OCS Study 

BOEM 2015-027 

FGBNMS 2015-001 

U.S. Department of the Interior 

Bureau of Ocean Energy Management 

Gulf of Mexico OCS Region 

National Oceanic and Atmospheric Administration 

Flower Garden Banks National Marine Sanctuary

Long-Term Monitoring at East and 

West Flower Garden Banks

National Marine Sanctuary, 2011–2012

Volume 1: Technical Report
OCS Study 

BOEM 2015-027 

 FGBNMS 2005-001 

Published by 

U.S. Department of the Interior 

Bureau of Ocean Energy Management 

Gulf of Mexico OCS Region

New Orleans, LA 

June 2015

Long-Term Monitoring at East and 

West Flower Garden Banks

National Marine Sanctuary, 2011–2012

Volume 1: Technical Report

Authors 

Michelle A. Johnston 

Marissa F. Nuttall 

Ryan J. Eckert 

John A. Embesi 

Niall C. Slowey 

Emma L. Hickerson 

George P. Schmahl 

Prepared under BOEM Interagency Agreement 

M09PG00011 

by 

U.S. Department of Commerce 

NOAA Flower Garden Banks National Marine Sanctuary 

Avenue U, Bldg. 216 

Galveston, TX 77551 
iii 

 DISCLAIMER 

This report was prepared under an interagency agreement between the Bureau of Ocean Energy 

Management (BOEM) and National Oceanic and Atmospheric Administration’s Flower Garden 

Banks National Marine Sanctuary (NOAA FGBNMS). This report has been technically reviewed 

by BOEM, and it has been approved for publication. Approval does not necessarily signify that 

the contents reflect the views and policies of BOEM, nor does mention of trade names or 

commercial products constitute endorsement or recommendation for use. 

REPORT AVAILABILITY 

To download a PDF file of this Gulf of Mexico OCS Region report, go to the U.S. Department of 

the Interior, Bureau of Ocean Energy Management, Environmental Studies Program Information 

System website and search on OCS Study BOEM 2015-027. 

This report can be viewed at select Federal Depository Libraries. It can also be obtained from the 

National Technical Information Service; the contact information is below. 

U.S. Department of Commerce 

National Technical Information Service 

5301 Shawnee Rd. 

Springfield, Virginia 22312 

Phone: (703) 605-6000, 1(800)553-6847 

Fax: (703) 605-6900 

Website: http://www.ntis.gov/ 

CITATION 

Johnston, M.A., M.F. Nuttall, R.J. Eckert, J.A. Embesi, N.C. Slowey, E.L. Hickerson, and G.P. 

Schmahl. 2015. Long-term monitoring at East and West Flower Garden Banks National 

Marine Sanctuary, 2011–2012, volume 1: technical report. U.S. Dept. of Interior, Bureau 

of Ocean Energy Management, Gulf of Mexico OCS Region, New Orleans, Louisiana. 

OCS Study BOEM 2015-027. 194 p. 

ABOUT THE COVER 

The cover photograph features NOAA Flower Garden Banks National Marine Sanctuary diver 

Ryan Eckert capturing a benthic scene in the East Flower Garden Bank. He is using a camera 

mounted on an aluminmum T-frame on a random transect line. Photograph by G.P. Schmahl 

(NOAA FGBNMS). 
v 

ACKNOWLEDGMENTS 

We thank the individuals, listed below, who contributed their time and expertise to make this 

long-term monitoring effort successful. We are grateful to the NOAA and BOEM staff for their 

invaluable institutional knowledge. In particular, we acknowledge James Sinclair, Michelle 

Nannen, Greg Boland, and Matthew Johnson for their support and dedication to this project. 

NOAA FGBNMS PERSONNEL AND ROLE 

Michelle A. Johnston, Ph.D. Project Manager, Data Acquisition, Analysis, and 

Report Compilation 

Marissa Nuttall Cruise Logistics, Data Acquisition and Analysis 

Ryan Eckert Technical Support, Data Acquisition and Analysis 

John Embesi Field Management, Data Acquisition and Analysis 

Emma L. Hickerson Sanctuary Research Coordinator, Data Acquisition 

G.P. Schmahl Sanctuary Superintendent, Data Acquisition 

PROJECT DIVERS 2011–2012 

Lindy Arbuckle Michelle Johnston G.P. Schmahl 

Ryan Eckert Doug Jones James Sinclair 

John Embesi Kaitlin McGraw Scott Sorsett 

Steve Gittings Marissa Nuttall Charles Vance 

Emma Hickerson Randy Rudd 

 

REPORT CONTRIBUTERS AND REVIEWERS 

Flower Garden Banks National Marine Sanctuary staff would like to acknowledge the support 

and efforts of subject area experts who assisted with this technical report. The report benefited 

significantly from the following individuals who either provided a peer review or provided 

comments, content, images, and data: Matthew Johnson (Bureau of Ocean Energy Management), 

James Sinclair (Bureau of Safety and Environment Enforcement), Gregory Boland (Bureau of 

Ocean Energy Management), Steve Gittings (NOAA’s Office of National Marine Sanctuaries), 

George Sedberry (NOAA’s Office of National Marine Sanctuaries Southeast Region), William 

Kiene (NOAA’s Office of National Marine Sanctuaries Southeast Region), Niall Slowey (Texas 

A&M University), and Eleanor Yudelman (Texas A&M University). 
vii 

CONTENTS 

LIST OF FIGURES ....................................................................................................................... xi 

LIST OF TABLES ........................................................................................................................ xii 

LIST OF ABBREVIATIONS ........................................................................................................ xi 

EXECUTIVE SUMMARY ....................................................................................................... xxiii

CHAPTER 1.0: Introduction........................................................................................................1 

1.1. Coral Reef Monitoring at East and West Flower Garden Banks ....................................... 1

1.2. Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico ........................ 4

1.2.1. Habitat Description ............................................................................................... 4

1.2.2. East and West Flower Garden Banks ................................................................... 5

1.3. BOEM and FGBNMS Protective Measures ...................................................................... 8

CHAPTER 2.0: Study Sites ........................................................................................................ 11 

2.1. Study Site Methods .......................................................................................................... 11

2.1.1. 10,000 m2 Study Sites ........................................................................................ 11 

2.1.2. Repetitive Deep Stations .................................................................................... 15

CHAPTER 3.0: Random Transects ........................................................................................... 19 

3.1. Random Transect Methodological Rationale ................................................................... 19

3.2. Random Transect Methods .............................................................................................. 19 

3.2.1. Random Transect Field Methods ....................................................................... 19

3.2.2. Random Transect Data Processing ..................................................................... 20

3.2.3. Random Transect Statistical Analyses ............................................................... 21

3.3. Random Transect Results ................................................................................................ 22 

3.3.1. Random Transect Univariate Analysis ............................................................... 28

3.3.2. Random Transect Multivariate Analysis ............................................................ 29

3.3.3. Historical Comparison of Random Transect Benthic Cover .............................. 30

3.4. Random Transect Discussion ........................................................................................... 35

3.4.1. Historical Comparison of Random Transect Benthic Cover .............................. 37

CHAPTER 4.0: Repetitive Quadrats......................................................................................... 41 

4.1. Repetitive Quadrat Methodological Rationale ................................................................. 41

4.2. Repetitive Quadrat Methods ............................................................................................ 41

4.2.1. Repetitive Quadrat Field Methods ..................................................................... 41

4.2.2. Repetitive Quadrat Data Processing ................................................................... 42 

4.2.3. Repetitive Quadrat Statistical Analyses ............................................................. 43 

4.3. Repetitive Quadrat Results .............................................................................................. 44 

4.3.1. Repetitive Quadrat Analysis ............................................................................... 44 

 4.3.2. Repetitive Deep Station Percent Cover .............................................................. 56 

4.3.3. Repetitive Quadrat Planimetric Analysis ........................................................... 67
viii 

4.4. Repetitive Quadrat Discussion ......................................................................................... 70

4.4.1. Study Site Repetitive Quadrats ........................................................................... 70

4.4.2. Repetitive Deep Stations .................................................................................... 72

4.4.3. Planimetry .......................................................................................................... 72 

CHAPTER 5.0: Lateral Growth ................................................................................................ 75 

5.1. Lateral Growth Methodological Rationale ...................................................................... 75

5.2. Lateral Growth Methods .................................................................................................. 75 

5.2.1. Lateral Growth Field Methods ........................................................................... 75 

5.2.2. Lateral Growth Data Processing ......................................................................... 76 

5.2.3. Lateral Growth Data Presentation and Analysis ................................................ 77

5.3. Lateral Growth Results .................................................................................................... 78 

5.3.1. Historical Comparison of Lateral Growth Results ............................................. 79

5.4. Lateral Growth Discussion .............................................................................................. 80

CHAPTER 6.0: Sclerochronology ............................................................................................. 87 

6.1. Sclerochronology Methodological Rationale .................................................................. 87

6.2. Sclerochronology Methods .............................................................................................. 88

6.2.1. Why Orbicella faveolata? .................................................................................. 88 

6.2.2. Sclerochronology Field Methods ....................................................................... 89

6.2.3. Sclerochronology Data Processing ..................................................................... 89

6.2.4. Sclerochronology Data Presentation and Analysis ............................................ 90

6.3. Sclerochronology Results ................................................................................................ 90

6.4. Sclerochronology Discussion........................................................................................... 95

