS 2017a). Specific mitigation criteria the 

Permits Division considers when issuing permits include: (1) whether alternative nonendangered species or population stocks can and should be used, (2) how the research is not 

unnecessarily duplicative of other work, (3) how the applicant will coordinate activities with 

other Permit Holders; and (4) how the applicant will minimize impacts of the activities, in 

particular to avoid or minimize mortality. 

In addition to the minimization and avoidance measures in the research permit or specified as a 

condition of the permit, the Permits Division has proposed an adaptive management approach 

that will continuously update and improve the mitigation measures. The mitigation measures 

included in sea turtle research permits authorized under the program can be modified by the 

Permits Division at any time based on investigation into a researcher reported incident of take, 

new information regarding potential impacts of authorized activities, or demonstrated 

improvements to the standard protocols for turtle research. 

8.3 Sea Turtle Exposure to Stressors 

Exposure analyses identify the ESA-listed species that are likely to co-occur with the actions’ 

effects on the environment in space and time, and identify the nature of that co-occurrence. The 

exposure analysis also identifies, as possible, the number, age or life stage, and gender of the 

individuals likely to be exposed to the actions’ effects and the population(s) or subpopulation(s) 

those individuals represent. 

The annual number of sea turtle takes requested by researchers, authorized by the Permits 

Division, and actually conducted is expected to fluctuate somewhat over the course of the 

Program. Requested takes may vary due to changes in researcher objectives or available funding 

sources. Authorized takes may vary due to changes in requested take levels, sea turtle population 

sizes, trends or health, or other factors affecting maximum mortality limit levels. Actual takes 

may also vary due to changes in authorized take levels, distribution and abundance of sea turtles, 

and effectiveness of capture gear. Authorized take numbers for ‘survey-only’ methods (Section 

3.5) are expected to significantly decrease because of NMFS’ new internal policy defining 

‘harass’ under the ESA (NMFS 2016c). Thus, a significant portion of the takes authorized for 

stand-alone surveys should no longer be needed. Future authorized take numbers are expected to 

be more in line with the annual reported take data for surveys that occur in conjunction with 

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vessel-based captures or research procedures. Despite the unpredictable nature of sea turtle 

directed research total take numbers, the proposed lethal take limits establish program-wide 

limits on the number of sea turtles that may be killed during research activities. 

Data from the past ten years of sea turtle research (June 2007 to May 2017) represent the best 

available information regarding the exposure of sea turtles to activities authorized as part of the 

Program (Table 22). However, we recognize that these numbers are subject to change in the 

future. 

Table 22. Total authorized takes of sea turtles by capture method in permits from June 

2007 to May 2017. 

Species 

Sea Turtle Capture Method 

Hand 

or Dip Tangle Seine Cast Pound Trawl Breakaway Hoop 

Encircle 

Strike 

Green 14,509 11,672 1,890 4,180 1,480 1,227 2,285 1,210 

Hawksbill 6,250 2,126 215 2,465 215 185 1,115 95 

Kemp’s ridley 4,590 4,034 1,400 2,475 1,400 1519 2,005 1,680 

Leatherback 1,255 174 150 575 150 84 885 130 

Loggerhead 10,663 5,337 3,076 5,350 3,020 3,933 4,250 1,030 

Olive ridley 1,936 146 106 100 50 15 100 0 

Unidentified 213 136 136 211 136 36 213 2 

The number of animals that may be taken non-lethally in the Permit Division’s program as a 

whole will be unlimited. However, the Permits Division expects the number of applicants to 

remain at current levels for the foreseeable future (NMFS 2017a). Thus, they do not expect the 

overall magnitude of cumulative authorized take numbers for sea turtles in the Program to 

increase significantly. Modest growth in reported takes annually for each capture method is 

estimated at approximately ten percent (NMFS 2017a), with the exception of trawling captures 

which are expected to increase by approximately 25 percent (Amy Hapeman, NMFS OPR, pers. 

comm. to Maureen Trnka, NMFS OPR, November 21, 2017) (Table 23). 

In order to insure that the proposed action is not likely to jeopardize any of these species, we 

analyze the impacts to the species as if 100 percent of the average authorized sea turtle capture 

takes over the last ten years will occur each year into the foreseeable future. 

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Table 23. Number of sea turtle exposures by capture type projected over the next ten 

years based on previously authorized takes and future growth estimates for each 

method. 

Species 

Sea Turtle Capture Method 

Hand or 

Dip 

(+10%) 

Tangle 

(+10%) 

Seine 

(+10%) 

Cast 

(+10%) 

Pound 

(+10%) 

Trawl 

(+25%) 

Breakaway 

Hoop 

(+10%) 

Encircle 

Strike 

(+10%) 

TOTAL 

(10 

years) 

Green 15,960 12,839 2,079 4,598 1,628 1,534 2,514 1,331 42,482 

Hawksbill 6,875 2,339 237 2,712 237 231 1,227 105 13,960 

Kemp’s 

ridley 5,049 4,437 1,540 2,723 1,540 1,899 2,206 1,848 21,241 

Leatherback 1,381 191 165 633 165 105 974 143 3,756 

Loggerhead 11,729 5,871 3,384 5,885 3,322 4,916 4,675 1,133 40,915 

Olive ridley 2,130 161 117 110 55 19 110 0 2,701 

Unidentified 234 150 150 232 150 45 234 2 1,197 

TOTAL 

(10 years) 43,358 25,988 7,670 16,892 7,096 8,749 11,938 4,562 

Based on past research and sea turtle takes, most research authorized under the Program will be 

for the take of juveniles, subadults and/or adults often in some grouped combination (e.g., 

subadult and adults). Sea turtle takes are usually authorized in nearshore waters (i.e., neritic 

zone). Very few permits authorize takes specifically for post-hatchlings as only a few researchers 

have objectives or study designs specific to this life stage. In most cases where researchers have 

requested takes for posthatchlings, these takes are authorized in combination with other life 

stages because sampling of this life stage is opportunitstic and/or the capture gear is nonselective. In almost all cases, takes are authorized for males and females combined; it is rare that 

a researcher has an objective that is gender-specific. 

Additionally, we cannot predict the number of research procedures that will be performed on 

individual turtles. In general, most turtles captured are typically subjected to a basic suite of 

procedures including morphometrics (e.g., weight, measurements), identification marking (e.g., 

flipper tag, PIT tag), marking (e.g., carapace painting, shell etching), and sampling (e.g., blood, 

tissue, fecal, urine). Some turtles will be subjected to additional procedures such as transmitter 

attachment(s), gastric lavage, laparoscopy, internal tissue sampling, and non-invasive imaging. 

In order to insure that the action is not likely to jeopardize listed sea turtles, we base our analysis 

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on the estimated number of sea turtles captured (Table 23), with the assumption that all captured 

turtles could be exposed to any research procedures that are a part of the Program. 

Although the Program would not establish limits on sub-lethal takes from capture or research 

procedures, by proxy sea turtle captures are limited in effect by the lethal take limits. That is, if a 

ten-year lethal take limit is reached for a particular species (or DPS) and ocean basin, no more 

captures (and therefore no more procedures) would be authorized within that ten-year period for 

that species (or DPS) and ocean basin. To reduce the likelihood of this occurring, the Permits 

Division will closely monitor and manage lethal take limits, conservatively authorizing lethal 

take within individual permits, and retaining some lethal take as “reserve” for unexpected events 

that may result in higher levels of mortality than anticipated. Any mortality that is caused by a 

research activity will be reported promptly due to permit terms and conditions. Further, the 

circumstances that lead to the death of the turtle, will be assessed and reviewed under the 

adaptive management process, which could lead to changes in the research techniques or 

activities conducted in the future. In addition, consistent with its obligations under the ESA, the 

Permits Division will effectively limit captures and procedures to only those it determines are 

necessary to achieve the objectives of research that will aid in the recovery of ESA-listed 

species. 

8.4 Sea Turtle Responses to Stressors 

The potential and likely responses of sea turtles exposed to stressors associated with the research 

activities is summarized below consistent with the stressors previously identified (Section 8.1). 

8.4.1 Research Vessel Interactions 

Interactions between research vessels and sea turtles create stressors of vessel presence, sounds, 

and potential vessel/propeller strikes. Research vessels will be used to observe, track, and pursue 

turtles for capture. They will also serve as platforms to deploy various equipment such as AUS, 

ROV, autonomous underwater vehicles, or acoustic monitoring devises. 

The mere presence of research vessels is not known to disturb sea turtles. Boats routinely 

approach sea turtles in the wild with turtle exhibiting little to no behavior response. Sounds 

created by the vessel are also not known to elicit a strong behavioral response from sea turtles. 

The combination of vessel presence (turtle visually noticing the vessel) and the sounds produced 

by the vessel may create a minor behavioral response of swimming or diving away from the 

vessel. Such behavior is within the normal repertoire of sea turtle behavior. Vessels deploying 

equipment to capture or monitor sea turtles generally operate at low speeds (two to seven knots) 

when near sea turtles. 

The reporting of striking of a sea turtle by a permitted researcher has always been a requirement 

of research permits. Throughout the history of the Permits Division, no reports of a vessel 

striking a sea turtle have been submitted. Researchers engaging in the hand capture of sea turtles 

would use vessels to closely approach turtles. Purposeful close approach to sea turtles to hand 

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capture it may increase the risk of striking a turtle. Researchers would use highly skilled vessel 

operators that can safely position the vessel near the target individual, only near enough for a 

researcher to jump near the target sea turtle. Risk of vessel strike is not an issue for cast or dip 

netting because vessels will be stopped or moving very slowly when sea turtles are captured. 

Because, no permit holders have reported a vessel strike of a sea turtle in the history of the 

Permit Division’s program we believe there is very low risk of vessel-strike to sea turtles. We do 

not expect vessel strikes to occur while encirclement netting is conducted as the vessel is making 

a wide circle around the animal rather than directly approaching it in close proximity. 

In summary we expect the responses, if any, of sea turtles to research vessels to be minor 

behavioral responses in the form of swimming away from the vessel or diving below the water 

surface. 

8.4.2 Surveys by Manned and Unmanned Aircraft 

Aerial surveys using manned aircraft create stressors of aircraft presence and sound. Sea turtles 

may or may not respond to the presence of a manned aircraft, depending upon the altitude of and 

proximity of the aircraft to the turtle. Studies of the reaction of sea turtles to aerial surveys are 

not available in the literature. This may be because scientists and researchers have generally not 

considered aerial surveys to pose a substantial threat to sea turtles. Although little data exist for 

sea turtle research, manned aerial surveys have been conducted on marine mammals by several 

researchers (e.g., (Acevedo-Whitehouse et al. 2010; Durban et al. 2015; Goebel et al. 2015; 

Hodgson et al. 2013)). Marine mammals show either no reaction to the aircraft, or minor shortterm evasive behaviors such as swimming away or diving. 

In decades of aerial surveys by the NMFS Southwest Fisheries Science Center, researchers have 

very rarely observed behavior indicative of a startle or evasive response (e.g., change in travel 

direction or surfacing behavior) by turtles when flying overhead at 650 feet in altitude in 

Partenavia and Twin Otter aircraft; these two aircraft types are among the quietest available for 

marine wildlife surveys. Other sea turtle researchers have reported minor swimming or diving 

responses to aerial surveys. 

Unmanned aircraft (i.e., UAS) are a technological advance of already permitted and analyzed 

aerial surveys using manned aircraft. Since UASs are smaller and quieter than manned aircraft, 

they are expected to result in similar or less startle and evasive responses in the sea turtles than 

manned aircraft. In general, UAS platforms elicit fewer, if any, behavioral responses compared 

to manned aircraft or vessel approaches on targeted marine mammal species (Smith et al. 2016). 

The NMFS Southwest Fisheries Science Center used UAS over killer whales and found that at 

thirty feet, there were no behavioral reactions to UAS. The use of UAS was permitted in 2008 

over humpback whales in Alaska, and no observed reactions were noted in the permit annual 

report (see Table 1 in (Smith et al. 2016). Because researchers are just starting to employ UAS 

for sea turtle research, the Permits Division is gathering information on behavioral responses of 

sea turtles to their operation to validate that assumption. To date, the information provided by 

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researchers suggests that even minor behavioral responses rare when UAS are operated for 

momentary observation of sea turtles. 

Sea turtles may exhibit temporary startle and evasive such as swimming and diving behaviors in 

response to manned or unmanned aircraft. Swimming and diving are normal and routine sea 

turtle behaviors that may be associated with stressor avoidance, foraging, or migration. In 

addition, researchers would be required as a condition of a permit to document any behavioral 

responses to inform management decisions on the continued and future use of UAS. 

8.4.3 Underwater Tracking by Remotely Operated and Autonomous Vehicles 

The tracking of sea turtles using ROV or autonomous underwater vehicles is new technology 

developed within the last decade. This type of research is expected to continue and increase 

because it allows researchers to collect behavioral and biological data, and in some cases, 

alleviates the necessity to attach instruments to target animals. We expect that sea turtles would 

have little to no response to underwater tracking by ROV and AUV units. The target animals 

may not even be aware of the vehicle’s presence. Animals that are aware of its presence may 

have varied behavioral responses ranging from approaching the unit for investigation to a startle 

response or evasive behaviors, moving away from the vehicle (Smolowitz et al. 2015). 

Smolowitz et al. (2015) documented a suite of intra-and inter-specific behaviors by sea turtles 

indicating that the presence of the ROV did not appear to substantially disrupt the species’ 

behavior. Likewise, Patel et al. (2016) noted that any response to the ROV were seen only 7.3 

percent of the time. When turtles did react, responses were brief and included circling the ROV, 

or rubbing, biting or head butting the vehicle. Animals are expected to resume their prior 

behaviors and recover from any incurred stress as soon as the encounter ends. 

The tethers on ROVs are thick and somewhat rigid, such that we do not believe they pose a 

substantive risk of entanglement to the target animals or to other marine life. Smolowitz et al. 

(2015) reported no entanglements in encounters with 70 loggerhead sea turtles using a 250 meter 

tether. Patel et al. (2016) noted a couple cases in which the tether became briefly hooked around 

a flipper of a sea turtle from which the animal quickly swam out. 

Sea turtles may exhibit temporary startle and evasive such as swimming away from an ROV or 

autonomous underwater vehicle. They may also approach an underwater vehicle to investigate, 

bump, or rub it. 

8.4.4 Acoustic Surveys and Sonar Transducers 

Multibeam, side-scan, and imaging sonars (e.g., DIDSON) are acoustic devices used to detect 

sea turtles. High-frequency sound pulses (120 kHz to 1.8 MHz) are transmitted by the sonar 

transducers and reflect off the seafloor and objects in the water column, producing real-time 

acoustic backscatter images of bottom topography and location of sea turtles in the study area. 

When testing the effectiveness of a particular type of acoustic gear for detecting and/or imaging 

sea turtles, turtles may be followed at a distance once they are detected, to keep them within the 

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acoustic beam. The duration of this type of directed acoustic effort will not exceed five to ten 

minutes. 

All of the acoustic survey methods are remote activities that involve no more than brief 

encounters with the target sea turtles. Sea turtles may exhibit temporary startle and evasive such 

as swimming and diving behaviors in response to acoustic devices similar to behaviors that may 

be associated with stressor avoidance, foraging, or migration. 

8.4.5 Capture 

Capture of sea turtles by hand, dip net, cast net, breakaway hoop, encircle net, entanglement net, 

pound net, seine net and trawl net is a stressor that may involve the brief pursuit/following of 

animals by the research vessel. Capture may be selective for an identified individual or nonselective as is the case with pound, seine or trawl nets. Some nets are continuously monitored 

with others are not. Potential responses to capture are rapid swimming, diving, biting, and other 

attempts to escape, and physiological stress. 

We have previously noted that swimming and diving are routine and normal behaviors that are 

associated with predator avoidance, feeding, and migration. Biting and other aggressive 

behaviors or a prolonged increase in swimming effort in attempts to evade capture are expected 

in some turtles. This behavior may last several seconds to several minutes until individuals 

escape or are captured. Capture can cause stress responses in sea turtles (Gregory 1994; Gregory 

and Schmid 2001; Hoopes et al. 1998; Jessop et al. 2003; Jessop et al. 2004; Thomson and 

Heithaus 2014). The physiological response of releasing stress hormones has been documented 

by multiple researchers (Gregory et al. 1996; Gregory and Schmid 2001; Harms et al. 2003; 

Hoopes et al. 2000; Stabenau et al. 1991). This stress is similar to the stress of evading a predator 

and may incur a metabolic cost of energy expected during evasive behavior as well as forgone 

foraging opportunities. 

The Program’s mitigation measures are designed to minimize the stress of capture on sea turtles. 

Because many of the effects of capture are similar across methods, discussion of effects are 

grouped here for efficiency. 

8.4.5.1 Selective Capture Methods: Hand Capture, Dip Net, Cast Net, Breakaway Hoop, and 

Encircle Net 

Capture by hand, and with cast, breakaway hoop, dip and encircle nets pose low risk to the target 

sea turtles because researchers are able to immediately remove captured individuals from the 

water and eliminate the possibility of drowning or other injury. Hoop netting has been used 

successfully by researchers to catch pinnipeds and small cetaceans (Asper 1975). This method 

has been adapted for turtles by researchers at Dalhousie University and has been employed 

successfully on Atlantic leatherbacks in a study by researchers from the National Aquarium in 

Baltimore as well as by NMFS science center staff to capture loggerhead, green, olive ridley, and 

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leatherback sea turtles in the Eastern Tropical Pacific. These capture methods are considered 

simple and non-invasive but may result in raised levels of stressor hormones. 

Although individuals will be rapidly removed from these net types, responses associated with 

subsequent stressors will continue. For example, handling has been shown to result in 

progressive changes in blood chemistry indicative of a continued stress response (Gregory and 

Schmid 2001; Hoopes et al. 2000). Studies conducted to assess the effects of direct capture on 

Atlantic leatherback turtles indicated relatively stable physiologic status and mild adrenocortical 

stress response associated with one-hour capture duration, and supported the general safety of 

direct capture in this species (Innis et al. 2010). Further, given that captures for leatherbacks will 

be performed with a veterinarian on-board vessels to continuously monitor the turtle and 

respond, if necessary, according to established veterinarian approved protocols, the risk of 

serious injury or mortality from hoop net capture is not expected for this species. There is a 

minimal risk of vessel-strike to sea turtles with the method of hand capture, and little to no risk 

for cast nets, dip nets, and encirclement netting as discussed in the Research Vessel Interaction 

Section (8.4.1). 

The NMFS Pacific Islands Fisheries Science Center Marine Turtle Research Program captures 

ESA-listed sea turtles (green, hawksbill, loggerhead, leatherback and olive ridley) using various 

methods including scoop nets, tangle nets, pens, and by hand. Based on strandings data from the 

NMFS Pacific Islands Marine Turtle Research Program, none of the dead stranded 135 turtles 

(combined species) that were previously tagged and released turtles (from 1982 through 

February 2006) by the program had died as a result of research related stressors (NMFS 2006c). 

NMFS does not expect that individual turtles would experience more than short-term stress and 

temporary physiological changes during these type of captures. No injury or mortality would be 

expected from these capture methods when following the Permit Division’s standard mitigation 

measures. Potential impacts from repeated capture of an individual sea turtle in a short period of 

time during research is not expected. Such impacts can be minimized by temporarily marking the 

carapace to avoid unintentional recaptures within the same field season. If recapture occurs, most 

animals will have sufficient time to recover from the stress of capture before recapture is likely 

to occur days later. 

8.4.5.2 Non-Selective Capture Methods: Entanglement Net, Pound Net, Seine Net, and Trawl 

Sea turtles that are forcibly submerged undergo respiratory and metabolic stress that can lead to 

severe disturbance of their acid-base balance. While most voluntary dives by sea turtles appear to 

be aerobic, showing little if any increases in blood lactate and only minor changes in acid-base 

status (pH level of the blood) (Lutz and Bentley 1985), sea turtles that are stressed as a result of 

being forcibly submerged through entanglement consume oxygen stores, triggering an activation 

of anaerobic glycolysis, and subsequently disturbing their acid-base balance, sometimes to lethal 

levels. It is likely that the rapidity and extent of the physiological changes that occur during 

forced submergence are functions of the intensity of struggling as well as the length of 

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submergence (Lutcavage and Lutz 1997). Other factors to consider in the effects of forced 

submergence include the size of the turtle, ambient water temperature, and multiple 

submergences. Larger sea turtles are capable of longer voluntary dives than small turtles, so 

juveniles may be more vulnerable to the stress due to handling. During the warmer months, 

routine metabolic rates are higher, so the impacts of the stress may be magnified. With each 

forced submergence, lactate levels increase and require a long (even as much as 20 hours) time 

to recover to normal levels. Turtles are probably more susceptible to lethal metabolic acidosis if 

they experience multiple captures in a short period of time, because they would not have had 

time to process lactic acid loads (Lutcavage and Lutz 1997). 

Entaglement Net 

Entanglement nets are a type of passive, stationary fishing gear that incidentally captures turtles. 

Sea turtles readily enter this net and usually are able to come to the surface to breathe. Thus, they 

are minimally stressed within the confines of the net. However, turtles may attempt to swim 

vigorously, attempting to elude capture. Turtles will become entangled in the webbing of the net 

itself, which results in constriction marks around their head and flippers and may lead to their 

death due to forced submergence and traumatic injury. Forced submergence from entanglement 

in or impingement on net gear is likely comparable to forced submergence in other kinds of 

fishing gear, given that both instances involve sea turtles unable to reach the surface in a 

relatively stressful situation. Sea turtles forcibly submerged in any type of restrictive gear 

eventually suffer fatal consequences from prolonged anoxia and/or seawater infiltration of the 

lung (Lutcavage and Lutz 1997). Types of injuries sustained during net capture include abrasions 

and injury from other taxa caught in nets (e.g., stingrays, sharks). Leatherback sea turtles may be 

more vulnerable to injury than other species because of their delicate skin and bone structure 

(Ryder et al. 2006). Sea turtles may also experience damage to appendages if the entanglement is 

prolonged and compromises blood flow. 

Capture could result in restricted access to air, intense struggling, and physiologic injuries such 

as induction of a systemic stress response, hypoxia, or various other changes in blood chemistry 

(Gregory et al. 1996, Jessop et al. 2004). Because sea turtles rely on anaerobic metabolism 

during periods of activity, struggles to escape nets would likely result in the build-up of lactate, 

metabolic acidosis, and changes in ion concentrations in sea turtles’ blood that could have 

deleterious effects on normal physiological function (Gregory and Schmid 2001; Harms et al. 

2003; Hoopes et al. 2000; Stabenau et al. 1991; Stabenau and Vietti 2003). 

Hoopes et al. (2000) noted that blood lactate levels of turtles caught by entanglement nets were 

only slightly elevated over captive reared animals compared to lactate concentrations in trawl 

caught turtles as reported by others. While it appears that captures have the potential to result in 

temporary changes in blood chemistry of sea turtles, it also appears that animals quickly returned 

to the marine environment after removal from the gear can recover from the short-term stress of 

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capture (Hoopes et al. 2000). Hoopes et al. (2000) concluded that entanglement netting is an 

appropriate “low stress” method for researchers working on turtles in shallow, coastal areas. 

The rapidity and extent of the physiological changes that occur during forced submergence likely 

are functions of the intensity of struggling as well as the duration of submergence (Lutcavage 

and Lutz 1997). Additional factors that may influence the intensity of effects resulting from 

capture include the size or species of the turtle, location in the net, ambient water temperature, 

and multiple submergences. Larger sea turtles are capable of longer voluntary dives than small 

turtles, so juveniles may be more vulnerable to entanglement stress. Larger turtles have a larger 

lung capacity than smaller turtles and, the bigger the turtle, the greater chance it has of reaching 

the surface after being entangled. During warmer months, routine metabolic rates are higher, so 

the impacts of the stress due to entanglement may be magnified at that time. 

While capture in non-research entanglement nets has been shown to result in injuries, such 

injuries are not anticipated as a result of the Permit Division’s permitted research due to standard 

mitigation measures that researchers would be required to follow. In particular, researchers 

would be required to continuously monitor and physical check entanglement nets, thus allowing 

them to respond quickly to remove captured turtles from the net and safely bring aboard the 

research vessel. Entanglement time, depth of entanglement, and severity of entanglement may 

have an effect on the health status of turtles upon release from the net and effect probability of 

post-release survival (Snoddy et al. 2009). Prolonged anaerobiosis due to entanglement in fishing 

gear or restraint may leave sea turtles exhausted and vulnerable to other threats upon release 

from gear (Snoddy et al. 2009). Sea turtles subjected to forced submergence may require an 

extended period of time at the surface to rest, recover, and repay oxygen debt (Stabenau and 

Vietti 2003). Holding the animals on deck while conducting research procedures provides 

animals time to recover from the capture event. For this reason, we expect most animals to 

recover from the physiological effects of capture. Entanglement nets have been successfully and 

safely employed by the NMFS Southwest Fisheries Science Center permitted researchers to 

sample green turtles in San Diego Bay, California since the early 1990s and in the San Gabriel 

River/Los Alamitos Bay/Seal Beach National Wildlife Refuge since 2010. 

Pound Net 

If a sea turtle cannot breathe properly or cannot reach the surface for air, the turtle can drown as 

a result of forced submergence (Sasso and Epperly 2006). Pound nets are a passive, stationary 

fishing gear that enclose animals in a pen, usually allowing them to surface and breathe until the 

turtles are removed from the pound. Forced submergence from entanglement in or impingement 

on pound net gear is comparable to forced submergence in other kinds of fishing gear, given that 

both instances involve sea turtles unable to reach the surface in a relatively stressful situation. 

Rarely, turtles are entangled in the webbing of the pound net itself, the tunnel, heart, or the lead 

which results in constriction marks around their head and flippers. This may lead to their death 

due to forced submergence, as occurred in three cases reported by the NMFS Southeast Fisheries 

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Science Center for Permit No. 16733. As a result, in June 2017, the Permit’s Division revised 

mitigation requirements for pound nets by reducing the allowable stretched mesh size to one and 

three quarters inches to prevent future entanglements. Since this change, we expect future pound 

net captures to have a very low potential for mortality. 

Seine Net and Trawl 

Trawls pose a greater risk of impacts from forced submergence to sea turtles than the other 

authorized capture gears. A study examining the relationship between tow time and sea turtle 

mortality showed that mortality was strongly dependent on trawling duration, with no mortality 

or serious injury in tows of 50 minutes or less, but increasing rapidly to 70 percent mortality after 

90 minutes (Epperly et al. 2002; Henwood and Stuntz 1987). In line with this data (the best 

information available at the time), the Permit’s Division previously allowed tow times for up to 

50 minutes. NMFS researchers updated and reanalyzed the association between tow times and 

sea turtle deaths (Epperly et al. 2002; Sasso and Epperly 2006). Seasonal differences in the 

likelihood of mortality for sea turtles caught in trawl gear were apparent. For example, the 

observed mortality exceeded one percent after ten minutes of towing in the winter (defined by 

the authors as December through February), while the observed mortality did not exceed one 

until after 50 minutes in the summer (March through November) (Sasso and Epperly 2006). 

Intermediate tow times (10 to 200 minutes in summer and 10 to 150 minutes in winter) result in a 

rapid escalation of mortality, and eventually reach a plateau of high mortality, but will not equal 

100 percent, as a sea turtle caught within the last hour of a long tow will likely survive (Epperly 

et al. 2002; Sasso and Epperly 2006). In both seasons, a rapid escalation in the mortality rate did 

not occur until after 50 minutes (Sasso and Epperly 2006) as had been found by Henwood and 

Stuntz (1987). 

Though rare, mortality has been observed in summer trawl tows as short as 15 minutes (Sasso 

and Epperly 2006). Serious injury and mortality, when it occurs, is likely due to acid-base 

imbalances resulting from accumulation of carbon dioxide and lactate in the bloodstream 

(Lutcavage and Lutz 1997); this imbalance can become apparent in captured, submerged sea 

turtles after a few minutes (Stabenau et al. 1991). Although extremely rare, sea turtles entangled 

in nets exhibiting lethargy can die even with professional supportive care, possibly due to severe 

exertion resulting in muscle damage (Phillips et al. 2015). Fahlman et al. (2017) correlate trawl 

gear depth with the risk of developing gas embolisms and their severity in loggerhead sea turtles. 

Though trawl captures for research would not be deployed for the durations and at the depths 

typically used in commercial fisheries, we recognize there is risk of gas embolism and 

decompression sickness in sea turtles captured in trawls. Even at trawl depths of up to 20 meters, 

moderate to severe gas embolisms that go untreated could result in death (Fahlman et al. 2017). 

For this reason, trawls may pose an added risk of delayed mortality after the capture event that 

goes unseen and undocumented. Most animals are expected to have a very low likelihood of 

delayed mortality; most animals that are captured are observed to be in good physical condition, 

consistent with Category 1 of NMFS’ post-interaction mortality guidance (NMFS 2017b). 

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To minimize the risk of mortality, the Permits Division has set forth requirements of the permit: 

trawl tows and seine pulls must be limited to 30 minutes bottom time and trawl tow depths no 

deeper than 20 meters. In July 2017, a permit holder (Permit No. 19621) reported the death of an 

emaciated loggerhead while in transit to a rehabilitation facility after capture by trawl. This was a 

rare event. In most cases, we do not expect observed mortalities because captured sea turtles 

have time to recover from the stress of capture during holding for examination prior to release. 

This holding time should help minimize risks from the accumulation of other stressors that can 

cumulatively impair physiological function or result in sublethal or delayed effects that cannot be 

observed upon capture. In addition, veterinary assistance would be sought for any comatose, 

injured or compromised animals as a requirement of the permit. Researchers must also try to 

resuscitate any comatose animals. 

Five comatose turtles were reported during research trawling activities conducted under a section 

10(a)(1)(A) permit (Permit No. 1245) from 2000 to 2003. The trawl tow times that resulted in the 

capture of comatose turtles were 30 minutes, the maximum tow time authorized under sea turtle 

research permits. Four of these turtles were intubated successfully and returned to the wild in 

good condition. The fifth turtle, a loggerhead, exhibited limited movement after capture and 

became very lethargic (Stender 2001). The individual was intubated, which resulted in the 

disabled turtle moving around the deck. Alternating periods of activity and lethargy occurred 

repeatedly. At one point, the turtle was so active that it was tagged in anticipation of release, but 

again showed signs of problems. The turtle was returned to the lab for observation, blood 

samples were taken, and the turtle was kept in a covered, outdoor tank with a minimal amount of 

water for observation overnight. By 9:00 am the next day, the turtle had died. A necropsy 

showed that the turtle was healthy in all respects except that water had caused the anterior lobes 

of the lungs to swell and cease to function properly. There have been no other reports of 

comatose sea turtles as a result of research trawl capture since 2003. 

Satellite tracking data is available in published studies on sea turtles released after research 

trawling (Arendt et al. 2012a; Arendt et al. 2012b; Arendt et al. 2012c). Satellite tagged turtles 

caught by trawl in these studies all behaved normally, including normal dive patterns, migrations 

and movements between foraging and breeding grounds, following release. Transmitters 

remained attached from 7 days to over 400 days, with most having transmissions and tracks for 

at least several months. One study trawl captured 34 juvenile loggerhead sea turtles between 

May 2004 and August 2007 with tow bottom times ranging from 9 to 21 minutes (Arendt et al. 

2012c). In another study, 29 adult male loggerheads were captured by trawling from April 2006 

through April 2007 with a tow bottom time of 15 minutes (Arendt et al. 2012b). There were no 

apparent injuries or health risks to any trawl captured turtles in these studies. 

8.4.5.3 Summary of Sea Turtle Response to Capture 

Sublethal effects that might have an impact on sea turtles are the turtle’s ability to swim, forage, 

or migrate. These remain very difficult to quantify or monitor. For capture, to result in significant 

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fitness consequences to live animals, we would have to assume that an individual turtle could not 

compensate for lost feeding opportunities by either immediately feeding at another location, by 

feeding shortly after release, or by feeding at a later time. There is no indication this is the case. 

Similarly, temporary disruptions of swim speed or direction are expected to be inconsequential 

because they can resume these behaviors almost immediately following release. Further, these 

sorts of behavioral disruptions may be similar to natural disruptions such as those resulting from 

predator avoidance, or fluctuations in oceanographic conditions. Therefore, in most cases, 

behavioral responses of sea turtles to capture in a net are unlikely to lead to fitness consequences, 

reduced reproductive success, or long-term implications for the population. 

All capture methods are expected to result in some level of stress to the target animals and 

temporarily disrupt activities such as resting, foraging, and migration. However, these 

interruptions for individual turtles are relatively short-lived and any physiological effects are 

expected to be compensated by intrinsic homeostatic mechanisms. The harassment of turtles 

during capture can result in raised levels of stressor hormones and can cause some discomfort. 

Based on past observations of similar research, these effects are expected to dissipate within a 

day (Stabenau and Vietti 2003). A number of factors, such as size, species, water temperature, 

severity of entanglement, and others can intensify the effects resulting from capture. A small 

number of turtles may die as a direct result of forced submergence in the net. Such observed 

mortalities are expected to be uncommon as evidenced by historical reported take data. Trawls 

also have the potential to result in delayed mortality that cannot be observed. Additionally, these 

methods will not affect the physical or biological environment. No long-term, population level 

effect is expected from any capture method. 

8.4.6 Recapture 

Turtles could be captured more than once during a sampling day. Cumulative physiological 

stress can result from capture and handling of captured sea turtles. Recaptured animals that have 

not properly recovered from stressors associated with the previous capture have a higher risk of 

mortality. As a mitigation measure to minimize the risks associated with recapture, as a condition 

of the permit, turtles may be sampled no more than two times during the same permit year. With 

this mitigation measure in place, permit holders will have incentive to avoid recapturing the 

same sea turtles if it can be easily determined (through markings, tag number, etc.) that a sea 

turtle has already been sampled. Although recaptures may still occur, we anticipate they will be 

limited in number because of this permit condition. For recaptured turtles, researchers will still 

be required to adhere to the sampling protocols and mitigation measures for safe handling of sea 

turtles and ensure they are active and healthy prior to release. Recaptured turtles may need more 

time to achieve full recovery prior to release. 

While the recapture of sea turtles in a given day may result in increased levels of stress 

responses, those responses are not likely to manifest into any long-term adverse effects, reduced 

fitness, or mortality. This conclusion can be reached as long as all of the sampling protocols, 

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mitigation measures, and any other required conditions of the sturgeon research permit are 

followed by all permit holders. 

8.4.7 Holding, Handling, and Transport 

Capture and handling activities may markedly affect metabolic rate (St. Aubin and Geraci 1988), 

reproduction (Mahmoud and Licht 1997), and hormone levels (Gregory et al. 1996). Handling 

has been shown to result in progressive changes in blood chemistry indicative of a continued 

stress response (Gregory and Schmid 2001; Hoopes et al. 2000). The additional on-board holding 

time imposes an additional stressor on these already acidotic turtles (Hoopes et al. 2000). It has 

been suggested that the muscles used by sea turtles for swimming might also be used during lung 

ventilation (Butler et al. 1984). Thus, an increase in breathing effort in negatively buoyant 

animals may have heightened lactate production. Understanding the physiological effects of 

capture methodology is essential to conducting research on endangered sea turtles, since safe 

return to their natural habitat is required. However, literature pertaining to the physiological 

effects of capture on sea turtles is scarce. Turtles would be worked up as quickly as possible to 

minimize stresses resulting from their capture. 

Animals obtained from other legal sources likely have experienced the same type of stress from 

capture as discussed above prior to research. In most cases, the Permit’s Division requires that 

animals must appear to be in good condition before they can be used for research. Researchers 

must forego research on animals that are injured, comatose or compromised. The exceptions to 

this requirement are rare cases when the Permit’s Division allows research on disentangled 

animals to collect much needed data on post-interaction survival in fishing gear as an identified 

management and conservation need to further recovery of the species. The decision to use a 

compromised sea turtle would be left to the discretion of the attending veterinarian, who upon 

assessment of each animal, determines whether the animal may undergo research procedures. 

Permit No. 15726 is such an example in which researchers may receive leatherbacks from the 

local disentanglement and stranding network once they are disentangled from pot gear at sea. 

Healthy and compromised animals may receive research procedures including a direct tag 

attachment while under the direction of an attending veterinarian onboard. Evidence shows that 

the subsequent use of disentangled turtles for research has no apparent adverse effects, with 

disentangled sea turtles returning to typical migrations and behavior after release (Innis et al. 

2010; López-Mendilaharsu et al. 2009). One instance has been documented of a very short 

duration of satellite tag transmission, which could indicate a mortality, or tag failure (Innis et al. 