CHAPTER 7.0: Perimeter Videography ................................................................................... 99 

7.1. Perimeter Videography Methodological Rationale ......................................................... 99

7.2. Perimeter Videography Methods ..................................................................................... 99

7.3. Perimeter Videography Results ....................................................................................... 99

7.3.1. EFGB Perimeter Lines ..................................................................................... 100

7.3.2. EFGB 360 Panoramic Views .......................................................................... 100

7.3.3. WFGB Perimeter Lines .................................................................................... 100

7.3.4. WFGB 360 Panoramic Views ......................................................................... 100

7.4. Perimeter Videography Discussion ................................................................................ 102

CHAPTER 8.0: Diver Observations ........................................................................................ 105 

8.1. Diver Observations Methodological Rationale .............................................................. 105 

8.2. Diver Observations Methods ....................................................................................... ..105

8.3. Diver Observations Results............................................................................................ 105

8.3.1. Wildlife Observations ....................................................................................... 105 

8.3.2. Coral Health Observations ............................................................................... 107 

8.3.3. Invasive Species Sightings ............................................................................... 109

8.4. Diver Observations Discussion ...................................................................................... 108

8.4.1. Wildlife Observations ....................................................................................... 110 

8.4.2. Coral Health Observations ............................................................................... 111 

8.4.3. Invasive Species Sightings ............................................................................... 111
ix 

CHAPTER 9.0: Water Quality ................................................................................................. 115

9.1. Water Quality Methodological Rationale ...................................................................... 115

9.2. Water Quality Methods.................................................................................................. 115

9.2.1. Sea-Bird Conductivity and Temperature Recorder .......................................... 115 

9.2.2. HoboTemp Thermographs ............................................................................... 116

9.2.3. YSI Probe ......................................................................................................... 116

9.2.4. Chlorophyll a and Nutrients ............................................................................. 117

9.3. Water Quality Results .................................................................................................... 118

9.3.1. Sea-Bird Temperature and Salinity .................................................................. 118 

9.3.2. HoboTemp Thermograph Data ........................................................................ 121

9.3.3. YSI Vertical Profiles ........................................................................................ 123

9.3.4. Water Samples .................................................................................................. 125 

9.4. Water Quality Discussion .............................................................................................. 129

9.4.1. Water Quality Parameters ................................................................................ 129 

9.4.2. Chlorophyll a and Nutrients ............................................................................. 133

9.4.3. Sea State ........................................................................................................... 137

CHAPTER 10.0: Fish Surveys ................................................................................................. 139 

10.1. Fish Surveys Methodological Rationale ...................................................................... 139

10.2. Fish Surveys Methods .................................................................................................. 139

10.3. Fish Surveys Data and Statistical Analysis .................................................................. 140

10.4. Fish Surveys Results .................................................................................................... 142 

10.4.1. Population Diversity ....................................................................................... 145 

10.4.2. Sighting Frequency and Occurrence .............................................................. 147 

10.4.3. Species Density .............................................................................................. 151 

10.4.4. Trophic Group Analysis ................................................................................. 152 

10.4.5. Biomass Analysis ........................................................................................... 155 

10.4.6. Diurnal Density Patterns ................................................................................ 162 

10.4.7. Abundance-Biomass Curves .......................................................................... 164 

10.4.8. Family Level Analysis .................................................................................... 166 

10.4.9. Long-Term Trends ......................................................................................... 167 

10.5. Fish Surveys Discussion .............................................................................................. 168

CHAPTER 11.0: Sea Urchin and Lobster Surveys ............................................................... 173

11.1. Sea Urchin and Lobster Surveys Methodological Rationale ....................................... 173

11.2. Sea Urchin and Lobster Surveys Methods ................................................................... 173 

11.3. Statistical Analysis of Sea Urchin and Lobster Surveys Data ..................................... 173

11.4. Sea Urchin and Lobster Surveys Results ..................................................................... 173 

11.4.1. Historical Comparison of Sea Urchin and Lobster Surveys ........................... 174

11.5. Sea Urchin and Lobster Surveys Discussion ............................................................... 176

CHAPTER 12.0: Recommendations ....................................................................................... 177

LITERATURE CITED ............................................................................................................ 179
xi 

LIST OF FIGURES 

Figure 1.2.1. Map of EFGB and WFGB in relation to the Texas-Louisiana continental 

shelf and other topographic features of the northwestern Gulf of Mexico 

(NOAA/FGBNMS). ........................................................................................... 5 

Figure 1.2.2. Bathymetric map of EFGB (NOAA/FGBNMS). ............................................... 6 

Figure 1.2.3. Bathymetric map of WFGB (NOAA/FGBNMS). .............................................. 7 

Figure 2.1.1. Bathymetric map of EFGB with long-term monitoring study site (LTM 

site), mooring buoy, and datasonde locations (NOAA/FGBNMS). ................. 12 

Figure 2.1.2. Bathymetric map of WFGB with long-term monitoring study site (LTM 

site), mooring buoy, and datasonde locations (NOAA/FGBNMS). ................. 13 

Figure 2.1.3. Divers install new permanent eye-bolts at the WFGB study site 

(NOAA/FGBNMS). ......................................................................................... 14 

Figure 2.1.4. Bathymetric map of EFGB with long-term monitoring study site (LTM 

site), mooring buoy, and repetitive deep photostation locations (EB Deep) 

(NOAA/FGBNMS). ......................................................................................... 16 

Figure 2.1.5. Bathymetric map of WFGB with long-term monitoring study site (LTM 

site), mooring buoy, and repetitive deep photostation locations (WB Deep) 

(NOAA/FGBNMS). ......................................................................................... 17 

Figure 3.2.1. NOAA scientific diver with camera and strobes mounted on aluminum tframe taking random transect photographs (NOAA/FGBNMS). .................... 20 

Figure 3.3.1. Mean percent cover + SE of four functional benthic categories from random 

transects at the FGB from 2011–2012. ............................................................. 23 

Figure 3.3.2. Mean percent cover + SE of observed dominant coral species from random 

transect photographs at EFGB in 2011 and 2012. ............................................ 26 

Figure 3.3.3. Mean percent cover + SE of observed dominant coral species from random 

transect photographs at WFGB in 2011 and 2012. .......................................... 26 

Figure 3.3.4. Two-dimensional MDS plot based on Bray-Curtis similarities showing the 

spatial representation of benthic community similarities between EFGB and 

WFGB in 2011 and 2012. ................................................................................. 29 

Figure 3.3.5. Historical representation of mean percent cover of coral, sponge, 

macroalgae, and CTB at (A) EFGB and (B) WFGB. ....................................... 31 

Figure 3.3.6. Two-dimensional MDS plot based on Bray-Curtis similarities comparing 

benthic cover analysis from 1994–2012 at EFGB and WFGB. ....................... 34 

Figure 3.4.1. Random transect mean percent coral cover + SE at EFGB and WFGB over 

time. .................................................................................................................. 36 

Figure 3.4.2. Historical representation of mean percent dominant coral cover at (A) 

EFGB and (B) WFGB. ..................................................................................... 40 
xii 

Figure 4.2.1. Repetitive quadrat station #761 at EFGB in 2012 (NOAA/FGBNMS). .......... 41 

Figure 4.3.1. Mean percent cover + SE of four functional benthic categories at the FGB 

in 2011 and 2012. ............................................................................................. 45 

Figure 4.3.2. Mean percent cover + SE of the dominant observed coral species in 

repetitive quadrats at EFGB in 2011 and 2010. ............................................... 48 

Figure 4.3.3. Mean percent cover + SE of the dominant observed coral species in 

repetitive quadrats at WFGB in 2011 and 2012. .............................................. 48 

Figure 4.3.4. Two-dimensional MDS plot based on Bray-Curtis similarities showing the 

spatial representation of repetitive quadrat benthic community cover 

similarities between EFGB and WFGB for 2011 and 2012. ............................ 51 

Figure 4.3.5. Historical representation of mean percent cover of coral, sponge, 

macroalgae, and CTB in repetitive quadrats at (A) EFGB and (B) WFGB. .... 53 

Figure 4.3.6. Two-dimensional MDS plot based on Bray-Curtis similarities comparing 

benthic cover analysis from 2002–2012 in repetitive quadrats at EFGB and 

WFGB. ............................................................................................................. 56 

Figure 4.3.7. Mean percent cover + SE of four functional benthic categories at the FGB 

repetitive deep stations in 2011 and 2012. ....................................................... 57 

Figure 4.3.8. Mean percent cover + SE of the observed dominant coral species at EFGB 

repetitive deep stations in 2011 and 2012. ....................................................... 60 

Figure 4.3.9. Mean percent cover + SE of the observed dominant coral species at WFGB 

repetitive deep stations in 2012. ....................................................................... 60 

Figure 4.3.10. Two-dimensional MDS plot based on Bray-Curtis similarities showing the 

spatial representation of benthic community similarities between the 2011 

and 2012 EFGB and 2012 WFGB repetitive deep stations. ............................. 63 

Figure 4.3.11. Mean percent cover + SE of the four functional benthic categories at the 

FGB repetitive deep stations (DS) and shallow station (SS) repetitive 

quadrats in 2011and 2012. ............................................................................... 64 

Figure 4.3.12. Repetitive deep station mean percent cover from 2003–2012 of coral, 

sponge, macroalgae, and CTB at EFGB. .......................................................... 66 

Figure 4.3.13. Mean percent change from repetitive quadrat planimetry analysis for 2011 

and 2012 at EFGB and WFGB repetitive quadrats and EFGB repetitive 

deep stations (EFGB Deep). ............................................................................. 67 

Figure 4.3.14. Mean percent change from coral species from repetitive quadrat planimetry 

analysis for 2011 and 2012 at EFGB and WFGB repetitive quadrats and 

EFGB repetitive deep stations (EFGB Deep). .................................................. 68 

Figure 4.4.1. Repetitive photostation 761 (re-named 102 in 2012) from EFGB in a time 

series from 2006–2012, showing a healthy and stable coral community: (A) 

2006; (B) 2007; (C) 2008; (D) 2009; (E) 2010; (F) 2011; (G) 2012 

(NOAA/FGBNMS). ......................................................................................... 71 
xiii 

Figure 4.4.2. An example of colonies selected for planimetric analysis include 1) 

Colpophylia natans, 2) Porites astreoides, and 3) Pseudodiploria strigosa

in photo (A), and colony planar outlines in (B), at repetitive quadrat station 

#10 at EFGB in 2012. ....................................................................................... 73 

Figure 5.2.1. Lateral growth station #108 on a Pseudodiploria strigosa colony with 

close-up framer at WFGB in 2011 (NOAA/FGBNMS). ................................. 76 

Figure 5.2.2. Image analysis of Pseudodiploria strigosa lateral growth margin at EFGB 

(NOAA/FGBNMS). ......................................................................................... 77 

Figure 5.3.1. Percent change ± SE in Pseudodiploria strigosa colonies at EFGB and 

WFGB during intervals from 2001–2012......................................................... 80 

Figure 5.4.1. Lateral growth station #10 on a Pseudodiploria strigosa colony with closeup framer at EFGB in 2012 displaying an overgrown margin and bolts 

(NOAA/FGBNMS) .......................................................................................... 81 

Figure 5.4.2. Lateral growth station #15 on a Pseudodiploria strigosa colony with closeup framer at EFGB in 2012 displaying algae overgrowth 

(NOAA/FGBNMS) .......................................................................................... 81 

Figure 5.4.3. Lateral growth station #10 on a Pseudodiploria strigosa colony with closeup framer at EFGB in (A) 2009 displaying a measurable margin, and (B) in 

2012 displaying an overgrown irregular margin that can no longer provide a 

comparable measurement (NOAA/FGBNMS) ................................................ 82 

Figure 5.4.4. Lateral growth station #34 on a Pseudodiploria strigosa colony with closeup framer at EFGB in (A) 2011 where the framer was not placed in the 

correct orientation, and (B) in 2012 displaying the correct orientation and 

bolt placement; however, the photo is no longer comparable to the previous 

year (NOAA/FGBNMS) .................................................................................. 82 

Figure 5.4.5. New lateral growth test station on a Pseudodiploria strigosa colony margin 

(A), and lateral photograph taken by placing the framer in the key hole 

plate (B) (NOAA/FGBNMS) ........................................................................... 83 

Figure 6.1.1. Example X-radiograph of Orbicella faveolata skeletal material from the 

FGB showing density banding (Slowey/TAMU). ............................................ 88 

Figure 6.3.1. Digitally created slab X-radiographs of Orbicella faveolata skeletal 

structure in the plane of corallite growth from coral cores taken in EFGB 

study site quadrants (NE=northeast, SE=southeast, SW=southwest) 

(Yudelman 2014). ............................................................................................. 91 

Figure 6.3.2. Digitally created slab X-radiographs of Orbicella faveolata

skeletalstructure in the plane of corallite growth from coral cores taken in 

WFGB study site quadrants (NW=northwest, NE=northeast, SE=southeast, 

SW=southwest) (Yudelman 2014). .................................................................. 92 

Figure 6.3.3. Mean annual extension rates determined from cores collected in 2012 at 

EFGB (Yudelman 2014). ................................................................................. 94 
xiv 

Figure 6.3.4. Mean annual extension rates determined from cores collected in 2012 at 

WFGB (Yudelman 2014). ................................................................................ 95 

Figure 7.3.1. A seismic cable drapped over a Colpophyllia natans coral head in 2011 

(A), the cable and scar in 2011 (B), and the recovered colony and shifted 

cable in 2012 (C) at EFGB (NOAA/FGBNMS). ........................................... 101 

Figure 7.3.2. A bleached Montastraea cavernosa colony in 2011 (A), and the same 

recovered colony in 2012 (B) at WFGB (note shift in line between years) 

(NOAA/FGBNMS). ....................................................................................... 108 

Figure 8.3.1. Marbled grouper (Dermatolepis inermis) visits diver at WFGB 

(NOAA/FGBNMS). ....................................................................................... 106 

Figure 8.3.2. Hawksbill sea turtle (Eretmochelys imbricata) at WFGB 

(NOAA/FGBNMS). ....................................................................................... 106 

Figure 8.3.3. Montastraea cavernosa "false bleaching" at WFGB (NOAA/FGBNMS). .... 107 

Figure 8.3.4. Fluorescent orange algae, Martensia pavonia, observed at EFGB in 2012 

(NOAA/FGBNMS). ....................................................................................... 108 

Figure 8.3.5. Arrow points to spawn leaving barrel of sponge at WFGB in 2012 

(NOAA/FGBNMS). ....................................................................................... 108 

Figure 8.3.6. Patches of orange cup coral (Tubastraea coccinea), an invasive species 

from the Pacific, at WFGB (NOAA/FGBNMS). ........................................... 109 

Figure 8.3.7. Invasive lionfish (Pterois spp.) at WFGB in 2012 (NOAA/FGBNMS). ....... 110 

Figure 8.4.1. Lionfish sightings from 1985–2012 (USGS). ................................................ 110 

Figure 9.2.1. Sea-Bird 37-SMP MicroCAT water quality instrument at EFGB 

(NOAA/FGBNMS). ....................................................................................... 116 

Figure 9.3.1. Sea-bird datasonde daily mean seawater temperature measured near the reef 

cap at EFGB from 2011–2012.. ...................................................................... 119 

Figure 9.3.2. Sea-bird datasonde daily mean seawater temperature measured near the reef 

cap at WFGB from 2011–2012. ..................................................................... 120 

Figure 9.3.3. Sea-bird datasonde daily mean salinity measured near the reef cap at EFGB 

and WFGB from 2011–2012. ......................................................................... 121 

Figure 9.3.4. HoboTemp thermographs daily mean seawater temperature measured at 

EFGB and WFGB repetitive deep stations from 2011–2012. ........................ 123 

Figure 9.4.1. Comparison of Sea-Bird and Hobo daily mean seawater temperature 

readings measured near the reef cap at EFGB from 2011–2012. ................... 130 

Figure 9.4.2. Comparison of Sea-Bird and Hobo daily mean seawater temperature 

readings measured near the reef cap at WFGB from 2011–2012. ................. 130 

Figure 9.4.3. Seawater temperature measured using Sea-Bird datasonde near the reef cap 

at EFGB in 2011 and 2012, and the historical long-term mean temperature 

from past monitoring periods. ........................................................................ 132 
xv 

Figure 9.4.4. Seawater temperature measured using Sea-Bird datasonde near the reef cap 

at WFGB in 2011 and 2012, and the historical long-term mean temperature 

from past monitoring periods. ........................................................................ 132 

Figure 9.4.5. Water samples taken at the surface, midwater, and on the reef cap at EFGB 

from 2002–2012. ............................................................................................ 135 

Figure 9.4.6. Water samples taken at the surface, midwater, and on the reef cap at WFGB 

from 2002–2012. ............................................................................................ 136 

Figure 10.4.1. Tropical species accumulation curve. ............................................................. 145

Figure 10.4.2. MDS plot displaying two-dimensional fish occurrence similarity between 

years and banks. ............................................................................................. 150 

Figure 10.4.3. MDS plot displaying two-dimensional fish density similarity between years 

and banks. ....................................................................................................... 151 

Figure 10.4.4. MDS plot displaying two-dimensional trophic guild density similarity 

between years and banks. ............................................................................... 153 

Figure 10.4.5. EFGB size distribution by trophic guild. ........................................................ 154 

Figure 10.4.6. WFGB size distribution by trophic guild........................................................ 155 

Figure 10.4.7. MDS plot displaying two-dimensional biomass similarity between years 

and banks. ....................................................................................................... 156 

Figure 10.4.8. FGB size distribution by trophic guild: (A) Herbivores, (B) Invertivores, 

(C) Piscivores, and (D) Planktivores. ............................................................. 157 

Figure 10.4.9. MDS plot displaying two-dimensional trophic guild similarity between 

years and banks. ............................................................................................. 158 

Figure 10.4.10. MDS plot displaying two-dimensional similarity between morning and 

afternoon surveys. .......................................................................................... 163 

Figure 10.4.11. Abundance-Biomass curves for (A) EFGB 2011, (B) WFGB 2011, (C) 

EFGB 2012, and (D) WFGB 2012, with average w values for all surveys at 

the year and location. ...................................................................................... 165 

Figure 10.4.12. Mean biomass (g/m2

) of the fish community at EFGB and WFGB from 

2006–2012. ..................................................................................................... 167 

Figure 10.4.13. Mean fish density (g/100m2) at EFGB and WFGB from 2002–2012. ........... 167 