2010). More recently, Dr. Lutcavage’s research has shown that holding compromised 

leatherback sea turtles for tagging aids the animal’s ability to physiologically recovery from the 

stress of entanglement. Analysis of paired blood samples (post-capture and pre-release samples) 

from this study suggests that increased respiration during holding ameliorates observed acidosis 

in leatherbacks (Innis et al. 2014) 

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8.4.8 Morphometrics and Monitoring of Vital Parameters 

Once sea turtles have been captured, individuals may be handled and exposed to various 

activities of greater or lesser degrees of invasiveness. Each sea turtle may be exposed to 

morphometric measurement, including carapace size and individual weight. Although these 

activities are not considered invasive, we expect individual sea turtles to experience a continued 

stress response due to the handling and restraint necessary to conduct these activities. 

Turtles should be handled in such a way as to avoid injury to the turtles themselves and to the 

researchers. Measuring and weighing can result in raised levels of stressor hormones in sea 

turtles. The additional on-board holding time imposes an additional stressor on these already 

acidotic turtles (Hoopes et al. 2000). It has been suggested that the muscles used by sea turtles 

for swimming might also be used during lung ventilation (Butler et al. 1984). Thus, an increase 

in breathing effort in negatively buoyant animals may have heightened lactate production. 

The measuring and weighing procedures are simple, non-invasive, with a relatively short time 

period and NMFS does not expect that individual turtles would normally experience more than 

short-term stresses as a result of these activities. No injury is expected from these activities, and 

turtles will be worked up as quickly as possible to minimize stresses resulting from their capture. 

We expect that the general monitoring of vital parameters of turtles would not elicit any long 

lasting discomfort or stress to the animals. Visually monitoring respiration would have no 

expected impact on sea turtles as it does not require contacting the animal. Ultrasound and heart 

rate monitoring procedures would involve handling and restraint, as well as imaging with a 

device emitting sound pulses well above the levels audible to sea turtles. Such monitoring will 

not have any more than short-term effects on sea turtles. Although a temperature probe could be 

mildly uncomfortable to the turtle, the probe would be sterile and no tissue surface would be 

pierced. We do not expect that the cloacal temperature recording would cause any significant 

additional stress or discomfort to the turtle beyond what was experienced during other research 

activities. 

Bioelectrical Impediance Analysis (BIA) is expected to be fast, safe, and non-invasive. BIA has 

been used previously in other animals, including humans, and we believe that it can be used on 

sea turtles with no harmful effects. The amount of current in the body during testing is too small 

to be felt by a human. A review of this procedure can be found in “Body composition analysis of 

animals: A handbook of non-destructive methods” (Speakman 2001). Due to its non-invasive 

design, we do not expect the BIA testing to cause any additional stress or discomfort to the turtle 

beyond what was experienced during capture, collection of measurements, and tagging. 

Similarly, a pulse oximeter is a non-invasive method. It would not result in any additional stress 

to the animal and would provide beneficial information that could be used to manage stress and 

other effects of research activities on the animal. 

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8.4.9 Shell Marking 

Marking the sea turtles for identification can include carapace painting, shell etching, and 

plastron marking. Researchers have temporarily marked turtle shells for over a decade with no 

visible effects to turtles when following the Permit Division’s standard permit requirements. 

Temporary marks must be non-toxic. Previous permit holders have reported that temporary 

marks wore off of the shell within weeks and showed no evidence of any problems associated 

with it. NMFS believes that the turtle would feel the vibration of the etching tool but would not 

experience pain. 

We do not expect that individual turtles would experience more than short-term stresses as a 

result of this activity. No injury is expected from this activity, and turtles will be marked as 

quickly as possible to minimize stress. 

8.4.10 Oral and Ophthalmic Examination 

The mouth, eyes, and vent may be examined for signs of injury, ingestion of hooks or marine 

debris (plastics, tar balls), and tumors. Ophthalmic exam procedures are considered invasive, but 

with minimal risk. When conducted by trained personnel, we do not expect the procedure to 

result in injury or harm. NMFS researchers have conducted oral measurements on more than 200 

turtles with no detectable ill effects. The turtle may experience discomfort while its mouth is 

gagged for oral measurements, but no lasting negative effect is anticipated. Aseptic requirements 

are designed to minimize the risk of either introducing a new pathogen into a population or 

amplifying the rate of transmission from animal to animal of an endemic pathogen when 

handling animals. Given the precautions that would be taken by the researchers to ensure the 

safety of the turtles and the permit conditions relating to handling, NMFS expects that the 

activities would have minimal and insignificant effects on the animals. 

8.4.11 Flipper and Passive Integrated Transponder Tagging 

Flipper and PIT tagging involve the implantation of tags in or through skin and/or muscle of the 

flippers. The PIT tags remain internal while flipper tags have both internal and external 

components. For both, internal tag parts are expected to be biologically inert. In addition to the 

stress sea turtles are expected to experience by handling and restraint associated with inspection 

and tagging, we expect an additional stress response associated with the short-term pain 

experienced during tag implantation (Balazs 1999) although this will be reduced by a standard 

injection of an anesthetic. Internal PIT tags should be sterilized and the area of insertion should 

be disinfected. Turtles should be injected with a PIT tag into the shoulder muscle area of the 

right front flipper. If any bleeding occurs after the tag has been injected, researchers should hold 

a swab soaked in povidone iodine to the injection site until the bleeding has stopped. 

We expect disinfection methods should mitigate infection risks from tagging. Wounds are 

expected to heal without infection. Researchers that have recaptured individuals report never 

seeing evidence of infection resulting from tagging. Tags are designed to be small, 

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physiologically inert, and not hinder movement or cause chafing; we do not expect the tags 

themselves to negatively impact sea turtles (Balazs 1999). The proposed methods are standard 

worldwide and not widely known to result in decreased survival, reproduction, or prolonged 

health effects (Balazs 1999; NMFS SEFSC 2008; Stapleton and Eckert 2008). The proposed 

tagging methods have been regularly employed in sea turtle research with little lasting impact on 

the individuals tagged and handled (Balazs 1999). 

These tagging activities are minimally invasive and all tag types have negative effects associated 

with them, especially concerning tag retention. Plastic tags can become brittle, break and fall off 

underwater, and titanium tags can bend during implantation and thus not close properly, leading 

to tag loss. Flipper tags occasionally come off turtle flippers, which may cause tissue ripping and 

subsequent trauma and infection risk. However, individuals who have lost flipper tags have not 

been observed to be in any different body condition than turtles lacking tags or those who retain 

their tags. Turtles that have lost external tags would be re-tagged if captured again later, which 

subjects them to additional effects of tagging. PIT tags have the advantage of being encased in 

glass, which makes them inert, and are positioned inside the turtle where loss or damage over 

time due to abrasion, breakage, corrosion or age is virtually non-existent (Balazs 1999; 

MacDonald and Dutton 1996). Currently available PIT tags are designed with a coating that 

promotes growth of muscle fibers to heal and hold the PIT tag in place when injected into 

muscle. 

Turtles can experience some discomfort during the tagging procedures and these procedures will 

produce some level of pain. The discomfort is usually short and highly variable between 

individuals (Balazs 1999). Most barely seem to notice, while a few others exhibit a marked 

response. However, we expect the stresses to be minimal and short-term and that the small 

wound-site resulting from a tag applied to the flipper should heal completely in a short period of 

time. Similarly, turtles that must be re-tagged should also experience minimal short-term stress 

and heal completely in a short period of time. Re-tagging is not expected to appreciably affect 

these turtles. Given the precautions that would be taken by researchers to ensure the safety of the 

turtles and the permit conditions relating to handling and tagging and using aseptic techniques, 

we expect that the activities would have minimal and insignificant effects on the animals. We do 

not expect mortality or long-term adverse effects to the turtle due to attachment of the flipper 

tags or insertion of PIT tags. 

8.4.12 Oxytetracycline 

Tetracycline injections are performed in many species to establish tracers in bone growth so that 

once the animal dies, post-mortem procedures can determine the individual’s growth rate (Coles 

et al. 2001). In addition, this antibiotic likely has a short-term effect of boosting health by acting 

against many types of pathogenic bacteria, although a recent study showed significant bacterial 

resistance to oxytetracycline in sea turtles (Foti et al. 2009). A study of the pharmacokinetics of 

oxytetracycline in loggerhead sea turtles did not identify any negative effects (including lack of 

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response at the injection site, food consumption, flipper movement, and activity) (Harms et al. 

2004). However, a Kemp’s ridley sea turtle responded with skin exfoliation and ventral erythema 

after repeated injection; both conditions disappeared after oxytetracycline was discontinued 

(Harms et al. 2004). The single low dose (10 to 15 milligrams/kilogram) and intravenous or 

intramuscular administration of several smaller volume injections (less than 10 milliliters/site) 

will reduce the risk of these adverse effects. Several animals that have been injected in recent 

years by the Southwest Fisheries Science Center have been recaptured. Each of the animals was 

in good condition and no ill effects from oxytetracycline injection were observed. 

The results of these studies indicate that the dosage generally used to produce a tetracycline mark 

in the bones of sea turtles does not appear to harm either the animals injected or those in their 

immediate surroundings. Furthermore, although tetracycline injection can potentially result in 

bacterial resistance, it appears that wild individuals may already host tetracycline-resistant 

bacteria, suggesting a one-time injection of oxytetracycline would not cause the turtles harm in 

this respect. 

8.4.13 Biological Sampling 

Biological sampling activities can result in raised levels of stressor hormones in sea turtles and 

would be in addition to any stresses or effects already experienced during capture. Sterile 

techniques should be utilized to minimize the possibility of infection at the biopsy sites. 

Biological sampling should not be performed on any compromised animals (e.g., those that are 

emaciated or having heavy parasite loads, bacterial infections, etc.). 

8.4.13.1 Epibiota Collection 

Removal of epibiota would not be expected to significantly affect the animal because epibiota 

can be removed in a relatively non-invasive manner. Although the turtle may experience shortterm stress or discomfort, this stress would not be significant. Growth of barnacles, algae, and 

other marine life (epiphytes) on sea turtles is considered a negative factor for sea turtles, as this 

growth introduces additional mass and drag into the hydrodynamic performance of the individual 

sea turtle. Removal of these materials is expected to aid sea turtles by reducing their metabolic 

requirements for locomotion in water. Hence, we consider this activity beneficial to individual 

sea turtles. Therefore, we conclude that epibiota removal is not likely to adversely affect sea 

turtles. 

8.4.13.2 Swabs 

All forms of swabbing are minimally invasive or opportunistic. Any discomfort experienced by 

the turtle would be temporary and would not have any lasting effects. All the turtles sampled by 

the NMFS Southeast Fisheries Science Center Beaufort Laboratory exhibited normal behavior as 

they were released, and of those that have been recaptured, none have shown an adverse effect. 

We expect that the animal would experience discomfort but that the stress from these procedures 

would be insignificant and short-term. No injury is expected from these procedures. 

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8.4.13.3 Skin Biopsy 

During skin biopsy, it is not expect that individual turtles will experience more than short-term 

stresses during tissue sampling (for genetic and stable isotope analyses). It is no expected that the 

collection of a tissue sample will cause any additional significant stress or discomfort to the 

turtle beyond what was experienced during the other research activities. 

No adverse effects have been noted when tissue sampling animals in central California by the 

NMFS Southwest Fisheries Science Center (NMFS 2017a). Researchers who examined hardshelled turtles re-captured two to three weeks after initial capture and sample collection noted 

that the sample collection site was almost completely healed (NMFS 2017a). Sampling sites on 

turtles re-captured in San Diego Bay after several months to years have completely healed and 

have shown no signs of infection. In areas such as San Diego Bay, California, and St. Croix, U.S. 

Virgin Islands, animals remain in the study area long term, indicating that sampling does not 

produce any adverse effects on their behavior (NMFS 2017a). 

Sterile techniques will be utilized to minimize the possibility of infection at the biopsy site. All 

tissue biopsy samples would be collected, handled, stored, and shipped in such a manner as to 

ensure human safety from injury or zoonotic disease transmission as well as provide for the 

protection of the sea turtles that are sampled. Bjorndal et al. (2010) found that repeated skin 

sampling of the same individual loggerhead sea turtles did not alter growth, result in scarring, or 

impact other physiological or health parameters. 

8.4.13.4 Scute Scraping 

Scute scrapings would allow researchers to collect splinters of scute material in a non-invasive 

manner with little effect on the turtles. Keratin collected from the outermost edge of the marginal 

scutes is of sufficient thickness and texture to provide a sufficient sample mass while minimizing 

the risk of penetrating through the keratin layer. Whether via scrapings or a core, because the 

keratin layer has no nerve endings or blood vessels, sampling is not expected to result in 

discomfort or pain to the turtle and little to no bleeding. Researchers would avoid scraping too 

deeply and causing injury to the turtle; however, should a deep scrape occur, the result would be 

minor bleeding and minor discomfort to the turtle (less than what would be expected during a 

skin biopsy. Bjorndal et al. (2010) found that repeated scute sampling of the same individual 

loggerhead sea turtles did not alter growth, result in scarring, or impact other physiological or 

health parameters. Therefore, we do not expect that individual turtles would experience more 

than short-term stress from handling during this procedure. 

8.4.13.5 Blood Sampling 

Sea turtles are expected to experience a short-term stress response in association with the 

handling, restraint, and pain associated with blood sampling. Taking a blood sample from the 

sinuses in the dorsal side of the neck is a routine procedure (Owens 1999), although it requires 

knowledgeable and experienced staff to do correctly and requires the animal to be restrained 

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(DiBello et al. 2010; Wallace and George 2007). According to Owens (1999), with practice, it is 

possible to obtain a blood sample 95 percent of the time, and the sample collection time should 

be about 30 seconds in duration. Blood sampling volume would be conditioned to only allow a 

conservative amount of blood (Section 3.4.4.4) to be drawn during each event. Blood hormones 

and heart rate have been measured in animals that have had this amount of blood drawn from 

them and no stress has been observed (NMFS 2017a). 

No sea turtle mortalities have occurred during previous blood sampling activity from researchers, 

that we are aware of, nor are we aware of any meaningful pathological consequences by sampled 

individuals on the part of any researchers. Aseptic techniques would minimize the risk of 

infection and spread of pathogens. All blood samples would be collected, handled, stored, and 

shipped in such a manner as to ensure human safety from injury or zoonotic disease transmission 

as well as provide for the protection of the sea turtles that are sampled. Bjorndal et al. (2010) 

found that repeated blood sampling of the same individual loggerhead sea turtles did not alter 

growth, result in scarring, or impact other physiological or health parameters. 

8.4.13.6 Tear Collection 

Tear collection is not expected to result in any impact more than temporary discomfort to the 

animal. The method is minimally invasive. Therefore, we do not expect that individual turtles 

would experience more than short-term stress from handling during this procedure. 

8.4.13.7 Soft Tissue Biopsy 

Appropriate topical anesthesic will be employed to minimize any pain or discomfort associated 

with fat and larger tissue sampling of sea turtles. We do not expect that these methods will cause 

any additional stress or discomfort to the turtle beyond what was experienced during the capture, 

collection of measurements, and tagging. 

The NMFS Southeast Fisheries Science Center discussed the safety of the fat sampling 

procedure for sea turtles with several veterinarians (Drs. Greg Lewbart, Andy Stamper, Craig 

Harms, and Elizabeth Chittick). All agreed that this procedure is simple, routine, and that risk to 

the turtles can be managed. The amount of tissue removed would be small and would not deplete 

the turtle's fat stores. According to Dr. Harms, small pieces of fat are often intentionally 

discarded during clinical surgeries to improve visualization of the underlying musculature. The 

superficial incision would not penetrate the body cavity, making it minimally invasive. The main 

risk of the procedure is secondary infection at the incision site. However, required sterile 

techniques would reduce this risk. 

8.4.13.8 Urine and Fecal collection 

Fecal samples will be collected either after turtles have defecated during biological sampling or 

by digital extraction of feces from the cloaca using a lubricated, gloved finger, or by fecal loops, 

swabs, or cloacal lavage. Those turtles that do not defecate during the sampling period would be 

temporarily overturned onto the carapace and restrained. While wearing lubricated latex gloves, 

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a finger will be inserted into the cloaca of the turtle to feel for the presence of a fecal mass. The 

cloacal lavage is brief, lasting only minutes. No injury or lasting effects are expected from this 

procedure. Only sufficiently large turtles would be subject to digital extraction of feces. Urine 

sample collection will be collected on an opportunistic basis and is not expected to result in harm 

or injury of sea turtles. Researchers would not attempt to expel urine from captured sea turtles. 

We do not expect that individual turtles would normally experience more than short-term 

stresses and possibly some minor discomfort as a result of these activities. No injury or lasting 

effects are expected from this procedure. The NMFS Beaufort Laboratory conducted fecal 

sampling, and turtles exhibited normal behavior as they were released. 

8.4.14 Gastric Lavage 

The feeding habits of turtles can be determined by a variety of methods, but the method used 

under this research permit is gastric lavage or stomach flushing. This comparatively simple and 

reliable technique has been used to successfully sample the gut contents of various vertebrate 

animal groups without harm to the animal (Forbes 1999). This technique has been successfully 

used on green, hawksbill, olive ridley and loggerhead turtles ranging in size from twenty-five to 

one hundred and fifteen centimeters curved carapace length. Forbes (1999) stated that many 

individual turtles have been lavaged more than three times without any known detrimental effect. 

Individuals that have been recaptured from the day after the procedure up to three years later 

appear to be healthy and to feed normally. As well, laparoscopic examination of the intestines 

following the procedure has not detected any swelling or damage to the intestines. 

While individual turtles are likely to experience discomfort during this procedure, we do not 

expect individual turtles to experience more than short-term stress. Injuries and mortalities are 

not anticipated. This is supported in the literature by cases of animals repeatedly re-sighted, 

recaptured and in some cases resampled. Fuentes et al. (2006) noted that nine of seventy-six 

juvenile green sea turtles were resampled days to weeks after the initial capture (by free-dive) 

and lavage event. Seven of these animals were sampled twice within days of the original 

sampling; one animal was lavaged three times in one week, and one animal was sampled four 

times within a three-week period. Dr. Kristen Hart has recaptured twenty-one of the animals she 

has lavaged in the U.S. Virgin Islands (Permit No. 16146) and the Dry Tortugas (Permit No. 

17381) (NMFS 2017a). Some animals have been recaptured several times since first lavage, 

some as many as eleven times. All of these turtles had gained weight and increased in size upon 

recapture. In an earlier study, Dr. Hart documented recaptures of juvenile hawksbills in the U.S. 

Virgin Islands, demonstrating that lavage is a safe procedure that does not affect an animal’s 

residency, site fidelity, or ability to forage; reported growth rates were within other published 

ranges for the species, and in some cases higher than other areas (Hart et al. 2013b). Therefore, 

we do not believe that lavage will result in more than short-term stress from the actual lavage 

procedure; when performed by trained qualified researchers no injury or mortality is expected. 

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8.4.15 Laparoscopy, Internal Tissue Sampling, and Anesthesia 

Laparoscopy is a form of surgery that involves a small incision being made allowing access by a 

miniature camera and sampling equipment into the body cavity. This procedure allows direct 

viewing of organs and tissues (such as reproductive tracts to confirm sex) as well as sampling 

(such as biopsies of internal organs). However, as with any surgical procedure, laparoscopy 

introduces the risk of infection not only at the surgical site, but also within the body cavity. The 

procedure also requires veterinary staff experienced in the procedure and sea turtle anatomy in 

order to be performed safely. The procedure is likely to be very stressful for subjects, as it 

involves restraining the individual in a head-down position for an extended period. Although 

anesthesia (local and/or systemic) is also involved, a degree of pain can be expected at least with 

the sutured surgical site after the procedure is complete and anesthesia has worn off. 

Even though laparoscopy has the potential to cause lethal or major sub-lethal injury, few studies 

have been conducted evaluating the effects of laparoscopy on sea turtles. Owens (1999) reports a 

mortality rate of one to two percent associated with the procedure in sea turtles. The two most 

common sources of mortality are excessive bleeding due to poor placement and death due to 

non-specific symptoms in a turtle that has already been compromised due to other conditions. 

For example, sea turtles with a heavy parasite load, a severe bacterial infection, or obesity may 

succumb during surgery (Eckert et al. 1999b). Permit holders under this programmatic will avoid 

such risk because the procedure may not be performed on compromised animals. In addition, all 

laparoscopic procedures would be conducted by or under the direct guidance of a veterinarian. 

Some animals may float and be unable to dive properly after the procedure. When given 

adequate recovery time in controlled conditions, the animal can absorb or expel excess air. In 

cases where this does not occur, a special effort, such as reopening the suture site, to remove the 

excess air may have to be made. No animals would be released until they are swimming 

normally and a veterinarian has given approval for release. 

Even though laparoscopy has the potential to cause lethal or sub-lethal injury, few studies have 

been conducted evaluating the effects of laparoscopy on sea turtles. Perhaps the best study on the 

long-term effects of laparoscopy was conducted over thirty years ago when sea turtles were 

being farmed for commercial use. Wood et al. (1983b) performed laparoscopy on over fifty sea 

turtles in an aquaculture facility where all individuals were retained and monitored. No 

individual died or appeared to suffer long-term injury as a result of procedures conducted in less 

aseptic conditions and using less-refined methods than required by the Permit’s Division. 

More recently, Dobbs et al. (2007) reported findings after conducting laparoscopy on 225 freeranging adult nesting hawksbill sea turtles in Australia. Individuals were released following the 

procedure. The researchers found stitches were gone in individuals returning to lay additional 

nests, but those individuals that returned to lay additional nests took on average one day longer 

to return than individuals that did not undergo laparoscopy (Dobbs et al. 2007). Some individuals 

were re-sighted in subsequent nesting seasons (Dobbs et al. 2007). Of the 225 hawksbill sea 

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turtles, twenty-seven were injured during laparoscopy, which included (twenty-four of twentyseven received lung punctures and the other three injuries were blood vessel punctures of egg 

yolks or ovaries (Dobbs et al. 2007)). This may be a unique feature of hawksbill sea turtles, as 

researchers noted that hawksbill lungs extended around the gut when the turtle was inverted for 

laparoscopy; a condition that was not found in green or loggerhead sea turtles (Dobbs et al. 

2007). The researchers modified their methods so as to reduce the potential for injury (Dobbs et 

al. 2007). One sea turtle with lung puncture was seen to nest again the same season, and five 

were seen nesting in subsequent seasons (Dobbs et al. 2007). No such injuries or mortalities have 

been reported by permitted researchers in the Permit Division’s program from laparoscopy. In 

the NMFS Southeast Fisheries Science Center application for Permit No. 16733, the applicant 

noted that they have performed laparoscopies intermittently for twenty years, and fat biopsy in 

conjunction with laparoscopy for ten years, and none of the large numbers of turtles recaptured 

over the years (often multiple times) following these procedures has exhibited adverse effects. 

The purpose of administering anesthesia is to reduce the stress and pain associated with these 

procedures. These drugs have the potential for side effects that can be adverse, even in light of 

the potential benefits for which they are administered. Examples of animal recovery are provided 

here. Loggerhead sedation with a combination of medetomidine and 5 milligrams/kilogram 

ketamine and intubated with 0.5 to 2.0 percent sevoflurane was achieved in a mean time of just 

under nine minutes and anesthesia lasted 110 to 325 minutes in six juveniles (Chittick et al. 

2002). Recovery times took 5 to 124 minutes (Chittick et al. 2002). Breathing, blood acidity, 

oxygenation, and body temperature all remained within safe ranges (Chittick et al. 2002). Doses 

of 3 to 8 milligrams/kilogram were insufficient to fully sedate leatherback sea turtles and 

supplementary doses of 2 to 9 milligrams/kilogram had to be administered (Harms et al. 2007). 

No apparent ill effects were found and anaesthetized individuals were found to return at the same 

rate as non-anaesthetized individuals (Harms et al. 2007). Green sea turtles were anaesthetized 

underwater with 5 milligrams/kilogram ketamine without lasting effect (Harms et al. 2007). 

Anesthesia took 5 to 8 minutes to take effect and lasted 71 to 77 minutes (Harms et al. 2007). In 

another study, three loggerheads anesthetized with 18 milligrams/kilogram ketamine seemed to 

take full effect within 10 minutes (George et al. 1989). Ketamine alone appeared to cause only 

mild sedation and other drugs were necessary for deeper anesthesia (George et al. 1989). 

Recovery times of up to three hours were necessary (George et al. 1989). Leatherback recovery 

from sedation (6 milligrams/kilogram body weight of ketamine and 30 micrograms/kilogram 

body weight of dexmedetomidine) took 6 to 33 minutes in air, with an average time of 13.5 

minutes, with almost two hours from injection to full recovery (Harms et al. 2014). All 

individuals were released in good condition (Harms et al. 2014). Based on the expertise of the 

attending veterinarian and the Permit Division’s standard mitigation measures for performing 

these procedures, we believe that the risk of mortality or other complications is low. 

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8.4.16 Transmitter Attachments 

All external tag units would result in increased drag forces while the unit is attached; this varies 

widely from days to weeks or months based on the method of attachment. Invasive tag designs 

for leatherbacks also would result in temporary harm and injury at the tag site. Stomach pills 

may result in temporary discomfort during placement but should not result in injury. The 

standard mitigation measures for transmitters set forth by the Permits Division are designed to 

minimize impacts from drag forces, harm and injury to the animal and risk of entanglement. 

More details on the types of anticipated effects are provided for each attachment method below. 

8.4.16.1 Suction cup attachment 

Suction-cup mounted tags, such as animal-borne video and environmental data collection 

systems (AVEDS) or “Crittercams©”, would cause hydrodynamic drag for the turtles while tags 

are attached. However, we believe that they would have negligible effects on the movements of 

turtles. In a NMFS Southwest Fisheries Science Center study of Crittercam©-equipped green 

turtles, telemetered turtles exhibited normal diving behavior and swimming speeds (Seminoff et 

al. 2006). AVEDS would detach within about a day or less indicating that any effects would be 

very short-term. In a study of video camera equipped leatherback sea turtles, telemetered turtles 

exhibited normal diving behavior, and swimming speeds while foraging on jellyfish prey (NMFS 

2017a). Jones et al. (2011) conducted tests to quantify the drag forces of different externallyattached biotelemetry devices using 3-D sea turtle models. Measured drag forces varied widely 

based on tag placement, shape and size. Drag increases were high, in some cases over 100 

percent, for AVEDS-type units (Jones et al. 2011). However, the authors noted that although 

some of these tag designs are not in line within their overall recommendations, exceptions for 

these units are acceptable for short-term attachments where locomotion is not the animal’s 

primary activity (e.g., local foraging vs long migrations). Further, archival video camera tags 

attached by suction cups are designed for short-term deployments exclusively (i.e., hours). 

Deployment durations have typically been two to four hours with the longest deployment 

spanning five days before the apparatus fell off the carapace without assistance. Other types of 

suction-cup attached units typically last from 24 to 48 hours. Therefore, any unanticipated effects 

would be short-lived, and are not likely to translate to significant impacts, such as a permanent 

shift in habitat use or reduced reproductive success, to the tagged animal. 

8.4.16.2 Adhesive attachment 

Attachment of satellite, acoustic, or radio tags with epoxy is a commonly used and permitted 

technique by NMFS. Transmitters, as well as biofouling of the tag, attached to the carapace of 

turtles have the potential to increase hydrodynamic drag and affect lift and pitch. Because 

biofouling can increase drag and negatively affect tag transmissions if epibiota cover the 

saltwater switch, many researchers coat the majority of the tag with a biofouling paint before 

attachment. Watson and Granger (1998) performed wind tunnel tests on a full-scale juvenile 

green turtle and found that at small flow angles representative of straight-line swimming, a 

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transmitter mounted at the peak of the carapace increased drag by 27 to 30 percent, reduced lift 

by less than 10 percent and increased pitch moment by 11 to 42 percent. More recently, tests by 

Jones et al. (2011) determined that drag forces can be high depending on the shape, size and 

placement of the tag; however, drag can be substantially reduced to 17 percent or lower if the tag 

is shifted off the peak of the carapace (Jones et al. 2011). Based on the recommendations of 

Jones et al. (2011), the Permit’s Division no longer authorizes harness-based attachment designs 

for sea turtles. Further, our standard mitigation measures for transmitters are in line with the 

recommendations of the report, including requirements to make attachments as hydrodynamic as 

possible, reduce risk of entanglement, and attach tags off the peak of the carapace whenever 

possible. 

Researchers have successfully tracked turtles from nesting to foraging grounds (Hart et al. 2012; 

Hart et al. 2013a; Shaver et al. 2005; Van Dam et al. 2008). Shaver et al. (2017) has recorded 

females returning to nest after having a transmitter attached across inter-nesting seasons. Others 

have documented tagged animals using the same foraging areas, inter-nesting habitat, or home 

range after tagging (Hawkes et al. 2011; MacDonald et al. 2012; MacDonald et al. 2013; Madrak 

et al. 2016; Olson et al. 2012; Shaver et al. 2017). This information suggests that having a 

transmitter attached using adhesive methods does not impact a sea turtle’s migration, feeding, 

and mating behavior. Hatchlings, post-hatchlings, and juveniles grow much faster than subadult 

or adult individuals do. The attachment mechanism can impair growth if not flexible enough to 

either grow with the individual or break away as its base expands. Mansfield et al. (2012) 

evaluated potential impacts to tagging neonates by comparing tagged with non-tagged turtles and 

found no significant differences in growth, condition, swimming behavior and feeding, 

suggesting that the attachment does not pose more than minimal energetic costs. The authors also 

noted that because neonates are not continuously actively swimming, energetic costs may be 

further reduced to this age class. Taking information on turtle movements into account with the 

Permit Division’s standard mitigation measures for transmitters, we do not anticipate that the 

proposed methods pose any long-term risks to the turtle. The transmitters would not result in any 

serious injury. We expect that the proposed materials or methods would not significantly 

interfere with the turtles’ normal activities, growth, movement, feeding, or other critical life 

functions after they are released. 

Schmid noted that radio/sonic telemetered Kemp's ridley turtles exhibited surface durations of 

one to two seconds and submergence durations of one to two minutes upon release and 

continuing for several hours, but longer surface and submergence intervals were observed after 

24 hours and this respiratory pattern continued through the remainder of the monitoring sessions 

(Schmid et al. 2002). Furthermore, telemetric monitoring has demonstrated that Kemp's ridley 

turtles that were captured and handled resume their activities and foraging during their seasonal 

occurrence in nearshore waters (Schmid 2003; Schmid 2004; Schmid et al. 2002; Schmid et al. 

2003) and return to capture sites following winter migrations (Schmid and Witzell 2006). 

Recaptured turtles by Schmid have not displayed any noticeable long-term effects to capture and 

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repeated recapture. Multiple recaptures of turtles suggest that capture and tagging does not 

impede their site fidelity to nearshore foraging grounds (Schmid 1995; Schmid 1998; Witzell and 

Schmid 2003; Witzell and Schmid 2004). 

For tag attachments that require vessel-based tracking of animals, little to no disturbance of the 

target animal is expected as researchers do not intend to get close enough to influence the 

animal’s behavior. Further, in coastal areas where recreational and commercial boating activity is 

common in areas inhabited by turtles, they may become accustomed to these interactions and 

suffer no adverse effects. 

8.4.17 Drilling through Carapace 

Acoustic tags may be secured by wired or tied attachments. Pop-up archival tags may be attached 

to the caudal carapace by tether, and medial ridge direct attachment is specific for leatherback 

tag attachment. For much of the same reasons as provided above for adhesively tagged units, we 

do not expect long-term impacts from these tag methods (wires and tethered units). Wire 

attachments are often used in conjunction with an adhesive putty, the effects are expected to be 

similar, resulting in some level of drag to the animal. When placed on the marginal scutes versus 

the middle of the carapace, we expect that tags would result in less drag. 

Researchers studying the movements and home ranges of green turtles outfitted with both radio 

and sonic transmitters concluded that the transmitters and the tagging experience left no lasting 

effect on habitat use patterns (Seminoff et al. 2002). All tagged turtles in the study were 

resighted 444 times, ranging from 16 to 61 resightings each. The authors concluded that the tags 

had negligible impacts on tagged animals because “(1) telemetered turtles seemed to exhibit 

normal behavior, swimming ability and physical appearance; (2) during tracking efforts, turtles 

returned to areas of initial capture, suggesting that the transmitters and the tagging experience 

left no lasting effect on habitat use patterns; (3) the maximum weight of transmitter packages 

during this study was 1.2 percent of body mass, and studies on fish (Mellas and Haynes 1985) 

have shown that a transmitter will not cause negative effects if its weight is less than 2 percent of 

the tracked individual’s body mass; (4) the use of transmitter fairings as applied to the VHF 

transmitters used in this study has been shown to substantially reduce hydrodynamic drag of 

backpack mounted satellite transmitters in experimental conditions (Watson and Granger 1998); 

and (5) during tracking sessions, both telemetered and non-telemetered turtles were seen in the 

same areas exhibiting roughly similar surface behavior, even swimming within meters of our 

tracking vessel; thus, suggesting negligible effects of the transmitter packages.” 

Avens et al. (2003) investigated homing behavior in juvenile loggerhead sea turtles tagged with 

tethered radio transmitters. Turtles displayed fidelity to the site of capture, with some animals 

being recaptured in the same season or across years. Studies have not yet been done to evaluate 

the drag of a tethered tag unit. However, we have no reason to believe that impacts would be 

greater than those identified for adhesive attachment. Drilling through the shell is invasive but 

not likely to result in harm to the animal (Avens et al. 2003). No bleeding is expected because 

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the site is not vascularized and the animal should feel no pain. Once the tag is shed, the scute 

would grow back, resulting in no lasting effects to the carapace. A discussion of potential 

acoustic impacts is provided here for acoustic tags, which could be attached via epoxy, putty, 

and/or wire. 

8.4.17.1 Acoustic Tag Transmission 

Signals from sonic or acoustic tags would be tracked underwater using a directional hydrophone. 

Transmissions typically have a frequency of approximately 25 to 80 kHz. This frequency level is 

not expected to adversely affect turtles. Sea turtles have low-frequency hearing sensitivity and 

are potentially affected by sound energy in the band below 1,000 hertz (Lenhardt 2003). Bartol et 

al. (1999) found the effective bandpass of the loggerhead sea turtle to be between at least 250 

and 1,000 Hz. Ridgway et al. (1969) found the maximum sensitivity of green sea turtle hearing 

to fall within 300 to 500 Hz with a sharp decline at 750 Hz. Since these tags authorized for sea 

turtle tracking research would be well above this hearing threshold, these tags would not be 

heard by the turtles. We would not expect the transmitters to interfere with turtles’ normal 

activities after they are released. 

Another important consideration is whether the sounds emitted by these transmitters would 

attract potential predators, primarily sharks. Unfortunately, hearing data on sharks is limited. 

Casper et al. (2004) examined the hearing abilities of the nurse shark (Ginglymostoma cirratum), 

and results showed that this species detects low frequency sounds from 100 to 1,000 Hz with 

best sensitivity from 100 to 400 Hz. Although we don't have hearing information for all the 

sharks that could potentially prey on sea turtles, estimates for hearing sensitivity in available 

studies provided ranges of 20 to 1,000 Hz. In general, these studies found that shark hearing is 

not as sensitive as in other tested fishes, and that sharks are most sensitive to low frequency 

sounds (Banner 1967; Casper et al. 2003; Casper and Mann 2007; Casper and Mann 2009; 

Kritzler and Wood 1961). Thus, we do not expect acoustic transmitters would attract potential 

shark predators to the turtles, given the frequency of the tags is well above the 1,000 Hz 

threshold. 

8.4.17.2 Leatherback Long-term Attachments 

The medial ridge of the leatherback sea turtle provides enough dense tissue for an anchor and is 

far removed from any vital structures. We expect animals to experience minimal pain or 

discomfort because the integument at the site of attachment is not rich in nerve endings. 

Similarly, minimal bleeding is expected. The risk for carapacial infection or osteomyelitis (bone 

infection) is extremely low even in the case of hardware failure and breakout due in large part to 

the leatherback's inherent natural ability to heal from major natural injuries encountered in the 

environment. The overall risks of the deployments are less than the risks animals (e.g., females) 

face from courting males, fishing gear, and other natural or human-induced trauma. The size, 

shape, and footprint of the attachment is substantially smaller than the previously authorized 

harness method, thereby resulting in reduced hydrodynamic effects to the tagged animal (Jones 

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et al. 2011). For this reason, the Permit’s Division has stopped authorizing the use of harnesses 

on leatherback sea turtles since 2010. 

Dr. Lutcavage’s telemetry data also shows that these tags do not disrupt migration patterns to 

nesting beaches (Dodge et al. 2015; Dodge et al. 2014) and a review of Dr. Lutcavage’s annual 

reports (for Permit No. 15726) monitoring the health of animal’s post-tagging indicates that 

transmitter attachments do not appear to result in long-term harm or to appreciably reduce 

reproductive fitness (resightings on nesting beaches with no visible scars at the tagging location). 