Figure 11.4.1. Sea urchin and lobster densities at the FGB from 2004–2012. ...................... 174 

Figure 11.4.2. Two-dimensional MDS plot based on Bray-Curtis similarities comparing 

sea urchin and lobster densities at the FGB from 2004–2012. ....................... 175 
xvii 

LIST OF TABLES 

Table 2.1.1. Coordinates for EFGB and WFGB Study Site Permanent Mooring Buoys ..... 13 

Table 2.1.2. Cruise Dates at EFGB and WFGB for 2011 and 2012 ..................................... 13 

Table 3.3.1. Mean Percent Cover ± SE of Benthic Categories in Random Transects at 

EFGB and WFGB from 2011 and 2012 (listed from most to least abundant) . 24 

Table 3.3.2. Mean Percent Cover ± SE of Coral Condition Categories in Random 

Transects at EFGB and WFGB from 2011 and 2012 ....................................... 27 

Table 3.3.3. Results of ANOVA on Mean Percent Cover Estimates from Random 

Transects from 2011 and 2012 ......................................................................... 28 

Table 3.3.4. EFGB and WFGB Random Transect Data for Dominant Cover Categories ... 32 

Table 3.4.1. Percentage of Coral Cover on Living Reefs in the Western Atlantic and 

Caribbean Region ............................................................................................. 35 

Table 3.4.2. EFGB and WFGB Random Transect Data for Dominant Coral Cover ........... 38 

Table 4.3.1. Mean Percent Cover ± SE of Benthic Categories in Repetitive Quadrats at 

EFGB and WFGB in 2011 and 2012 (listed from most to least abundant) ...... 46 

Table 4.3.2. Mean Percent Cover ± SE of Coral Condition Categories in Repetitive 

Quadrats at EFGB and WFGB from 2011 and 2012 ........................................ 49 

Table 4.3.3. Results of ANOVA on Mean Percent Cover Estimates from Repetitive 

Quadrats from 2011 and 2012 .......................................................................... 50 

Table 4.3.4. EFGB and WFGB Repetitive Quadrat Data for Dominant Cover Categories 

from 1992–2012 ............................................................................................... 54 

Table 4.3.5. Mean Percent Cover ± SE of Benthic Categories in Repetitive Deep 

Stations at EFGB from 2011 and 2012, and at WFGB in 2012 (listed from 

most to least abundant) ..................................................................................... 58 

Table 4.3.6. Mean Percent Cover ± SE of Coral Condition Categories in Repetitive 

Deep Stations at EFGB from 2011 and 2012, and at WFGB in 2012 .............. 61 

Table 4.3.7. Results of ANOVA on Mean Percent Cover Estimates from EFGB 

Repetitive Deep Stations from 2011 and 2012 ................................................. 62 

Table 4.3.8. Results of ANOVA on Mean Percent Cover Estimates between EFGB and 

WFGB Repetitive Deep Stations in 2012 ......................................................... 62 

Table 4.3.9. Mean Percent Cover ± SE of Benthic Categories in Repetitive Deep 

Stations and Shallow Repetitive Quadrats at EFGB and WFGB from 2011 

and 2012 ........................................................................................................... 64 

Table 4.3.10. Results of ANOVA on Mean Percent Cover Estimates from Repetitive 

Deep Stations and Shallow Station Repetitive Quadrats from 2011 and 

2012 .................................................................................................................. 65 
xviii 

Table 4.3.11. EFGB and WFGB Repetitive Deep Station Data for Dominant Cover 

Categories from 2003–2012 ............................................................................. 66 

Table 4.3.12. Results of t-test on Percent Colony Change for Dominant Coral Species 

from Repetitive Quadrat Planimtery Analysis for 2011 and 2012 at EFGB 

and WFGB ........................................................................................................ 69 

Table 5.3.1. Comparable Lateral Growth Station Photographs from 2009–2012 ................ 78 

Table 5.3.2. Pseudodiploria strigosa Lateral Growth Stations and Percent of Margin 

Growing, Retreating, or Remaining Stable of Coral Tissue at EFB and 

WFGB from 2010–2011 and 2011–2012 ......................................................... 79 

Table 5.4.1. Historical Review of Pseudodiploria strigosa Lateral Growth Methods and 

Analyses Throughout the Monitoring Program ................................................ 82 

Table 6.3.1. Coral Growth at the FGB Determined from Cores Taken in 2012 .................. 93 

Table 9.2.1. Water Sampling Schedule, Depth, and Number of Samples Taken at EFGB 

and WFGB in 2011 and 2012 ......................................................................... 117 

Table 9.2.2. Standard USEPA Methods Used to Analyze Water Samples Taken at the 

FGB ................................................................................................................ 118 

Table 9.3.1. Summary of Sea-Bird Seawater Temperature Parameters from 2011–2012 . 119 

Table 9.3.2. Summary of Sea-Bird Salinity Parameters from 2011–2012 ......................... 121 

Table 9.3.3. Summary of HoboTemp Seawater Temperature Parameters from 2011–

2012 ................................................................................................................ 122 

Table 9.3.4. Summary of HoboTemp Seawater Temperature Parameters from 2011–

2012 at EFGB and WFGB Repetitive Deep Stations ..................................... 122 

Table 9.3.5. Summary of Opportunistic YSI Seawater Temperature Vertical Profiles 

from 2011–2012 at EFGB and WFGB ........................................................... 124 

Table 9.3.6. Chl-a Concentrations in Water Samples at EFGB and WFGB from 2011–

2012 ................................................................................................................ 125 

Table 9.3.7. Concentrations of Ammonia in Water Samples at EFGB and WFGB from 

2011–2012 ...................................................................................................... 126 

Table 9.3.8. Concentrations of Nitrate in Water Samples at EFGB and WFGB from 

2011–2012 ...................................................................................................... 127 

Table 9.3.9. Concentrations of TKN in Water Samples at EFGB and WFGB from 2011–

2012 ................................................................................................................ 126 

Table 10.4.1. Complete Species List for 2011 and 2012 at EFGB and WFGB Showing 

Abundance per 100 m2

 by Year and Bank ..................................................... 142 

Table 10.4.2. Species and Family Richness by Year and Bank ........................................... 145 

Table 10.4.3. Species Richness within Families between Years and Banks, and between 

all Surveys ...................................................................................................... 146 

Table 10.4.4. Shannon-Wiener Diversity and Evenness Indices for each Bank and Year ... 147 
xix 

Table 10.4.5. Percent Sighting Frequency for Species by Year and Bank, Including 

Sighting Frequency for All Surveys Conducted during the 2011–2012 

Reporting Period ............................................................................................. 147 

Table 10.4.6. Species Richness within Trophic Guilds between Years and Banks, and 

between all Surveys ........................................................................................ 152 

Table 10.4.7. Average Density per 100 m2 of Individuals from each Trophic Guild by 

Year and Bank, ± Standard Deviation ............................................................ 152 

Table 10.4.8. Total and Average Biomass, in g/m2, by Year and Bank, ± Standard 

Deviation ........................................................................................................ 155 

Table 10.4.9. Average Biomass, in g/m2, for each Trophic Guild by Year and Bank and 

between all Surveys, ± Standard Deviation .................................................... 157 

Table 10.4.10. Percent Contribution of Each Species to the Average Biomass of Each 

Trophic Guild ................................................................................................. 159 

Table 10.4.11. Number of Surveys Conducted During Various Times of the Day ............... 163 

Table 10.4.12. ANOSIM Results for Pair-Wise Comparisons of Creole Wrasse Density in 

Each Time Bracket ......................................................................................... 164 

Table 10.4.13. Average w values by Bank and Year, ± Standard Deviation ......................... 165 

Table 10.4.14. Average w Values by Bank and Year for the Grouper Family ...................... 166 

Table 10.4.15. Average w Values by Bank and Year for the Snapper Family ...................... 166 

Table 10.5.1. Percentage of Fishes Observed in the Listed Families at Reefs around the 

Gulf of Mexico and the Caribbean Region .................................................... 170 

Table 11.4.1. Number of Individual Sea Urchins and Lobsters Observed During Surveys 

in 2011 and 2012 ............................................................................................ 174 
xxi 

LIST OF ABBREVIATIONS 

AGRRA Atlantic and Gulf Rapid Reef Assessment 

ANOSIM Analysis of similarity 

ANOVA Analysis of variance 

BOEM Bureau of Ocean Energy Management 

BOEMRE Bureau of Ocean Energy Management, Regulation and Enforcement 

CCMA Center for Coastal Monitoring and Assessment 

CFB Concentrated fish biting 

CFR Code of Federal Regulations 

CPCe Coral Point Count with Microsoft® Excel® Extensions 

CRCP Coral Reef Conservation Program 

CREIOS Coral Reef Ecosystem Integrated Observing System 

CSA Continental Shelf Associates

CT Computerized tomography 

CTB Crustose Coralline Algae, Fine Turf Algae, and Bare Rock 

EA Environmental Assessment

EFGB East Flower Garden Bank 

ENSO El Niño Southern Oscillation 

FGB Flower Garden Banks (East and West Flower Garden Banks combined) 

FGBNMS Flower Garden Banks National Marine Sanctuary 

GOMEX Gulf of Mexico 

GREAT Gulf Reef Environmental Action Team 

IFB Isolated fish biting 

IMO International Maritime Organization 

IUCN International Union for Conservation of Nature 

JMP "Jump" statistical software®

MASC Montastraea annularis Species Complex 

MDS Multidimensional scaling

MMS Minerals Management Service 

MSD Marine sanitation device

NAZ No Activity Zone

NEPA National Environmental Policy Act 

NESDIS National Environmental Satellite Data and Information Service 

NIH National Institute of Health 

NOAA National Oceanic and Atmospheric Administration 

NOS National Ocean Service 

NRDA Natural Resource Damage Assessment 

OASC Orbicella annularis species complex 

OCS Outer Continental Shelf 
xxii 

ONMS Office of National Marine Sanctuaries 

PAR Photosynthetically active radiation 

PBSJ Post, Buckley, Schuh & Jernigan, Inc. 

PRIMER-E PRIMER® Enterprises 

PSU Practical salinity units

QA/QC Quality Assurance/Quality Control 

R/V Research vessel 

RDT Roving diver technique 

SCUBA Self-contained underwater breathing apparatus 

SD Standard deviation

SE Standard error

SIMPER Similarity percentage

SOW Scope of Work

SPMD Semipermeable membrane devices 

TAMU Texas A&M University 

TAMU-CC Texas A&M University Corpus Christi 

TAMUG Texas A&M University Galveston 

TKN Total Kjeldahl Nitrogen 

USA U.S. of America

USCG U.S. Coast Guard 

USDOI U.S. Department of Interior 

USEPA U.S. Environmental Protection Agency 

WFGB West Flower Garden Bank 

YSI Yellow Springs Instrument Company 
xxiii 

EXECUTIVE SUMMARY 

In the 1970s, because of concern about potential impacts of offshore oil and gas development, 

the Department of Interior (DOI) (initially through the Minerals Management Service, now the 

Bureau of Ocean Energy Management) started monitoring East and West Flower Garden Banks 

(EFGB and WFGB), which are now part of the Flower Garden Banks National Marine Sanctuary 

(FGBNMS). The purpose was to establish baseline data and determine if these reefs were 

impacted by nearby oil and gas exploration and production activities. In 1988, DOI established a 

long-term monitoring program to evaluate the potential ongoing impacts of oil and gas 

development to EFGB and WFGB. The long-term monitoring effort evaluates changes in living 

coral and benthic community cover, coral growth rates, reef fish population dynamics, water 

quality, and other indices of reef vitality within designated study sites. Though many coral reefs 

in the western Atlantic and Caribbean region have experienced significant declines in coral 

cover, the reefs of EFGB and WFGB support healthy coral and fish assemblages. Through a 

continued interagency agreement, this program is of significant interest to both NOAA and 

BOEM, who share responsibility of protecting and monitoring these important marine resources. 

In over 25 years of continuous monitoring, the coral reefs of EFGB and WFGB have maintained 

levels of coral cover above 50% and have suffered minimally from hurricanes, coral bleaching, 

and disease outbreaks; they support relatively diverse and abundant fish populations and other 

vertebrate and invertebrate species. No significant long-term changes have been detected in coral 

cover or coral diversity at the Flower Garden Banks (FGB, East and West Flower Garden Bank 

combined) since 1988 and likely not since the first measurements were made in the early 1970s; 

however, macroalgae cover has been increasing since 1999. During the 2011–2012 monitoring 

period, analyses indicated that coral cover at EFGB and WFGB averaged approximately 56%. 

Results of the 2011–2012 monitoring efforts illustrate the continued stability of the coral 

assemblage and associated fish populations of the FGB when compared to other reefs in the 

Caribbean. Random transect results revealed mean coral cover within the study site at EFGB to 

be 57% in 2011 and 52% in 2012. Mean coral cover at WFGB in 2011 was 60% and 55% in 

2012. These results are consistent with previous monitoring efforts of coral cover above 50% at 

the FGB highlighting the coral stability at the study site since the start of the monitoring 

program. 

Results of the random transect data indicate that Orbicella franksi was the principal component 

of mean percent coral cover at both banks. Mean cover of Orbicella franksi at EFGB was 

estimated at 26% in 2011 and 26% in 2012. At WFGB, mean cover was 24% in 2011 and 26% in 

2012. Pseudodiploria strigosa was the next most abundant species during this period, with 6% at 

EFGB in 2011 and 8% in 2012. WFGB estimates were 12% and 9% for the two years. The 

importance of the FGB, in terms of the Atlantic coral reef system as a whole, has been 

substantially elevated because the NOAA Fisheries Endangered Species Act lists all coral under 

the Orbicella annularis species complex as threatened; all are found at the FGB. 

In 2011 and 2012, macroalgae mean percent cover was more abundant than crustose coralline 

algae, fine turf algae, and bare rock (abbreviated as Crustose/Turf/Bare or CTB), ranging from 

approximately 30–38% at EFGB and 29–31% at WFGB. Despite continued stability in mean 

coral cover, macroalgae mean cover has been increasing since 1999. The most dominant 
xxiv 

components of macroalgal cover were fleshy algae, Dictyota spp., and Lobophora variegata. 

CTB was the second-ranked non-coral category of mean substratum percent cover, ranging from 

approximately 9–12% at EFGB and 10–12% at WFGB from 2011–2012. Mean sponge cover 

continues to be extremely low at both banks (less than 1%). An ANOVA and ANOSIM revealed 

that no significant differences between sites or years occured at EFGB and WFGB, this makes 

the banks similar in terms of benthic composition. 

Sclerochronology was used to measure the accretionary extension rates of Orbicella faveolata

coral cores. Annual extension of Orbicella faveolata at EFGB averaged 6.5 mm/year (sample 

range = 4.6–9.6 mm/year). At WFGB, annual growth averaged 5.6 mm/year (range = 3.3–10.3 

mm/year). Extension rates did not differ significantly between banks. 

Repetitive qudarats stations were photographed in 2011 and 2012 to monitor changes in 

specific coral reef locations over time. Mean coral cover in the repetitive quadrats averaged 

approximately 63% for both banks in all years. Macroalgae and CTB cover showed 

reciprocal patterns between banks. An ANOVA on the proportional cover of sponge and CTB 

showed significant differences between both bank and year. The incidences of bleaching, 

paling, and fish biting were low (ranging from 0.00–0.63% of area assessed) and there was 

little evidence of coral disease. The coral assemblages remained consistent at both banks, 

and the dominant corals were Orbicella franksi and Pseudodiploria strigosa. 

At repetitive photostations in 32–40 m depths, mean coral cover ranged between 72–76% in 

2011 and 2012. Orbicella franksi and Montastraea cavernosa were the dominant species in 

this depth range. Macroalgae averaged 19% and CTB averaged 7%. 

Seawater temperature and salinity were recorded at EFGB and WFGB using Sea-Bird 37-SMP 

MicroCAT datasondes from 2011–2012. During the 2011–2012 period, seawater temperature at 

EFGB ranged from 18.62°C to 30.49°C from 2011–2012, and at WFGB from 17.92°C to 

30.55°C. High seawater temperatures were observed during the late summer months, exceeding 

the 30°C coral bleaching threshold; however, because only limited time was spent above this 

temperature, the risk of bleaching was low. Though most Chl-a and nutrient concentrations were 

below detectable limits, total Kjeldahl Nitrogen (TKN) was detected in all water samples 

collected at the banks in 2011, with concentrations ranging from 1.3–45.2 mg/l (above the 0.55 

mg/l detection limit), and in 50% of the samples collected in 2012. 

Fish surveys were conducted using a modified Bohnsack and Bannerot (1986) method in 2011 

and 2012. Pomacentridae, Labridae, and Serranidae were the dominant fish families at both 

banks. Diversity varied between banks and years, with the greatest diversity occurring at WFGB 

in 2012. The most frequently sighted species during this study period were brown chromis 

(Chromis multilineata), closely followed by Spanish hogfish (Bodianus rufus), and bluehead 

(Thalassoma bifasciatum). Mean fish density (abundance per 100 m2

) was highest at WFGB in 

2012 and lowest at EFGB in 2012. 

Invertivores were the dominant fish guild; Pomacentridae and Labridae represented the largest 

density. The size-frequency distributions of invertivores were non-normally distributed, and the 

majority of individuals were small damselfish. The greatest mean biomass was seen in 2011 at 
xxv 

WFGB, where the piscivores possessed the highest mean biomass for all surveys, with over 50% 

of total biomass. Following the pattern of coral species present at the FGB (low diversity 

compared to Caribbean reefs, but high coral cover), the fish assemblages reflect a similar trend 

of low diversity and high abundance (Pattengill-Semmens and Gittings 2003). Although no 

lionfish (Pterois spp.) were observed within the fish surveys conducted, in 2012 lionfish were 

sighted within the study site after first being observed to invade sanctuary waters in 2011. 

Sea urchin surveys documented continued low densities of Diadema antillarum at WFGB in 

2011 (3.75 per 100 m2) and 2012 (12.5 per 100 m2). No sea urchins were observed at EFGB. 

These populations have not recovered to pre-1984 levels, which were at least 140 per 100 m2 at 

EFGB and 50 per 100 m2 at WFGB (Gittings et al. 1998). 