During previous telemetry deployments using no longer authorized harness-based attachments 

from central California foraging grounds, most leatherback turtles (greater than 70 percent) 

returned to areas of initial capture after over-wintering in tropical latitudes (Benson et al. 2011), 

suggesting that the transmitters and the tagging experience left no lasting effect on habitat use 

patterns. The use of satellite-linked transmitters designed for attachment to medial ridge of a 

leatherback carapace have been shown to substantially reduce hydrodynamic drag in comparison 

with transmitters attached with previously authorized shoulder harnesses (Jones et al. 2011). 

Hence, the Permit’s Division believes that more streamlined medial ridge attached tags will 

lessen impacts to this species while still providing valuable long-term data on migrations and 

movements. The Permits Division requires researchers to attach tags so that they are not placed 

at the peak height of the carapace to reduce drag effects as recommended by Jones et al. (2011). 

In addition, Casey and Southwood (2008) observed that turtles tagged with the medial ridge 

method did not visibly react to the procedure and the tag site on the carapace looked healthy 

post-tagging. 

Casey and Southwood (2008) tagged female leatherbacks under Permit No. 1557 in this manner 

while ovipositing during the nesting season on St. Croix; they noted that twelve of nineteen 

females returned to the beach to nest again indicating that nesting was not impacted by the tag 

attachment. All twelve animals behaved normally and the wound site did not have signs of 

infection, chaffing, or necrosis. Two of the twelve tags had shed prior to the animal’s return to 

the beach. Of the seven females that did not return to nest, four turtles begin a post-nesting 

migration with the tag attached, some of which are thought to have nested elsewhere based on 

movements. Tags transmitted for at least one to two months each. The remaining three tags are 

believed to have been shed by the turtles based on the two observed animals that returned to the 

St. Croix nesting beach without tags. Researchers reported for Permit No. 1557 (in 2009 and 

2010) tagging twelve and three turtles, respectively, noting a similar ease of tagging and 

behavior of animals. Transmissions from all tags ranged between 150 to 300 days and 

demonstrated that animals continued to migrate across the North Atlantic, possibly to nesting 

beaches. Based on these reports, the proposed tagging method would not be expected to reduce 

the numbers, distribution, or reproduction of sea turtles in the wild or reduce the likelihood of 

survival and recovery of these species. 

Several researchers have directly attached satellite tags and TDRs to the caudal peduncle (e.g., 

NMFS Southwest Fisheries Science Center in other countries and the NMFS Southeast Fisheries 

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Science Center in Florida) and medial ridge of leatherbacks, with no resulting mortalities or 

long-term injuries. Instruments are small, lightweight, and streamlined to minimize drag. From 

initial long-term tracks of leatherbacks, it appears that movement, survival, foraging, and 

predator avoidance are not affected. A nesting leatherback tagged by the NMFS Southeast 

Fisheries Science Center nested a second time with the tag attached to the caudal peduncle with 

no deleterious effects, suggesting that reproduction is not affected. 

8.4.18 Stomach Pills 

We expect no harm to the animal from the ingestion of a stomach pill and only minor, temporary 

stress. Insertion of the recorder is a quick procedure, with the turtle's mouth is usually held open 

for less than one minute. A previous study has shown that a stomach temperature pill, model 

STP3, inserted in this manner is eventually pushed into the stomach by peristaltic action and 

food ingestion (Southwood et al. 2005). The recorders are small enough to easily pass through 

the digestive tract of a turtle. Recordings of gastrointestinal tract temperatures are expected for 

approximately twelve to thirteen days using this technique (Casey et al. 2010). In a previous 

study, pills fed to leatherback turtles were excreted within ten days of ingestion (Southwood et 

al. 2005). Stomach pills were used by Casey et al. (2010) to infer foraging behavior by 

leatherback turtles during the inter-nesting period at Sandy Point National Wildlife Reserve, St. 

Croix, U.S. Virgin Islands. They reported that eleven of nineteen turtles returned to the Sandy 

Point National Wildlife Reserve to nest eight to thirty-one days following instrument 

deployments, and that all turtles that returned to nest there displayed normal nesting behavior. 

Furthermore, eight of nineteen turtles were re-sighted at the Sandy Point National Wildlife 

Reserve two years after instrument deployments. They reported that the external instrument 

attachment sites for the medial ridge tag unit had healed and were in good condition for all 

remigrants, providing evidence that the direct attachment technique is safe for use with 

leatherbacks and does not cause lasting damage to the carapace. 

8.4.19 Non-invasive Imaging 

X-ray, CT, MRI, and ultrasound are all non-invasive procedures that would be supervised by a 

veterinarian. These procedures would involve handling and restraint, as well as imaging with 

some devices emitting sound pulses that are well above the levels audible to sea turtles. Although 

the turtle may experience short-term stress or discomfort during imaging, this stress would not be 

significant. Any stresses associated with this activity are expected to be minimal and short-term. 

No lasting effects of imaging are expected. Exposure to radiation during x-ray is expected to be 

minimal and pose no more risk than for a human. X-ray is a routine procedure for animals in 

rehab. Exposure to an MRI would not be expected to affect an animal’s ability to orient when 

returned to the wild. To study mechanisms of sea turtle orientation and navigation, Fuxjager et 

al. (2011) exposed loggerhead hatchlings to different simulated magnetic fields to see how they 

behaved and oriented. The authors did not report any evidence of disorientation or harm to the 

subjects after exposure and all animals were released on the nesting beach after the trial was 

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completed. As discussed in the context of laparoscopy, sedation for imaging, has an inherent risk 

of mortality. However, animals would be under the constant care of a veterinarian in a facility 

that should allow them to respond to any emergency. Compromised animals would not be 

sedated. As a result, risk of death is expected to be very low. 

8.5 Sea Turtle Risk Analysis 

The risk to individual sea turtles posed by the Program is determined by assessing the effects of 

the responses of sea turtles to the stressors created by the research activities. Below we address 

the risks of sub-lethal effects, observed research mortality, and unobserved delayed mortality 

where a turtle dies after release but the death was the result of the research activity. Once the risk 

to individuals is determined, the risk to a population and species (including DPS) is assessed. 

8.5.1 Sub-lethal Effects 

Based on our response analysis above, we determine that many of the stressors created by the 

research activities would result in minor behavioral responses by individual sea turtles. The 

presence and sounds created by vessels, manned and unmanned aircraft, underwater tracking 

vehicles, acoustic sensor devices may not elicit any identifiable behavioral or physiological 

response. If a response is elicited, the response would probably be a turtle swimming or diving 

away from the stressor. This level of response would be temporary and not lead to a reduction in 

fitness of an individual sea turtle. Capture of turtles could result in behaviors indicative of 

avoidance or attempts to escape as well as physiological stress response. With the rare exception 

of mortality (discussed below) that could occur in non-selective capture gears, we do not expect 

that individual turtles would experience more than short-term stress and temporary physiological 

changes during capture and subsequent holding and handling. Based on previous researcher 

reports, there is some small risk that trawl captured sea turtles will be comatose upon capture. 

However, given the extensive mitigation measures and protocols in place for handling and 

resuscitating compromised sea turtles, we anticipate that, with the very rare exception of 

mortality that may occur (discussed above), compromised trawl captured sea turtles will be 

successfully rehabilitated prior to release. 

Stressors associated with many of the research procedures conducted on sea turtles will also 

result in sub-lethal effects of short-term stress and/or pain. These include shell marking, flipper 

and PIT tagging, oxytetracycline injection, epibiota collection, swabs, skin biopsies, scute 

scraping, blood sampling, tear collection, tissue biopsy, urine and fecal sampling, lavage, 

laparoscopy, anesthesia, stomach pills, and transmitter attachment involving drilling, epoxy or 

suction cups. Sub-lethal effects on sea turtles resulting from research activities authorized under 

the proposed action will be minimal, short-term, and are not likely to result in any reduced 

fitness or loss of fecundity to individual turtles. Mitigation measures and research protocols 

required as a condition of the research permit further reduce the risk of sub-lethal effects from 

authorized research activities. No serious injuries have been reported to the Permits Division by 

sea turtle researchers over the last ten years. While external tag units would result in increased 

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drag forces while the unit is attached, standard mitigation measures for transmitters set forth by 

the Permits Division are designed to minimize impacts from drag forces, harm and injury to the 

animal and risk of entanglement. Although they could remain attached for several weeks or 

months at a time, transmitters are not expected to result in the reduced fitness of individual 

turtles as long as the required mitigation measures and procedures are followed. 

Since sub-lethal effects are not likely to result in reduced fitness or fecundity of individuals, it 

follows that sub-lethal effects from research activities are not likely to negatively impact sea 

turtles populations. Therefore, we determine that the authorized sublethal take of sea turtles as 

part of the proposed action is not likely to affect the survival or recovery of ESA-listed sea turtle 

species or DPSs. These conclusions can be reached as long as all sampling protocols, mitigation 

measures, and any other required conditions of the sea turtle research permit are followed by all 

permit holders. In addition, as part of the adaptive management approach that is an integral part 

of the Program, the Permits Division will continuously monitor and evaluate the sub-lethal 

effects of authorized activities. If the sub-lethal effects associated with a particular activity are 

greater than anticipated, the Permits Division will reevaluate the authorization of the activity in 

permits and consider additional mitigation measures as necessary. 

8.5.2 Research Mortality 

Based on our response analysis above, we determine that stressors associated with the capture of 

sea turtles in non-selective gear (i.e., trawl, entanglement, pound, and seine nets) could result in 

the mortality of individual sea turtles. Based on past sea turtle research, mortalities due to 

capture are expected to be very rare. From 2007-2017 there were only five reported sea turtle 

research mortalities out of 9,881 reported captures (i.e., mortality rate of 0.0005). Four of the 

five were captured in pound nets (two Kemp ridley’s and two greens) and one was captured in a 

trawl net (loggerhead). 

Lethal take limits represent the maximum number of sea turtles that can be killed every ten years 

as part of the proposed action; the actual number of sea turtle mortalities resulting from the 

proposed action may be considerably smaller since mortalities are rare events. In addition, the 

Permits Division will take a conservative approach to authorizing lethal take in individual 

permits, and will not authorize the “reserve” lethal take up front as this will be retained as a 

buffer for unexpected events. Table 24 shows each species and DPS with their current abundance 

estimate, abundance trend, and ten-year lethal take limits that are part of the Program, and the 

impact to the population assuming the lethal take limit is reached. Lethal take limits for the 

Program would be established for each species and ocean basin. Since there is more than one 

green turtle DPS per ocean basin, the green turtle lethal take limits shown in Table 24 are based 

on the conservative assumption that the entirety of lethal take authorized within a ten-year period 

could come from a single DPS within a particular ocean basin (e.g., all 15 lethal takes from the 

North Atlantic DPS and zero from the South Atlantic DPS; or visa-versa). 

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Table 24. ESA-listed sea turtle species with abundance estimates, abundance trends, tenyear lethal take limits and population impact. 

Species 

Distinct 

Population 

Segment 

Abundance 

estimate 

Abundance 

Trend 

Lethal Take Limits for 

Research Mortality 

(Total over 10 years= 

Authorized + Reserve 

Buffer) 

Population 

Impact 

Over 10 

Years 

Green North Atlantic 167,424 

Nesting females1 Increasing11 15 0.0090% 

Green South Atlantic 63,332 

Nesting females1 Mixed11 15 0.0237% 

Green East Indian-West 

Pacific 

77,009 

Nesting females1 Mixed1 0 0 

Green Central West 

Pacific 

6,518 

Nesting females1 Unknown11 7 0.1074% 

Green Southwest Pacific 83,058 

Nesting females1 Increasing1 0 0 

Green Central South 

Pacific 

2,677 

Nesting females1 Unknown11 7 0.2615% 

Green Central North 

Pacific 

3,846 

Nesting females1 Increasing11 7 0.1820% 

Green East 

Pacific 

20,062 

Nesting females1 Mixed11 7 0.0349% 

Hawksbill Worldwide 22,004 

Nesting females2 Mixed11 15 

(Atlantic + Pacific) 0.0682% 

Kemp’s 

ridley Worldwide 4,872 Nesting females3 Unknown11 15 

(Atlantic only) 0.3079% 

Leatherback Northwest Atlantic 

subpopulation 

34,000 

Adults4 Stable11 15 0.0441% 

Leatherback West Pacific 

subpopulation 

562 

Nesting females5 Decreasing11 2 0.3559% 

Loggerhead Northwest Atlantic 53,000 

Nests annually6 Stable11 15 0.0283% 

Loggerhead Northeast Atlantic 12,000 

Nests annually7 Unknown12 0 0 

Loggerhead North Pacific 43,320 

Individuals8 Stable11 7 0.0162% 

Loggerhead South Pacific 200 

Nesting females9 Decreasing12 0 0 

Olive ridley Worldwide 1.39 million 

Adults10 Mixed11 15 

(Atlantic + Pacific) 0.0011% 

1 (Seminoff et al. 2015); 2 (NMFS and USFWS 2013a); 3 Derived from (NMFS and USFWS 2015); 4 (TEWG 2007); 5 Derived from (NMFS and USFWS 2013b); 6 (NMFS SEFSC 2009); 7 (Lino et al. 2010; Marco et al. 2010); 8 

(Matsuzawa 2011; Seminoff et al. 2014); 9 (Wabnitz and Andréfouët 2008); 10 (Eguchi et al. 2007); 11 (NMFS 

2017c); 12 (Conant et al. 2009). 

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The East Indian-West Pacific and Southwest Pacific DPSs of green and Northeast Atlantic 

Ocean DPS and South Pacific Ocean DPS of loggerhead are also included, despite being a 

foreign water population because these DPSs could be caught on the high seas through capture 

under another authority. The Permits Division would not authorize any lethal take for those four 

DPSs under the Program. 

8.5.3 Delayed Mortality 

Based on our response analysis above, we determine that stressors associated with the capture of 

sea turtles in trawl nets could result in the delayed (unobserved) mortality of individual sea 

turtles. Sea turtles caught by trawl have an increased risk of delayed mortality due to forced 

submergence. Underwater entrapment in fishing gear followed by rapid decompression may 

cause gas bubble formation within the blood stream (embolism) and tissues leading to organ 

injury, impairment, and even mortality in some individuals. 

As part of our risk analysis, we evaluate the anticipated delayed mortality from trawl capture. 

Available information for estimating a delayed mortality rate due to sea turtle research activities 

is sparse. Based on historical data, the Permits Division calculated an observed research 

mortality rate of 0.0005 from reported take data for all species combined over a ten-year period 

(i.e., five observed mortalities out of 9,881 reported capture takes over the previous ten years). 

As an assessment of the potential for delayed mortality, based on expert opinion the Permits 

Division predicts that the delayed mortality rate may be as high as twice the observed research 

mortality rate, or 0.0010, of all sea turtles captured (i.e., all species combined) (NMFS 2017a). 

On average, permitted researchers reported taking approximately 1,100 sea turtles by capture (all 

methods) in a given year. Using the above estimates for delayed mortality rate and captures 

(0.0010 and 1,100), this translates to an annual delayed mortality estimate of approximately 1.11 

turtles, all species combined. 

Although the above approach provides us with an estimate of delayed mortality, we have 

identified several shortcomings for using this approach in our risk analysis. First, the doubling of 

the observed research mortality rate to determine the delayed mortality rate is based on expert 

opinion rather than empirical data. Second, while the observed mortality rate was based on 

turtles captured using all capture methods, our turtle response analysis indicates that the risk of 

delayed mortality from turtle research capture is only from capture in trawl nets. Third, the 

estimated number of delayed mortalities is expressed for all species combined; however, for our 

risk analysis we must separately assess the risk to each species or DPS. 

To address these shortcomings, we developed an estimate of delayed mortality based on 

information on turtle health as provided in past sea turtle researcher annual reports. We focused 

on reports from researchers who used trawl nets to capture sea turtles. Since sea turtle delayed 

mortality is likely related to trawl tow time (Fahlman et al. 2017), to take a conservative 

approach we used data from trawl captured sea turtles with 30 minute tow times, the maximum 

that would be authorized under the Program. We found only one research permit that met the 

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criteria for our delayed mortality estimate (Permit No. 1245). Under this permit, from 2000 to 

2003, 3,020 trawling events resulted in 925 loggerheads, 67 Kemp’s ridley, and 8 green sea 

turtles captured. Of those 1,000 turtles captured, five were collected comatose and required 

intubation. Four intubated turtles were returned to the wild after normal behavior was observed. 

The fifth turtle also appeared to return to normal health and at one point was so active that it was 

tagged in anticipation of release. However, the turtle became lethargic again and eventually died 

in the lab (see Section 8.3.2 for more details). The necropsy showed that the turtle was healthy in 

all respects except that water had caused the anterior lobes of the lungs to swell and cease to 

function properly. Although the death occurred in the lab and not after release into the wild, this 

incident indicates that, although very rare, delayed mortality after trawl capture is possible, even 

after the turtle has shown initial signs of returning to normal health. Based on this information, 

we assign an estimated delayed mortality rate of 0.1 percent (i.e., one out of 1,000 turtles 

captured in trawls using 30 minute tow times). 

Next, we apply the delayed mortality rate estimated above to the anticipated number of trawl 

captures in the Program for each species or DPS. The average annual number of authorized turtle 

takes from trawl capture over the last ten years (June 2007 to May 2017) by species are as 

follows: green, 122.7; hawksbill, 18.5; Kemp’s ridley, 151.9; leatherback, 8.4; loggerhead, 

393.3; olive ridley, 1.5; and unidentified, 3.6. This equates to the following proportions of the 

trawl captures by species: 17.53 percent green, 2.64 percent hawksbill, 21.70 percent Kemp’s 

ridley, 1.20 percent leatherback, 56.19 percent loggerhead, and 0.21 percent olive ridley. Based 

on our exposure analysis above, we estimate the proposed action will result in 8,749 sea turtle 

captures by trawl (Table 23) over any given ten-year period. This is a highly conservative 

estimate of trawl captures because, since it is based on past authorized levels, it assumes that 100 

percent of authorized trawl captures will be utilized by researchers. From 2007 to 2017, only 16 

percent of authorized trawl captures resulted in actual trawl capture take as reported by 

researchers. 

Using these proportions, we estimate the number of turtles that may be captured by trawl for 

each species, and calculate the estimated number of delayed mortalities that may result from 

these trawl captures over a ten-year period (Table 25). For species with more than one DPS, we 

make the conservative assumption that 100 percent of the estimated trawl captures for the species 

could potentially come from any of the individual DPSs (e.g., all 1,533.7 trawl captures of green 

turtles could be from the North Atlantic DPS). The estimated delayed mortalities were 

conservatively rounded up to the nearest integer and added to the anticipated observed research 

mortalities (based on lethal take limits) to arrive at the total estimated mortalities over ten-years 

for each species or DPS. 

The Permits Division will re-evaluate delayed mortality rates if the program has a substantial 

increase in 1) reported mortalities over several years, or 2) reported take levels for all activities 

that require capture or handling animals beyond historic levels. As with the research mortality 

rate, the delayed mortality rate will be re-assessed and adjusted as more data are collected or new 

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information indicates an increased risk of delayed mortality from research methods. For 

example, delayed mortality resulting from the stress of capture may change if new data on 

decompression sickness from trawl capture becomes available. The Permits Division will also 

evaluate all new procedures for their risk to cause mortality (or a reduction of fitness) based on 

the best available data. Because the Permits Division will know how many takes are authorized 

for capture and handling of turtles each year, as part of monitoring the program, they will be able 

to provide us with an update on whether the estimated delayed mortality rate changes when 

reporting annually to the Interagency Cooperation Division. The impact of mortality on sea turtle 

populations as a result of the proposed action is estimated by dividing the total estimated 

mortality by the abundance estimate for each species (or DPS) as shown in Table 25. 

8.5.4 Summary 

Based on our risk analysis, accidental mortality as a result of research activities authorized under 

the Program will likely have an extremely small impact on ESA-listed sea turtles at the species 

or DPS level. For most species and DPSs, research related mortalities will result in a decrease of 

less than 0.15 percent of the population every ten years. The populations that could potentially be 

most impacted are (in order of impact): West Pacific DPS of leatherback (0.53 percent), Kemp’s 

ridley (0.35 percent), Central South Pacific DPS of green turtle (0.34 percent), and Central North 

Pacific DPS of green turtle (0.25 percent). Considering that such changes are projected over a ten 

year period, these estimated declines still represent a very small proportion of each population 

(i.e., from 0.025 to 0.053 percent annually). Since the abundance estimates used to calculate 

these proportions are of nesting females only, the estimated population impacts could be even 

smaller since some of the mortalities will likely be males or juveniles. In addition, as discussed 

above, several conservative assumptions were made in estimating the anticipated observed 

research and delayed mortalities for each species (or DPS). Thus, the proportion of each ESAlisted sea turtle population lethally taken (as shown in Table 25) likely represents a highly 

conservative estimate of the impact on these populations. In summary, there is no indication that 

the anticipated small amount of lethal take resulting from turtle research activities authorized as 

part of the Program poses a threat to the recovery of any ESA-listed sea turtle species or DPS. 

8.6 Non-Target Species Exposure and Response Analysis 

Several non-target ESA-listed species will be exposed to activities conducted under the Program. 

These species are Atlantic salmon, smalltooth sawfish, Atlantic sturgeon, shortnose sturgeon, 

green sturgeon, Gulf sturgeon, Nassau grouper, and scalloped hammerhead. Below we address 

the exposure, response, and risk to these species. 

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Table 25. Proportion of all trawl captures, anticipated trawl captures, ten-year lethal take 

limits, estimated delayed mortalities, abundance estimates and population impact for 

each turtle species or distinct population segment. 

Number of Turtles 

Over 10 Year Period 

Species and DPS 

Proportion 

of All Trawl 

Captured 

Sea Turtles 

by Species 

Anticipated 

trawl captures 

over 10 years 

(proportion of 

8,749 turtles) 

Estimated 

Delayed 

Mortality 

(0.1% of trawl 

captures) 

Lethal 

Take 

Limits 

Total 

Estimated 

Mortality 

Abundance 

estimate 

Population 

Impact 

(Total 

mortality 

divided by 

abundance) 

Green 

North Atlantic 17.53% 1,533.70 1.53 15 17 

167,424 

Nesting 

females 

0.0101% 

Green 

South Atlantic 17.53% 1,533.70 1.53 15 17 

63,332 

Nesting 

females 

0.0268% 

Green Central 

West Pacific 17.53% 1,533.70 1.53 7 9 

6,518 

Nesting 

females 

0.1380% 

Green Central 

South Pacific 17.53% 1,533.70 1.53 7 9 

2,677 

Nesting 

females 

0.3362% 

Green Central 

North Pacific 17.53% 1,533.70 1.53 7 9 

3,846 

Nesting 

females 

0.2340% 

Green 

East Pacific 17.53% 1,533.70 1.53 7 9 

20,062 

Nesting 

females 

0.0449% 

Hawksbill 2.64% 230.97 0.23 15 16 

22,004 

Nesting 

females 

0.0727% 

Kemp’s ridley 21.70% 1,898.53 1.90 15 17 

4,872 

Nesting 

females 

0.3489% 

Leatherback 

Northwest Atlantic 

subpopulation 

1.20% 104.99 0.10 15 16 34,000 

Adults 0.0471% 

Leatherback 

West Pacific 

subpopulation 

1.20% 104.99 0.10 2 3 

562 

Nesting 

females 

0.5338% 

Loggerhead 

Northwest Atlantic 56.19% 4,916.06 4.92 15 20 

53,000 

Nests 

annually 

0.0377% 

Loggerhead 

North Pacific 56.19% 4,916.06 4.92 7 12 43,320 Individuals 0.0277% 

Olive ridley 0.21% 18.37 0.02 15 16 1.39 million 

Adults 0.0012% 

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8.6.1 Vessel Interactions 

Sea turtle research vessels could potentially interact with the following non-target ESA-listed 

fish species as part of the proposed action: Atlantic salmon, smalltooth sawfish, Atlantic 

sturgeon, shortnose sturgeon, green sturgeon, Gulf sturgeon, Nassau grouper, and scalloped 

hammerhead. Vessel strike is identified as a threat to populations of Atlantic and shortnose 

sturgeon (ASSRT 2007; SSSRT 2010), but these interactions are limited mostly to shipping 

vessels heading to and from major ports in river environments. Green sturgeon, Gulf sturgeon 

and smalltooth sawfish may also be affected by vessel strike, although there is little available 

information on the impact of this threat on these or any other ESA-listed fish species considered 

in this opinion. While a sea turtle research vessel strike could result is serious injury or death, the 

likelihood of this occurring is extremely small (i.e., discountable) given that (1) there has never 

been a reported incident of a vessel strike on any species (listed or non-listed) by a NMFS 

permitted sea turtle researcher (NMFS 2017a), (2) vessel strikes of any marine fish species are 

generally a rare event, (3) turtle research vessels account for a very small fraction of vessel 

activity in the action area, and (4) research vessel operators are expected to be vigilant and 

proceed carefully to minimize risk of vessel strike and unnecessary disturbance when ESA-listed 

species may be in the area. In the unlikely event that a research vessel strikes an ESA-listed 

species, the researcher will be required to report the incident to the Permits Division. 

The presence of a research vessel may disturb non-target fishes resulting in their movement away 

from the vessel for a short time. Reactions may include a brief startle response, diving, 

submerging, or attempting to evade the vessel or personnel. Based on the anticipated responses, 

any disruptions are expected to be temporary in nature, with animals resuming normal behaviors 

shortly after the exposure. No reduction in fitness or overall health of individual fish is 

anticipated due to the presence of sea turtle research vessels. 

8.6.2 Capture by Entanglement, Pound, Seine, or Trawl Nets 

Nets used by researchers to capture sea turtles could potentially interact with the following nontarget ESA-listed fish species within the action area: Atlantic salmon, smalltooth sawfish, 

Atlantic sturgeon, shortnose sturgeon, green sturgeon, Gulf sturgeon, Nassau grouper, and 

scalloped hammerhead. The non-selective capture methods authorized as part of the Program 

that could result in the incidental capture of fish species are entanglement nets, pound nets, 

seines, and trawls. Some interactions between ESA-listed fish species and turtle research gear 

would likely occur as a result of the proposed action. If any non-target ESA-listed species is 

incidentally captured or harmed by research activities, all activities would be suspended until the 

Permits Division has granted approval to continue research. 

Animals entangled or captured in nets can become stressed, harmed, injured, and/or die. Animals 

may experience additional stress and other adverse effects during subsequent handling for 

disentanglement and release. Signs of stress include reduced respiration and prolonged struggling 

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while being held. Impacts to each species or taxa that may be affected by the proposed action are 

described below. 

Except for pound nets, permits authorizing stationary netting would require that nets be 

continuously monitored for entanglements. This will ensure that all incidentally captured animals 

will be freed from the net as quickly as possible. As a result, the effects of temporary 

entanglement are, in most instances, expected to be minor and short-term, with resumption of 

normal behaviors to occur shortly after release. Pound nets are required to be checked every 24-

hrs. However, fish should be able to swim freely within the pound until researchers are able to 

release them. Sea turtle research permits that authorize trawling would set a limit on the tow 

duration to minimize impacts to turtles and incidentally caught non-target species. Additional 

mitigation measures, as a condition of sea turtle research permits, designed to minimize effects 

on particular species, are describe below. Even with the required mitigation measures in place, 

we anticipate that some very small proportion of these interactions will result in mortality due to 

the effects of capture (e.g., entanglement in trawl net or other capture gear). The anticipated 

number of takes (lethal and sublethal) of ESA-listed fish species as a result of sea turtle research 

authorized under the Program is provided below for each non-target species or DPS that may be 

affected. 

8.6.2.1 Atlantic Salmon, Gulf of Maine Distinct Population Segment 

Adult Atlantic salmon ascend GOM rivers beginning in the spring and continuing into the fall, 

with the peak occurring in June. Salmon smolts leave the rivers and enter the sea during May and 

June to begin their ocean migration. Sea turtle research that occurs in the spring and early 

summer has the greatest potential for interacting with migrating adult and juvenile salmon. Based 

on currently authorized sea turtle research permits, the spatial overlap between research gear and 

GOM Atlantic salmon occurs exclusively in the marine environment. While future turtle research 

may occur in the lower portions of GOM rivers, we anticipate that sea turtle research in this 

region will continue to occur primarily in the marine environment. 

Given the typical mesh size, location, set times, and water depth of sea turtle research gear, there 

is a low likelihood of Atlantic salmon incidental capture. Large net mesh sizes, that are often 

used for turtle research, are expected to have no effect on juvenile Atlantic salmon as these fish 

are too small to be vulnerable to entanglement. Interactions with adult Atlantic salmon are also 

not expected to occur with net mesh sizes of 12" or greater for the same reason. Incidental 

capture of large adult Atlantic salmon by sea turtle researchers could potentially occur with net 

mesh sizes of 12” or less. As smolts migrate from the rivers they tend to travel near the water 

surface. Atlantic salmon in the ocean are pelagic and also highly surface oriented (Kocik and 

Sheehan 2006). As such, Atlantic salmon are likely more vulnerable to sea turtle capture gears 

that occupy that upper portion of the water column. If an Atlantic salmon is taken as part of the 

proposed action it is most likely to be caught in an entanglement net or trawl. 

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While adult Atlantic salmon may be present in the action area year-round, based on historical 

commercial fisheries bycatch data, they are rarely captured in fishing nets in the marine 

environment. Northeast Fisheries Observer Program data indicate a total of 15 individual 

Atlantic salmon caught from 1989 through 2013 (NMFS 2013c). There is no information 

available on the genetics of these fish, so we do not know how many of these salmon were part 

of the GOM DPS. Of the observed incidentally caught Atlantic salmon, ten were listed as 

“discarded” (presumably alive) and five were listed as mortalities. The incidental takes of 

Atlantic salmon occurred using sink gillnets (11) and bottom otter trawls (4). Incidental capture 

of Atlantic salmon in sea turtle research nets are expected to be considerably lower than those 

reported by the Northeast Fisheries Observer Program since turtle research effort is extremely 

small compared to observed commercial fishing effort within the action area. 

When captured in nets, Atlantic salmon mortality is usually the result of suffocation, exacerbated 

by high water temperatures and/or low DO. Wilkie et al. (1997) showed that salmon suffered 30 

percent mortality when stressed for just six minutes in 23oC water. Elevated water temperatures 

also make salmon more vulnerable to delayed mortality associated with their capture, which can 

occur for up to three days after being released (Wilkie et al. 1997). Atlantic salmon also suffer 

from impaired respiratory abilities when DO is below 5 milligrams per liter (Kazakov and 

Khalyapina 1981). 

Capturing and handling salmon causes physiological stress and can result in physical injury such 

as scale loss. Although relatively high mortality rates have been reported for salmon captured in 

commercial gillnets, mortality risk can be effectively reduced when appropriate mitigation 

measures are implemented. While Atlantic salmon captured in turtle research gear could be 

injured due to stress from capture and handling, in most cases long-term or delayed effects of 

properly handled adult salmon are expected to be minimal, assuming researchers follow the 

sampling procedures and mitigation measures specified in their permit. 

Although interactions between turtle research gear and GOM Atlantic salmon are expected to 

occur infrequently, it is likely that some small amount of incidental take will occur as part of the 

Program. While the incidental capture of GOM Atlantic salmon in capture gear used by turtle 

researchers (i.e., entanglement nets, pounds nets, seines and trawls) may result in short-term 

negative effects (i.e., elevated stress levels, net abrasion), with the exception of those extremely 

rare instances of capture mortality, these activities are not expected to result in reduced fitness or 

have any long-term adverse effects on individual fish. This conclusion can be reached as long as 

all of the sampling protocols, mitigation measures, and any other required conditions of the sea 

turtle research permit are closely followed by all permit holders. 

We estimate that the Program will result in the take of up to three GOM DPS Atlantic salmon, 

including the lethal take of up to one GOM DPS Atlantic salmon, over any ten-year period. To 

arrive at this estimate we considered the history of sea turtle research interactions with Atlantic 

salmon, the mitigation measures in place to avoid future interactions, and the potential future 

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GOM DPS population growth that could increase the risk of exposure to sea turtle research 

sampling gear. 

8.6.2.2 Smalltooth Sawfish, U.S. Portion of Range Distinct Population Segment 

Spatial overlap documented in the ranges of sea turtle species and the U.S. portion of range 

smalltooth sawfish DPS is the main variable considered in anticipating future interactions with 

smalltooth sawfish and research authorized under the Program. Smalltooth sawfish are found in 

the peninsula of Florida, most commonly in the Everglades region at the southern tip of the state. 

This is also one of the most active geographic areas for sea turtle researchers. The Permits 

Division anticipates issuing several sea turtle research permits within the range of the smalltooth 

sawfish as part of the Program (NMFS 2017a). Sawfish coastal migratory behavior by individual 

adults and large juveniles in northeast Florida has been documented. These migratory 

movements are limited largely by cold intolerance (about 16 to 18 degrees Celsius and also by 

the lack of appropriate coastal foraging and habitat. Thus, the likelihood of turtle research gear 

interacting with sawfish becomes increasingly more remote as you move north up the Atlantic 

coast. 

The morphology of the smalltooth sawfish causes it to be particularly vulnerable to entanglement 

in any type of non-selective netting gear used in sea turtle research, including the relatively 

small-mesh webbing used in trawls, seines, and entanglement nets. The long toothed rostrum of 

the species penetrates easily through nets, causing the animal to become entangled when it 

attempts to escape. The entanglement nets and trawl nets used in sea turtle research can result in 

the take of smalltooth sawfish based on historical data on incidental captures in commercial 

fisheries (Simpfendorfer and Wiley 2005). Henshall (1894) noted that the smalltooth sawfish 

“does considerable damage to turtle nets and other set nets by becoming entangled in the meshes 

and is capable of inflicting severe wounds with its saw, if interfered with.” Reports of smalltooth 

sawfish becoming entangled in fishing nets are common in the early literature from areas where 

they were once common, but are now rare (if not extirpated), including Florida (Snelson 1981), 

Louisiana (Simpfendorfer 2002), and Texas (Baughman 1943). Reported smalltooth sawfish 

injuries and mortalities in commercial fishing operations were due largely to the difficulty of 

safely removing sawfish from fishing gear without damaging the gear. This often meant removal 

of the saw before returning the fish to the water to starve to death, or killing the sawfish in the 

net and dropping the carcass overboard. The Permits Division has implemented the following 

mitigation measures designed to minimize adverse effects and the risk of mortality if a sawfish is 

captured incidentally: 

• Researchers operating in areas where sawfish are present are required to be trained by a 

member of the NMFS sawfish recovery team to discuss proper handling procedures. 

• When attempting to handle and release an incidentally captured sawfish, researchers must 

use caution and follow safe-handling procedures specified in the NMFS Sawfish 

Handling and Release Guidelines. 

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• Researchers must keep the fish in the water at all times and cutting the net from the 

rostrum and body of the animal (no attempts should be made to disentangle the rostrum 

from the net). 

• Adverse interactions with sawfish should be documented, including any pertinent details 

of the interaction (e.g., gear type, what was done to handle and release the animals, 

location, date, size, water and air temperatures, and photos if possible). 

Although interactions between turtle research gear and smalltooth sawfish are expected to occur 

infrequently, it is likely that some small amount incidental take will occur as part of the Program. 

A total of four smalltooth sawfish interactions have been reported by researchers or commercial 

vessels in the last 15 years in the northern range of sawfish; one lethal and three non-lethal. 

Incidental take statements in a 2016 batched biological opinion for three sea turtle permit actions 

(Permit Nos. 18926, 19528, and 19621) authorized up to five smalltooth sawfish takes (all nonlethal) over the five years of the permitted actions. While the incidental capture of smalltooth 

sawfish in capture gear used by turtle researchers (i.e., entanglement nets, pounds nets, seines 

and trawls) may result in short-term negative effects (i.e., elevated stress levels, net abrasion), 

with the exception of those extremely rare instances of capture mortality, these activities are not 

expected to result in reduced fitness or have any long-term adverse effects on individual fish. 

This conclusion can be reached as long as all of the sampling protocols, mitigation measures, and 

any other required conditions of the sea turtle research permit are closely followed by all permit 

holders. 

We estimate that the Program will result in the take of up to five U.S. portion of range DPS of 

smalltooth sawfish, including the lethal take of up to two smalltooth sawfish, over any ten year 

period. To arrive at this estimate we considered the history of sea turtle research interactions with 

smalltooth sawfish, the mitigation measures in place to avoid or minimize the effects of future 

interactions, and the potential future smalltooth sawfish population growth that could increase 

the risk of exposure to sea turtle research sampling gear. 

8.6.2.3 Sturgeon Species 

The proposed action anticipates multiple sea turtle research permits may be issued within the 

ranges of all five DPSs of Atlantic sturgeon, shortnose sturgeon, Gulf sturgeon, and Southern 

DPS green sturgeon. There have been no reported incidental takes of sturgeon during permitted 

sea turtle research. However, the use of non-selective capture gear (e.g., entanglement nets and 

trawls) by turtle researchers could result in the future incidental capture of these sturgeon 

species. Due to their life history, all four sturgeon species considered in this opinion could 

potentially interact with sea turtle research gear in marine, coastal, and estuarine environments. 