An ongoing monitoring program at the FGB is critical to ensure data are available to disinguish 

among the drivers of ecosystem variation in the northern Gulf of Mexico. The relatively stable 

conditions on the reef since the beginning of the monitoring program, combined with the 

historical data collection and the proximity to oil and gas development, makes the FGB an ideal 

sentinel site for continued support of a long-term monitoring program. Problems that affect coral 

reefs throughout the region, including land-based sources of pollution and disease have not had a 

major impact at the FGB, partially due to their relative isolation and depth; however, increased 

incidence of bleaching events, algal cover, and invasive species, are reasons for increased 

vigilance and perhaps concern for the future of the resources. Continued monitoring will 

document long-term changes in condition and will be useful for management decisions and 

future research focused on the dynamics of the robust benthic communities and the fish 

populations they support. 
1 

CHAPTER 1.0: INTRODUCTION 

1.1. CORAL REEF MONITORING AT EAST AND WEST FLOWER GARDEN

BANKS

The biotic assemblages of East and West Flower Garden Banks (EFGB and WFGB), part 

of Flower Garden Banks National Marine Sanctuary (FGBNMS), constitute a healthy 

community of coral and fish assemblages (Gittings et al. 1992; CSA 1996; Dokken et al. 

1999, 2001, 2003; Pattengill-Semmens and Gittings 2003; Precht et al. 2006; Zimmer et al. 

2010; Johnston et al. 2013). Although coral species richness is lower at the Flower Garden 

Banks (FGB) than at other Caribbean reefs, 31 species of scleractinian corals have been 

documented (Schmahl et al. 2008). In more than 25 years of continuous monitoring, the 

coral reefs of EFGB and WFGB have maintained high levels of coral cover compared to 

reefs in the Caribbean region; suffered minimally from hurricanes, coral bleaching and 

disease outbreaks; and supported relatively diverse and abundant fish and invertebrate 

populations (Pattengill-Semmens and Gittings 2003). No significant long-term changes 

have been detected in coral cover or coral diversity in coral monitoring study sites at EFGB 

and WFGB from 1988–2010 (Zimmer et al. 2010; Johnston et al. 2013), and probably not 

since the first measurements were taken in the mid-1970s (Gittings, 1998). The Caribbean has 

experienced declines in zooxanthellate scleractinian coral cover (Gardner et al. 2003) and 

subsequent increases in macroalgal cover; however, the coral cover at EFGB and WFGB 

has remained above 50% in the northwest Gulf of Mexico. These reefs, therefore, represent 

a natural laboratory for understanding factors influencing stability and change in reef systems. 

The importance of EFGB and WFGB as representative western Atlantic coral reefs has 

been substantially elevated by the regional decline of corals, as well as by the listing of all 

coral under the Orbicella annularis species complex as threatened (79 FR 

53851). Consequently, the risk of loss would be elevated for FGBNMS in the event of a 

severe industrial accident or other significant change in environmental conditions (Gittings 

et al. 1992; ONMS 2008). 

The long-term monitoring program was initiated in 1988 by the Department of the 

Interior’s Minerals Management Service (now the Bureau of Ocean Energy Management 

[BOEM]) to ensure protective measures regulating potential impacts of offshore oil and gas 

development in the northwestern Gulf of Mexico were effective. Gittings et al. (1992) 

established a single, 100 x 100 m (10,000 m2

) study site at both EFGB and WFGB to 

monitor benthic community structure from 1988 to 1991 using coral cover, relative 

dominance, species diversity, evenness, accretionary and encrusting growth rates, and 

water quality parameters as potential indicators of reef health. Comparisons between their 

1988–1991 results and those of previous studies from 1978–1982 (Rezak et al. 1985) 

showed no significant differences in any of the parameters, which suggests some degree of 

ecological stability over the period examined. During this time, mean coral cover was 

approximately 50% and dominated by the Montastraea annularis species complex (25%), 

now known as the Orbicella annularis species complex, and Diploria strigosa (8%), now 

known as Pseudodiploria strigosa (Gittings et al. 1992). Gittings et al. (1992) considered 

spills from oil tankers, discharges of mud and drill cuttings during oil and gas exploration 
2 

and production, noise from seismic surveys, and accidents on platforms leading to spills to 

be the greatest localized threats to these reefs. 

No significant changes in coral community structure were reported between 1992–1995 by 

CSA (1996). However, variation in mean percent cover of individual coral species was 

detected between banks and among sampling years in 1992, 1994, and 1995. Minor 

occurences of coral bleaching were documented in individual colonies in repetitive 

photostations in 1992 (91 colonies) and 1994 (24 colonies), and 1995 (429 colonies) was 

the first main bleaching event documented at the FGB coinciding with seawater 

temperatures in excess of 30°C for prolonged periods (Hagman and Gittings 1992; Dokken 

et al. 1999, 2001, 2003). Montastraea cavernosa and Millepora alcicornis were the species 

most affected by bleaching, but post-bleaching mortality rates were low at 0.2%–2.8% 

(1992–1995). The small-scale spatiotemporal variation reported by CSA did not appear to 

affect long-term landscape-scale trends in coral cover or composition. 

Dokken et al. (1999, 2003) continued the monitoring effort from 1996 through 2001 and 

documented no significant changes in coral growth or condition at the 10,000 m2

 study 

sites at EFGB and WFGB; however, macroalgae levels increased ranging from 6.1–24.7% 

at EFGB and 0.1–25.4% at WFGB. Biodiversity inventories were conducted for algae and 

mollusks: 72 species of algae were documented and 100 new species were added to the 

catalog of 4,294 mollusks found at the FGB (Dokken et al. 2001, 2003). Fish assemblages 

were also documented and 177 species were identified (Pattengill 1998). 

Using the Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol in 1999, 

Pattengill-Semmens and Gittings (2003) observed mean coral cover of approximately 50% 

at 20–28 m, dominated by large coral colonies (mean diameter 81–93 cm), with a level of 

partial colony mortality (recent and long-dead portions of colonies) of only 13%. In 

concordance with earlier findings, turf was the dominant functional group of algae, 

whereas macroalgae accounted for less than 10% cover (Pattengill-Semmens and Gittings 

2003). 

Continued monitoring of the study sites in 2002 and 2003 by Precht et al. (2006) highlighted 

the stability of the coral reef communities since the start of monitoring efforts. Mean coral 

cover was approximately 50% at both banks during those years, macroalgae cover averaged 

12%, and no significant diseases were detected. The relative dominance of coral species also 

remained consistent with past findings. Repetitive quadrat data from 2002 and 2003 revealed 

low prevalence of paling and bleaching (<0.61%) and no evidence of disease. Planimetry 

results showed an increase in surface area of selected corals at both banks. Fish population 

surveys were added to the long-term monitoring protocol in 2002 and sea urchin (Diadema 

antillarum) and lobster (Panulirus spp.) abundance remained low. 

Zimmer et al. (2010) continued the monitoring effort from 2004 through 2008 and 

documented the relative stability of the coral reef community and associated fish 

populations at the monitoring study sites at EFGB and WFGB. Mean coral cover averaged 

over 50% at both banks, macroalgae cover increased to an average of 18%, and the 

Orbicella annularis species complex remained the dominant component of coral cover. 
3 

On September 23, 2005 Hurricane Rita (Category 3 on the Saffir-Simpson Index) passed 

approximately 93 km from EFGB on its route north to the mainland of the United States. 

Two months later, Precht et al. (2008a) conducted a post-hurricane assessment and 

reported that approximately 10% of the coral in repetitive quadrat stations at EFGB were 

bleached. This was the highest level of bleaching reported for the FGB since the bleaching 

event of 1995; however, there was no evidence of coral disease in any of the repetitive 

quadrats analyzed from 2004 through 2008. It should be noted that it was known the FGB 

bleaching event was ongoing before the hurricane, because 2005 was a severe bleaching 

year throughout the Caribbean (Eakin et al. 2010). After Hurricane Rita passed through the 

Gulf of Mexico, the seawater temperature at the FGB dropped considerably, which may 

have helped counteract the bleaching event. 

On September 12, 2008, Hurricane Ike (Category 3 on the Saffir-Simpson Index) passed 

directly over EFGB. To monitor changes in coral reef community structure due to the passage 

of Hurricanes Rita and Ike, repetitive 8 m2 photo quadrats and perimeter videos of the study 

sites were collected in November 2005 and November 2008, respectively, and assessed for 

hurricane damage. The results of the post-hurricane cruise conducted in November 2005 

were published in a separate report (Precht et al. 2008). An estimated total area of 

approximately 2.3 m2 of coral was missing from the study-site repetitive quadrat stations 

between June 2007 and November 2008 at EFGB and WFGB, most likely due to 

Hurricane Ike. The greatest loss in terms of both the number of missing coral colonies 

and the total loss in area of coral cover occurred at EFGB. Hurricane impacts (i.e., 

dislodged colonies of Pseudodiploria strigosa) were observed only in videos taken along 

the perimeter of the study site at EFGB. No obvious hurricane impacts were observed 

along perimeter lines at WFGB. The observed hurricane impacts were likely an 

underestimate of the actual hurricane damages because 1) only a portion of the perimeter 

surveys were comparable between June 2007 and November 2008 due to the loss of some 

corner locations and shifts in line placement, and 2) the 2008 perimeter video was recorded 

at an angle of 90o to the substrate due to operator error (rather than at 45o as in previous 

surveys), providing a smaller area of view and fewer coral colonies for comparison. 