Entanglement in research nets used to capture sea turtles can constrict a sturgeon’s gills, 

resulting in increased stress and risk of suffocation (Collins et al. 2000; Kahn and Mohead 2010; 

Moser et al. 2000). Sturgeon stress and mortality associated with capture in nets has been 

directly related to environmental conditions. However, except for very rare instances, results 

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from previous sturgeon research indicate that capture in nets does not cause any effects on the 

vast majority of fish beyond 24 hours. For all species of sturgeon, research has revealed that 

stress from capture is affected by temperature, DO, and salinity, and this vulnerability may be 

increased by the research-related stress of capture, holding, and handling (Kahn and Mohead 

2010). Other factors affecting the level of stress or mortality risk from netting include the amount 

of time the fish is caught in the net, mesh size, net composition, and, in some instances, the 

researcher’s experience level or preparedness. Analysis of the empirical evidence suggests that 

individuals collected in high water temperatures and low DO concentrations, combined with 

longer times between net checks, were more at risk of elevated stress and mortality (Kahn and 

Mohead 2010). As a condition of their permit, turtle researchers will be required to take 

necessary precautions while deploying capture gear to ensure target and non-target ESA-listed 

species are not unnecessarily harmed, including: (1) continuously monitoring nets, (2) removing 

animals from nets as soon as capture is recognized, and (3) limiting the time and depth for use of 

trawling gear. These actions are expected to substantially reduce the likelihood of injuring or 

killing sturgeon during research activities. Sturgeon may also be incidentally captured in pound 

nets and seines during sea turtle research. Since fish trapped in these gears would typically be 

free swimming, as opposed to gilled or confined, the likelihood of stress or injury from pound 

nets or seines is lower than from entanglement nets or trawls. 

Although interactions between turtle research gear and ESA-listed sturgeon species are expected 

to occur infrequently, it is likely that some small amount incidental take will occur as part of the 

Program. Only one currently active sea turtle permit has an ITS for an ESA-listed species of 

sturgeon (Permit No. 19621 ITS for Atlantic and shortnose sturgeon take). While the incidental 

capture of ESA-listed sturgeon species in capture gear used by turtle researchers (i.e., 

entanglement nets, pounds nets, seines and trawls) may result in short-term negative effects (i.e., 

elevated stress levels, net abrasion), with the exception of those extremely rare instances of 

capture mortality, these activities are not expected to result in reduced fitness or have any longterm adverse effects on individual sturgeon. This conclusion can be reached as long as all of the 

sampling protocols, mitigation measures, and any other required conditions of the sea turtle 

research permit are closely followed by all permit holders. While the proposed mitigation 

measures will likely minimize the adverse effects of this take, a very small number of sturgeon 

mortalities may still occur due to the stress and injury associated with capture and handling. 

We estimate that the Program will result in the take of up to six Atlantic sturgeon (all five DPSs 

combined), including the lethal take of up to one Atlantic sturgeon, over any ten year period. We 

estimate that the Program will result in the take of up to three shortnose sturgeon, including the 

lethal take of up to one shortnose sturgeon, over any ten year period. We estimate that the 

Program will result in the take of up to five Gulf sturgeon, including the lethal take of up to one 

Gulf sturgeon, over any ten-year period. We estimate that the Program will result in the take of 

up to two Southern DPS green sturgeon, including the lethal take of up to one Southern DPS 

green sturgeon, over any ten-year period. 

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To arrive at these estimates we considered the history of sea turtle research interactions with 

ESA-listed sturgeon species, the mitigation measures in place to avoid or minimize the effects of 

future interactions, and the potential future sturgeon population growth that could increase the 

risk of exposure to sea turtle research sampling gear. 

8.6.2.4 Nassau Grouper 

Nassau grouper’s distribution include Bermuda, Florida, Bahamas and the Caribbean Sea. Due to 

their life history, Nassau grouper presence would overlap with sea turtle research in both marine 

and coastal environments. Although there have been no reported interactions with Nassau 

grouper by permitted sea turtle researchers, this species could potentially be captured in trawls, 

seines or pound nets used for sea turtle capture. Incidental capture in entanglement nets is less 

likely given the large net mesh sizes typically used by turtle researchers in comparison with the 

body size (or girth) of Nassau grouper. Nassau grouper form large aggregations to spawn, which 

makes them particularly vulnerable to capture in fishing gear during these times of year. To 

mitigate the potential interaction with Nassau grouper at times of spawning, as part of the 

Program the Permits Division would require researchers to avoid known spawning aggregation 

areas when using non-selective capture methods. 

While the incidental capture of Nassau grouper in capture gear used by turtle researchers (i.e., 

entanglement nets, pounds nets, seines and trawls) may result in short-term negative effects (i.e., 

elevated stress levels, net abrasion), these activities are not expected to result in reduced fitness 

or have any long-term adverse effects on individual fish. This conclusion can be reached as long 

as all of the sampling protocols, mitigation measures, and any other required conditions of the 

sea turtle research permit are closely followed by all permit holders. 

We estimate that the Program will result in the take of up to two Nassau grouper, including the 

lethal take of up to one Nassau grouper, over any ten year period. To arrive at this estimate we 

considered the history of sea turtle research interactions with Nassau grouper, the mitigation 

measures in place to avoid or minimize the effects of future interactions, and the potential future 

Nassau grouper population growth that could increase the risk of exposure to sea turtle research 

sampling gear. 

8.6.2.5 Scalloped Hammerhead Shark 

The scalloped hammerhead shark is circumglobal species inhabiting warm temperate and 

tropical seas. They can be found over continental and insular shelves as well as adjacent deep 

waters, ranging from intertidal and surface to depths exceeding 400 meters. As part of the 

Program, sea turtle research permits may be issued within the range of any of the three scalloped 

hammerhead DPSs (Eastern Pacific, Central and Southwest Atlantic, and Indo-West Pacific) 

considered in this opinion. Scalloped hammerhead sharks are commonly caught in commercial 

gillnet and trawl fisheries (Miller et al. 2013). Although there have been no reported interactions 

with scalloped hammerhead by permitted sea turtle researchers, this species could potentially be 

captured incidentally in any of the non-selective capture gears used for to capture sea turtles. 

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Turtle researchers at the NMFS Pacific Islands Fisheries Science Center have listed this species 

as a potential bycatch in past research permits. 

Hammerhead sharks are obligate ram ventilators and have been known to suffer high mortality 

rates in bottom longline fisheries (Macbeth and Macbeth 2009; Morgan and Burgess 2007). 

However, longlines will not be authorized for sea turtle research under the Program. Sharks can 

also experience high mortality rates in commercial gill (entanglement) net fisheries with long 

(i.e., 12 to 48 hour) soak times. However, as a condition of the permit, all bycatch must be 

released immediately upon capture and all sea turtle research gear, except pound nets, must be 

monitored continuously. With continuous net monitoring, turtle researchers will be able to 

respond quickly to bycatch in order minimize the effects of capture on individual sharks. If a 

scalloped hammerhead shark is incidentally captured by a sea turtle researcher, we anticipate the 

effects to be minor in nature (i.e., short-term stress) and dissipate shortly after release. While the 

incidental capture of scalloped hammerhead sharks in capture gear used by turtle researchers 

(i.e., entanglement nets, pounds nets, seines and trawls) may result in short-term negative effects 

(i.e., elevated stress levels, net abrasion), these activities are not expected to result in reduced 

fitness or have any long-term adverse effects on individual fish. This conclusion can be reached 

as long as all of the sampling protocols, mitigation measures, and any other required conditions 

of the sea turtle research permit are closely followed by all permit holders. 

Although interactions between turtle research gear and scalloped hammerhead sharks are 

expected to occur infrequently, it is likely that some small amount incidental take will occur as 

part of the Program. While the incidental capture of scalloped hammerhead sharks in capture 

gear used by turtle researchers (i.e., entanglement nets, pounds nets, seines and trawls) may 

result in short-term negative effects (i.e., elevated stress levels, net abrasion), with the exception 

of those extremely rare instances of capture mortality, these activities are not expected to result 

in reduced fitness or have any long-term adverse effects on individual sharks. This conclusion 

can be reached as long as all of the sampling protocols, mitigation measures, and any other 

required conditions of the sea turtle research permit are closely followed by all permit holders. 

We estimate that the Program will result in the take of up to two scalloped hammerhead sharks 

from any of the three DPSs (Eastern Pacific, Central and Southwest Atlantic, and Indo-West 

Pacific) combined, including the lethal take of up to one scalloped hammerhead shark, over any 

ten year period. To arrive at this estimate we considered the history of sea turtle research 

interactions with scalloped hammerheads, the mitigation measures in place to avoid or minimize 

the effects of future interactions, and the potential future scalloped hammerhead population 

growth that could increase the risk of exposure to sea turtle research sampling gear. 

8.7 Non-Target Species Risk Analysis 

Based on our exposure and response analysis of the effects of the Program on non-target ESAlisted fish species, we anticipate that a small number of takes will occur as a result of incidental 

capture in sea turtle research gear. The large majority of these takes are not expected to result in 

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reduced fitness or have any long-term adverse effects on individual fish. However, a small 

number of interactions could result in mortality (i.e., lethal take) of individual fish from any of 

the following ESA-listed species: Atlantic salmon, smalltooth sawfish, Atlantic sturgeon, 

shortnose sturgeon, green sturgeon, Gulf sturgeon, Nassau grouper, and scalloped hammerhead. 

Lethal interactions would reduce the population size, compared to their numbers in the absence 

of the proposed action, assuming all other variables remained the same. Lethal interactions 

would also result in a potential reduction in future reproduction, assuming some individuals 

would be females and would have otherwise survived to reproduce. A lethal capture of an adult 

female would remove this level of reproductive output from the species. Whether the reductions 

in numbers and reproduction of the species or DPS would appreciably reduce its likelihood of 

survival depends on the probable effect the changes in numbers and reproduction would have 

relative to current population sizes and trends. As part of our risk analysis, we assess the likely 

effects those mortalities may have on the viability of the populations those individuals represent, 

and the species those populations comprise. 

8.7.1 Atlantic Salmon, Gulf of Maine Distinct Population Segment 

The observed declines in Atlantic salmon suggests that the combined impacts from ongoing 

activities described in the Environmental Baseline, Cumulative Effects, and the Status of ESAListed Species are continuing to cause the population to deteriorate. For the population to remain 

stable, Atlantic salmon must replace themselves through successful reproduction at least once 

over the course of their reproductive lives, and at least one offspring must survive to reproduce 

itself. If the survival rate to maturity is greater than the mortality rate of the population, the loss 

of breeding individuals would be exceeded through recruitment of new breeding individuals 

from successful reproduction of Atlantic salmon that were not seriously injured or killed. 

The most recent data available on the population trend of Atlantic salmon indicate that their 

abundance within the range of the GOM DPS has been generally declining since the 1800s (Fay 

et al. 2006a). Contemporary estimates of abundance for the entire GOM DPS have rarely 

exceeded 5,000 individuals in any given year since 1967, and appear to have stabilized at very 

low levels since 2000 (Fay et al. 2006a). After a period of slow population growth between the 

1970s and the early 1980s, adult returns of salmon in the GOM DPS peaked around 1985 and 

declined through the 1990s and early 2000s. Adult returns have been increasing again over the 

last few years. The population growth observed in the 1970s is likely attributable to favorable 

marine survival and increases in hatchery capacity. Marine survival remained relatively high 

throughout the 1980s, and salmon populations in the GOM DPS remained relatively stable until 

the early 1990s. In the early 1990s, marine survival rates decreased, leading to the declining 

trend in adult abundance observed throughout 1990s and early 2000s. The increase in the 

abundance of returning adult salmon observed between 2008 and 2011 may be an indication of 

improving marine survival. Adult returns for the GOM DPS remain well below conservation 

spawning escapement (CSE) goals that are widely used (ICES 2015) to describe the status of 

individual Atlantic salmon populations. When CSE goals are met, Atlantic salmon populations 

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are generally self-sustaining. When CSE goals are not met (i.e., less than 100 percent), 

populations are not reaching full potential; and this can be indicative of a population decline. For 

all GOM DPS rivers in Maine, current Atlantic salmon populations (including hatchery 

contributions) are well below CSE levels required to sustain themselves (Fay et al. 2006a), which 

is further indication of their poor population status. 

While the abundance trend information for Atlantic salmon is either stable or declining, we 

believe the extremely small numbers of anticipated lethal interactions attributed to sea turtle 

research will not have any measurable effect on that trend. We anticipate no more than one GOM 

Atlantic salmon mortality every ten years, or 0.1 mortalities per year on average, due to the 

proposed action. This represents about 0.01 percent of the estimated adult returns in 2015, and 

about 0.02 percent of the lowest value of estimated adult returns (i.e., 405 fish in 2014) over the 

past several decades (USASAC 2016). The anticipated mortalities represent an even smaller 

proportion of the number of adult Atlantic salmon that are stocked in Maine rivers every year 

(e.g., 3,066 in 2015). Similarly, we do not anticipate any long-term adverse effects on either 

individual fish or the GOM DPS resulting from the capture and live release of Atlantic salmon 

by turtle researchers. 

Recent efforts to help Atlantic salmon recover include hatchery supplementation, dam removal, 

improving road crossings that block passage or degrade stream habitat, protecting riparian 

corridors, reducing the impact of irrigation water withdrawals, limiting effects of recreational 

and commercial fishing, reducing the effects of finfish aquaculture, outreach and education, and 

research activities. Improving the survival of Atlantic salmon in the marine environment is an 

important part of meeting the objective of GOM DPS Atlantic salmon recovery. 

The proposed research activities have numerous mitigation measures intended to reduce the 

probability of interaction and to minimize the probability of mortality in the event of 

interactions. In summary, there is no indication that the anticipated extremely small amount of 

Atlantic salmon take (lethal or sublethal) resulting from turtle research activities poses a threat to 

the recovery of the GOM DPS of Atlantic salmon. 

8.7.2 Smalltooth Sawfish, U.S. Portion of Range Distinct Population Segment 

The abundance of smalltooth sawfish in U.S. waters has decreased dramatically over the past 

century. However, recent information indicates the smalltooth sawfish population is likely stable 

or increasing (Carlson and Osborne 2012; Carlson and Simpfendorfer 2015). Data analyzed from 

the Everglades portion of the smalltooth sawfish range suggests that the population growth rate 

for that region may be around five percent per year (Carlson and Osborne 2012; Carlson et al. 

2007). Intrinsic rates of growth (λ) for smalltooth sawfish have been estimated at 1.08-1.14 per 

year and 1.237-1.150 per year by Simpfendorfer (2000) and Carlson and Simpfendorfer (2015) 

respectively. Although this rate is very slow, any potential lethal interactions and probable 

nonlethal interactions with turtle sampling gear are not likely to occur at levels sufficient to 

reverse these trends. Chapman et al. (2011) found the remnant smalltooth sawfish population 

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exhibits high genetic diversity (allelic richness, alleles per locus, heterozygosity) and will likely 

retain greater than 90 percent of its current genetic diversity over the next century. NMFS is 

currently funding several actions identified in the recovery plan for smalltooth sawfish including 

adult satellite tagging studies and monitoring take in commercial fisheries. Additionally, NMFS 

has developed safe handling guidelines for the species. 

We expect that the very small numbers of lethal interactions (i.e., up to two every ten years) 

attributed to sea turtle research will not have any measurable effect on the smalltooth sawfish 

population trend. Similarly, we do not anticipate any long-term adverse effects on either 

individual fish or the population resulting from the capture and live release of smalltooth sawfish 

by turtle researchers. In summary, there is no indication that the anticipated small amount of 

smalltooth sawfish take resulting from turtle research activities authorized as part of the Program 

poses a threat to the recovery of the U.S. portion of the range DPS of this species. 

8.7.3 Sturgeon Species 

Due to their life history traits, sturgeon populations are more sensitive to adult mortality than 

many other species of fish (Boreman 1997; Gross et al. 2002; Secor et al. 2002). Given their 

large body size and high fecundity, mortality of adult sturgeon can result in negative population 

levels impacts, especially in very small sturgeon subpopulations found within some particular 

river systems. The viability of some sturgeon populations may also be highly sensitive to 

increases in juvenile mortality that result in chronic reductions in the number of subadults that 

recruit into the adult breeding population (Anders et al. 2002; Gross et al. 2002; Secor et al. 

2002). The mortality of any individual fish from a population represents the loss of 100 percent 

of that fish’s reproductive potential. For long-lived species, such as Atlantic and shortnose 

sturgeon, mortality of juveniles or subadults affects future reproductive potential and could have 

effects on a population for decades. 

The largest estimated adult Atlantic sturgeon river populations are currently found within the 

New York Bight DPS (3,000 in Hudson River; 1,305 in Delaware River), the South Atlantic DPS 

(1,325 in the Altamaha River; 745 in the Savannah River), GOM DPS (865 in Kennebec River), 

and the Chesapeake DPS (705 in the James River). The Carolina DPS of Atlantic sturgeon likely 

has the smallest adult population size among the five ESA-listed DPSs, although a population 

estimate has only been published for one river system (Roanoke) within this DPS. Published 

estimates of Atlantic sturgeon juvenile abundance are available in the following river systems: 

4,314 age 1 fish in the Hudson in 1995 (Peterson et al. 2000); 3,656 age 0-1 fish in the Delaware 

in 2014(Hale et al. 2016); between 1,072 to 2,033 age 1-2 fish on average from 2004-2007 in the 

Altamaha - (Schueller and Peterson 2010); and 154 age 1 fish in 2010 in the Satilla (Fritts et al. 

2016). 

The 2010 SSSRT conducted a three-step risk assessment for shortnose sturgeon at a riverine 

scale: (1) assess population health, (2) populate a “matrix of stressors” by ranking threats, and 

(3) review assessment by comparing population health scores to stressor scores. The Hudson 

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River had the highest estimated adult abundance (30,000 to 61,000), followed by the Delaware 

(12,000), Kennebec Complex (9,000), and Altamaha (6,000) (SSSRT 2010). The SSSRT found 

evidence of an increasing abundance trend for the Kennebec Complex and ACE Basin 

populations; a stable trend for the Merrimack, Connecticut, Hudson, Delaware, Winyah Bay 

Complex, Cooper, Savannah, Ogeechee, and Altamaha populations; and a declining trend only 

for the Cape Fear population (all other populations had an unknown trend) (SSSRT 2010). 

The largest estimated populations of Gulf sturgeon are found in the Suwannee (14,000), 

Choctawhatchee (3,314), and Yellow (911) rivers (USFWS and NMFS 2009). The most recent 

population estimates for the other four rivers with known reproducing populations are all below 

500. In general, gulf sturgeon populations in the eastern portion of the range appear to be stable 

or slightly increasing, while populations in the western portion are associated with lower 

abundances and higher uncertainty (USFWS and NMFS 2009). 

Based on survey data from 2010-14, the total number of adults in the Southern DPS population is 

estimated to be 1,348 (95 percent confidence interval ± 524) (Mora 2015; NMFS 2015c). The 

recovery potential for Southern DPS green sturgeon is considered moderate to high; however, 

certain life history characteristics (e.g., long-lived, delayed maturity) indicate recovery could 

take many decades, even under the best circumstances (NMFS 2010a). 

Although sturgeon populations can be particularly sensitive to anthropogenic sources of 

mortality, the number of sturgeon mortalities resulting from the proposed action are expected to 

be extremely small relative to the population sizes of the affected ESA-listed species or DPSs. 

For Atlantic sturgeon, only one lethal take is anticipated every ten years for any of the five ESAlisted DPSs combined. Similarly, we anticipate that the proposed action will result in the lethal 

take of up to one Gulf sturgeon, one Southern DPS green sturgeon, and one shortnose sturgeon 

over any ten-year period. These lethal take estimates represent a very small fraction of the total 

population, even for the smallest sturgeon populations, based on available abundance 

information. One mortality every ten years also represents a mortality rate that is several orders 

of magnitude lower than the commercial fishing bycatch mortality rate of three percent estimated 

by Kahnle et al. (1998) to keep the Hudson River Atlantic sturgeon population stable or 

increasing. 

We expect that the very small numbers of lethal interactions (i.e., up to one every ten years) 

attributed to sea turtle research will not have any measurable effect on sturgeon population sizes 

or abundance trends. Similarly, we do not anticipate any long-term adverse effects on either 

individual fish or the population resulting from the capture and live release of sturgeon by turtle 

researchers. In summary, there is no indication that the anticipated small amount of take resulting 

from turtle research activities authorized as part of the Program poses a threat to the recovery of 

any of the five DPSs of Atlantic sturgeon, shortnose sturgeon, Gulf sturgeon, or the Southern 

DPS of green sturgeon. 

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8.7.4 Nassau Grouper 

There is no range-wide abundance estimate or population growth rate available for Nassau 

grouper. Although relative abundance has been reduced compared to historical levels, spawning 

still occurs and abundance is increasing in some locations, such as the Cayman Islands and 

Bermuda. Available information from observations of spawning aggregations has shown steep 

declines (Aguilar-Perera 2006; Claro and Lindeman 2003; Sala et al. 2001); however, some 

aggregation sites are comparatively robust and show signs of increase (Vo et al. 2014; Whaylen 

et al. 2004). 

We expect that the very small numbers of lethal interactions (i.e., one every ten years) attributed 

to sea turtle research will not have any measurable effect on Nassau grouper population size or 

growth rate. Similarly, we do not anticipate any long-term adverse effects on either individual 

fish or the population resulting from the capture and live release of Nassau grouper by turtle 

researchers. While Nassau grouper populations are particularly vulnerable to anthropogenic 

mortality during the formation of large spawning aggregations, the Program includes mitigation 

measures designed to minimize this risk during these critical periods in the species life history. In 

summary, there is no indication that the anticipated small amount of take resulting from turtle 

research activities authorized as part of the Program poses a threat to the recovery of Nassau 

grouper. 

8.7.5 Scalloped Hammerhead Shark 

According to the most recent stock assessment, the Northwestern Atlantic and Gulf of Mexico 

scalloped hammerhead stock has declined to a relatively low level of abundance in recent years 

(Hayes et al. 2009). Populations in other parts of the world are assumed to have suffered similar 

declines, however data to conduct stock assessments on those populations are currently lacking. 

Historical estimates of effective population size in the Eastern Pacific DPS range from 34,995 to 

43,551 individuals (Nance et al. 2011). Nance et al. (2011) estimate that the current effective 

population size is significantly smaller (one to three orders of magnitude) than the historical 

effective population size, indicating that scalloped hammerheads in the eastern Pacific 

experienced a bottleneck and suffered significant declines. Although abundance estimates and 

quality catch data are unavailable for the Central and Southwest Atlantic DPS, the evidence of 

heavy fishing pressure off the coast of Brazil, Central America, and the Caribbean, with 

documented large numbers of juvenile and neonate landings, suggests this DPS is likely 

approaching a level of abundance and productivity that places its current and future persistence 

in question (Miller et al. 2014). Abundance estimates are also lacking for the Indo-West Pacific 

DPS, although documented trends in abundance in particular areas suggest significant depletions 

of local populations. 

Scalloped hammerhead sharks have a life history that is susceptible to overharvesting (i.e., longlived, late maturity, low reproductive rates). Although data are limited, the available information 

indicates that the three DPSs of scalloped hammerhead that occur within the action area remain 

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at risk from both directed and incidental take by commercial fisheries. Any additional sources of 

anthropogenic mortality will compound the risk to hammerhead populations from fishing 

operations. However, the anticipated number of mortalities (one every ten years for any of the 

three DPSs combined) resulting from the proposed action are orders of magnitude smaller than 

the anticipated mortalities from future commercial fisheries based on historical data. In addition, 

we do not anticipate any long-term adverse effects on either individual fish or the population 

resulting from the capture and live release of scalloped hammerhead sharks by turtle researchers. 

In summary, there is no indication that the anticipated small amount of take resulting from turtle 

research activities authorized as part of the Program poses a threat to the recovery of the 

following scalloped hammerhead DPSs: Eastern Pacific, Central and Southwest Atlantic, and 

Indo-West Pacific. 

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9 CUMULATIVE EFFECTS 

“Cumulative effects” are those effects of future state or private activities, not involving Federal 

activities, that are reasonably certain to occur within the action area of the Federal action subject 

to consultation (50 CFR 402.02). Future Federal actions that are unrelated to the proposed action 

are not considered in this section because they require separate consultation pursuant to section 7 

of the ESA. 

This section attempts to identify the likely changes present in the future and their impact on 

ESA-listed or proposed species and their critical habitats in the action area. This section is not 

meant to be a comprehensive socio-economic evaluation, but a brief outlook on future changes 

on the environment. Projections are based upon recognized organizations producing bestavailable information and reasonable rough-trend estimates of change stemming from these data. 

However, all changes are based upon projections that are subject to error and alteration by 

complex economic and social interactions. During this consultation, we searched for information 

on future state, tribal, local, and private (non-Federal) actions reasonably certain to occur in the 

action area. Based on this search, we expect the same threats currently facing the species as 

described in the Environmental Baseline (Section 7) will continue in the future. These include 

global climate change, habitat degradation, marine debris, pollutants, oil spills, anthropogenic 

sound, industrial and power generating plants, dredging, hydromodification projects, and 

fisheries bycatch. For sea turtles, stranding data indicate mortality can result from various natural 

causes, including cold stunning, as well as human activities, such as incidental capture in state 

fisheries, ingestion of or entanglement in debris, vessel strikes, and degradation of nesting 

habitat. We anticipate the effects of these stressors to continue in the future. While some of these 

threats would involve a federal nexus and be subject to future ESA section 7 consultation, others 

will be entirely under the jurisdiction of state, tribal, or local authorities. An increase in these 

threats could result in increased effects to ESA-listed species, and for some (e.g., global climate 

change and habitat degradation) an increase in the future is considered reasonably certain to 

occur. 

Probably one of the most certain future changes that ESA-listed species within the action area 

are likely to experience is that of global climate change. Even under predictions that consider 

stringent mitigation measures to reduce carbon dioxide emissions (IPCC Representative 

Concentration Pathway 2.5), by the end of the 21st century (relative to 1986 to 2005) global 

temperatures are likely to rise between 0.3 degrees Celsius and 1.7 degrees Celsius, sea level is 

expected to rise between 0.26 and 0.55 meters, and increased ocean acidification is almost 

certain (IPCC 2014). In less stringent Representative Concentration Pathways, greater increases 

in global temperature, sea level, and ocean pH are predicted. Other climate changes such as 

increase drought and/or precipitation in some areas and changes in the frequency of extreme 

weather events are also likely to occur (IPCC 2014). The impact of these changes on ESA-listed 

species are even more difficult to predict than the future climate scenarios themselves, but they 

will likely have direct, indirect, positive, and/or negative effects depending on the species and 

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the particular climatic changes. Nonetheless, future impacts from global climate change on ESAlisted species are virtually certain to occur. 

Anthropogenic threats that ESA-listed species experiences due to population growth, 

development, and land use changes are also likely to increase. Between 2014 and 2060 the U.S. 

population is expected to increase from 319 million to 417 million (Colby and Ortman 2014). 

With this population increase, the negative impacts of associated land use changes, pollution, 

contaminants, habitat degradation and destruction, and water quality issues described for ESAlisted species in the Environmental Baseline are likely to increase, although the level of which 

remain unknown at this time. For turtles, future beachfront development, lighting, and beach 

erosion control projects are likely to reduce or degrade sea turtle nesting habitats and/or interfere 

with hatchling movement to the sea. These ongoing activities will likely continue along the Gulf 

and Atlantic coasts as coastal populations continue to grow in these regions. 

The harmful effects of marine debris on sea turtles and other ESA-listed species are expected to 

continue into the future, and may increase in some parts of the action area. Ribic (2010), 

documented regional differences in amounts and trends of marine debris along the U.S. Atlantic 

coast from 1997 to 2007. The Northeast region, with a relatively small percentage population 

increase, had low land-based and general-source debris loads and no increases over the ten-year 

study period. The Mid-Atlantic region, with an increasing coastal population, had heavy landbased and general-source debris loads that increased over time. The Southeast Atlantic region 

had low land-based and general-source debris loads and no increases despite the largest 

percentage increase in coastal population over the study period. Ribic (2010) assessed trends of 

marine debris for the U.S. Pacific Coast and Hawaii from 1998 to 2007. They found that debris 

loads decreased over time for all source categories (i.e., land-based, general source, and oceanbased) in all regions except for land-based and general-source loads in the North Pacific Coast 

region, which were unchanged. 

For the remainder of activities and associated threats to the ESA-listed species identified in the 

Environmental Baseline, and other unforeseen threats, the magnitude of increase and the 

significance of any anticipated effects remain unknown. Thus, this opinion assumes effects in the 

future would be similar to those in the past and, therefore, are reflected in the anticipated trends 

described in the Status of the Species (Section 6) and Environmental Baseline (Section 7). 

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10 INTEGRATION AND SYNTHESIS 

The Integration and Synthesis section is the final step in our assessment of the risk posed to 

species due to implementation of the proposed action. In this section, we add the Effects of the 

Action (Section 8) to the Environmental Baseline (Section 7) and the Cumulative Effects 

(Section 9) to formulate the agency’s biological opinion as to whether the proposed action is 

likely to appreciably reduce the likelihood of both the survival and recovery of a ESA-listed 

species in the wild by reducing its numbers, reproduction, or distribution. These assessments are 

made in full consideration of the Status of the Species (Section 6). 

10.1 Sea Turtles 

In this section, we summarize the status of sea turtle species and DPSs in light of past, current, 

and anticipated future threats as presented in the Environmental Baseline and Cumulative Effects 

sections of this opinion. Finally, we integrate the results of our sea turtle exposure, response, and 

risk analyses to evaluate the probable risk the proposed action poses to the survival and recovery 

of the sea turtle species and DPSs considered in this opinion. 

10.1.1 Sea Turtle Research Permitting Program: Summary 

As discussed throughout this opinion, there are several key components of the Permits Division’s 

Program that are designed to minimize adverse effects on individual sea turtles and to mitigate 

risks to the survival and recovery of sea turtle populations. While the proposed lethal take limits 

determine the upper limit on research allowed, the Permits Division would continually evaluate 

each permit application to ensure that the proposed research (including requested take levels) is 

necessary for the conservation and recovery of sea turtle populations. The Permits Division 

proposes to issue more invasive procedures, which have a higher risk associated with adverse 

effects, with caution and conservatively. 

ESA regulations require that all research and enhancement permits issued by the Permits 

Division must meet specific regulatory issuance criteria. These include: (1) the permit will be 

used in a manner consistent with the ESA goal of listed-species conservation and will not be 

used to the disadvantage of species, (2) the research is bona fide and necessary for the survival 

and recovery of species, (3) a surrogate (non-listed) species cannot be used instead, (4) the 

permit holder has the necessary expertise, facilities, or other resources to achieve research 

objectives, and (5) the validity and need for the proposed research is reviewed by other 

researchers and species experts. These criteria are designed to reduce adverse effects and risk by 

decreasing the likelihood that ESA-listed species will be exposed to stressors from research 

activities that are either duplicative, extraneous or will not result in information (e.g., data, 

published papers) that can be used for the conservation of ESA-listed species. 

In addition to regulatory issuance criteria, all permit holders authorized under the Program are 

required to follow general permit terms and conditions. These include: (1) reporting 

requirements that are necessary to track take (lethal and sublethal) and monitor the effects of 

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authorized research activities on sea turtle populations, (2) notification and coordination 

requirements designed to maximize efficiency and minimize duplicative research efforts that 

could result in higher levels of exposure to stressors than absolutely necessary, and (3) 

requirements related to the qualifications, responsibilities, and designation of personnel designed 

to assure that mitigation measures are closely followed and all procedures are performed using 

the required standard protocols. Also included in all research and enhancement permits issued by 

the Permits Division are terms and conditions related to permit modification, suspension, and 

revocation. These assure that the Permits Division can take the appropriate measures a permit 

holder’s actions result in increased risk to individual sea turtles (or other ESA-listed species) or 

to the populations they comprise, beyond what was authorized in the permit. In addition, the 

Permits Division can modify a research or enhancement permit if, based on new information, it 

determines that the previously authorized activities will unnecessarily expose individual turtles 

to stressors or will result in a greater risk to the survival and recovery of threatened and 

endangered species. 

Another integral component of the Program for reducing risk and avoiding jeopardy or adverse 

modification over time is the adaptive management approach. This is particularly important 

considering that the Program (and this opinion) does not have a sunset date. Based on historical 

data, over time the development of new and improved sea turtle research protocols, required as a 

condition of the permit, have greatly reduced adverse effects and mortalities resulting from 

research activities. The adaptive management approach allows the Permits Division to 

continually update mitigation measures designed specifically to reduce adverse effects on sea 

turtles as well as ESA-listed species taken incidentally as part of the proposed action. Also part 

of the adaptive management approach, as new information is made available regarding risks to 

sea turtles from certain capture methods or procedures, the Permits Division can make program 

level or individual permit level changes, as necessary, to further reduce the risk to ESA-listed 

species or their critical habitat. 

The adaptability and flexibility of the Program is viewed as a beneficial feature for addressing 

the potential impacts of climate change on ESA-listed species considered in this opinion. As 

discussed in Section 7.1 above, environmental changes resulting from climate change may affect 

sea turtles in a number of ways. The Program’s adaptive management approach allows Permits 

Division to respond to any changes in the status, health, or distribution of sea turtle populations 

due to climate change, and make the necessary and timely program-level or permit level 

adjustments to avoid jeopardy or adverse modification to ESA-listed species in the action area. 

Continued close collaboration and an on-going dialogue between the Permits Division and the 

Interagency Cooperation Division will also be an important component of the proposed adaptive 

approach to managing the Program. Annual program reports and periodic program evaluations 

(every 5-years or more often as needed) will allow NMFS OPR to evaluate if the assumptions 

made in the effects analysis for this opinion are still valid. If new information indicates that a 

procedure has greater impacts than those analyzed in this opinion, the Permits Division will 

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consult (either informally or formally) with the Interagency Cooperation Division and use the 

additional documentation to modify individual permits as needed. 

10.1.2 Current Status and Threats: Summary 

As discussed in the Environmental Baseline (Section 7), the major anthropogenic stressors that 

contributed to the sharp decline of sea turtle populations in the past include habitat degradation, 

direct harvest, commercial fisheries bycatch, and marine debris. While sea turtle populations are 

still at risk, efforts made over the past few decades to reduce the impact of these threats have 

slowed the rate of decline for many sea turtle populations. Increasing abundance trends have now 

been reported for several populations (or subpopulations) of ESA-listed sea turtles (see Table 24 

above for details). 

Bycatch reduction devices have reduced the incidental take of sea turtles in many U.S. 

commercial fisheries. TEDs, which are required in federal shrimp trawl fisheries, are estimated 

to have reduced mortality of sea turtles by approximately 95 percent (NMFS 2014c). Mitigation 

measures required in other federal and state fisheries (e.g., gill net, pelagic longline, pound nets) 

have also resulted in reduced sea turtle interactions and mortality rates (see Section 7.14.1 for 

details). In 2001, NMFS published as a final rule (66 FR 67495) requiring people participating in 

scientific research or fishing activities to handle and resuscitate (as necessary) incidentally 

caught sea turtles to help further reduce sea turtle mortalities and injuries due to capture. 

Increased conservation awareness at the international scale has led to greater global protection of 

sea turtles. All six ESA-listed sea turtles are listed in CITES Appendix I and many countries now 

have regulations banning turtle harvest and export. Among the countries that still allow directed 

take of sea turtles, harvest has decreased by more than 60 percent over the past three decades 

(Humber et al. 2014). Implementation of the Clean Water Act of 1972 resulted in estuarine and 

coastal water quality improvements throughout the range of many sea turtle species. While 

vessel strikes, power plants, dredging, pollutants, oil spills, and hydromodification still represent 

sources of mortality, sea turtle mortalities resulting from these activities within the action area 

are expected to either remain at current levels, or possibly decrease with additional research 

efforts, conservation measures, and the continued implementation of existing environmental 

regulations. In addition, many activities that result in sea turtle take have already undergone 

formal section 7 consultation and are covered for take by an existing ITS; some of which would 

presumably need to reinitiate consultation with NMFS in the future to continue the activity. 

Based on our Cumulative Effects analysis (Section 9), it is likely that some current threats to sea 

turtles will increase in the future. These include global climate change, marine debris, and habitat 

degradation. It is difficult to predict the magnitude of these threats in the future or their impact 

on sea turtle populations, particularly considering that the Program has no sunset date. 

10.1.3 Sea Turtle Exposure, Response, and Risk Analyses: Summary 

The proposed action would have both sublethal and lethal effects on ESA-listed sea turtles. 

Based on our Sea Turtle Response Analysis (Section 8.4), we determine that sub-lethal effects 

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resulting from research activities authorized under the proposed action will be minimal, shortterm, and are not likely to result in any reduced fitness or loss of fecundity to individual turtles. 

Mortality of sea turtles will be limited in the proposed action by the ten-year observed research 

lethal take limits established for each species (or DPS) within each ocean basin (i.e., Atlantic and 

Pacific). The proposed action may also result in a very low level of delayed mortality of sea 

turtles captured using trawl nets. From our Sea Turtle Risk Analysis (Section 8.5), we determine 

that the anticipated mortality resulting from the proposed action (observed research mortality 

plus delayed mortality) is not likely to impact the survival or recovery of any of the sea turtle 

species or DPSs considered in this consultation. The anticipated levels of mortality represent an 

extremely small fraction of the estimated female nesting or adult population sizes of the sea 

turtle species and DPSs evaluated. For most species and DPSs, research related mortalities will 

result in a decrease of less than 0.15 percent of the population every ten years. The populations 

that could potentially be most impacted are (in order of impact over a ten-year period): West 

Pacific DPS of leatherback (0.53 percent), Kemp’s ridley (0.35 percent), Central South Pacific 

DPS of green turtle (0.34 percent), and Central North Pacific DPS of green turtle (0.25 percent). 

Considering that such changes are projected over any ten year period into the future, these 

estimated declines represent a very small proportion of each population (i.e., from 0.025 to 0.053 

percent annually). The proportion of each ESA-listed sea turtle population impacted likely 

represents a highly conservative estimate based on several conservative assumptions that went 

into our risk assessment. As described above, the effects of these activities are expected to be 

low-level, short-duration stress that individual turtles would experience. The research authorized 

under this Program, including research dealing with fisheries bycatch issues, is expected to have 

a net benefit to the species as a whole, which will lead to more-informed management decisions. 

Therefore, we do not anticipate a decline of even this small proportion of the population in every 

year going forward. In summary, there is no indication that the anticipated small number of 

lethal take resulting from turtle research activities authorized as part of the Program poses a 

threat to the survival or recovery of any ESA-listed sea turtle species or DPS. A decline in any 

ESA-listed sea turtle species population could trigger reinitiation (see Section 14). 

10.1.4 Overall Summary 

Several components of the proposed action would mitigate adverse effects and assure that 

research activities permitted under the Program are for the benefit of ESA-listed species and their 

designated critical habitat. These include: (1) regulatory issuance criteria designed to reduce 

adverse effects and risk resulting from research activities that are either duplicative, extraneous 

or will not result in information that can be used for species recovery, (2) general permit terms 

and conditions that provide the Permits Division with the information necessary to manage their 

Program, monitor take and the impacts on ESA-listed species, evaluate permit compliance, and 

modify or revoke permits as necessary to mitigate adverse effects to individuals and reduce the 

risk to the survival and recovery of ESA-listed populations, (3) species and habitat specific terms 

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listed species resulting from particular research activities, (4) proposed sea turtle research 

mortality limits that limit the lethal take (and by proxy sublethal take) that can be authorized for 

each species or DPS, and (5) an adaptive management approach that provides the Permits 

Division flexibility to make program level changes as new information regarding species status, 

threats, effects of research activities, improved protocols or technologies is made available. 

Efforts made over the past few decades to reduce the impact of major threats from directed 

harvest, fisheries bycatch, habitat degradation and pollution have slowed the rate of decline for 

many sea turtle populations. Some sea turtle populations within the action area have experienced 

an increasing abundance trend in recent years. The sub-lethal effects on sea turtles resulting from 

research activities authorized under the proposed action will be minimal, short-term, and are not 

likely to result in any reduced fitness or loss of fecundity to individual turtles. The anticipated 

level of research related sea turtle mortalities, in combination with mortalities from outside 

threats (as described in the Environmental Baseline, Section 7 and Cumulative Effects, Section 

9), does not significantly alter the likelihood of survival and recovery of these sea turtle species. 

Additionally, as has been demonstrated in the past, adverse effects (sublethal and lethal) to sea 

turtles and other ESA-listed species resulting from research activities are expected to continue to 

decrease over time with new mitigation measures, research techniques, and technologies. 

In summary, we determine that the proposed action will not appreciably reduce the likelihood of 

both the survival and recovery of any of the ESA-listed sea turtle species or DPSs considered in 

this consultation. 

10.2 Gulf of Maine Atlantic Salmon 

The GOM DPS Atlantic salmon was listed as endangered in response to population decline 

caused by many factors, including overexploitation, degradation of water quality and damming 

of rivers, all of which remain persistent threats (Fay et al. 2006a). There are a number of actions 

underway or planned to help Atlantic salmon recover including hatchery supplementation, dam 

removal, protecting riparian habitat, reducing the impact of irrigation water withdrawals, and 

limiting the effects of recreational and commercial fishing. Even with current conservation 

efforts, returns of adult Atlantic salmon to the GOM DPS rivers remain extremely low. The total 

number of adult returns to U.S. rivers in 2015 was 921, the majority (eighty percent) of which 

were of hatchery origin. The DPS likely has a low resilience to additional perturbations (NOAA 

2016). 

Based on our Exposure and Response Analysis above (Section 8.6), we estimate that the 

proposed action will result in the death of no more than one GOM DPS Atlantic salmon every 

ten years. While the abundance trend information for Atlantic salmon is either stable or 

declining, based on our Risk Analysis (Section 8.7.1) we believe the very small numbers of 

lethal interactions attributed to sea turtle research will not have any measurable effect on that 

trend. Similarly, we do not anticipate any long-term adverse effects on either individual fish or 

the GOM DPS resulting from the capture and live release of Atlantic salmon by turtle 

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researchers. In summary, we determine that the proposed action will not appreciably reduce the 

likelihood of both the survival and recovery of the GOM DPS of Atlantic salmon. 

10.3 Smalltooth Sawfish, U.S. Portion of Range 

The abundance of smalltooth sawfish has decreased dramatically over the past century and the 

U.S. population may be at less than five percent of historic levels based on the contraction of the 

species’ range (Simpfendorfer 2002). The decline in the abundance of smalltooth sawfish has 

been attributed to fishing (primarily commercial and recreational bycatch), habitat modification 

(including changes to freshwater flow regimes due to climate change), and life history 

characteristics (i.e., slow-growing, relatively late-maturing, and long-lived species) (NMFS 

2009c; Simpfendorfer et al. 2011). These factors continue to threaten the smalltooth sawfish 

population. However, recent information indicates the smalltooth sawfish population is likely 

stable or increasing (Carlson and Osborne 2012; Carlson and Simpfendorfer 2015). The remnant 

population exhibits high genetic diversity and that inbreeding is rare (Chapman et al. 2011). The 

female population size is estimated at around 600 (Carlson and Simpfendorfer 2015). Chapman 

et al. (2011) estimate the effective genetic population size as 250 to 350 adults. The abundance 

of juveniles encountered in recent studies (Poulakis et al. 2014; Seitz and Poulakis 2002; 

Simpfendorfer and Wiley 2004) suggests that the smalltooth sawfish population remains 

reproductively viable. 

Based on our Exposure and Response Analysis above (Section 8.6), we estimate that the 

proposed action will result in the death of no more than two smalltooth sawfish every ten years. 

Based on our Risk Analysis (Section 8.7.2), we expect that the very small numbers of lethal 

interactions attributed to sea turtle research will not have any measurable effect on the smalltooth 

sawfish population trend. Similarly, we do not anticipate any long-term adverse effects on either 

individual fish or the population resulting from the capture and live release of smalltooth sawfish 

by turtle researchers. In summary, we determine that the proposed action will not appreciably 

reduce the likelihood of both the survival and recovery of the smalltooth sawfish. 

10.4 Sturgeon: Atlantic, Shortnose, Green, and Gulf 

ESA-listed sturgeon populations within the action area have declined sharply over the past 

century. As discussed in the Environmental Baseline section, the major anthropogenic stressors 

that contributed to the sharp decline of sturgeon populations were commercial fisheries, habitat 

curtailment and alteration from dams and dredging, and degraded water quality. While sturgeon 

are still at risk from anthropogenic threats, some of the major threats that contributed to sharp 

population declines in the past have either been eliminated or reduced. Efforts made over the past 

few decades to reduce the impact of these threats have slowed the rate of decline for many 

sturgeon populations. 

The GOM DPS of Atlantic sturgeon is listed as threatened and includes six river systems. The 

Kennebec River is the primary spawning and nursery area for GOM Atlantic sturgeon. The 

removal of the Edwards Dam in 1999 resulted in 17 additional miles of historical spawning 

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habitat accessible to Kennebec River Atlantic sturgeon and improved water quality. The New 

York Bight DPS of Atlantic sturgeon is listed as endangered and includes seven river systems, 

only three of which are known spawning subpopulations: Delaware, Hudson River, with 

intermittent spawning in the Connecticut. Long-term surveys indicate that the Hudson River 

subpopulation has been stable and/or slightly increasing since 1995 in abundance (ASSRT 

2007). Some of the stressors to New York Bight DPS Atlantic sturgeon, while still present, have 

been reduced over the past few decades. Water quality in the Hudson has improved markedly 

since the 1980s and is no longer considered a major threat to this subpopulation (ASSRT 2007). 

Similarly, restrictions on dredging in the upper portions of the Delaware have likely had 

beneficial impacts on Atlantic sturgeon spawning success. The Chesapeake DPS of Atlantic 

sturgeon is listed as endangered and includes seven river systems, only two of which are known 

spawning subpopulations (James and York rivers). A recent study by Balazik and Musick (2015) 

indicates that two races of Atlantic sturgeon repeatedly spawn during two different times (spring 

and fall) and places in the James River, and possibly the groups have become genetically distinct 

from each other. The Carolina DPS of Atlantic sturgeon is listed as endangered and includes 

eight river systems, only one of which is a known spawning subpopulation (Roanoke River). 

Smith et al. (2015) identified fall spawning in the Roanoke River, suggesting there may be two 

populations (spring and fall) of spawners in this system. The South Atlantic DPS of Atlantic 

sturgeon is listed as endangered and includes ten river systems. Currently, this DPS supports six 

known spawning subpopulations: ACE Basin, Savannah, Ogeechee, Altamaha, Satilla, and St. 

Mary’s. Farrae et al. (2017) found genetically distinct fall- and spring-spawned Atlantic sturgeon 

in the Edisto River (part of the ACE Basin), and genetic diversity of both groups was on the 

higher end of published population diversity values. There are no known major existing threats 

in any of the ten river populations within this DPS; several face minor threats, mainly water 

quality and bycatch. 

For shortnose sturgeon, the largest adult subpopulations are found in the Northeastern rivers (i.e., 

Hudson, Delaware, Kennebec and St. John). Shortnose sturgeon subpopulations in southern 

rivers are considerably smaller by comparison with the largest in this region occurring in the 

Altamaha and Savannah Rivers. Population trend estimates are available for six shortnose 

sturgeon spawning stocks: St John, Kennebec, Hudson, and Satilla are all decreasing slightly (-1 

percent); Delaware and Ogeechee are stable (0 percent). The SSSRT evaluated the extinction risk 

for three shortnose subpopulations (Hudson, Cooper, and Altamaha) and concluded that the 

estimated probability of extinction was zero for all three under the default assumptions, despite 

the long (100-year) horizon and the relatively high year-to-year variability in fertility and 

survival rates. 

Many of the principle factors considered when listing Southern DPS green sturgeon as 

threatened in 2006 are relatively unchanged. Confirmation of spawning in the Feather River is 

encouraging and the decommissioning of the Red Bluff Diversion Dam and breach of Shanghai 

Bench makes spawning conditions more favorable, although Southern DPS green sturgeon still 

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encounter impassible barriers in the Sacramento, Feather and other rivers that limit their 

spawning range (NMFS 2015c). Entrainment as well as stranding in flood diversions during high 

water events also negatively affect Southern DPS green sturgeon. The prohibition of retention in 

commercial and recreational fisheries has eliminated a known threat and likely had a very 

positive effect on the overall population, although recruitment indices are not presently available. 

The recovery potential for Southern DPS green sturgeon is considered moderate to high; 

however, certain life history characteristics (e.g., long-lived, delayed maturity) indicate recovery 

could take many decades, even under the best circumstances (NMFS 2010a). 

The decline in the abundance of gulf sturgeon has been attributed to targeted fisheries in the late 

19th and early 20th centuries, habitat loss associated with dams and sills, habitat degradation 

associated with dredging, de-snagging, and contamination by pesticides, heavy metals, and other 

industrial contaminants, and certain life history characteristics (e.g., slow growth and late 

maturation) (56 FR 49653). In general, gulf sturgeon populations in the eastern portion of the 

range appear to be stable or slightly increasing, while populations in the western portion are 

associated with lower abundances and higher uncertainty (USFWS and NMFS 2009). 

Based on our Exposure and Response Analysis above (Section 8.6), we estimate that the 

proposed action will result in the death of no more than one Atlantic sturgeon (all DPSs 

combined), shortnose sturgeon, Southern DPS of green sturgeon, or Gulf sturgeon every ten 

years. Based on our risk analysis (Section 8.7.3), we expect that the very small numbers of lethal 

interactions attributed to sea turtle research will not have any measurable effect on the population 

trends of these ESA-listed sturgeon species. Similarly, we do not anticipate any long-term 

adverse effects on either individual fish or their populations resulting from the capture and live 

release of sturgeon by turtle researchers. In summary, we determine that the proposed action will 

not appreciably reduce the likelihood of both the survival and recovery of the following ESAlisted sturgeon species: Atlantic sturgeon DPSs (Gulf of Maine, New York Bight, Chesapeake, 

Carolina, and South Atlantic), shortnose sturgeon, Southern DPS of green sturgeon, and Gulf 

sturgeon. 

10.5 Nassau Grouper 

The most serious ongoing threats to Nassau grouper are fishing at spawning aggregations and 

inadequate law enforcement. Many Caribbean countries have banned or restricted Nassau 

grouper harvest, and it is believed that current areas of higher abundance are correlated with 

effective regulations. In some locations, spawning aggregations are increasing. Although harvest 

has decreased due to management measures, Nassau grouper populations remain vulnerable to 

unregulated harvest. 

Based on our Exposure and Response Analysis above (Section 8.6), we estimate that the 

proposed action will result in the death of no more than one Nassau grouper every ten years. 

Based on our Risk Analysis (Section 8.7.4) we believe the very small numbers of lethal 

interactions attributed to sea turtle research will not have any measurable effect on the Nassau 

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grouper population trend. Similarly, we do not anticipate any long-term adverse effects on either 

individual fish or the population resulting from the capture and live release of Nassau grouper by 

turtle researchers. In summary, we determine that the proposed action will not appreciably 

reduce the likelihood of both the survival and recovery of Nassau grouper. 

10.6 Scalloped Hammerhead 

The primary factors responsible for the decline of the ESA-listed scalloped hammerhead DPSs 

are overutilization, due to both catch and bycatch of these sharks in fisheries, and inadequate 

regulatory mechanisms for protecting these sharks, with illegal fishing identified as a significant 

problem (Miller et al. 2014). The threat of overfishing is likely to continue into the future as 

scalloped hammerheads remain unprotected throughout wide portions of their range. 

Based on our Exposure and Response Analysis above (Section 8.6), we estimate that the 

proposed action will result in the death of no more than one scalloped hammerhead (all DPSs 

combined) every ten years. Based on our Risk Analysis (Section 8.7.5) we believe the very small 

numbers of lethal interactions attributed to sea turtle research will not have any measurable effect 

on the population trends for the scalloped hammerhead DPSs considered in this opinion. 

Similarly, we do not anticipate any long-term adverse effects on either individual fish or the 

population resulting from the capture and live release of scalloped hammerhead by turtle 

researchers. In summary, we determine that the proposed action will not appreciably reduce the 

likelihood of both the survival and recovery of the following scalloped hammerhead DPSs: 

Eastern Pacific, Central and Southwest Atlantic, and Indo-West Pacific. 

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11 CONCLUSION 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the North Atlantic DPS of green sea turtle or to 

destroy or adversely modify its designated critical habitat. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the following green sea turtle DPSs: South 

Atlantic, East Indian-West Pacific, Central West Pacific, Southwest Pacific, Central South 

Pacific, Central North Pacific, and East Pacific. No critical habitat has been designated or 

proposed for these DPSs; therefore, none will be affected. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the hawksbill sea turtle or to destroy or adversely 

modify its designated critical habitat. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the Kemp’s ridley sea turtle. No critical habitat 

has been designated or proposed for this species; therefore, none will be affected. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the leatherback sea turtle or to destroy or 

adversely modify its designated critical habitat. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the Northwest Atlantic loggerhead sea turtle or to 

destroy or adversely modify its designated critical habitat. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the following loggerhead sea turtle DPSs: 

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Northeast Atlantic, North Pacific, and South Pacific. No critical habitat has been designated or 

proposed for these DPSs; therefore, none will be affected. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the following olive ridley sea turtle populations: 

Mexico’s Pacific coast and all other breeding populations. No critical habitat has been designated 

or proposed for this species; therefore, none will be affected. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the GOM DPS of Atlantic salmon or to destroy or 

adversely modify its designated critical habitat. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the U.S. portion of range DPS of smalltooth 

sawfish or to destroy or adversely modify its designated critical habitat. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence or to destroy or adversely modify designated critical 

habitat of the following Atlantic sturgeon DPSs: Gulf of Maine, New York Bight, Chesapeake 

Bay, Carolina, and South Atlantic. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of shortnose sturgeon. No critical habitat has been 

designated or proposed for this species; therefore, none will be affected. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of Southern DPS of green sturgeon or to destroy or 

adversely modify its designated critical habitat. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

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likely to jeopardize the continued existence of Gulf sturgeon or to destroy or adversely modify 

its designated critical habitat. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of Nassau grouper. No critical habitat has been 

designated or proposed for this species; therefore, none will be affected. 

After reviewing the current status of the ESA-listed species, the environmental baseline within 

the action area, the effects of the proposed action, any effects of interrelated and interdependent 

actions, and cumulative effects, it is NMFS’s biological opinion that the proposed action is not 

likely to jeopardize the continued existence of the following DPSs of scalloped hammerhead 

shark: Eastern Pacific, Central and Southwest Atlantic, and Indo-West Pacific. No critical habitat 

has been designated or proposed for these DPSs; therefore, none will be affected. 

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12 INCIDENTAL TAKE STATEMENT 

Section 9 of the ESA and Federal regulations pursuant to section 4(d) of the ESA prohibit the 

take of endangered and threatened species, respectively, without a special exemption. “Take” is 

defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt 

to engage in any such conduct. Harm is further defined by regulation to include significant 

habitat modification or degradation that results in death or injury to ESA-listed species by 

significantly impairing essential behavioral patterns, including breeding, feeding, or sheltering. 

Harass is further defined as an act which “create the likelihood of injury to wildlife by annoying 

it to such an extent as to significantly disrupt normal behavioral patterns which include, but are 

not limited to, breeding, feeding, or sheltering” (NMFS 2016c). Incidental take is defined as take 

that is incidental to, and not the purpose of, the carrying out of an otherwise lawful activity. 

Section 7(b)(4) and section 7(o)(2) provide that taking that is incidental to an otherwise lawful 

agency action is not considered to be prohibited taking under the ESA if that action is performed 

in compliance with the terms and conditions of this ITS. 

12.1 Amount or Extent of Take 

Section 7 regulations require NMFS to specify the impact of any incidental take of endangered 

or threatened species; that is, the amount or extent, of such incidental taking on the species (50 

CFR § 402.14(i)(1)(i)). The amount of take represents the number of individuals that are 

expected to be taken by the proposed action. The extent of take represents the “extent of land or 

marine area that may be affected by an action” and may be used if we cannot assign numerical 

limits for animals that could be incidentally taken during the course of an action (51 FR 19953). 

As discussed in our Sea Turtle Risk Analysis (Section 8.5), there is a risk of delayed mortality 

associated with sea turtles captured in trawl nets as part of the Program. To conduct our risk 

analysis, we estimated the number of delayed mortalities that may occur within the Program for 

each species or DPS (as shown in Table 25 above) based on assumptions regarding the number 

of trawl captures and our calculated estimate of the delayed mortality rate based on researcher 

reports. The Program establishes a lethal take limit (as shown in Table 1) by species and ocean 

basin only for turtle mortalities that are observed and reported by researchers. However, these 

limits would not account for delayed mortalities, which would not be observed and, therefore, 

would not be authorized to researchers in individual permits. Therefore, for purposes of this 

programmatic opinion, we include the estimated sea turtle delayed mortalities that we anticipate 

will occur under the Program as part of the incidental take statement for this opinion. The 

anticipated incidental lethal take of sea turtles resulting from research trawl captures authorized 

under the Program, over any given ten-year period, is shown by turtle species in Table 26. These 

numbers are based on rounding up of the delayed mortality estimates calculated for our Sea 

Turtle Risk Analysis above. For sea turtle species with more than one DPS within the action 

area, incidental take is expressed as a combined take limit for the species due to the difficulty of 

predicting the number of takes by DPS in any given year. 

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As part of the proposed action, any incidental take (lethal or nonlethal) of non-target sea turtle 

species (or DPS) that is observed and reported by researchers will be included with the directed 

take for that particular species (or DPS), and therefore will not be covered under this ITS. This 

could occur if a sea turtle researcher captures a turtle species or DPS that their permit does not 

authorize them to take. 

Activities authorized as part of the Program may also result in the incidental take of non-target 

ESA-listed species. Atlantic salmon, Atlantic sturgeon, shortnose sturgeon, Gulf sturgeon, green 

sturgeon, Nassau grouper, and scalloped hammerhead may be exposed to stressors resulting from 

incidental capture in non-selective capture gears (entanglement or gill nets, trawls, pound nets 

and seines) used to capture sea turtles. Anticipated incidental take of non-target species was 

determined based on our evaluation of the proposed action and information provided by the 

Permits Division in its BA (Table 26). Incidental take estimates of the numbers of individuals by 

species, were developed by considering the following: (1) level of historical incidental take that 

has occurred under sea turtle research permits authorized by the Permits Division, (2) mitigation 

measures in place to avoid future incidental take of non-target species, (3) population trends of 

each non-target species (as available), and (4) projected changes in environmental conditions or 

sea turtle research focus that could potentially affect the spatial/temporal overlap between nontarget species and turtle research activities. For the five DPSs of Atlantic sturgeon and three 

DPSs of scalloped hammerhead that occur in the action area, incidental take is expressed as a 

combined take limit for each species due to the difficulty of predicting the number of takes by 

DPS in any given year. 

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Table 26. Authorized incidental take of sea turtles due to delayed mortality and of 

incidentally captured non-target ESA-listed species resulting from the Program over any 

given ten-year period. 

ESA-listed species or 

Distinct Population Segment 

Non-lethal Take 

(Number of individuals 

over 10 years) 

Lethal Take 

(Number of individuals 

over 10 years) 

Green Sea Turtle 

All DPSs combined: North Atlantic, 

South Atlantic, West Pacific, South 

Pacific, North Pacific, and East Pacific 

None 2 

Hawksbill Sea Turtle None 1 

Kemp’s ridley Sea Turtle None 2 

Leatherback Sea Turtle 

All DPSs combined: Northwest 

Atlantic and West Pacific 

None 1 

Loggerhead Sea Turtle 

All DPSs combined: Northwest 

Atlantic and North Pacific 

None 5 

Olive ridley Sea Turtle None 1 

Atlantic Salmon 

Gulf of Maine DPS 3 1 

Smalltooth Sawfish 

U.S. Portion of Range DPS 5 2 

Atlantic Sturgeon 

All DPSs combined: Gulf of Maine, 

New York Bight, Chesapeake, 

Carolina, and South Atlantic 

6 1 

Shortnose Sturgeon 3 1 

Gulf Sturgeon 5 1 

Green Sturgeon 

Southern DPS 2 1 

Nassau Grouper 2 1 

Scalloped Hammerhead 

All DPSs combined: Eastern Pacific, 

Central and Southwest Atlantic, and 

Indo-West Pacific 

2 1 

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12.2 Effects of the Take 

In this opinion, we have determined that the amount of anticipated incidental take of sea turtles 

due to delayed mortality, coupled with other effects of the proposed action, is not likely to result 

in jeopardy to any of the ESA-listed sea turtle species or DPSs evaluated in this opinion. We 

have also determined that the amount of anticipated take, coupled with other effects of the 

proposed action, is not likely to result in jeopardy to any of the following non-target species: 

Atlantic salmon GOM DPS; smalltooth sawfish U.S. portion of range DPS; Atlantic Sturgeon 

DPSs (Gulf of Maine, New York Bight, Chesapeake, Carolina, and South Atlantic), shortnose 

sturgeon, Gulf sturgeon, green sturgeon Southern DPS, Nassau grouper, and scalloped 

hammerhead DPSs (Eastern Pacific, Central and Southwest Atlantic, and Indo-West Pacific). 

Refer to Section 8.3 Exposure, Response and Risk Analysis for details regarding how we reached 

these determinations. 

12.3 Reasonable and Prudent Measures 

“Reasonable and prudent measures” are nondiscretionary measures to minimize the amount or 

extent of incidental take (50 CFR 402.02). Section 7(b)(4) of the ESA requires that when a 

proposed agency action is found to be consistent with section 7(a)(2) of the ESA and the 

proposed action may incidentally take individuals of ESA-listed species, NMFS will issue a 

statement that specifies the impact of any incidental taking of endangered or threatened species. 

To minimize such impacts, reasonable and prudent measures, and terms and conditions to 

implement the measures, must be provided. Only incidental take resulting from the agency 

actions and any specified reasonable and prudent measures and terms and conditions identified in 

the ITS are exempt from the taking prohibition of section 9(a), pursuant to section 7(o) of the 

ESA. 

The measures described below are nondiscretionary, and must be undertaken by the Permits 

Division so that they become binding conditions for the exemption in section 7(o)(2) to apply. 

NMFS believes the reasonable and prudent measures described below are necessary and 

appropriate to minimize the impacts of incidental take on threatened and endangered species: 

Reasonable and prudent measure #1: All section 10(a)(1)(A) sea turtle research permits 

authorized as part of the proposed action will include required terms and conditions (as described 

below) to minimize the impacts of incidental take on non-target ESA-listed species. 

Reasonable and prudent measure #2: The Permits Division will monitor and evaluate the 

incidental take of ESA-listed species resulting from the proposed action and report the impacts of 

such incidental take to the Interagency Cooperation Division. 

12.4 Terms and Conditions 

To be exempt from the prohibitions of section 9 of the ESA, the Permits Division must comply 

with the following terms and conditions, which implement the Reasonable and Prudent Measures 

described above and outlines the mitigation, monitoring and reporting measures required by the 

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section 7 regulations (50 CFR 402.14(i)). These terms and conditions are nondiscretionary. If the 

Permits Division fails to ensure compliance with these terms and conditions and their 

implementing reasonable and prudent measures, the protective coverage of section 7(o)(2) may 

lapse. 

Terms and Conditions Required to Implement Reasonable and Prudent Measure # 1 

The Permits Division will assure that all section 10(a)(1)(A) sea turtle research permits 

authorized as part of the proposed action will include the following required terms and 

conditions: 

All Non-target ESA-listed Species 

1. All incidentally captured species (e.g., fishes) must be released alive as soon as possible. 

2. If any ESA-listed non-target species are taken (captured, injured, etc.) during research, 

Researchers must stop activities and submit an incident report (see Section 3.2.1.5 Reports 

for details). Adverse interactions must be documented in the report, including any pertinent 

details of the interaction (gear type, what was done to handle and release the animals, 

location, date, size, water and air temperature, and photos if possible). 

Smalltooth Sawfish Specific Terms and Conditions 

3. Researchers operating in areas where sawfish are present are required to contact the 

smalltooth sawfish recovery coordinator in the NMFS Southeast Regional Office for training 

requirements on proper handling procedures. 

4. When attempting to handle and release an incidentally captured sawfish, researchers must 

use extreme caution, following procedures specified in the NMFS Sawfish Handling and 

Release Guidelines (Appendix F), or as otherwise modified by NMFS in the future to reflect 

best management practices for handling and releasing sawfish. 

5. Researchers must keep the fish in the water at all times while cutting the net from the rostrum 

and body of the animal (no attempts should be made to disentangle the rostrum from the net). 

6. Adverse interactions with sawfish should be documented, including any pertinent details of 

the interaction (type of gear type, what was done to handle and release the animals, location, 

date, size, water & air temp, and photos if possible). 

Terms and Conditions Required to Implement Reasonable and Prudent Measure # 2 

1. The Permits Division will include an incidental take section in their annual Program report 

(see Section 3.8, Reporting to the Interagency Cooperation Division). This section of the 

report will include the following: 

a) The number of individuals incidentally taken by species (or DPS), life stage, and type of 

take (i.e., nonlethal and lethal) 

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b) A copy of each incident report, which includes the dates, locations, gear types, and any 

other relevant information that may assist in evaluating the impacts of incidental take on 

ESA-listed populations, DPS(s), or species 

c) Any permits modifications (e.g., changes in protocols, methods, or mitigation measures) 

made by the Permits Division in response to an incidental take occurrence in order to 

minimize the chance of additional incidental take by the permit holder in the future. 

2. In addition to the annual reporting requirement, the Permits Division will maintain a file with 

real-time updates on incidental take numbers (by species/DPS and type of take) resulting 

from the proposed action. This file will be stored on a shared network drive accessible to the 

Interagency Cooperation Division. 

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13 CONSERVATION RECOMMENDATIONS 

Section 7(a)(1) of the ESA directs Federal agencies to use their authorities to further the 

purposes of the ESA by carrying out conservation programs for the benefit of the threatened and 

endangered species. Conservation recommendations are discretionary agency activities to 

minimize or avoid adverse effects of a proposed action on ESA-listed species or critical habitat, 

to help implement recovery plans or develop information (50 CFR 402.02). 

• We recommend that the Permits Division continue to work collaboratively with the 

Interagency Cooperation Division to explore opportunities for developing and consulting 

on research programmatics for other ESA-listed species and/or taxa (e.g., cetaceans and 

pinnipeds). 

• We recommend that the Permits Division considering requesting that researchers collect 

and report information on any ESA-listed fish species captured incidentally during sea 

turtle research. This may include collection of biological data, morphometrics, or tag 

information. Depending on the species, turtle researchers may need special training for 

handling and collecting information from ESA-listed fish. 

• We recommend that the Permits Division encourage researchers to conduct research that 

will help improve our understanding of the delayed mortality risk for sea turtles subjected 

to research activities, particularly trawl captured turtles. 

• We recommend that the Permits Division consider requiring that researchers report 

satellite tracking study information that could be used to assess post-release survival and 

health of sea turtles. This could include number of days tracked, movement, diagnostic 

data on satellite tag status and reason for tag failure (Hays et al. 2007), as well as data on 

recaptured turtles (e.g., overall health, growth rate). 

• When issuing permits for sea turtle research conducted within the range of GOM Atlantic 

salmon, we recommend that the Permits Division consider limitations on the use of small 

net mesh capture gear (i.e., less than12 inches) to minimize potential interactions with 

adult salmon. 

• We recommend the Permits Division consider modifying the required reporting form for 

research permits to collect additional information that can further assist managers in 

protecting and conserving ESA-listed species. For example, the Permits Division could 

request researchers to provide population abundance estimates as they become available 

(e.g., unpublished data). Such information would not only better inform the Permits 

Division’s future issuance of research permits, but could also be used in recovery plans 

and five-year species status reviews. 

• We recommend that the Permits Division work to establish protocols for data sharing 

among permitted researchers. While many researchers in the community collaborate, 

having a national standard for data sharing among researchers could improve the quality 

of research produced. Data sharing may also reduce adverse impacts to ESA-listed 

species and critical habitat by minimizing duplicative research efforts. 

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• We recommend that the Permits Division continue to work collaboratively with the 

NMFS’s Regional Offices to organize meetings and workshops to ensure that the results 

of all research programs or other studies on specific threatened or endangered species are 

communicated and coordinated among the different investigators and other interested 

parties. Meeting participants should include regional species recovery coordinators, 

academic institutions, researchers, USFWS species experts, state agencies, and other 

stakeholders. 

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14 REINITIATION NOTICE 

This concludes formal consultation for the OPR Permits and Conservation Division proposal to 

implement a program for the issuance of permits for research and enhancement activities on 

ESA-listed sea turtles. Since the Program does not have a definitive sunset (or expiration) date, 

there is no pre-determined end date on this biological opinion. As discussed above (see 

Integration and Synthesis Section 10), the dynamic and adaptive elements of the Program (i.e., 

adaptive management approach) are critically important for reducing risk and avoiding jeopardy 

or adverse modification over time. The standard reinitiation triggers, which apply to all 

biological opinions, provide an additional safeguard against jeopardy or adverse modification 

over time. As 50 CFR 402.16 states, reinitiation of formal consultation is required where 

discretionary Federal agency involvement or control over the action has been retained (or is 

authorized by law) and if (1) the amount or extent of incidental take is exceeded, (2) new 

information reveals effects of the agency action that may affect ESA-listed species or critical 

habitat in a manner or to an extent not considered in this opinion, (3) the agency action is 

subsequently modified in a manner that causes an effect to the ESA-listed species or critical 

habitat that was not considered in this opinion, or (4) a new species is ESA-listed or critical 

habitat designated that may be affected by the action. Each of these standard reinitiation triggers 

is discussed below in the context of this consultation. 

As described in Section 12 (above), the proposed action may result in some small level of 

incidental take of the following ESA-listed species or DPSs: Atlantic salmon GOM DPS; 

smalltooth sawfish U.S. portion of range DPS; Atlantic Sturgeon DPSs (Gulf of Maine, New 

York Bight, Chesapeake, Carolina, and South Atlantic), shortnose sturgeon, Gulf sturgeon, green 

sturgeon Southern DPS, Nassau grouper, and scalloped hammerhead DPSs (Eastern Pacific, 

Central and Southwest Atlantic, and Indo-West Pacific). The proposed action may also result in 

some small level of incidental (lethal) take of the sea turtle species and DPSs due to delayed 

mortality from the effects of trawl capture. Reinitiation of formal consultation is required if the 

incidental take of any of these species (or DPSs) exceeds the anticipated levels (trigger #1) 

specified in Table 26 (above). Since delayed mortality would not be observed or reported by 

researchers, this incidental take would be exceeded if the assumptions regarding the anticipated 

number of trawl captures or the delayed mortality rate are exceeded. 

Given the adaptive management approach that is built into the proposed action, we anticipate 

that reinitiation trigger #2 (above) will have limited application in the context of this 

consultation. That is, the Program is structured such that new information regarding the effects of 

research activities on ESA-listed species and/or critical habitat can be incorporated into the 

Program without the need for reinitiation, assuming such changes are designed to be more 

protective, or at least equally protective, as those evaluated in this consultation. Some examples 

may include: (1) changes in general permit conditions to improve the monitoring of take or 

administration of the Program, (2) adding new mitigation measures to further minimize adverse 

effects (either directed or incidental) on ESA-listed species, or (3) applying updated information 

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regarding delayed mortality risk from certain capture methods (e.g., trawls) or research 

procedures to the management of the sea turtle lethal take limits established by the Program. 

Reinitiation trigger #2 could also apply if new information indicates that any of the key 

assumptions that went into the effects analysis have been violated. For this opinion, this includes 

assumptions regarding the number of sea turtles annually exposed to capture in trawl nets as part 

of the Program and how sea turtles respond to capture in research trawl nets. 

Based on information obtained from permit holders or other sources, the Permits Division may 

determine that one of the ten-year lethal take limits for observed sea turtle mortalities (as shown 

in Table 1) for a particular species (or DPS) has been exceeded. While exceeding a mortality 

limit may adversely affect ESA-listed species in a manner or to an extent not considered in this 

opinion, depending on the particular circumstances, such an incident may not automatically 

trigger reinitiation of formal consultation. Given the flexibility and adaptability built into the 

Program, we anticipate that, in many instances, adverse effects resulting from exceeding a lethal 

take limit can be addressed through informal consultation and Program modifications not 

requiring reinitiation of formal consultation. Continued close collaboration and an on-going 

dialogue between the Permits Division and the Interagency Cooperation Division will be an 

important component of the proposed adaptive approach to managing the Program. As soon as it 

is determined that a ten-year lethal take limit is likely to be or has been exceeded, the Permits 

Division and the Interagency Cooperation Division will consult informally to evaluate the 

impacts on the affected sea turtle population and species (or DPS), and work collaboratively on 

solutions for mitigating adverse effects. Reinitiation of formal consultation may be required if 

informal consultation does not result in Program changes that adequately address the adverse 

effects resulting from exceeding a lethal take limit. 