Continued monitoring of the study sites in 2009 and 2010 was conducted by FGBNMS in 

partnership with BOEM. Johnston et al. (2013) highlighted the continued relative stability 

of the coral assemblage at the study site and associated fish populations. Random transect 

results revealed the mean coral cover within study sites at both banks from 2009 to 2010 to 

be approximately 57%. Macroalgae cover was significantly higher at EFGB (32%) than 

WFGB (26%). High seawater temperatures were observed during the late summer months 

of 2010, exceeding the 30°C coral bleaching threshold; however, minimal bleaching was 

observed within the study sites during sampling as signs of bleaching did not manifest until 

late fall in 2010. Fish populations continued to be robust; however, Diadema antillarum and 

Panulirus spp. abundance remained low. 

April 20, 2010 marked the beginning of the Deepwater Horizon explosion, oil spill, and 

subsequent response; an estimated 53,000 barrels per day escaped from the well before it 

was capped. NOAA acted as the lead science support agency to the U.S. Coast Guard 

during the spill response. The spill site was approximately 520 km from EFGB, but 
4 

because of the size of the spill, the potential for impact to the resources of the sanctuary 

was of great concern. As part of the Natural Resource Damage Assessment (NRDA) 

activities, FGBNMS personnel were assigned to the shallow and deep water coral response 

groups. In addition, semi-permeable membrane devices (SPMDs) were deployed at EFGB 

and WFGB, and at Stetson and Sonnier Banks, and total petroleum hydrocarbons were 

added to the suite of analysis parameters for the May 2010 water quality sampling at EFGB 

and WFGB. 

Though the oil spill caused damage to wildlife and marine habitats in other areas of the 

Gulf of Mexico, no visible oil or immediate oil-related impacts were observed in or near 

the FGBNMS. Total petroleum hydrocarbon concentrations were undetectable (<5 mg/L) 

in all water samples collected at the surface, midwater, and reef cap at both EFGB and 

WFGB. Nevertheless, the long-term monitoring data would have provided a valuable 

baseline from which impacts could have been detected, if they occurred. 

1.2. FLOWER GARDEN BANKS NATIONAL MARINE SANCTUARY IN THE GULF

OF MEXICO

1.2.1. Habitat Description 

East and West Flower Garden Banks, located in the northwestern Gulf of Mexico, are part 

of a discontinuous arc of reef environments along the outer continental shelf (Rezak et al. 

1985; Figure 1.2.1). These coral reef-capped banks are the largest Holocene carbonate 

accumulations in the northwestern Gulf of Mexico and the northernmost coral reefs in 

North America (Bright et al. 1984; Bright et al. 1985). Although coral and non-coral 

dominated communities exist on neighboring banks (e.g., Bright Bank, Geyer Bank, 

Sonnier Bank, Stetson Bank, McGrail Bank) and on the Florida Middle Grounds in the 

eastern Gulf, the reefs of Lobos-Tuxpan Flora and Fauna Protected Area near Cabo Rojo, 

Mexico are the nearest shallow-water coral reefs in the Gulf of Mexico. 

The large-scale topographic features of the FGB were created by geologic activity 

associated with salt diapirs of the Jurassic Louann Formation and subsequent loading and 

uplifting of sedimentary rocks (Rezak 1981). Many such diapirs exist in the northern Gulf 

of Mexico and dozens form substantial elevated banks. The caps of some of the banks 

extend into the photic zone in clear oceanic waters, where conditions are ideal for 

colonization by species of corals, algae, invertebrates, and fish typical of coral reefs found 

in the Caribbean and western central Atlantic (Figure 1.2.2 and Figure 1.2.3). Although 

coral species richness is lower at the FGB than on most Caribbean reefs, 31 species of 

scleractinian corals have been documented at the FGB (Schmahl et al. 2008) and 298 

species of tropical Atlantic fish have been reported sanctuary wide, including the deepwater 

communities (FGBNMS 2013). Salinity conditions at the FGB range from 34 to 36 PSU, 

with water temperatures ranging from 18°C (in mid-February) to 30°C (in late August). 

Water clarity across both banks is more then sufficient to transmit light to benthic 

photosynthetic organisms (40 m or more vertical visibility). 
5 

Figure 1.2.1. Map of EFGB and WFGB in relation to the Texas-Louisiana continental shelf and 

other topographic features of the northwestern Gulf of Mexico (NOAA/FGBNMS). 

1. Stetson Bank, 2. Applebaum Bank, 3. Claypile Bank, 4. Coffee Lump Bank, 5. West Flower

Garden Bank, 6. Horseshoe Bank, 7. East Flower Garden Bank, 8. MacNeil Bank, 9. 29 Fathom 

Bank, 10. Rankin Bank, 11. 28 Fathom Bank, 12. Bright Bank, 13. Geyer Bank, 14. Elvers Bank, 

15. McGrail Bank, 16. Bouma Bank, 17. Sonnier Bank, 18. Rezak Bank, 19. Sidner Bank, 20.

Parker Bank, 21. Alderdice Bank, 22. Sweet Bank, 23. Fishnet Bank, 24. Jakkula Bank, 25. Ewing 

Bank, 26. Diaphus Bank. Red lines represent sanctuary boundaries. 

1.2.2. East and West Flower Garden Banks 

East Flower Garden Bank (27o 54.5’ N, 93o 36.0’ W) is a pear-shaped dome located 

approximately 193 km (120 mi) southeast of Galveston, Texas. EFGB is 8.7 by 5.1 km in 

size, sloping from its shallowest point at 17 m to the terrigenous mud seafloor at a depth of 

100–120 m. The eastern and southern edges of the bank have steep slopes, whereas the 

northern and western edges descend more gently (Figure 1.2.2). West Flower Garden Bank 

(27o 52.4’ N, 93o 48.8’ W) is an oblong-shaped dome located 20 km west of EFGB and 172 

km southeast of Galveston. It is 11.0 by 5.0 km in size (Figure 1.2.3). The WFGB study 

site is located on the eastern knoll and is 18 m at its shallowest. Coral species diversity at 

both banks is low; 31 species from 18 genera are represented (Schmahl et al. 2008), 

compared to 67 species found on some Caribbean reefs (Goreau and Wells 1967). Shallowwater gorgonians and live acroporids have not been reported at the FGB. However, one 

colony of Acropora palmata was discovered in 2003 at WFGB, but is in decline due to 

stressors, such as damselfish predation, algal growth, and possible disease. Another living 

colony of Acropora palmata was discovered at EFGB, southeast of the study site in 2005 

and has a resident damselfish and minimal tissue loss (Zimmer et al. 2006). 
6 

Figure 1.2.2. Bathymetric map of EFGB. 

EFGB is 8.7 by 5.1 km in size, capped by 1.43 sq. km of coral reef rising 17 m to the surface 

(NOAA/FGBNMS). 
7 

Figure 1.2.3. Bathymetric map of WFGB. 

WFGB is 11.0 by 5.0 km, capped by 0.42 sq km of coral reef starting 18 meters below the 

surface (NOAA/FGBNMS). 

Five habitat zones have been delineated at EFGB and WFGB. This zonation scheme was 

updated by Schmahl et al. (2008) and includes the coral reef zone, the coral community 

zone, the coralline algal zones (which consist of coralline algal reefs and/or algal nodules), 

the deep coral zone, and the soft bottom zone. All monitoring at both banks was conducted 

within the coral reef zone, which is the shallowest portion of the bank, referred to as “the 

reef cap.” 
8 

1.3. BOEM AND FGBNMS PROTECTIVE MEASURES

Oil and gas activity in the vicinity of FGBNMS has been ongoing since the 1970s. The 

former Minerals Management Service (MMS) of the U.S. Department of the Interior (DOI) 

has regulated the development of the oil and gas industry on the Gulf of Mexico outer 

continental shelf. In 2010, MMS was reorganized and renamed the Bureau of Ocean 

Energy Management, Regulation and Enforcement (BOEMRE). In October 2011, the 

agency was again reorganized and the agency partnering in this monitoring effort is now 

called the Bureau of Ocean Energy Management (BOEM). 

The first coral reef assessment of the FGB took place at WFGB in 1972 (Bright and 

Pequegnat 1974). In 1973, BOEM (then the Bureau of Land Management) conducted a 

program of protective activities at the FGB coral reefs and sponsored numerous studies of 

the banks. The Topographic Features Stipulation (since 1973) was designed to protect 

sensitive biological resources in the northwestern Gulf of Mexico, from the adverse effects 

of routine oil and gas activities (USDOI, MMS 2002) and, in particular, from the discharge 

of drilling effluents. Since 1983 the stipulation has protected the biota of the FGB from 

physical damage associated with oil and gas activities including anchoring and rig 

emplacement, and potential toxic and smothering effects from drilling muds and cuttings 

discharges (USDOI, MMS 2002). The Stipulation defines a No Activity Zone (NAZ) 

around each of the banks using boundaries based on the “1⁄4, 1⁄4, 1⁄4 system”, where lease 

blocks are divided into smaller sections by successively breaking each section into quarters 

(USDOI, MMS 1998). The boundary of the NAZ overlaps the 100–120 m isobaths at 

WFGB and the 100–130 m isobaths at EFGB. No oil or gas structures, drilling rigs, 

pipelines, or anchoring are allowed within the NAZ. The Stipulation also defines a “4 Mile 

Zone” outside of the NAZ, within which operators are to shunt all drill cuttings and drilling 

fluids to within 10 m of the seafloor. Note that the FGB are the only topographic features 

with a NAZ defined by the 1⁄4, 1⁄4, 1⁄4 system. The NAZ of all other BOEM protected banks 

follow defined isobaths surrounding the bank. 