Reinitiation trigger #3 (above) could be invoked if the Permits Division modifies the proposed 

action such that the adverse effects to ESA-listed species or designated critical habitat are greater 

than those effects considered in this opinion under the Program. For example, any proposed 

increase in the ten-year mortality limits shown in Table 1 could result in adverse effects to sea 

turtle populations beyond those considered in this opinion. Such a change to the Program, 

therefore, would trigger reinitiation of formal consultation. The Permits Division would initiate 

discussions with the Interagency Cooperation Division about reinitiation if all Column A (Table 

1) lethal takes for a species/ocean basin have been authorized for a given ten-year period, and at 

least one authorized lethal take has been drawn from the buffer reserve (Column B, Table 1). 

Since additional risks may be associated with new or experimental procedures, the Permits 

Division will only authorize a new procedure (i.e., one that is not explicitly discussed above) as 

part of the Program if, after reviewing the best available scientific information, they determine 

that (1) the procedure is effective at achieving the research objectives, and (2) any adverse 

effects on sea turtles resulting from the procedure are less than or equal to the adverse effects of 

any of the procedures previously authorized or described above for the same research objectives. 

Therefore, the Permits Division does not expect new research methods or changes in protocols to 

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result in a level of impact not evaluated as part of this programmatic consultation. If the adverse 

effects are greater than considered in this programmatic opinion, reinitiation is required. 

As discussed in the Description of the Proposed Action (Section 3), the Permits Division would 

work closely with the Interagency Cooperation Division throughout implementation of its 

Program. The two divisions will routinely (e.g., every 5 years or more frequently as needed) 

check-in on how the Program is functioning overall, and determine whether new information 

indicates that the Permits Division should request re-initiation of this consultation. 

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346 
Appendix A: Endangered Species Scientific Research and Enhancement Permit Application 

Instructions 

National Marine Fisheries Service 

Endangered Species Scientific 

Research and Enhancement Permit 

Application 

OMB No. 0648-0084 

Expires: 12/31/2019 
2

Endangered Species Scientific Research and 

Enhancement Permit Application

TABLE OF CONTENTS

INTRODUCTION .......................................................................................................... 3

APPLICATION INSTRUCTIONS........................................................................... 5

PROJECT INFORMATION ....................................................................................................................... 5

PROJECT DESCRIPTION PAGE............................................................................................................. 6

PROJECT SUPPLEMENTAL INFORMATION........................................................................................13

PROJECT LOCATIONS ..........................................................................................................................16

NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) CONSIDERATIONS ....................................19

PROJECT CONTACTS............................................................................................................................20

SUBMIT APPLICATION..........................................................................................................................23

ADDITIONAL INFORMATION ............................................................................. 23

PAPERWORK REDUCTION ACT STATEMENT ...................................................................................24
3

Introduction 

What is this application for? 

• This application is for requesting an Endangered Species Act (ESA) scientific 

research or enhancement permit to take1, import, or export National Marine 

Fisheries Service (NMFS) protected species, including: 

• Sawfish (largetooth and smalltooth) 

• Sea turtles (in-water)

• Sturgeon (Atlantic and shortnose) 

What is this application not for?

• Research or enhancement activities on sea turtles on land or in rehabilitation

• Research or enhancement activities on marine mammals

• Only importing, exporting, or receiving protected species parts 

• Commercial or educational photography 

• Public display 

• To apply for one of these permits, visit: 

http://www.nmfs.noaa.gov/pr/permits/types.html

When should I apply?

• At least 1 year before your project will begin

What is the process for getting a permit?

1. Follow these instructions and contact the Permits and Conservation Division at 

301-427-8401 with any questions. 

2. Submit your application via APPS (https://apps.nmfs.noaa.gov/). 

a. An assigned permit analyst will contact you and review the application.

3. Address any questions on the application. To facilitate processing, reference the 

application File No. in all correspondence. 

a. Once complete, we will publish a notice in the Federal Register, which 

starts a mandatory 30-day public comment period. 

b. Concurrently, we will send your application to subject matter experts in 

partner institutions and federal and state agencies for review. 

c. We will also request consultation under section 7 of the ESA to assess 

impacts to ESA-listed species. The ESA consultation can take up to 6 

months. 

4. Address any questions received during the comment period and consultation. 

a. We will then draft the permit and supporting documentation (including 

National Environmental Policy Act analyses and documentation of ESA 

issuance criteria), which will be reviewed by various NMFS offices 

including a legal review by General Counsel.

 

1 A take under the ESA means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or 

attempt to do any of the preceding.
4

b. A Biological Opinion will be issued to determine if the activity will 

jeopardize the species or adversely modify critical habitat.

c. The Office Director will make a final decision. 

Important information

• If you do not follow these instructions, your application will be withdrawn and 

you will be asked to resubmit a new application that includes the information 

required. 

• If we request additional information and do not receive it within 60 days, we may 

withdraw your application. 

• Your permit may only authorize what is in your application; therefore, it must be 

a stand-alone document that describes all proposed activities even when you 

reference previous permits or published literature. 

• When a question does not apply (i.e., N/A), explain why.

• Your application should be free of grammatical errors and readable to a lay 

person. 

• You are highly encouraged to contact us at 301-427-8401 with questions in 

advance of submitting your application.

How do I use APPS?

• Refer to Chapter 2 (“How to Use the System”). 

• When starting from your portfolio, click on the link of your file number under the 

File Number column to take you to the application. 

• Save your application every 20 minutes or you will lose information! 

• You do not have to complete an application in one session. Your application will 

remain in draft mode until you submit. 

• An * means it is a required field.

• If you cut and paste from Word, special characters and formatting may be lost. 

• Attachments cannot be larger than 10MB – contact us if you have larger files.

Questions?

• Contact the Permits and Conservation Division at 301-427-8401. 
5

Application Instructions 

Project Information

File Number 

• This number is automatically generated and cannot be changed. To facilitate 

processing, reference this File No. in correspondence with our office. 

*Project Title (up to 255 characters)

• Provide a concise title to include the activity, species (or taxa if multiple species), 

location, and purpose of the study. For example: 

• Vessel surveys, sampling, and tagging sea turtles in the Gulf of Mexico to 

characterize population structure, forging ecology, and movement 

patterns.

*Project Status 

• The project status (New or Renewal) is automatically selected based on your 

answers in the pre-application guide (PAG). Do not change this field. 

Previous Federal or State Permit #

• If applicable, enter your most recent and closely related NMFS permit number. 

Otherwise leave blank. State permit numbers are not applicable. 

*Permits Requested

• One or more permit will be listed based on your answers in the PAG. If the 

options listed are incorrect, please call us at 301-427-8401 for assistance. 

*Where Will the Activities Occur?

• One or more general locations will be listed based on your answers in the PAG. 

If a location is incorrect, please call us at 301-427-8401 for assistance. 

*Research Timeframe

• Enter the desired start and end dates of the entire project in the following format: 

MM/DD/YYYY. The start date must not be prior to the date you submit the 

application and should be at least 1 year after the date you submit. The end date 

must be within five years of the start date because permits are generally valid for 

a five-year period. In some cases, a ten-year permit may be authorized.

*Sampling Season/Project Duration (up to 1,000 characters)

• Describe the annual field season(s) including the months and frequency of 

fieldwork (i.e., how many times per year and how frequently will you conduct 

your activities?). If this includes year-round research, indicate when activities are 

most likely to occur and how frequently. 
6

*Abstract (up to 2,000 characters) 

• Federal regulations require the following information be published in the Federal 

Register Notice of Receipt that initiates a mandatory 30-day public comment 

period: 

• Purpose of the research or enhancement

• Target and non-target species (common and scientific names)

• Proposed take activities (e.g., capture, sampling, tagging), import, or 

export 

• Numbers of animals to be taken or imported/exported or number of 

animals from which specimens will be imported/exported, by species or 

taxa, annually 

• Specific geographic locations of take and locations from which animals or 

samples will be imported or to where they will be exported, if applicable

• Requested duration of the permit 

Project Description Page

*Project Purpose: Hypothesis/Objectives and Justification (up to 64,000 characters) 

• Discuss the purpose of your project including your hypotheses and/or objectives. 

• Briefly summarize published findings related to your objectives. If you 

previously held or worked under a permit, use literature citations from that work 

to show how you previously met your objectives; or, use other published literature 

on the subject. Describe how this study is different from, builds upon, or 

duplicates past research. 

• If proposing novel procedures, include a discussion on results from pilot studies 

or studies on other species, if available. 

• Explain how you determined your sample size/take numbers. For example, did 

you base your numbers on previous encounter rates or abundance estimates for 

your study area? If appropriate for your study, include a power analysis or other 

sample size estimation to show whether the sample size is sufficient to provide 

statistically significant or otherwise robust results appropriate for your study. 

• The information above should support how your proposed research is bona 

fide, including how the results of your research are likely to published in a 

refereed scientific journal. 

• Discuss why your project must involve ESA-listed species. 

• Discuss how your project will, as applicable: 

• contribute to the objectives identified in the species’ recovery plan or 

otherwise respond to recommendations of a scientific body charged with 

management of the species; 
7

• contribute significantly to understanding the basic biology or ecology of the 

species; and 

• contribute significantly to identifying, evaluating, or resolving conservation 

problems. 

• For enhancement, describe how your work will enhance the survival and recovery 

of the species in the wild, or will enhance the propagation of the species for 

recovery purposes. 

*Project Description (up to 64,000 characters) 

• Your permit may only authorize what you describe in your application. 

• Provide a brief overview of a day on the water of the suite of activities you intend 

to perform on each animal during an encounter or capture event including where 

your work would happen, especially if different projects occur in different 

locations. 

• For sturgeon, provide location (i.e. river, bay, ocean basin) for each Take 

Action2 you describe. 

• Methods: Provide clear descriptions of all methods for each species, by 

Distinct Population Segment (DPS) where applicable, and the number of 

animals by age class3 and sex you expect to take by each method/procedure 

annually. 

• The methods must match what is in the take table. 

• There should be a narrative description for each Take Action, 

Observe/Collect Method4, and Procedure5 in the take table, and the take 

numbers and procedures in the narrative must match the table. 

• Reference take table lines in the narrative that correspond to the take 

actions and procedures, as needed. 

• If you have multiple projects, it is helpful to name them by project number 

or title and include project names in the Details column of the take table. 

• Indicate the number of times known individuals will be intentionally taken in 

a year as driven by your objectives and study design (e.g., recapture for 

instrument retrieval or multiple biopsy samples per year). If recapturing animals, 

 

2 The Take Action is a generalized overview of how animals will be taken. You may only have one Take 

Action for each Take Row. Examples: Capture/handle release; Harass.

3 Define how age classes (e.g., early life stage fishes (ELS; includes eggs and larvae), post-hatchling turtles, 

juvenile, subadult, adult) are differentiated, by taxa or species. 

4 The Observe/Collect Method is the method of observation (e.g., survey, vessel) or capture (e.g., net). 

Select only one observe/collect method per take table row.

5 Procedures are the individual activities you conduct on animals that have been captured/taken by a certain 

Take Action and Observe/Collect Method. Examples: sample, blood, fin clip, and swabs; external tagging. 
8

indicate whether they will be immediately released without processing or fully or 

partially processed (i.e., what will be done to them on recapture). 

• If some animals may be unintentionally recaptured in a year estimate how many 

and indicate whether they will be immediately released without processing or 

fully or partially processed.

• If some animals will only get a subset of procedures, list them on separate rows 

in the take table and make sure it is clear in the narrative. Explain how you 

decide which animals receive which procedures.

• If animals are being captured under another legal source (e.g., bycaught in 

commercial federal fishery) prior to research, identify the legal authority (e.g., 

ESA section 7 biological opinion with incidental take statement; another ESA 

section 10 permit) for the capture of these animals. Note: Annual take numbers 

requested for your research activities cannot exceed the number authorized for the 

original capture. 

• Describe the size of animals for which you are requesting take. 

• For turtles, indicate the minimum size of the animals for the procedures 

you are requesting.

• For sturgeon: 

o Include total length for each age class proposed. 

o Make sure you have indicated in the Objectives section above the 

purpose of working with each life stage/size. 

o In the details of the Take Table, define the size range of the 

targeted life stage.

• Figures and photographs are useful to illustrate your methods (e.g., tags and 

instrument attachments, nets and net deployment), especially for ESA 

consultations. You can attach them on the Supplemental Information page. 

• Cite references for the methods where applicable, but do not substitute a 

literature citation for a complete description of the methods. 

• Include a brief statement on the purpose of each procedure/how it relates to 

meeting your objectives. 

• Mitigation measures that are standard protocols may be included in this 

methodology, or in Mitigation section below. 

• See table below for examples of information to include when describing your 

methods. 
9

Take action/ 

procedures

Example details to include in methods 

Active acoustics -Sound source (e.g., sidescan sonar, underwater speaker, acoustic deterrent 

device)

-Source depth in water column 

-Frequency (bandwidth) 

-Maximum source level

-Maximum received level

-Distance to target and non-target animals

-Signal duration and duty cycle

-Duration of exposure

-Ambient sound level, when known 

-Propagation loss model results, when available 

-Post playback monitoring

Administer 

drugs or other 

substances (e.g., 

stable isotopes, 

bone marking, 

anesthesia)

-Name of each drug/chemical and its purpose

-Name of any drug reversal or emergency response drugs

-Dosage of each

-Delivery method and route (e.g., intramuscular, intravenous, subcutaneous, 

topical, immersion) 

-Location of administration on body 

-Duration of drug

-Personnel that would administer drug (e.g., veterinarian or veterinary 

technician; state license requirements)

-Post drug administration monitoring

Aerial and vessel 

surveys 

(manned)

-Type of survey craft and vessel

-Type of survey (e.g., line transect, photogrammetry) 

-Number of surveys per year

-Minimum and maximum altitude/approach distance 

-Air/ vessel speed

-Protocols for breaking track to ID species 

-Duration spent with group or individual/day

Auditory 

brainstem 

response or 

evoked potential

-Type of measurement equipment (suction cup or needle electrodes )

-Handling/restraint methods 

-Handling duration 

-Data collection and analysis method

-Whether animal will be transported to a facility (complete the Transport 

Section in Take Table) 

Captive 

experiments

-In addition to describing the procedures that will be performed on the 

animals, describe their care and maintenance, including a complete 

description of the facilities where they will be maintained. This includes 

but is not limited to: 

• dimensions of the pools or other holding facilities 

• number, sex, and age of animals by species to be held in each 

tank/enclosure 

• water supply, amount, and quality 

• diet, amount and type 

• sanitation practices.

-Indicate the final disposition of animals after completion of experiments. 
10

Take action/ 

procedures

Example details to include in methods 

Capture and 

restraint

-Type of capture (e.g., hand or net (gill [drift or anchored], trawl, seine) and 

gear description

-Deployment methods (e.g., boat approach and net set, tow or soak times)

-Configuration, duration, and monitoring of net sets (how often net set is 

checked)

-Numbers of animals captured at a time

-Number of animals processed at a time

-Anesthesia/sedation (see drug administration)

-Dimensions and type of holding container

-Number and roles of personnel (must be adequate to perform all activities 

without harming excess captured animals; else they must be released 

immediately)

-Additional equipment or personnel necessary for capturing and handling 

excess numbers

-Duration of restraint/holding from capture to release

-Sea turtles: If handling sea turtles without a veterinarian present, identify 

an on-call veterinarian or nearby permitted rehabilitation facility available 

for emergencies

-Release

Export/import 

samples

-Type of sample (e.g., blood, muscle, gonad)

-Country sending samples to, country of origin, or high seas

-Designated port of entry/import or export

-How sample/animal is taken in foreign country or on the high seas and 

legal take authority

-Type of storage/shipping, including preservatives, etc.

-Analysis 

-Re-import/export if samples remain after analysis

External 

instruments (a 

table is helpful 

for multiple tag 

types)

-Type of instrument

-Location on body

-Dimensions 

-Mass in air or water

-Percentage of body mass

-Minimum size of animal to receive each tag type

-Maximum footprint/maximum number of tags/animal

-Method of attachment (e.g., remote suction cup; restraint and epoxy/resin; 

monofilament line)

-For remote deployment: number of attempts per animal/day, minimum 

approach distance and angle

-Pain management if required (see Administration of Drugs)

-Will it be coated with antifouling paint?

-Duration of attachment procedure

-Duration of instrument retention on animal

-Release mechanism or recapture to remove

-Type of data collection (e.g., archival requiring retrieval)

-Type of data collection

-How will you determine which animals receive which tags or more than 

one tag? 

-Post-tag monitoring
11

Take action/ 

procedures

Example details to include in methods 

Internal 

instruments

-Type of instrument

-Dimensions 

-Mass in air or water

-Percentage of body mass

-Size of animals (including minimum size) to receive an internal instrument 

-Location within body 

-Cleaning/sterile preparation

-Insertion method (e.g., surgical implant, injection, stomach tube) and any 

applied coating on the tag (e.g., antibiotic) 

-Local anesthetic or anesthesia/sedation (see Administer drugs) if 

applicable

-Personnel that would implant tag

-Duration of insertion procedure 

-Duration of instrument retention 

-How stomach pills are voided 

-For sea turtles: include veterinary-approved protocol for stomach pills 

-Type of data collection 

Intrusive 

sampling (e.g., 

blood, digital 

fecal extraction, 

laparoscopy, 

lavage, muscle, 

scute, skin, 

swabs); remote or 

under restraint

-Type of tissues

-Size or volume of sample (diameter and depth or total volume) 

-Location on body 

-Number of samples per animal per capture event and per year, sampling 

intervals (e.g., for serial blood samples)

-Sampling equipment description and disinfection 

-If restrained: cleansing site; left open or wound closure 

-If remote: collection method (e.g., pole sampling), minimum approach 

distance, number of attempts per animal 

-Minimum size of animal to receive each procedure

-Pain management or sedation (drugs and dosages as above) 

-Whether animal will be transported to a facility for temporary holding (see 

Transport information in Take Table below)

-Personnel that would perform intrusive procedures (see Personnel section 

below to include details on training and experience)

-For sea turtles, include a veterinary-approved protocol for laparoscopy, 

tumor removal surgery, and bone biopsy 

-Sample storage and analysis 

Marking (e.g., 

bone mark (OTC, 

fluorescent), 

flipper tag, 

Floy/dart tags, 

paing, PIT tag, 

shell etching) 

-Type of mark

-Location on body 

-Method of application 

-Disinfection procedures

-Duration of mark 

-Dimensions of tag or mark 

-Size of animals to receive tags including minimum size

-Total number and combination of tags or marks on each animal 

-For turtles: 

-Local anesthetic for PIT tagging turtles <30 cm SCL

-Veterinary-approved protocol for PIT tagging turtles <15 cm SCL 

-Type of paint (non-toxic only)
12

Take action/ 

procedures

Example details to include in methods 

Non-intrusive

sampling (e.g., 

behavioral 

observations, 

diagnostic 

imaging, 

collecting voided 

feces and urine, 

photogrammetry) 

-Approach method 

-Sampling method (e.g., X-ray; genetic tissue from fin)

-Minimum and maximum approach distance 

-Within sight of animals or not (e.g., from a blind)? 

-Frequency of observations/sampling/day

-Duration of observations/sampling/day

-Data or sample collection and analysis 

-Whether animal will be transported to a facility for temporary holding (see 

Transport information in Take Table below)

Unmanned 

Aircraft Systems

(UAS) or 

Underwater 

Remotely 

Operated 

Vehicles (ROVs)

For UAS, same details for aerial surveys and also:

-Type of UAS – fixed wing or vertical takeoff and landing 

-Payload components – what is the UAS carrying and for what purpose? 

-Size and mass of UAS

-Will the UAS ever be beyond the line of sight? 

-Does the device have an auto-return feature should the device fail?

-Ground control station description (what it is, where it will be located - on 

shore or on vessel, number of stations, and how close the station will be to 

animals)

-Spotter roles (e.g., one spotter monitoring the UAS, another for monitoring 

the ground control station) 

-Battery life 

-Do you have the appropriate FAA permits/authorizations (including pilot 

licenses)? 

For ROV, same details as for vessel surveys and also:

-Description and size of ROV

-Whether it is tethered or wireless

-Battery life

-Deployment method, in relation to capture and release of animal, if 

applicable

-Whether there will be a live video feed on the boat

Non-target species and conspecifics: Indicate the estimated number and type of nontarget species that may be encountered in your study area annually, and whether and 

how they may be incidentally harassed, captured, or otherwise affected. This includes 

but is not limited to marine mammals and ESA-listed species such as fish, sea turtles, sea 

birds and plants. 

• For ESA species designated by DPS, specify the DPSs that are likely to be 

encountered. 

• Explain how you will avoid them or minimize impacts to them (e.g., not in area 

during time of study; would not approach closer than 100 meters; would halt 

operations until non-target species moved out of study area). 

• If takes to non-target animals may occur, include these on separate rows in the 

Take Table to include incidental take (e.g., harassment or capture) of non-target 

conspecifics. 
13

Project Supplemental Information

Attach a Supplemental Information File

• You may attach supplemental files here. 

*Status of the Affected Species (up to 2,000 characters) 

• As applicable, indicate the status of the species or stock as follows: 

• ESA - threatened or endangered; and

• Convention on International Trade in Endangered Species of Wild Fauna 

and Flora (CITES) - Appendix I, I, or III 

Species information is available at the following web sites: 

 http://www.nmfs.noaa.gov/pr/species/

http://www.fws.gov/

http://www.cites.org/

*Lethal Take (up to 2,000 characters) 

• If authorization for harm6 or mortalities7 (euthanasia/intentional8 or 

accidental/unintentional) is proposed: 

• What activities could result in harm or mortality? 

• Explain why it’s not feasible to use other methods that won’t result in harm or 

mortality. 

• For euthanasia, indicate if it is for humane reasons (e.g., if working with 

compromised/comatose animals) or euthanasia for directed lethal take.

• If a wild fish or turtle is requested for directed lethal take where it is 

required to be euthanized for scientific research purposes, explain how the 

research will directly benefit the species or fulfill a critically important 

research need with a conservation benefit. 

• Directed research requiring euthanasia of captive sturgeon is an optional 

disposition for such animals. 

• What is the maximum number of animals of each species/DPS and age class 

that could be harmed, unintentionally die, or be euthanized annually? Over 

the life of the permit?

 

6 Harm is defined an act which actually kills or injures fish or wildlife. Such an act may include significant 

habitat modification or degradation where it actually kills or injures fish or wildlife by significantly 

impairing essential behavioral patterns, including breeding, spawning, rearing, migrating, feeding or 

sheltering. 

7 Caused by the presence or actions of researchers including but not limited to harm or deaths resulting 

from infections related to intrusive procedures, sustained during capture and handling, or while attempting 

to escape capture. 

8 This includes unintentional euthanasia for humane reasons (e.g., if working with compromised/comatose 

animals). Only in rare instances may wild fish or turtles be sacrificed in directed research, unless there are 

clear, documented conservation benefits outweighing the loss. 
14

• Justify the number of mortalities. 

• How is euthanasia decided, conducted, and who conducts it?

• For sea turtles, euthanasia must be determined and performed by an oncall veterinarian or permitted rehabilitation facility. 

• What are the protocols for necropsy and carcass disposal?

*Anticipated Effects on Animals (up to 64,000 characters) 

• Using the best available science (i.e., literature citations or other cited data 

sources) and your experience (e.g., personal communication), discuss how each 

take action and procedure listed in the take table (e.g., tissue sampling, marking, 

and instrumentation) will affect target and non-target animals (short-term and 

long-term).

• Include such things as typical behavioral and physiological responses, worstcase responses, % of animals that normally respond, how long it takes for animals 

to recover, and the time it takes wounds to heal. 

• Also include an assessment of such things as: 

• condition of animals on recapture/resight

• recovery from sedation and handling 

• post-release behavior (immediate and long-term)

• habitat use for animals in resident populations (e.g., telemetry data, 

resightings) 

• healing from intrusive sampling 

• healing from intrusive tag deployments 

• tag retention

• effects to nesting female sea turtles if working during the nesting period

• Condition of bycaught non-target species. Will they be released alive or is a 

certain percentage expected to be unintentionally harmed or killed? 

• For novel procedures or operating in more extreme environmental 

conditions, discuss the most likely anticipated responses based on literature from 

studies on other species, if available. 

• Summarize any mortalities that have occurred during the previous ten years of 

your permitted research using the same or similar techniques; include 

circumstances and cause of death.

• Discuss the anticipated effects on the species or DPS, especially if mortalities or 

reproductive effects are possible. On what is your determination based? 
15

*Measures to Minimize Negative Effects (up to 64,000 characters)

• Mitigation and monitoring: You may include mitigation and monitoring 

protocols here, in the Project Description section, or in the Anticipated Effects 

section. If included in another section, simply reference the section where the 

following information is found: 

• For each Take Action, Observe/Collect Method, and Procedure, describe your 

standard mitigation to avoid or minimize the potential for adverse impacts 

identified above. 

• Describe your short- and long-term post-procedure monitoring protocols. 

• If monitoring or mitigation is not feasible for specific procedures, species, 

situations, etc., explain why. 

• For sea turtles: if a proposed method (as indicated in the above methods 

table) or your institution requires a veterinary-approved protocol, attach the 

full protocol, any veterinary comments/recommendations, and the signed 

approval. This protocol may include an approved Institutional Animal Care 

and Use Committee (IACUC)9

 proposal to aid our assessment of impacts of 

your work under the ESA. 

• Research Coordination: Describe how you will collaborate or coordinate with 

other researchers in your action area. Who are they? Explain how this will occur. 

For example, will it involve sharing vessels, samples, or data? Will it involve 

timing surveys to avoid disturbance or repeated captures of the same animals? 

Attach a References File

• Attach a bibliography of references cited in this application. Referenced 

materials must be made available upon request, as needed for evaluation of the 

application, or preparation of any necessary ESA or NEPA analyses. 

*Resources Needed to Accomplish Objectives (up to 2,000 characters and attach files if 

necessary)

• Explain how your expertise, facilities, and resources are adequate to accomplish 

your proposed objectives and activities. 

• Attach copies of any relevant formal research proposals, contracts, grant awards, 

or letters of agreement that would demonstrate financial or logistical resources. 

• Indicate the status of any other international, federal, state, or local authorizations 

you have applied for, secured, or will apply for. 

 

9 For sea turtle research: NMFS researchers are required to submit the NMFS IACUC-approved 

protocols and assurance letter.
16

*Disposition of Tissue Samples (up to 2,000 characters) 

• Indicate the disposition of any remaining samples after your project is complete.

• State whether samples will be consumed in analysis, destroyed, or 

exported back to facility/researcher

• If applicable, list the name and location of the person or institution that 

will store/curate samples. Indicate if you will retain legal custody of the 

archived samples or if you wish to permanently transfer the samples once 

your project is complete. 

*Public Availability of Product/Publications (up to 800 characters) 

• Describe the end products of your proposed project and how they will be made 

available to the public. 

Project Locations 

• You will first describe where you plan to work. Then, for each location, you will 

use the Take Table to list the species you expect to encounter and the take 

procedures you will conduct in those locations. 

• Add New Location: provide information about one (or more) study areas 

• General area (ocean basin)

• State(s), as applicable.

• Enter Location Details, as applicable:

• Waterbody: enter names of rivers, estuaries, bays, etc. 

• Latitude and longitude of your study area 

• River miles (Begin Mile and End Mile)

• Limits of your study area (e.g., to the U.S. EEZ, to the edge of the 

continental shelf, to 50m depth) 

• Names of land masses where research will occur (e.g., islands, rookeries). 

• Attach File: Attach a high quality map(s) with the correct scale that clearly shows 

the location of your proposed activity and any environmental aspects of interest. 

If possible, include a shapefile, Google Earth kmz/kml, or ASCII text file with 

lat/long data and the associated basic metadata with your electronic application 

submission. 

Take Table 

The take table represents the estimated number of animals you may take annually

during your research. 

The options that appear in the dropdown menus in the take table are based on the species 

group you indicated in the Pre-application Guide and the location that you have selected. 

If you are having difficulties, please first check that the previous fields were entered 

correctly.
17

Columns you will fill out in the take table: 

1) Select: Leave this box blank unless you need to copy, move, or delete the line 

following the instructions above. 

2) Species: Use the drop down list to select. Species are listed alphabetically by 

common name and/or category (e.g., dolphin, bottlenose). If the species you are 

looking for is not on the drop-down menu, double check your location (species 

are populated based on location). If you are still having problems, contact us at 

301-427-8401. 

3) Listing Unit/Stock: Select the applicable ESA listing unit/stock. Choose Rangewide if, for example, your location has multiple stocks of the same species and 

you cannot distinguish between them while in the field. 

4) Production/Origin: Select from the drop-down list. Categories include Wild, 

Captive, Rehabilitation Facility (for marine mammals only), or All. 

5) Life Stage: Select from the drop-down list. You may enter take information for 

more than one life stage (e.g., adult versus juvenile) on separate rows or select a 

combination of life stages for one take category. Include specified ages if they 

differ for each procedure in the Details column. 

6) Sex: Select from the drop-down list. If your activity targets only one sex, 

indicate which. If it targets both and they can be targeted separately, enter 

separate rows for male and female; otherwise select Male and Female.

7) Expected Take: This represents a reasonable estimate of the maximum number 

of individuals you will take, import, or export, annually. 

For vessel surveys of sea turtles that do not involve capture, you will be 

required to count every animal you approach within 50 yards, regardless of 

whether a behavioral reaction has occurred. Count 1 take per animal observed per 

day when you know it is the same animal. If unable to identify the animal, count 

each turtle seen as a new take.

For aerial surveys of sea turtles flown at an altitude lower than 700 ft10, count 1 

take per sea turtle observed per day, regardless of the number of passes over the 

same animal. 

8) Takes Per Animal: Estimate the number of times the same individual will be 

taken annually, if known. 

 

10 We are looking for data to establish minimum thresholds for when take is likely to occur from vessel 

and aerial approaches.
18

9) Take Action: The “take action” is a generalized overview of how animals will be 

taken. If more than one action is proposed, you must enter the takes on separate 

rows.

10) Observe/Collect Method: Select the method of observation (e.g., survey, vessel) 

or collection/capture. Select only one observe/collect method per row. If various 

methods will be used, you must provide take information in separate rows for 

each observe method.

11) Procedures: Provide specific information on the research activities that will be 

conducted. A separate pop-up window will appear with a species-specific list of 

activities. Hold down the Control key to select all activities to be performed 

concurrently. Choose Other if your proposed activity is not listed. In the Details 

box (see below), briefly describe what the Other means. 

12) Transport: If you chose transport as a Procedure, enter information about the 

transport. 

a) Mode(s) of transportation: Describe the mode of transportation. Include a 

description of the vehicle or other platform used to transport animals. 

b) The name of the transportation company, if applicable, and the 

qualifications of the common carrier to transport live animals: If a contractor 

or other entity will do the transportation, enter information in the box. Otherwise, 

click on N/A. 

c) Maximum length of time from capture to arrival at destination: How long 

will the animals be in transport?

d) Description of the container (e.g., cage, tank) used to hold the animal 

during transit: Include the material of the container and its dimensions. 

e) Any special care procedures (e.g., moisture, medicines) to be administered 

during transport: How will the animals be cared for during transport?

f) A statement as to whether the animals will be accompanied by a 

veterinarian or some similarly qualified person: If so, give the name, 

affiliation, contact information for each person. 

g) Destination: Use the drop down list to select the destination. If your 

destination is not on the list, click on the “New Facility” button to add it. If the 

animals will be taken to a laboratory or aquarium, provide details of the location. 

If the animals will be released in another waterbody, provide details of the 

location. 
19

h) How will the animals be contained at the destination facility?: Describe the 

containment system for the animals, quarantine procedures, and effluent 

treatment. 

i) The final disposition of the animals: Describe, for example, whether the 

animal will be released or retained in permanent captivity. 

13) Begin Date: Populated with the Begin Date you entered on the Project 

Information page. You may change the date to coincide with a specific project 

time shorter than the overall duration of the project. You cannot enter a date that 

is earlier than your original Begin Date. 

14) End Date: Populated with the End Date you entered on the Project Information 

page. You may change the date to coincide with a specific project time shorter 

than the overall duration of the project. You cannot enter a date that is later than 

the End Date you previously entered. 

15) Details: Enter up to 255 characters in this text box to provide details on each take 

table row. This is especially useful for clarifying age class, takes, specific 

activities, or projects.

National Environmental Policy Act (NEPA) Considerations

In addition to providing information on effects to the target and non-target species in 

other sections of the application, provide information as requested below on potential 

environmental effects to determine if your activity may be categorically excluded from 

the requirement to prepare an environmental assessment or environmental impact 

statement under NEPA. If you believe any of the criteria are “not applicable” you must 

explain why. 

1) If your activities will involve equipment (e.g., scientific instruments) or 

techniques that are new, untested, or otherwise have unknown or uncertain 

impacts on the biological or physical environment, please describe the equipment 

and techniques and provide any information about the use of these in the natural 

environment. In addition, please discuss the degree to which they are likely to be 

adopted by others for similar activities or applied more broadly. 

2) Describe the physical characteristics of your project location, including: 

a. Whether you will be working in or near unique geographic areas including but 

not limited to Critical Habitat for endangered or threatened species, Essential 

Fish Habitat, National Marine Sanctuaries, Marine Protected Areas, State or 

National Parks, Wilderness Areas, Wildlife Refuges, Wild and Scenic Rivers, 

etc. 

b. Next, discuss how your activities could impact the physical environment in 

those locations, such as by direct alteration of substrate during use of 
20

anchoring vessels or buoys, erecting blinds or other structures, or ingress and 

egress of researchers, and measures you will take to minimize these impacts.

c. Is there potential to cause direct or indirect physical, chemical or biological 

alterations of the waters or substrate, including loss of, or injury to, benthic 

organisms (e.g., sea grass, corals), prey species and their habitat, and other 

ecosystem components? Could your actions reduce the quality and/or quantity 

of Essential Fish Habitat? If so, please provide additional details below: 

• What is the degree of alteration (low, medium, high)? 

• Approximately how much area (square footage) of habitat/substrate (e.g., 

seafloor, estuary or river bed) will be disturbed? 

3) Briefly describe important scientific, cultural, or historic resources (e.g., 

archeological resources, animals used for subsistence, sites listed in or eligible for 

listing in the National Register of Historic Places) in your project area and discuss 

measures you will take to ensure your work does not cause loss or destruction of 

such resources. 

4) Discuss whether your project involves activities known or suspected of 

introducing or spreading invasive species, intentionally or not, (e.g., transporting 

animals or tissues, discharging ballast water, use of boats/equipment at multiple 

sites). Describe measures you would take to prevent the possible introduction or 

spread of non-indigenous or invasive species, including plants, animals, microbes, 

or other biological agents. 

Project Contacts

As the person entering the application, you will automatically be assigned the following 

roles: Applicant/Permit Holder, Principal Investigator, and Primary Contact. See 

Chapter 2 for directions on how to change who is assigned to these roles, and the table 

below. 

Project Contact

Must be named 

in the permit 

application

Able to make changes to application, 

request changes to the permit, and 

submit reports; will receive 

automatic emails from APPS.

Description of

qualifications 

required

Applicant/ 

Holder

Permit 

Applicant or 

Responsible Party* 

Principal Investigator

Primary Contact

Co-Investigator

Authorized Recipients

Research Assistants

* The Applicant or Responsible Party may also be the PI or a CI if participating in the research; therefore, 

the description of qualifications is required if they are listed as the PI or a CI. 
21

To prevent duplicate entries, you MUST ALWAYS SEARCH the database for the 

person before entering a new contact. To facilitate the search, start with only putting 

the last name in APPS search box.

A project must have a Responsible Party if the Applicant/Permit Holder is an 

organization, institution, or agency. The Responsible Party or Applicant/Permit Holder is 

an official who has the legal authority to bind the organization, institution, or agency and 

is ultimately responsible for the activities of any individual operating under the authority 

of the permit.

The Principal Investigator (PI) is the individual primarily responsible for the take, 

import, export, and any related activities conducted under the permit. There can only be 

one PI on a permit. The PI:

• must have qualifications, knowledge and experience relevant to the activities 

authorized by the permit 

• must be on site during activities conducted under the permit unless a CoInvestigator is present to act in place of the PI 

• may also be the Applicant/Permit Holder and Primary Contact.

Co-investigators (CIs) are individuals who are qualified and authorized to conduct or 

directly supervise activities conducted under a permit without the on-site supervision of 

the PI. 

• You may add CIs to the application if the PI will not always be present during the 

permitted activities. 

• CIs can also be added or removed once a permit has been issued. 

Authorized Recipients (ARs) are persons or institutions authorized to receive samples 

for the purposes of analysis or curation related to the objectives of your permit. The PI 

and CIs may also be ARs. ARs should not be CIs if they are only performing the analysis 

and are not overseeing the study or publishing the results (i.e., they are only providing an 

analytical service). 

Include a table listing the names of the PI and CIs, and the specific procedures they will 

oversee or conduct. Attach the following table on the Supplemental Information 

page. 
22

Example Table Attachment: Personnel Roles

Name/Affiliation Role Activities

Researcher name, 

Affiliation, City, 

State

Principal Investigator, Coinvestigator, or Authorized 

Recipient

Specific activities they will conduct 

under the permit and whether they are 

supervising 

John Smith, Ph.D., 

University A, City, 

State

Principal Investigator and 

Authorized Recipient 

Supervise and perform all activities 

under the permit

Jane Smith, 

Institution B, City, 

State

Co-investigator All activities excluding anesthesia 

during captures and UAS 

Jane Doe, Ph.D., 

Institution C, City, 

State

Co-investigator Oversee and conduct captures, 

anesthesia, and surgical implantation 

of sonic tags

John Doe, Ph.D., 

University D, City, 

State

Co-investigator and 

Authorized Recipient 

Collect skin biopsy samples and 

create cell lines 

Laboratory E, City, 

State

Authorized Recipient Receive subset of fin clip samples for 

DNA sequencing

Qualifications and Experience

Federal Regulations require that persons authorized as the PI or CIs have qualifications 

commensurate with their duties. In addition, the names of the PI and CIs are sent to the 

NOAA Office of Law Enforcement to determine if any violations of the ESA and other 

environmental laws have occurred. 

The permit applicant is therefore required to submit the following information about the 

qualifications and experience of the PI and all CIs to demonstrate they have qualifications 

commensurate with their duties as stipulated in the Personnel Table. A CV or resume 

must be up to date and contain all relevant information below. If sufficient 

experience is not provided, additional information will be required and the personnel will 

not be authorized to conduct the proposed activities unless sufficient experience is 

demonstrated. 

1) Contact information - All documentation submitted will be publicly available.

DO NOT include personal information (e.g., social security number, date of 

birth, nationality, or home phone/ address-unless it is also the business 

phone/address). 

• Name (first middle last) 

• Business phone, e-mail, and mailing address 

2) Relevant education and training 

• Degree, major, name of institution, year received 

• Applicable certificates or licenses, year received

• Other relevant training or certification, year received 
23

3) Relevant experience

• Job title, affiliation/location, and dates of relevant experience

• Detailed description of when and how the individual obtained training and 

experience in the methods they will be conducting and/or supervising as 

outlined in the Personnel Table. This should include objective metrics 

such as: 

• The specific level of training received and who trained them

• The number of hours/months/years they have been performing the 

activities

• Which and how many procedures they have performed successfully and 

on what species/age class (this is especially important for intrusive 

procedures such as blood and biopsy sampling, intrusive tagging, etc.) 

• Whether and to what extent they have performed the activities without 

supervision or supervised the proposed activities 

• What permits they have been PI or CI under and for what species and 

activities

4) List of grants awarded demonstrating available resources relevant to the 

proposed activities or history of securing resources for similar work

5) Annotated publication history relevant to the activities being conducted 

under the permit

Submit Application 

See Chapter 2 for how to submit your application and check on its status. 

Additional Information 

Under section 10(a)(1)(A) of the ESA, persons may be authorized to take threatened and 

endangered species for purposes of scientific purposes or enhancing the survival or 

propagation of the species. Interested persons are required to submit an application in 

accordance with the ESA and the implementing regulations at 50 CFR part 222. These

instructions for applying for a research or enhancement permit are drawn from, but do not 

substitute for, ESA regulations. These regulations are available at the following web site: 

http://www.gpo.gov/. ESA section 10(a)(1)(A) is available at: 

http://www.nmfs.noaa.gov/pr/pdfs/laws/esa_section10.pdf. Under NEPA, Federal 

agencies must assess the effects of federal actions on the environment. Under section 7 

of the ESA, Federal agencies must ensure that the permitted activities will not jeopardize 

the continued existence of the species or result in adverse modification of critical habitat.
24

Paperwork Reduction Act Statement 

The information requested in this application is required and is used to determine whether 

the activities described in the application are consistent with the purposes and policies of 

the Acts and their implementing regulations. 

Public reporting burden for this collection of information is estimated to average 50 

hours per response, including the time for reviewing instructions, searching existing 

data sources, gathering and maintaining the data needed, and completing and reviewing 

the collection of information. Send comments regarding this burden estimate or any other 

aspect of this collection of information, including suggestions for reducing this burden, to 

the Chief, Permits and Conservation Division, Office of Protected Resources, F/PR1, 

NOAA/National Marine Fisheries Service, 1315 East-West Highway, Silver Spring, MD 

20910. 

All permit documentation, including the application, permit and amendments, reports, 

inventory information, and any other associated documents are considered public 

information and as such, are subject to the Freedom of Information Act. 

Notwithstanding any other provision of the law, no person is required to respond to, nor 

shall any person be subject to a penalty for failure to comply with, a collection of 

information subject to the requirements of the Paperwork Reduction Act, unless that 

collection of information displays a currently valid OMB Control Number. 

OMB No. 0648-0084 

Expires: 12/31/2019 
Appendix B. Application Review Checklist for Section 10(a)(1)(A) and NEPA Criteria 

Protected Resources Permits and Conservation Division 

Review of Protected Species Research or Enhancement Permit Application

File No. Applicant: 

Species/location: ____________________________________________________ 

Criterion Criterion 

met?(Y/N)

How? 

Application Requirements

Followed all instructions and used 

current OMB-approved version 

Application signed by appropriate 

person (individual applicant or 

Responsible Party verified)

Application Requirements and Information for Section 7 Consultation

Objectives are tied to recovery 

priorities (see issuance criteria 

below)

Methods are described in 

sufficient detail to evaluate 

potential effects by 

species/age/sex/location including 

critical habitat

Sample size is justified/ 

reasonably likely to occur

Best available science is used to 

discuss possible adverse impacts 

and how they would be minimized 

or mitigated

Proposed monitoring is 

appropriate to evaluate effects of 

research and recovery of animals 

post-handling or sampling

Lethal take is justified

Provisions for disposition of 

species at conclusion are described

Have applied for, secured, or will 

apply for funding; and/or, have 

demonstrated record of securing 

funding 

Issuance Criteria the Office Director Considers (50 CFR 222.308(c))
2

Criterion Criterion 

met?(Y/N)

How? 

The permit has been “applied for 

in good faith:” i.e., the applicant 

has demonstrated their intent to act 

consistent with the requirements of 

the ESA, regulations, and permit 

conditions; and their capability is 

consistent with what they purport 

to accomplish

The proposed activity “will not 

operate to disadvantage of listed 

species:” 

Consistent with the purposes of 

the ESA (section 2), results would 

contribute to the objectives 

identified in the species’ recovery 

plan or otherwise respond to 

recommendations of a scientific 

body charged with management of 

the species; contribute 

significantly to understanding the 

basic biology or ecology of the 

species; and contribute 

significantly to identifying, 

evaluating, or resolving 

conservation problems.

Would further a bona fide and 

necessary or desirable scientific 

purpose; or enhance propagation 

or survival

Personnel have adequate 

qualifications to carry out the 

proposed action and adequate 

facilities for captive care 

Proposed activities cannot be 

conducted using an alternative 

species or stock (not listed)

Expert opinions have been 

considered and addressed

Applicant has demonstrated 

compliance with IACUC 

requirements (required for NMFS 

turtle applicants only)

NEPA NAO 216-6A Extraordinary Circumstances – if not met, EA or EIS required
3 

Criterion Criterion 

met?(Y/N)

How? 

Applicant has described methods

and mitigation with sufficient 

detail for PR1 to evaluate potential 

effects on target and non-target 

species and the physical 

environment

No potentially significant effect on 

human health or safety

No potentially significant effect on 

a geographic area with unique 

environmental characteristics (e.g., 

park lands, prime farmlands, 

wetlands and floodplains, wild and 

scenic rivers, sole source aquifers, 

marine protected areas, national 

marine sanctuaries, national 

estuarine reserves, or national 

marine monuments) 

No potentially significant effect on 

species or habitats protected by the 

ESA, MMPA, MSA, or MBTA

No potential generation, use, 

storage, transport, or disposal of 

significant quantities of hazardous 

or toxic substances, (e.g., materials 

used at laboratories or 

maintenance facilities

No potentially significant effect on 

properties listed or eligible for 

listing on the National Register of 

Historic Places authorized by the 

NHPA, National Historic 

Landmarks designated by the 

Secretary of the Interior, or the 

National Monuments designated 

through the Antiquities Act; 

Federally recognized Tribal and 

Native Alaskan lands, cultural or 

natural resources, or religious or 

cultural sites

No disproportionately high or 

adverse effect on the health or the 
4 

Criterion Criterion 

met?(Y/N)

How? 

environment of minority or lowincome communities

No significant potential to 

introduce or spread invasive 

species (e.g., zebra mussels, 

cordgrass

No potential violation of Federal, 

State, or local law or requirements 

imposed for protection of the 

environment

No uncertain environmental 

effects or unique or unknown risks

Analyst: Date: 
Appendix C. Section 10(a)(1)(A) Permit Template 

Permit No. XXXXX-0X

Expiration Date: month dd, yyyy 

Reports Due: month dd, annually 

PERMIT TO TAKE PROTECTED SPECIES1

0F FOR SCIENTIFIC PURPOSES

I. Authorization 

This permit is issued to Name of Permit Holder, Affiliation, address (hereinafter “Permit 

Holder;” Responsible Party: Name), pursuant to the provisions of the Endangered Species Act 

of 1973 (ESA; 16 U.S.C. 1531 et seq.) and the regulations governing the taking, importing, and 

exporting of endangered and threatened species (50 CFR Parts 222-226). 

II. Abstract

The objective(s) of the permitted activity, as described in the application, is/are to [briefly 

summarize objectives]. 

III. Terms and Conditions 

The activities authorized herein must occur by the means, in the areas, and for the purposes set 

forth in the permit application, and as limited by the Terms and Conditions specified in this 

permit, including appendices and attachments. Permit noncompliance constitutes a violation and 

is grounds for permit modification, suspension, or revocation, and for enforcement action. 

A. Duration of Permit 

1. Personnel listed in Condition C.1 of this permit (hereinafter “Researchers”) may 

conduct activities authorized by this permit through month dd, yyyy. This permit 

may be extended by the Director, NMFS Office of Protected Resources, pursuant 

to applicable regulations and the requirements of the ESA. 

2. Researchers must immediately stop permitted activities and the Permit Holder or 

Principal Investigator must contact the Chief, NMFS Permits and Conservation 

Division (hereinafter “Permits Division”) for written permission to resume: 

 

1 “Protected species” include species listed as threatened or endangered under the ESA, and marine mammals.
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

2

a. If serious injury or mortality21F of protected species occurs / reaches that 

specified in Tables X of Appendix 1. 

b. If authorized take 32 F is exceeded in any of the following ways: 

i. More animals are taken than allowed in Tables X of Appendix 1. 

ii. Animals are taken in a manner not authorized by this permit. 

iii. Protected species other than those authorized by this permit are 

taken.

c. Following incident reporting requirements at Condition E.2. 

3. The Permit Holder may continue to possess biological samples 4

3F acquired54F under 

this permit after permit expiration without additional written authorization 

provided a copy of this permit is kept with the samples and they are maintained as 

specified in this permit. 

B. Number and Kinds of Protected Species, Locations and Manner of Taking 

1. The tables in Appendix 1 outlines the authorized species or distinct population 

segment (DPS) authorized; number of animals to be taken; number of animals 

from which parts may be received, imported and exported; and the manner of 

take, locations, and time period. 

2. Researchers working under this permit may collect images (e.g., photographs, 

video) and audio recordings in addition to the photo-identification or behavioral 

photo-documentation authorized in Appendix 1 as needed to document the 

permitted activities, provided the collection of such images or recordings does not 

result in takes. 

3. The Permit Holder may use visual images and audio recordings collected under 

this permit, including those authorized in Table X of Appendix 1, in printed 

 

2 This permit allows for /does not allow for unintentional serious injury and mortality caused by the presence or 

actions of researchers up to the limit in Table X of Appendix 1. This includes, but is not limited to: deaths of 

dependent young by starvation following research-related death of a lactating female; deaths resulting from 

infections related to sampling procedures or invasive tagging; and deaths or injuries sustained by animals during 

capture and handling, or while attempting to avoid researchers or escape capture. Note that for marine mammals, a 

serious injury is defined by regulation as any injury that will likely result in mortality. [Use as applicable]

3 By regulation, a take under the MMPA means to harass, hunt, capture, collect, or kill, or attempt to harass, hunt, 

capture, collect, or kill any marine mammal. This includes, without limitation, any of the following: the collection 

of dead animals, or parts thereof; the restraint or detention of a marine mammal, no matter how temporary; tagging a 

marine mammal; the negligent or intentional operation of an aircraft or vessel, or the doing of any other negligent or 

intentional act which results in disturbing or molesting a marine mammal; and feeding or attempting to feed a 

marine mammal in the wild. Under the ESA, a take means to harass, harm, pursue, hunt, shoot, wound, kill, trap, 

capture, or collect, or attempt to do any of the preceding.

4 Biological samples include, but are not limited to: carcasses (whole or parts); and any tissues, fluids, or other 

specimens from live or dead protected species; except feces, urine, and spew collected from the water or ground. 5 Authorized methods of sample acquisition are specified in Appendix 1.
taking: 

 

a. Capture/Surv

1. Hand Ca

a.

b.

2. Breakaw

a. R

m

p

3

materials (including commercial or scientific publications) and presentations 

provided the images and recordings are accompanied by a statement indicating 

that the activity was conducted pursuant to NMFS ESA Permit No. XXXXX. 

This statement must accompany the images and recordings in all subsequent uses 

or sales. 

4. The Chief, Permits Division may grant written approval for personnel performing 

activities not essential to achieving the research objectives (e.g., a documentary 

film crew) to be present, provided: 

a. The Permit Holder submits a request to the Permits Division specifying 

the purpose and nature of the activity, location, approximate dates, and 

number and roles of individuals for which permission is sought. 

b. Non-essential personnel/activities will not influence the conduct of 

permitted activities or result in takes of protected species. 

c. Persons authorized to accompany the Researchers for the purpose of such 

non-essential activities will not be allowed to participate in the permitted 

activities.

 d. The Permit Holder and Researchers do not require compensation from the 

individuals in return for allowing them to accompany Researchers.

5. Researchers must comply with the following conditions related to the manner of 

ey Methods 

pture and Dip Net 

Researchers must be aware of the increased stress and 

physiological alterations that accompany capture and 

minimize these effects by keeping in-water chase activities 

and associated exertion as brief as possible. For capture by 

dip net, turtles must be removed from the net as quickly 

and safely as possible.

The number of attempts to capture an individual turtle is 

limited to 3 attempts per day.

ay Hoop Net 

esearchers must follow the procedures for handling and 

onitoring leatherbacks included as Attachment X to this 

ermit. 

NMFS Permit No. XXXXX-0X

Expiration Date: month day, year
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

4

b. Researchers must ensure that only personnel experienced with 

the hoop net capture technique conduct the capture using this 

technique. 

c. The Permit Holder must be aware of the increased stress and 

physiological alterations that accompany capture and minimize 

these effects by keeping in-water chase activities and 

associated exertion as brief as possible. This includes efficient 

and safe removal of turtles from the net. 

d. The number of attempts to capture a leatherback sea turtle with 

the hoop net is limited to 5 per 24-hour period. If Researchers 

are unsuccessful after the first 3 attempts, they must wait a 

minimum of 4 hours before making the final 2 attempts for the 

day. Unless otherwise stipulated in the permit, only turtles 

behaving normally with no evidence of external trauma may be 

approached.

3. Entanglement Net

a. Mesh size of net must be designed to minimize bycatch of nonsea turtle species.

b. Highly visible surface buoys must be attached to the float line 

of each net and spaced at intervals of every 10 yards or less. 

c. Nets must be checked at intervals of less than 30 minutes, and 

more frequently whenever turtles or other organisms are 

observed in the net. If water temperatures are ≤ 10o

C (50oF) or 

≥ 30oC (86oF), nets must be checked at less than 20-minute 

intervals. “Net checking” is defined as a thorough check of the 

net either by snorkeling the net in clear water (entire net must 

be visible) or by pulling up on the top line such that the full 

depth of the net is viewed along the entire length. The 

intervals given are the maximum time between viewing any 

single point of the net (i.e., each point of the net must be 

viewed every 30 or 20 minutes, depending on water 

temperature). 

d. The surface float line of all nets must be observed continuously 

for movement indicating an animal has encountered the net. 

When this occurs, the net must be immediately and thoroughly 

checked. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

5

e. Researchers must plan for unexpected circumstances or 

demands of the research activities and have the ability and 

resources to meet the net checking requirements at all times 

(e.g., if one animal is very entangled and requires extra time 

and effort to remove from the net, researchers must have 

sufficient staff and resources to continue checking the rest of 

the net at the same time). Contingencies for inclement weather 

must be in place (e.g., if inclement weather is predicted that 

would prevent meeting the net checking requirements, the net 

must be removed in advance). 

f. Marine Mammals: Nets must not be deployed when marine 

mammals are observed within the vicinity of the study area; 

marine mammals must be allowed to either leave or pass 

through the area safely before net deployment is initiated. 

i. Should any marine mammals enter the research area 

after the nets have been deployed, the lead line must be 

raised and dropped in an attempt to make marine 

mammals in the vicinity aware of the net. 

ii. If marine mammals remain within the vicinity of the 

study area, nets must be removed. 

iii. If a marine mammal becomes entangled or dies, 

Researchers must:

A. Stop netting activities immediately.

B. If the animal is alive, immediately free it from the 

net in a same manner (including cutting the net as 

necessary) and proceed to step D.

C. If the animal is dead, hold the carcass and follow 

the directions of the NMFS Regional Stranding 

Coordinator. 

D. Notify the appropriate NMFS Regional Stranding 

Coordinator within 8 hours (see Attachment X or 

go to: 

http://www.nmfs.noaa.gov/pr/health/coordinators.h

tm), 

E. Report the incident as specified in Condition E.2, 

and

F. Suspend permitted activities until the NMFS 

Permits Division has granted approval to continue 

research per Condition E.2. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

6

g. Netting in Areas Where Fibropapilloma (FP) is Known to 

Occur: Nets used at sites where FP is known to occur must be 

thoroughly cleaned and disinfected prior to use in areas where 

FP is either not known to be present, is considered uncommon, 

or where there is limited or no information on FP prevalence. 

Nets must be disinfected using a broadcidal solution and the 

product-recommended contact time or by thoroughly drying 

nets in sunlight to inactivate FP-associated herpesvirus. 

Appropriate disinfectants include 70% isopropyl alcohol, 10% 

bleach, and other viricidal solutions with proven efficacy 

against herpesviruses. 

4. Trawl

a. Tow times must not exceed 30 minutes bottom time and depth 

may not exceed 20 m. 

b. Marine Mammals

i. Trawling must not be initiated when marine mammals, 

except dolphins or porpoises, are observed within the 

vicinity of the study area, and the marine mammals 

must be allowed to either leave or pass through the area 

safely before trawling is initiated. 

ii. Researchers must make every effort to prevent 

interactions with marine mammals. Researchers must 

be aware of the presence and location of marine 

mammals at all times as they conduct trawling 

activities. 

iii. If a marine mammal enters the net, becomes entangled 

or dies, Researchers must: 

A. Stop trawling activities immediately.

B. If the animal is alive, immediately free it 

from the net in a safe manner and proceed to 

step D.

C. If the animal is dead, hold the carcass and 

follow the directions of the NMFS Regional 

Stranding Coordinator. 

D. Notify the appropriate NMFS Regional 

Stranding Coordinator within 8 hours (see 

Attachment X or go to: 
http://www.nmfs.noaa.gov/pr/health/coordin

ators.htm). 

E. Report the incident as specified in Condition 

E.2. 

F. Suspend permitted activities until the NMFS 

Permits Division has granted approval to 

continue research per Condition E.2. 

5. Pound Net 

a. Pound nets and leaders must be thoroughly checked every 24 

hours or less. Net checking is defined as a thorough check of 

the net such that the full depth of the net and leader are visible 

along the entire length.

b. Unless otherwise authorized under ESA Section 7 or ESA 

Section 10(a)(1)(B), the Permit Holder must set, maintain, and 

manage his/her own pound nets, must not participate as part of 

a fishery, and must not retain any fish bycatch. 

c. Mesh size of the pound and heart must be 1 3/4” stretched 

mesh or less to reduce sea turtle entanglement and minimize 

sea turtle mortality.

6. Seine Net 

a. Seine net pulls must not exceed 30 minutes. 

b. Marine Mammals: The net must not be pulled when marine 

mammals are observed within the study area, and the marine 

mammals must be allowed to either leave or pass through the 

area safely before net pulling is initiated. Should marine 

mammals enter the study area after the net has been deployed, 

the net must be raised and dropped in an attempt to make 

marine mammals in the vicinity aware of the net. If marine 

mammals remain within the study area, the net must be 

removed. 

7. Aerial Surveys for Following, Hovering or Circling over Turtles 

 Manned Aircraft 

a. Aerial surveys must be flown at an altitude of 300' or higher. 

b. Each encounter must not exceed 45 min. 

NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

7
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

8

c. Aerial surveys must not be conducted over marine mammal 

haul out areas. Avoid flying over marine mammals to prevent 

harassment.

 Unmanned Aircraft Systems (UAS) 

a. You are authorized to use a fixed wing/vertical take-off and 

landing (VTOL) unmanned aircraft system (UAS). 

b. Each encounter must not exceed 45 min. 

c. UAS must be flown at an altitude of XXX feet.

 b. Turtles Captured Under Another Authority Prior to Research Activities 

1. Research activities may be performed on sea turtles from other sources 

only if the Permit Holder can demonstrate that the sea turtles were 

taken legally (e.g., covered by the incidental take statement [ITS] of an 

ESA Section 7 biological opinion with a “no jeopardy” conclusion or 

an ESA Section 10 permit such as an ESA incidental take permit or 

scientific research permit). 

2. Researchers must only use turtles that have been freed by the 

disentanglement network if the proposed actions are reasonably 

expected not to alter the course of the turtle’s recovery or survival 

outcome. 

 

c. General Handling, Resuscitation, and Release

1. Researchers must:

a. Use care when handling live animals to minimize any possible 

injury. 

b. Use the following resuscitation techniques on any comatose 

turtle. 

i. Place the turtle on its plastron so that the turtle is right 

side up and elevate its hindquarters at least 6 inches for 

a period of 4 up to 24 hours. The amount of the 

elevation depends on the size of the turtle; greater 

elevations are needed for larger turtles. Periodically, 

rock the turtle gently left to right and right to left by 

holding the outer edge of the carapace and lifting one 

side about 3 inches then alternate to the other side. If 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

9

the turtle is not moving, gently touch the eye and pinch 

the tail (reflex test) periodically to see if there is a 

response. 

ii. Sea turtles being resuscitated must be shaded and kept 

damp or moist but under no circumstance be placed into 

a container holding water. A water-soaked towel 

placed over the head, carapace, and flippers is the most 

effective method in keeping a turtle moist.

iii. A turtle is determined to be dead if the muscles are stiff 

(rigor mortis) and/or the flesh has begun to rot, or if 

cardiac arrest is determined by Doppler, ECG, or 

ultrasonography. Otherwise, the turtle is assumed to be 

comatose or inactive and resuscitation attempts are 

necessary. Return all dead turtles to shore for necropsy. 

c. Have an experienced veterinarian on call for emergencies and a 

permitted rehabilitation facility(ies) identified should 

veterinary care be required on shore (e.g., treatment of an 

injured or distressed turtle). Both the veterinarian and facility 

should be made aware of the dates and times of the research 

activity to ensure availability. 

2. If an animal becomes highly stressed, injured, or comatose during 

capture or handling, or is found to be compromised or injured upon 

capture, Researchers must forego or cease activities that will further 

stress the animal (erring on the side of caution) and contact the on call 

veterinarian as soon as possible. Compromised turtles include animals 

that are obviously weak, lethargic, positively buoyant, emaciated, or 

that have severe injuries or other abnormalities resulting in 

debilitation. One of the following options must be implemented (in 

order of preference):

a. Follow the instructions of the veterinarian, and, if necessary, 

immediately transfer the animal to the veterinarian or to a 

permitted rehabilitation facility to receive veterinary care. 

b. If the veterinarian or permitted rehabilitation facility cannot be 

reached, the Permit Holder should err on the side of caution 

and bring the animal to shore for medical evaluation and 

rehabilitation, at a permitted rehabilitation facility, as soon as 

possible. 

c. If the animal cannot be taken to a permitted rehabilitation 

facility due to logistical or safety constraints, allow it to 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

10

recuperate as conditions dictate, and return the animal to the 

water. 

3. In addition to Condition A.2, the Permit Holder is responsible for 

following the status of any sea turtle transported to rehab as a result of 

permitted activities and reporting the final disposition (death, 

permanent injury, recovery and return to wild, etc.) of the animal to 

the NMFS Permits Division. Every effort must be made to release the 

animal at the site of capture. 

4. In the event an animal dies or is sent to rehab as a result of research 

activities, the Permit Holder must, within two weeks, submit an 

incident report as described in Condition E.2. A necropsy should be 

performed, except where not feasible such as in remote areas with 

limited personnel. Gross necropsy findings should be included as part 

of an incident report. Final necropsy findings (e.g., histology and 

other analyses) must be submitted when complete. 

5. While holding sea turtles out of water, Researchers must: 

a. Protect sea turtles from temperature extremes (ideal air 

temperature range is between 70°F (21.1°C) and 80°F 

(26.7°C). 

b. Provide adequate air flow. 

c. Keep sea turtles moist when the temperature is ≥ 75°F 

(23.9°C). 

d. Prevent sea turtles from sustaining any injuries.

e. Keep the area surrounding the turtle free of materials that could 

be accidentally ingested. 

6. During release, turtles must be lowered as close to the water’s surface 

as possible to prevent injury. 

7. Researchers must carefully monitor newly released turtles’ apparent 

ability to swim and dive in a normal manner. If a turtle is not 

behaving normally upon release, recapture the turtle, if safely feasible, 

and contact your on-call veterinarian (see condition c.2 above). 

For research activities occurring aboard commercial fishing vessels or 

in conjunction with other NMFS research, Researchers must carefully 

observe newly released turtles and record observations on the turtle’s 

apparent ability to swim and dive. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

11

8. Extra care must be exercised when handling, sampling and releasing 

leatherbacks. Field and laboratory observations indicate that 

leatherbacks have more friable skin and softer bones and are more 

susceptible to certain types of external trauma. Researchers must:

a. only board leatherbacks if they can be safely brought on board 

the vessel. 

b. handle and support leatherbacks from underneath. 

c. not turn leatherbacks on their carapace. 

d. Handling, Measuring, Weighing, and Marking 

1. Refer to Attachment X for more information on the requirements for 

handling and sampling sea turtles. 

2. Researchers must:

a. Clean and disinfect all equipment (tagging equipment, tape 

measures, etc.) and surfaces that come in contact with sea 

turtles between the processing of each turtle.

b. Maintain a designated set of instruments for use on turtles with 

fibropapillomas (FP). Items that come into contact with sea 

turtles with FP should not be used on turtles without tumors. 

All measures possible should be exercised to minimize 

exposure and cross-contamination between affected turtles and 

those without apparent disease, including use of disposable 

gloves and thorough disinfection of equipment and surfaces. 

Appropriate disinfectants include 70% isopropyl alcohol, 10% 

bleach, and other viricidal solutions with proven efficacy 

against herpesviruses. 

c. Examine turtles for existing flipper and passive integrated 

transponder (PIT) tags before attaching or inserting new ones. 

All flippers must be checked. No more than one external 

flipper tag, per flipper, may be attached (includes existing 

flipper tags). If existing tags are found, all tag identification 

numbers must be recorded and promptly reported to the 

Cooperative Marine Turtle Tagging Program (CMTTP) at the 

Archie Carr Center for Sea Turtle Research (ACCSTR): 

http://accstr.ufl.edu/resources/report-a-tag/ or by email: 

accstr@ufl.edu. Researchers must have PIT tag readers 

capable of reading 125, 128, 134.2, and 400 kHz tags. 

d. Clean and disinfect:
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

12

i. flipper tags (e.g., to remove oil residue) before use; 

ii. tag applicators, including the tag injector handle, 

between sea turtles; and 

iii. the application site before the tag pierces the animal’s 

skin. 

3. Flipper Tagging 

a. The application site must be cleaned and then scrubbed with a 

medical disinfectant solution (e.g., Betadine, Chlorhexidine) 

followed by 70% alcohol before the applicator pierces the 

animal’s skin.

b. Animals less than 20 cm straight carapace length (SCL), nuchal 

notch to pygal tip, may not be flipper tagged. 

c. For turtles 20-30 cm SCL, only 1005 series tags or similar (~ 

4.8 x 11.1 mm) may be used. 

d. Standard 681 tags can only be used for turtles greater than 30 

cm SCL.

e. No more than one tag per flipper and two flipper tags per turtle 

may be applied.

4. Passive Integrated Transponder (PIT) Tagging 

a. Use a new, sterile needle each time. 

b. The application site must be cleaned and then scrubbed with 

two replicates of a medical disinfectant solution (e.g., Betadine, 

Chlorhexidine) followed by 70% alcohol 

(disinfectant/alcohol/disinfectant/alcohol) before the applicator 

pierces the animal’s skin. If it has been exposed to fluids from 

another animal, the injector handle must be disinfected 

between animals.

c. Turtles must be at least 16 cm SCL to receive a PIT tag under 

standard field conditions. 

d. For turtles 16-30 cm SCL: 

i. Researchers must have specialized experience to tag 

small turtles of this size.
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

13

ii. Only 10 mm PIT tags and a 16 gauge injector needle 

may be used.

iii. PIT tags must be inserted into the thickest part of the 

triceps superficialis muscle. The tag must occupy no 

more than an estimated 20% of the muscle’s total 

volume and length. To determine eligibility, pinch the 

muscle forward and assess the tag size relative to the 

muscle size. Alternative sites may be used provided: 

1) there is sufficient mass to accommodate the tag (< 

20%) and 2) there is minimal risk of injury to vital 

structures or other anatomical features.

iv. Local anesthetic (e.g., carbocaine, lidocaine) must be 

used prior to PIT tag injection. 

5. Marking the Carapace

a. Researchers must use non-toxic paints or markers that do not 

generate heat or contain xylene or toluene. 

b. Markings should be easily legible using the least amount of 

paint or marker necessary to re-identify the animal.

 

e. Biological Sampling

1. Blood Sampling 

a. Blood samples must be directly taken by or supervised by 

experienced personnel. 

 

b. New disposable needles must be used on each animal. 

c. Collection sites must be thoroughly swabbed with a medical 

disinfectant solution (e.g., Betadine, Chlorhexidine) followed 

by 70% alcohol before sampling. Two (2) applications of 

alcohol may be used if disinfectant solutions may affect 

intended analyses.

d. Samples must not be taken if an animal cannot be adequately 

immobilized for blood sampling or conditions on the 

boat/holding platform preclude the safety and health of the 

turtle. 

e. Attempts (needle insertions) to extract blood from the neck 

must be limited to a total of four, two on either side. Best 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

14

practices must be followed, including retraction of the needle 

to the level of the subcutis prior to redirection to avoid 

lacerating vessels and causing other unnecessary soft tissue 

injury and immediate removal of the needle if the animal 

begins to move. Individual needles can only be used for one or 

two attempts before the needle must be replaced. Needles must 

be changed immediately if they contact other surfaces or 

otherwise become contaminated or damaged. 

f. Blood Volume Limits 

i. Sample volume. The volume of blood withdrawn must 

be the minimal volume necessary to complete permitted 

activities. A single sample must not exceed 3 ml per 1 

kg of animal. 

ii. Sampling period. Cumulative blood volume taken from 

a single turtle must not exceed the maximum safe limit 

described above within a 45-day period. If more than 

50% of the maximum safe limit is taken, in a single 

event or cumulatively from repeat sampling events, 

from a single turtle within a 45-day period that turtle 

must not be re-sampled for 3 months from the last 

blood sampling event. 

iii. Research coordination. Researchers must, to the 

maximum extent practicable, attempt to determine if 

any of the turtles they blood sample may have been 

sampled within the past 3 months or will be sampled 

within the next 3 months by other researchers. The 

Permit Holder must make efforts to contact other 

researchers working in the area that could capture the 

same turtles to ensure that none of the above limits are 

exceeded.

iv. Turtles weighing 1 kg or less. A single sample must not 

exceed 6% of total blood volume. Total blood volume 

is estimated as 7% of total body weight. If additional 

samples are to be taken in less than 2 months on the 

same turtle, sample size must not exceed 3 ml/kg of 

turtle. 

2. Biopsy Sampling 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

15

a. A new sterile biopsy punch, scalpel blade or scissors must be 

used on each turtle. 

b. Turtles brought on-board the vessel for sampling: 

i. Samples may only be taken from the limbs, neck, 

carapace, or shoulder region as described in the 

application. Sensitive areas must be avoided. 

ii. For small skin samples (6 mm diameter or smaller): 

Aseptic techniques must be used at all times. At a 

minimum, the tissue surface must be thoroughly 

swabbed with a medical disinfectant solution (e.g., 

Betadine, Chlorhexidine) followed by 70% alcohol 

before sampling. Two applications of alcohol may be 

used if disinfectants may interfere with analyses. The 

procedure area and Researchers’ hands must be clean. 

iii. For larger skin and fat samples: 

1. A veterinary-approved pain management 

protocol must be followed. 

2. Sterile techniques must be used. For 

procedures conducted on vessels or under 

other field conditions, a designated surgery 

area should be utilized and kept as clean as 

possible (e.g., use of disposable surgical 

drapes) to minimize risk of contamination.

c. Turtles not boarded for sampling: 

i. Turtles must be sampled [using a pole-biopsy (6 mm 

diameter or smaller) or for leatherbacks via shallow 

carapacial scrapes] in the location most safely and 

easily accessed by the Researcher.

ii. Samples may be collected from anywhere on the limbs 

or neck, avoiding the head. 

d. If it can be easily determined (through markings, tag number, 

etc.) that a sea turtle has been recaptured and has been already 

sampled under this permit, turtles may be sampled no more 

than two times during the same permit year.

3. Gastric Lavage
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

16

a. Lavage must be directly taken by or supervised by experienced 

personnel. 

b. The washing must not exceed three minutes. 

c. Once the samples have been collected, water must be turned 

off and water and food allowed to drain until all flow has 

stopped. The posterior of the turtles must be elevated slightly 

to assist in drainage. 

d. Researchers must thoroughly clean and disinfect equipment 

after each use.

e. Compromised animals must not be lavaged. 

4. Cloacal Lavage

a. Use a new catheter or thoroughly disinfect catheters between 

turtles.

b. Lubricate the catheter prior to insertion. 

c. Do not attempt to further insert the catheter once resistance is 

encountered. 

5. Fecal Sampling: Turtles must be larger than 50 cm SCL for digital 

extraction of feces.

6. Laparoscopy and Internal Tissue Sampling 

a. Compromised animals must not be subjected to laparoscopy. 

b. This procedure must be performed or directly (in-person) 

overseen by an experienced veterinarian.

c. A veterinary-approved pain management protocol must be 

followed. 

d. Any use of sedation or anesthesia must be under a veterinaryapproved protocol and directly attended by a veterinarian. 

f. Instrument Attachments

1. [Placeholder to specify max. # tags on an animal at one time and tag 

combinations as needed. Example: No more than 2 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

17

transmitters/instruments on an animal at one time, no more than one of 

which may be a satellite tag.]

2. External units: TDRs, acoustic or satellite tags, and Crittercams 

Telemetry devices and attachment material selection and protocol 

should first use best available, current published methods, especially 

with regard to risk for thermal injury. Products not previously used for 

animal attachment should be tested (including monitoring of 

temperature) by mock application prior to use on sea turtles. The 

following considerations must be incorporated into tag selection and 

application: 

a. The frontal area of the tag must be minimized and the tag must 

have a low profile. 

b. The tag must be streamlined and cover as small of an area on 

the sea turtle as possible.

c. Adhesives, use of base plates, and building up of adhesive 

material should be minimized.

d. To the degree possible, avoid placing the tag at the peak height 

of the carapace. Place tags slightly anterior or posterior to the 

peak where uplinks will be maintained and the salt water 

switch will still be exposed to the air during breathing but the 

frontal area is minimized.

e. The antenna length and diameter must be minimized to reduce 

risk of entanglement and/or drag. 

f. Each attachment must be made so that there is minimal risk of 

entanglement. The transmitter attachment must contain a weak 

link (where appropriate) or have no gap between the 

transmitter and the turtle that could result in entanglement. For 

tethered instruments, the lanyard length must be less than half 

of the turtle's carapace length. It must include a corrosive, 

breakaway link that will release the unit after its battery life.

g. Adequate ventilation must be provided around the head of the 

turtle during the attachment of transmitters if attachment 

materials produce fumes. Turtles must not be held in water 

during application to prevent skin or eye contact with harmful 

chemicals.
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

18

h. For hard-shelled turtles, procedures for drilling through 

marginal scutes must follow aseptic techniques with two 

alternating applications of medical disinfectant (e.g., Betadine, 

Chlorhexidine) followed by 70% alcohol. A separate drill bit 

must be used for each turtle. Bits may be reused if sterilized by 

autoclave or cold sterilization (e.g., gluteraldehyde) before 

reuse. Similar aseptic protocols must be used for direct 

attachment of devices to leatherbacks, with sterilized drill bits 

used for each turtle. 

i. Crittercam: Attachments must be made so that turtles are able 

to move freely without impairment.

3. Stomach pills: Use of “smart” pills or other devices intended to be 

ingested and passed or otherwise retrieved must be used according to a 

veterinary-approved protocol that includes the minimum size of sea 

turtle to be used and clear explanation of safety relative to body size 

and monitoring of transmitter, administration of the pill, and 

anticipated risk for obstruction and complications. 

g. Holding 

1. Maximum holding time of an animal from the time of capture/removal 

from the net to release must not exceed:

• 1 hour for standard work-up (no transmitter attachments);

• 3 hours if receiving a transmitter attachment;

• 36 hours for animals temporarily held in a facility. 

2. Turtles temporarily held in a facility must be transported, maintained 

and cared for following the "Standard Permit Conditions for Care and 

Maintenance of Captive Sea Turtles" issued by the U.S. Fish and 

Wildlife Service (available at: 

https://www.fws.gov/northflorida/seaturtles/Captive_Forms/20130213

_revised%20_standard_permit_conditions_for_captive_sea_turtles.pdf

) and if in the State of Florida, following Florida Fish and Wildlife 

Conservation Commission Marine Turtle Conservation Handbook, 

Section 4, Holding Turtles in Captivity. 

3. Any use of sedation or anesthesia, such as for imaging, must be under 

a veterinary-approved protocol and directly attended by a veterinarian. 

-------------------------------------------------------------------------------------------------------------------

Non-Target Species [include based on applicable methods and species overlap with the 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

19

action]

1. Bycatch: All incidentally captured species (e.g., fishes and birds) must be 

released alive as soon as possible. 

2. [placeholder for manatee conditions.] 

3. If any listed non-target species are taken (captured, injured, etc.) during research, 

Researchers must stop activities per Condition A.2 and submit an incident report 

per Condition E.2. Adverse interactions must be documented in the report,

including any pertinent details of the interaction (gear type, what was done to 

handle and release the animals, location, date, size, water and air temperature, and

photos if possible).

4. Smalltooth Sawfish requirements

1. Researchers operating in areas where sawfish are present are required to 

contact Adam Brame, at (727) 209-5958 or adam.brame@noaa.gov, for 

training requirements on proper handling procedures. 

2. When attempting to handle and release an incidentally captured sawfish,

Researchers must use extreme caution, using procedures specified in NMFS

Sawfish Handling and Release Guidelines, found at: 

http://www.nmfs.noaa.gov/sfa/hms/compliance/workshops/protected_species

_workshop/sawfish_sturgeon/sawfish_release_guidelines_placard.pdf 

3. Researchers must keep the sawfish in the water at all times and cut the net 

from the rostrum and body of the animal (do NOT disentangle the rostrum

from the net).

4. In the event a sawfish is incidentally captured, in addition to following

Conditions A.2 and E.2, the Permit Holder must notify Adam Brame at the 

NMFS Southeast Regional Office at (727) 209-5958 or 

adam.brame@noaa.gov. 

5. Submerged Aquatic Vegetation (SAV; e.g., seagrass), Coral Communities, Hard 

and Live Bottom Habitat 

a. Researchers must take all practicable steps including the use of charts, 

GIS, sonar, fish finders, or other electronic devices to determine 

characteristics and suitability of bottom habitat prior to using gear to 

identify SAV, coral communities, and live/hard bottom habitats and avoid 

setting gear in such areas. 

b. No gear may be set, anchored on, or pulled across SAV, coral or hard/live 

bottom habitats.
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

20

c. If research gear is lost, diligent efforts would be made to recover the lost 

gear to avoid further damage to benthic habitat and impacts related to 

“ghost fishing.” 

d. Johnson’s seagrass and critical habitat. No research activities will be 

conducted over, on, or immediately adjacent to Johnson’s seagrass or in 

Johnson’s seagrass critical habitat. 

 e. Other seagrass species. Researchers must avoid setting and deploying 

gear over, on, or immediately adjacent to any non-listed seagrass species. 

If these non-listed species cannot be avoided, then the following 

avoidance/minimization measures must be implemented:

 

i. To reduce the potential for seagrass damage, anchors must be set by 

hand when water visibility is acceptable. Anchors must be placed in 

unvegetated areas within seagrass meadows or areas having relatively 

sparse vegetation coverage. Anchor removal must be conducted in a 

manner that would avoid the dragging of anchors and anchor chains. 

 

ii. Researchers must take great care to avoid damaging any seagrass 

species and if the potential for anchor or net drag is evident 

Researchers must suspend research activities immediately. 

iii. Researchers must be careful not to tread or trample on seagrass and 

coral reef habitat. 

 

6. North Atlantic Right Whale 

If a right whale is seen, Researchers must maintain a distance of at least 460 

meters (500 yards) from the animal. Please report all right whale sightings to 

NMFS Sighting Advisory System:

• in any location to the U.S. Coast Guard on channel 16, 

• from VA to ME to 978-585-8473, and 

• from NC to FL to 904-237-4220. 

7. For Humpback Whales in Hawaii 

If a humpback whale is observed in the area, Researchers and vessels must 

maintain a distance of at least 91.4 meters (100 yards) and aircraft must maintain 

a distance of at least 300 meters (1,000 feet). 

8. Hawaiian Monk Seals

a. To minimize disturbance of Hawaiian monk seals: 

Consult with the NMFS Hawaiian Monk Seal Research Program and 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

21

either the U.S. Fish and Wildlife Service (USFWS) at Midway or the State 

of Hawaii Department of Land and Natural Resources (DLNR) at Kure for 

approval of any land-based activities to avoid harassment of monk seals; 

i. Do not enter the water when monk seals are present, and if approached 

by a seal, leave the area.

 

ii. Report any opportunistic monk seal sightings to the NMFS Pacific 

Islands Fisheries Science Center, Hawaiian Monk Seal Research 

Program, NOAA IRC, 1845 WASP Blvd, Building 176, Honolulu, HI 

96818. 

In the main Hawaiian Islands: Tracy Mercer; 

Tracy.Mercer@noaa.gov; phone (808)725-5718; fax (808)725-5567 

In the Northwestern Hawaiian Islands: Thea Johanos; Thea.JohanosKam@noaa.gov; phone (808)725-5709; fax (808)725-5567 

6. Transfer of Sea Turtle Biological Samples

a. Samples may be sent to the Authorized Recipients listed in Appendix 2 

provided that 

i. The analysis or curation is related to the research objectives of this 

permit. 

ii. A copy of this permit accompanies the samples during transport 

and remains on site during analysis or curation. 

b. Samples remain in the legal custody of the Permit Holder while in the 

possession of Authorized Recipients. 

c. The transfer of biological samples to anyone other than the Authorized 

Recipients in Appendix 2 requires written approval from the Chief, 

Permits Division. 

d. Samples cannot be bought or sold. 

 

C. Qualifications, Responsibilities, and Designation of Personnel 

1. At the discretion of the Permit Holder, the following Researchers may participate 

in the conduct of the permitted activities in accordance with their qualifications

and the limitations specified herein: 

a. Principal Investigator – [name]. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

22

b. Co-Investigator(s) – [names and duties] /or/ See Appendix 2 for list of 

names and corresponding activities. 

c. Research Assistants – personnel identified by the Permit Holder or 

Principal Investigator and qualified to act pursuant to Conditions C.2, C.3, 

and C.4 of this permit. 

2. Individuals conducting permitted activities must possess qualifications 

commensurate with their roles and responsibilities. The roles and responsibilities 

of personnel operating under this permit are as follows:

a. The Permit Holder is ultimately responsible for activities of individuals 

operating under the authority of this permit. Where the Permit Holder is 

an institution/facility, the Responsible Party is the person at the 

institution/facility who is responsible for the supervision of the Principal 

Investigator. 

b. The Principal Investigator (PI) is the individual primarily responsible for 

the taking, import, export and related activities conducted under the 

permit. This includes coordination of field activities of all personnel 

working under the permit. The PI must be on site during activities 

conducted under this permit unless a Co-Investigator named in Condition 

C.1 is present to act in place of the PI. 

c. Co-Investigators (CIs) are individuals who are qualified to conduct 

activities authorized by the permit, for the objectives described in the 

application, without the on-site supervision of the PI. CIs assume the role 

and responsibility of the PI in the PI’s absence. 

d. Research Assistants (RAs) are individuals who work under the direct and 

on-site supervision of the PI or a CI. RAs cannot conduct permitted 

activities in the absence of the PI or a CI.

3. Personnel involved in permitted activities must be reasonable in number and 

essential to conduct of the permitted activities. Essential personnel are limited to: 

a. individuals who perform a function directly supportive of and necessary to 

the permitted activity (including operation of vessels or aircraft essential 

to conduct the activity), 

b. individuals included as backup for those personnel essential to the conduct 

of the permitted activity, and 

c. individuals included for training purposes. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

23

4. Persons who require state or Federal licenses or authorizations (e.g., veterinarians, 

pilots – including UAS operators) to conduct activities under the permit must be 

duly licensed/authorized and follow all applicable requirements when undertaking 

such activities.

5. Permitted activities may be conducted aboard vessels or aircraft, or in cooperation 

with individuals or organizations, engaged in commercial activities, provided the 

commercial activities are not conducted simultaneously with the permitted 

activities, except as specifically provided for in an Incidental Take Statement or 

Incidental Take Permit for the specific commercial activity.

6. The Permit Holder cannot require or receive direct or indirect compensation from 

a person approved to act as PI, CI, or RA under this permit in return for 

requesting such approval from the Permits Division. 

7. The Permit Holder or PI may add CIs by submitting a request to the Chief, 

Permits Division that includes a description of the individual’s qualifications to 

conduct and oversee the activities authorized under this permit. If a CI will only 

be responsible for a subset of permitted activities, the request must also specify 

the activities for which they would provide oversight. 

7. The Permit Holder or PI may designate additional CIs without prior approval 

from the Chief, Permits Division provided: 

a. A copy of the letter designating the individual and specifying their duties 

under the permit is forwarded to the Permits Division by facsimile or 

email on the day of designation. 

b. The copy of the letter is accompanied by a summary of the individual’s 

qualifications to conduct and supervise the permitted activities.

c. The Permit Holder acknowledges that the designation is subject to review 

and revocation by the Chief, Permits Division. 

8. Where the Permit Holder is an institution/facility, the Responsible Party may 

request a change of PI by submitting a request to the Chief, Permits Division that 

includes a description of the individual’s qualifications to conduct and oversee the 

activities authorized under this permit. 

9. Submit requests to add CIs or change the PI by one of the following: 

a. the online system at https://apps.nmfs.noaa.gov; 

b. an email attachment to the permit analyst for this permit; or 

c. a hard copy mailed or faxed to the Chief, Permits Division, Office of 

Protected Resources, NMFS, 1315 East-West Highway, Room 13705, 

Silver Spring, MD 20910; phone (301)427-8401; fax (301)713-0376. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

24

D. Possession of Permit 

1. This permit cannot be transferred or assigned to any other person. 

 2. The Permit Holder and persons operating under the authority of this permit must 

possess a copy of this permit when: 

 

a. Engaged in a permitted activity. 

b. A protected species is in transit incidental to a permitted activity. 

c. A protected species taken or imported under the permit is in the possession 

of such persons. 

 3. A duplicate copy of this permit must accompany or be attached to the container, 

package, enclosure, or other means of containment in which a protected species or 

protected species part is placed for purposes of storage, transit, supervision or 

care.

E. Reporting 

1. The Permit Holder must submit incident, annual, and final reports containing the 

information and in the format specified by the Permits Division. 

a. Reports must be submitted to the Permits Division by one of the 

following: 

i. the online system at https://apps.nmfs.noaa.gov; 

ii. an email attachment to the permit analyst for this permit; or 

iii. a hard copy mailed or faxed to the Chief, Permits Division. 

b. You must contact your permit analyst for a reporting form if you do not 

submit reports through the online system. 

2. Incident Reporting 

a. If a serious injury or mortality occurs/the total number of mortalities is 

reached, or authorized takes have been exceeded as specified in 

Conditions A.2 and B.5.x, the Permit Holder must:

i. Contact the Permits Division by phone (301-427-8401) as soon as 

possible, but no later than 2 business days of the incident; 

ii. Submit a written report within 2 weeks of the incident as specified 

below; and 

iii. Receive approval from the Permits Division before resuming work. 

The Permits Division may grant authorization to resume permitted 

activities based on review of the incident report and in 

consideration of the Terms and Conditions of this permit. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

25

b. Any time a serious injury or mortality of a protected species occurs, a 

written report must be submitted within two weeks. 

c. The incident report must include 1) a complete description of the events 

and 2) identification of steps that will be taken to reduce the potential for 

additional serious injury and research-related mortality or exceeding 

authorized take. 

3. Annual reports describing activities conducted during the previous permit year 

(from month/day to month/day) must:

a. be submitted by [insert date here and at top of first page] each year for which 

the permit is valid, and 

b. include a tabular accounting of takes and a narrative description of activities 

and their effects. 

4. A final report summarizing activities over the life of the permit must be submitted 

by (insert date 90 days post expiration), or, if the research concludes prior to 

permit expiration, within 90 days of completion of the research. 

5. Research results must be published or otherwise made available to the scientific 

community in a reasonable period of time. Copies of technical reports, 

conference abstracts, papers, or publications resulting from permitted research 

must be submitted the Permits Division.

6. The Permit Holder must submit with the annual report data on disturbance rates of 

marine mammals specific to UAS operations. Details should include, but not be 

limited to: species, altitude and angle of approach, context of exposure (e.g., 

behavioral states), and observed behavioral responses to the UAS. 

F. Notification and Coordination 

1. NMFS Regional Offices are responsible for ensuring coordination of the timing 

and location of all research activities in their areas to minimize unnecessary 

duplication, harassment, or other adverse impacts from multiple researchers. 

2. The Permit Holder must ensure written notification of planned field work for each 

project is provided to the NMFS Regional Offices listed below at least two weeks 

prior to initiation of each field trip/season. 

a. Notification must include: 

i. locations of the intended field study and/or survey routes; 

ii. estimated dates of activities; and 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

26

iii. number and roles of participants (for example: PI, CI, 

veterinarian, boat driver, safety diver, animal restrainer, Research 

Assistant “in training”). 

b. Notification must be sent to the following Assistant Regional 

Administrators for Protected Resources as applicable to the location of 

your activity: 

For activities in WA, OR, CA, and Antarctic: 

West Coast Region, NMFS, 501 West Ocean Blvd., Suite 4200, Long 

Beach, CA 90802-4213; phone (562)980-4005; fax (562)980-4027 

Email (preferred): WCR.research.notification@noaa.gov; 

For activities in HI, American Samoa, Guam, and Northern Mariana 

Islands: 

Pacific Islands Region, NMFS, 1845 Wasp Blvd., Building 176, Honolulu, 

HI 96818; phone (808)725-5000; fax (808)973-2941 

Email (preferred): nmfs.pir.research.notification@noaa.gov; 

For activities in NC, SC, GA, FL, AL, MS, LA, TX, PR, and USVI: 

Southeast Region, NMFS, 263 13th Ave South, St. Petersburg, FL 33701; 

phone (727)824-5312; fax (727)824-5309 

Email (preferred): nmfs.ser.research.notification@noaa.gov; and

For activities in ME, VT, NH, MA, NY, CT, NJ, DE, RI, MD, and VA:

Greater Atlantic Region, NMFS, 55 Great Republic Drive, Gloucester, 

MA 01930; phone (978)281-9328; fax (978)281-9394 

Email (preferred): NMFS.GAR.permit.notification@noaa.gov 

3. Researchers must coordinate their activities with other permitted researchers to 

avoid unnecessary disturbance of animals or duplication of efforts. Contact the 

applicable Regional Offices listed above for information about coordinating with 

other Permit Holders. 

G. Observers and Inspections 

1. NMFS may review activities conducted under this permit. At the request of 

NMFS, the Permit Holder must cooperate with any such review by

a. allowing an employee of NOAA or other person designated by the 

Director, NMFS Office of Protected Resources to observe and document 

permitted activities; and 

b. providing all documents or other information relating to the permitted 

activities.

H. Modification, Suspension, and Revocation 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

27

1. Permits are subject to suspension, revocation, modification, and denial in 

accordance with the provisions of subpart D [Permit Sanctions and Denials] of 15 

CFR Part 904. 

2. The Director, NMFS Office of Protected Resources may modify, suspend, or 

revoke this permit in whole or in part: 

a. in order to make the permit consistent with a change made after the date of 

permit issuance with respect to applicable regulations prescribed under 

Section 4 of the ESA; 

b. in a case in which a violation of the terms and conditions of the permit is 

found; 

c. in response to a written request 6

5F from the Permit Holder; 

 d. if NMFS determines that the application or other information pertaining to 

the permitted activities (including, but not limited to, reports pursuant to 

Section E of this permit and information provided to NOAA personnel 

pursuant to Section G of this permit) includes false information; and

 e. if NMFS determines that the authorized activities will operate to the 

disadvantage of threatened or endangered species or are otherwise no 

longer consistent with the purposes and policy in Section 2 of the ESA. 

3. Issuance of this permit does not guarantee or imply that NMFS will issue or 

approve subsequent permits or modifications for the same or similar activities 

requested by the Permit Holder, including those of a continuing nature. 

I. Penalties and Permit Sanctions 

1. A person who violates a provision of this permit, the MMPA, ESA, or the 

regulations at 50 CFR 216 and 50 CFR 222-226 is subject to civil and criminal 

penalties, permit sanctions, and forfeiture as authorized under the ESA, and 15 

CFR Part 904. 

2. The NMFS Office of Protected Resources shall be the sole arbiter of whether a 

given activity is within the scope and bounds of the authorization granted in this 

permit. 

 

 

6 The Permit Holder may request changes to the permit related to: the objectives or purposes of the permitted 

activities; the species or number of animals taken; and the location, time, or manner of taking or importing protected 

species. Such requests must be submitted in writing to the Permits Division in the format specified in the 

application instructions. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

28

a. The Permit Holder must contact the Permits Division for verification 

before conducting the activity if they are unsure whether an activity is 

within the scope of the permit. 

b. Failure to verify, where the NMFS Office of Protected Resources 

subsequently determines that an activity was outside the scope of the 

permit, may be used as evidence of a violation of the permit, the MMPA, 

the ESA, and applicable regulations in any enforcement actions. 

J. Acceptance of Permit

1. In signing this permit, the Permit Holder: 

 a. agrees to abide by all terms and conditions set forth in the permit, all 

restrictions and relevant regulations under 50 CFR Parts 216, and 222-226, 

and all restrictions and requirements under the MMPA, and the ESA; 

 b. acknowledges that the authority to conduct certain activities specified in 

the permit is conditional and subject to authorization by the Office

Director; and

 c. acknowledges that this permit does not relieve the Permit Holder of the 

responsibility to obtain any other permits, or comply with any other 

Federal, State, local, or international laws or regulations. 

 

Donna S. Wieting Date Issued

Director, Office of Protected Resources 

National Marine Fisheries Service

 

[name of Permit Holder or Responsible Party] Date Effective

[permit holder’s/RP’s title and institution]

Permit Holder /or/ Responsible Party 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

29

Appendix 1: Tables Specifying the Kind(s) of Protected Species, Location(s), and 

Manner of Taking

Appendix 2: NMFS-Approved Personnel and Authorized Recipients for Permit 

No. XXXXX-0X. 

The following individuals are approved to act as Co-Investigators pursuant to the terms and 

conditions under Section C (Qualifications, Responsibilities, and Designation of Personnel) of 

this permit.

Name of Co-Investigator Activities 

Dr. John Smith Aerial surveys

Dr. Jane Doe All research activities

Biological samples authorized for collection or acquisition in Table(s) X of Appendix 1 may be 

transferred to the following Authorized Recipients for the specified disposition, consistent with 

Condition B.6 of the permit: 

Authorized Recipient Sample Type Disposition

Researchers name, affiliation, 

City, State

Whole blood and serum Analysis and curation of 

remaining samples

Researcher’s name, affiliation, 

City, State

Skin Analysis (samples consumed in 

analysis)

Attachment 1: Procedures for handling and monitoring leatherbacks during 

leatherback capture-related work (revised 7/20/2017).

The following is the protocol for handling turtles captured under Permit No. XXXXX. These 

requirements incorporate recommendations made by a panel of veterinarians with experience 

capturing leatherback turtles in the Pacific, Atlantic, and Gulf of Mexico.

Personnel requirements

To effectively monitor leatherback turtles during capture and handling, researchers must have a 

designated medical observer on each capture outing team. Whenever possible, this observer 

should be an experienced6F

7 veterinarian; however, a licensed/registered veterinary technician7F8 is 

 

7 “Experienced” refers to a documented history of working with sea turtles under conditions requiring proficiency in 

emergency procedures and resuscitation. 8

 Must be trained in the methods defined herein and legally authorized to administer emergency medications within 

the area of study, which may vary by State/Territory. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

30

also acceptable if the period of restraint8 F

9 will be 30 minutes or less. If a technician serves this 

role, a veterinarian must be reachable by cellular or satellite phone or radio (as appropriate) in 

case of emergency. The observer must be a veterinarian if the period of restraint will last longer 

than 30 minutes or if any surgical procedures will be performed (excludes superficial skin 

biopsy). For any captures, at least one individual must have the dedicated role of monitoring 

vital rates, behavior, and ensuring temperature control. This individual should not have any 

other duties that limit their attentiveness to these responsibilities. Moreover, monitoring and 

delegation of responsibilities should be coordinated such that the period of restraint is as brief as 

required to accomplish research objectives. 

Capture, boarding, handling time, monitoring 

The number of attempts to capture an individual leatherback sea turtle is limited to 5 per 24-hour 

period. If researchers are unsuccessful after the first 3 attempts, they must wait a minimum of 4 

hours before making the final 2 attempts to capture that individual on the day. Unless otherwise 

stipulated in the permit, only turtles observed to be normal (e.g., normal swimming and diving 

behavior) and with no evidence of external traumatic wounds may be approached. Any animal 

deemed to be in distress at any time during the pre-capture period must be avoided.

Upon capture, the turtle should be immediately released if it is found to have any previously 

unapparent traumatic injuries, abnormal behavior, or other abnormalities that are deemed by the 

research leader or veterinarian/technician to create an additional risk of complication. The 

period of restraint should not exceed one hour unless deemed medically necessary (e.g., for 

attempted CPR, medical assessment, treatment); an interval of 30 minutes or less is preferred. 

The following monitoring is required for short and prolonged periods of restraint. A “fill-in-theblank” observation sheet is used and must be retained as part of each animal’s permanent capture 

record. 

Restraint interval <30 minutes 

Parameter Frequency

Responsiveness/activity level Throughout

Respiration rate Upon capture, every 20 minutes

Heart rate*( by Doppler, ultrasound, or ECG)) Upon capture, every 20 minutes 

Restraint interval >30 minutes 

Parameter Frequency

Responsiveness/activity level Throughout

Respiration rate Upon capture, every 20 minutes

Heart rate*(by Doppler, ultrasound, or ECG) Upon capture, every 20 minutes

Point-of-care analyzer* (for blood gases, electrolytes, glucose) Upon capture, every 30 minutes

Body temperature* Upon capture, every 20 minutes

*Only conducted if boarded/accessible

 

9

 Defined as time from entering the net until release. 
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

31

Below are general guidelines based on previous studies and medical opinion regarding alteration 

of these parameters that should trigger immediate assessment by the medical observer and chief 

scientist:

Parameter Trigger threshold

Responsiveness Reduction in response to procedures or noxious stimuli

Respiration rate Apnea for periods >2 min.

Heart rate <20 bpm

Blood pH <7.2 (temperature corrected)

Potassium >6.8 mmol/l

Glucose <60 mg/dl

Body temperature Alteration of initial body temperature by >2 ̊F or 1 ̊C (or if 

temperature exceeds 86 ̊F/30 ̊C) 

The chief scientist for each outing must be trained by a veterinarian in the following 

information and procedures:

• Acceptable parameters for responsiveness, respiration rate, heart rate, blood gas 

parameters, potassium concentration, and temperature. 

• Recognition and appropriate response to situations that suggest abortion of further animal 

work, and initiation of release. 

• Safe water reintroduction and monitoring of a turtle in possible distress. 

• Appropriate first aid measures for animals in distress. These measures may include 

intubation, artificial respiration, and administration of pharmaceuticals to stimulate 

respiration and/or cardiac contraction (to be administered by a veterinarian or licensed technician 

under consultation with a veterinarian). 

In addition to animal monitoring equipment, each outing must include an emergency field kit for 

intervention. This kit will be available to the medical observer and includes, but is not limited to, 

the following: 

• Means of ventilatory support (e.g., oxygen cylinder, demand breathing valve, 5 L Ambu bag)

• Endotracheal tubes (non-cuffed 10, 12, 14, and 16; other sizes as appropriate)

• Oral speculum and appropriate sized blade 

• Water-based lubricant 

• Disinfectants (e.g., betadine scrub, isopropyl alcohol)

• Sterile gauze

• Medical tape

• Needles, catheters, syringes, extension sets (size appropriate)

• Emergency medications: (e.g., doxapram, epinephrine, lidocaine, sodium bicarbonate, furosemide, and 

dexamethasone sodium phosphate; at discretion of attending veterinarian)

• Sterile saline
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

32

Attachment X: Requirements for Handling and Sampling Sea Turtles

Conditions have been included in the permit for research procedures that involve the handling 

and sampling of sea turtles. These conditions include requirements provided by a suite of expert 

veterinarians to minimize and mitigate potential impacts to the study animals. This information 

is being provided to help understand the permit requirements and standard veterinary protocols 

for sea turtles.

I. Permit requirements for antiseptic practices and research techniques

Measures required to minimize risk of infection and cross-contamination between individuals 

generally fall under the categories of clean, aseptic, and sterile techniques. Clean technique 

applies to noninvasive procedures that result in contact with skin or mucous membranes. 

Aseptic technique is used for brief, invasive procedures that result in any degree of internal 

contact, e.g. drawing blood. Sterile technique applies to longer invasive procedures, such as 

laparoscopy or surgery. Reusable instruments for procedures requiring aseptic or sterile 

technique should be sterilized by standard autoclave or cold sterilization procedures. 

Instruments that do not have internal contact, e.g. tagging pliers and PIT tag applicators, should 

be disinfected using a broadcidal solution and the product-recommended contact time between 

individuals. 

Clean technique: 

1. Routine hand washing or use of non-sterile disposable gloves. 

2. Cleaning and disinfection of equipment between individuals. 

Aseptic technique: 

1. Disinfection of hands or use of new non-sterile disposable gloves (preferred) 

2. Disinfection of the turtle’s skin using a surgical scrub (e.g. betadine scrub or 

chlorhexidine gluconate)† followed by application of 70% alcohol (isopropyl or ethanol) 

(minimum requirement).*

3. Clean work area.

4. Use of sterile instruments or new disposable items (e.g. needles and punch biopsies) 

between individuals. 

† Alcohol alone may be used in lieu of surgical scrub if necessary to avoid interference 

with research objectives, e.g. isotopic analysis. 

* Multiple applications and scrubbing should be used to achieve thorough cleansing of 

the procedure site as necessary. A minimum of two alternating applications of surgical 

scrub and alcohol are to be used for PIT tag application sites and drilling into the 

carapace, due to potential increased risk of infection. 

 

Sterile technique: 

1. To be conducted in accordance with approved veterinary protocol that considers 

analgesia/anesthesia, use of antimicrobials, anticipated risks and response measures, and 

exclusionary criteria for animal candidacy.
NMFS Permit No. XXXXX-0X

Expiration Date: month day, year

33

2. Direct veterinary attendance

3. Disinfection of hands and use of sterile disposable gloves 

4. Dedicated site (surgery room) or work area modified to reduce contamination 

5. Surgical preparation of skin 

6. Sterile instruments

Research Procedure Required Technique

Handling, gastric lavage, and cloacal lavage Clean technique

Tissue sampling (6 mm diameter or smaller) Aseptic technique

Blood sampling Aseptic technique

PIT tagging Aseptic technique; 2 applications of 

surgical scrub and alcohol

Flipper tagging Aseptic technique

Carapace drilling for instrument attachment Aseptic technique; 2 applications of 

surgical scrub and alcohol

Laparoscopy (+/- biopsy) Sterile

Large skin, fat, or other tissue biopsy Sterile

II. Minimum requirements for pain management and field techniques 

Procedures used for sea turtle research include those anticipated to cause short term pain or 

distress, such as tagging, as well more invasive procedures where relatively longer periods of 

pain or discomfort may result. The minimum requirements below consider animal welfare and 

relative benefits and risks of different modes of pain management under field and laboratory 

conditions. Additional measures are encouraged whenever possible, including sedation or 

anesthesia for invasive procedures, e.g. laparoscopy, when release does not immediately follow 

the procedure and full recovery can be assessed. 

Research Procedure Minimum Requirement

Tissue sampling (6 mm diameter or smaller) None

Blood sampling None

PIT tagging Local anesthetic if <30 cm SCL

Flipper tagging None

Carapace drilling for instrument attachment Systemic analgesic

Laparoscopy Local anesthetic and systemic analgesic

Laparoscopy biopsy Local anesthetic, sedation, and 

systemic analgesic

Large skin, fat, or other tissue biopsy Local anesthetic and systemic analgesic
1 

Appendix D. Permits Division Annual Report Form for Section 10(a)(1)(A) Permit Holders 

Protected Species Permit 

Report Form

We highly recommend you submit your report via APPS at https://apps.nmfs.noaa.gov. 

If you do not submit your report online, request an electronic copy to complete and return

• by email attachment to the permit analyst for this permit; or 

• by hard copy mailed or faxed to the Chief, Permits Division, Office of Protected 

Resources, NMFS, 1315 East-West Highway, Suite 13705, Silver Spring, MD 20910; 

phone (301)427-8401; fax (301)713-0376. 

Permit Number: Date Prepared: 

Permit Holder’s Name: 

Reporting Period: (please check one)

☐ A nnual #1 [date to date]

☐ A nnual #2 [date to date]

☐ A nnual #3 [date to date]

☐ A nnual #4 [date to date]

☐ C om bined A nnual# 5/Final [date to date]

☐ A nnual #5 [date to date]

☐ A nnual #6 [date to date]

☐ A nnual #7 [date to date] 

☐ A nnual #8 [date to date]

☐ A nnual #9 [date to date]

☐ C om bined A nnual #10/Final [date to date]

Contact Name: Contact Email: 

Contact Phone Number: 

 (Contact = person submitting report)

___________________________________________________________________________ 

Part I: Take Table. 

Enter the actual number of animals taken during this annual reporting period.

Take tables from permits are inserted here with a column to be filled for “Actual number of 

animals taken.” 

If you conducted activities or took protected species for which you were not authorized, you 

must enter these takes on separate lines of the table. Explain what happened in Part II, #4 below.
2 

Part II: Narrative. 

Review Section E of your permit to ensure you address any reporting specific to your 

research. 

Provide complete answers to the best of your ability. We acknowledge that monitoring 

during and after certain research activities is often opportunistic. If a question is not 

applicable, explain why. 

1. What progress did you make toward meeting your objectives this year? Summarize what 

you did and if and how you met your objectives. List citations for any reports, publications, and 

presentations from this reporting period. We may request electronic copies. 

2. Summarize how animals reacted to specific activities. Include normal and abnormal 

responses of target and non-target animals. To the extent feasible, provide quantitative data and 

estimate the proportion of animals (%) that had those reactions. 

3. Explain your efforts to conduct follow-up monitoring. Report your findings. Photographs 

are useful to document things like wound healing. We are especially interested in: 

• animal responses to new/novel procedures 

• time it takes to resume normal in-water behavior after harassment

• time it takes to re-populate rookeries or haul outs after harassment 

• condition of animals on resight or recapture

• recovery from sedation and handling and post-release behavior 

• healing at site of intrusive sampling (e.g., biopsy) 

• healing at site of intrusive tag deployment (e.g., surgical tag implants requiring sutures, 

remotely deployed dart/barb, fully implantable, medial ridge, and pygal tags) 

• tag retention and tag breakage 

4. Did serious injuries or mortalities occur or did you take a protected species you were not 

permitted to take? If so, and you already submitted an incident report, please briefly describe 

the event here and refer to the incident report. 

If such an incident occurred and you have not yet reported it, provide a full description of the 

incident (date and location of event; species and circumstances of how the take occurred; 

photographs; necropsy and histopathology reports, or other information to confirm cause of 

death or extent of injuries; etc.). Also, include steps that were or will be taken to reduce the 

possibility of it happening again. 

5. Describe any other problems encountered during this reporting period and steps taken or 

proposed to resolve them. Examples include equipment failure, weather delays, safety issues, 

and unanticipated effects to habitats or other species. 
3 

6. What efforts did you make to coordinate with the applicable NMFS Regional Office(s) and 

collaborate with other researchers? How did you collaborate (for example, avoiding field work

at the same time or working together on the same animals, sharing vessels, sharing data)? 

Only for the FINAL REPORT: In addition to the questions above: 

7. Did you meet your objectives for the permit? What did you learn? 

8. If you did not meet your objectives, explain why. For example, if you did not tag or mark as 

many animals as needed to meet your sample size, explain why and how that impacted your

ability to meet the goals of your study. 

9. For ESA-listed or MMPA-depleted target species: Explain how the results of your permitted 

work benefitted or promoted their recovery or conservation. How did your research contribute to 

fulfilling Recovery or Conservation Plan objectives (as applicable)? Explain. 

10. Did you identify any additional or improved mitigation measures? 

Feedback (optional)

11. We appreciate any feedback on APPS and your permit. For example, did you have any 

problems using APPS? Were any permit conditions difficult to comply with or unclear? Were 

your permitted take numbers appropriate? 
1 

Appendix E. Locations (denoted by red stars) of Active Section 10(a)(1)(A) Sea Turtle Research 

Permits 

Active Permits in the Atlantic (with Florida Inset) as of June 30, 2017 

Atlantic 
2 

Active Permits in the Pacific as of June 30, 2017

Pacific 
Appendix F. NMFS Sawfish Handling and Release Guidelines
­

Sawfish Handling Sawfish Handling 

and Release and Release 

Guidelines Guidelines 

Do not remove the saw or injure the 

sawfish in any way. 

♦ Use line cutting poles, boltcutters, long-handled dehookers and boat hooks to aid in removing gear, including hooks, from the sawfish 

♦ If the sawfish is hooked and not entangled, cut the 

line as close to the hook as possible. Remove the 

hook with a dehooker, if possible 

♦ If the sawfish is hooked and line is tangled around 

the saw (rostrum), remove all line with a boat hook or 

line cutting pole, then cut the line as close to the 

hook as possible. Remove the hook with a dehooker, if possible 

♦ If hooked internally, do NOT attempt to remove the 

hook, use line cutting pole or boat hook to remove 

as much line as possible 

♦ Date and time of encounter 

♦ Location (GPS coordinates) 

♦ Habitat (water depth, bottom type) 

♦ Estimated total length of sawfish including saw 

♦ Description of gear that could not safely be removed 

from the animal 

♦ Markings, scars, wounds 

♦ If present, record tag number and type (shape and 

color) (tags are found on or below the dorsal fins), but 

do not remove the tag 

♦ Details of capture (bait, hook size/type, mesh size, 

length of gear) 

♦ Sex of sawfish, if known (male sawfish, like sharks, 

have two claspers at the base of the pelvic fins) 

Smalltooth sawfish are listed as endangered under the Endangered Species Act and “take” of 

listed species is prohibited under section 9 of the Endangered Species Act. Any sawfish 

caught while fishing must be released as quickly as possible. More information can be found 

at http://www.nmfs.noaa.gov/pr/species/fish/smalltoothsawfish.htm 

Keep as much of the sawfish in the water as possible. 

For sawfish caught on longline gear: 

For sawfish caught in trawl or gill net gear: 

In your logbook, document as much information as 

possible including: 

Use extreme caution when handling and releasing 

sawfish as the saw can thrash violently from side to side 

♦ DO NOT REMOVE THE FISH’S SAW (ROSTRUM) 

♦ Leave the sawfish, especially the gills, in the water 

as much as possible 

♦ Use line cutting pole or knife to cut any net tangled 

around the saw by cutting the mesh along the length 

of the saw 

♦ Once mesh is cut, work it free with a boat hook or 

line cutting pole 

With a little extra effort, and the proper use of 

required tools, endangered smalltooth sawfish can 

be returned to the water with little or no damage.