In addition to the protections provided by BOEM, the FGB were designated as an U.S. 

National Marine Sanctuary in 1992 (Code of Federal Regulations, 15 CFR Part 992, 

Subpart L, Section 922.120), and Stetson Bank was later added in 1996. In April 2012, 

FGBNMS released an updated Management Plan, because the original management plan 

for FGBNMS dated back to its designation (USDOC NOAA ONMS 2012). Detailed 

FGBNMS regulations can be found in Volume II Appendix 1 of this report. Though certain 

exceptions exist for oil and gas operations, FGBNMS regulates, restricts and prohibits: 

(1) anchoring or mooring of all vessels within the sanctuary boundaries; 

(2) discharge of any material or matter within the sanctuary boundaries; 

(3) any alteration of the seabed within the sanctuary boundaries; 

(4) any injury or removal or attempt of injury or removal of any living or non-living 

sanctuary resource; 

(5) taking of marine mammals and sea turtles; 

(6) possessing or using within the sanctuary boundaries any fishing gear except 

conventional hook and line gear; and 
9 

(7) possessing or using explosives within the sanctuary boundaries or releasing 

electrical charges within the sanctuary boundaries. 

In July of 2001, the U.S. delegation to the International Maritime Organization (IMO), 

submitted a proposal to ban anchoring in FGBNMS for vessels greater than 30.5 m (100 ft). 

The IMO, out of concern for impacts to corals, modified the proposal to prohibit all 

anchoring, but vessels 30.5 m (100 ft) and under would be allowed to moor using existing 

FGBNMS mooring buoys. The new international measure also ensured that no-anchoring 

zones are marked on all charts internationally. Code of Federal Regulations, 15 CFR Part 

922.122. amended FGBNMS regulations to align with IMO no-anchor rule within the 

sanctuary. 

From 1988 to 1995, BOEM monitored the FGB coral reefs to detect any incipient changes 

that may be caused by oil and gas activities, as well as by other disturbances (Gittings et al. 

1992; Gittings 1998). From 1996 until 2008, FGBNMS and BOEM partnered to continue 

the long-term monitoring of the FGB through a competitive contract. Since 2009, 

FGBNMS has conducted the long-term monitoring and BOEM continues to support half of 

the associated costs for the monitoring effort through an interagency agreement with 

FGBNMS. The decision to take on this contract in-house was driven mainly by the 

acquisition of the FGBNMS research vessel (R/V) Manta. FGBNMS has also built up a 

team of NOAA scientific divers and researchers to conduct both the field work and analysis 

of the monitoring data. 
11 

CHAPTER 2.0: STUDY SITES 

2.1. STUDY SITE METHODS

EFGB and WFGB are located roughly 190 km offshore in water depths of 17 m and 

greater. The monitoring effort was conducted from the NOAA R/V Manta. Data was 

collected within 100 x 100 m (10,000 m2 or 1 hectare) study sites located at each bank. The 

benthos (with an emphasis on corals and algae) was examined along random 10 m transects 

and stationary repetitive photoquadrats. Sclerochronology was used to document the 

accretionary growth rate of specific coral colonies, and photography was used at permanent 

stations to monitor the lateral growth of corals. General aspects of coral condition were 

documented along study sites perimeter lines at EFGB and WFGB. During each annual 

monitoring cruise, observations of general coral reef health within the study sites, and 

notable biological and oceanographic events were qualitatively assessed and documented. 

Water quality was assessed to characterize the reef cap and water column environment of 

the FGB. Fish surveys were conducted at randomly located sites and sea urchin and lobster 

surveys were conducted along the study site perimeter lines. 

2.1.1. 10,000 m2 Study Sites 

Water depth at EFGB ranges from 17 m to 134 m and 18 m to 140 m at WFGB (Figures 

2.1.1 and 2.1.2). For the long-term monitoring program, data were collected within 10,000 

m2 study sites (hereafter referred to as “study sites”) located on the shallow reef cap at each 

bank. Within the locations of the study sites, depths range between 17 m to 27m at EFGB 

and 18 m to 25 m at WFGB. Divers installed reference lines to mark the perimeters of the 

study sites and the north-south and east-west centerlines (hereafter referred to as the 

“crosshairs”). Establishment of the perimeter and crosshairs divided each site into four 25 x 

25 m quadrants (Volume II Appendix 2). The lines aided divers in orientation-navigation 

through the study site and they allowed for efficient completion of monitoring tasks. 

Established in 1988, the study sites are marked by permanent mooring buoys: FGBNMS 

permanent mooring No. 2 at EFGB and mooring No. 5 at WFGB (Figure 2.1.1, Figure 

2.1.2, and Table 2.1.1). Data were collected within the study sites at EFGB and WFGB in 

2011 and 2012 (Table 2.1.2). 

Within each study site at EFGB and WFGB, permanent monitoring stations were established 

at the beginning of the monitoring program. There are two types of permanent monitoring 

stations within the study sites: 1) lateral growth stations on Pseudodiploria strigosa colonies, 

which are marked by two short rods per station; and 2) repetitive quadrats, the centers of 

which are marked by 0.5 m tall rods. Historically, 40 repetitive quadrats and 60 lateral growth 

stations were maintained at each bank. The repetitive growth stations have been maintained 

over time and the lateral growth stations have been replaced as stations become overgrown. 
12 

Figure 2.1.1. Bathymetric map of EFGB with long-term monitoring study site (LTM site), 

mooring buoy, and datasonde locations (NOAA/FGBNMS). 
13 

Figure 2.1.2. Bathymetric map of WFGB with the long-term monitoring study site (LTM 

site), mooring buoy, and datasonde locations (NOAA/FGBNMS). 

Table 2.1.1. 

 

Coordinates for EFGB and WFGB Study Site Permanent Mooring Buoys 

EFGB Mooring No. 2 WFGB Mooring No. 5 

Year Lat (DDM) Long (DDM) Year Lat (DDM) Long (DDM) 

2011 27°54.319 N 93°35.490 W 2011 27°52.519 N 93°48.889 W 

2012 27°54.516 N 93°35.831 W 2012 27°52.501 N 93°48.918 W 

Table 2.1.2. 

 

Cruise Dates at EFGB and WFGB for 2011 and 2012 

EFGB WFGB 

11-12 July 2011 13-14 July 2011 

23-25 July 2012 25-27 July 2012 
14 

2.1.1.1. Study Site Refurbishment 

In 2012, the monitoring team conducted study site rehabilitation at EFGB and WFGB. This 

was necessary to install permanent study site corner markers that had been lost or loosened 

over the years. Permanent eye-bolts were also installed at the 25 m, 50 m, and 75 m marks 

along each perimeter and crosshair line location to allow each perimeter line and crosshair 

to be clipped into these guide pins when the study site boundary lines are placed (Figure 

2.1.3). These modifications ensure consistent location of study site lines from year to year. 

Permanent mooring buoys were reinstalled to the center location of each study site (Table 

2.1.1). 

Also during study site rehabilitation, repetitive 5 m2

 quadrat photostations were 

renumbered and tagged to create custom numbers based on bank and quadrant to avoid 

confusion among stations. Eye bolts were used to remark the repetitive stations, and 

numbered tags were attached to the eye bolts. These 5 m2

 repetitive quadrat photostations 

were mapped in relation to corner and/or center eyeblots on perimeter lines or crosshairs. 

The distance and heading to each station was obtained by divers using measuring tapes and 

compasses. This information was incorporated into the master maps, to assist with locating 

stations and study site navigation (Volume II Appendix 2). It should be noted that when the 

long-term monitoring study site boundaries were adjusted to make accurate 100 x 100 m sites, 

the corner locations shifted slighty. For this reason, some of the repetitive quadrat stations that 

are monitored are now located outside of the study site boundaries (Volume II Appendix 2). 

Figure 2.1.3. Divers install new permanent eye-bolts at the WFGB study site (NOAA/FGBNMS). 
15 

2.1.2. Repetitive Deep Stations 

Eleven repetitive deep photostations are located outside the study site at EFGB (Figure 2.1.4). 

Nine original deep stations were established in April 2003 for comparison with the shallower 

repetitive quadrat photostations already in place (Precht et al. 2005), and two more stations 

were added in 2012. The photostations were located east of EFGB study site at depths 

between 32 m and 40 m (Precht et al. 2005). 

Twelve repetitive deep photostations are located outside the study site at WFGB near buoy 

No. 2 (Figure 2.1.5). These deep stations were established in 2012 for comparison with EFGB 

deep photostations and the shallower repetitive quadrat photostations already in place. The 

stations were located 78 m north of the WFGB study site mooring at depths between 24 m and 

38 m. Deep station information is incorporated into the master maps to assist with locating 

stations and site navigation (Volume II Appendix 2). 
16 

Figure 2.1.4. Bathymetric map of EFGB with long-term monitoring study site (LTM site), 

mooring buoy, and repetitive deep photostation locations (EB Deep) 

(NOAA/FGBNMS). 

 
17 

Figure 2.1.5. Bathymetric map of WFGB with long-term monitoring study site (LTM site), 

mooring buoy, and repetitive deep photostation locations (WB Deep) 

(NOAA/FGBNMS). 
19 

CHAPTER 3.0: RANDOM TRANSECTS 

3.1. RANDOM TRANSECT METHODOLOGICAL RATIONALE

To estimate the areal coverage of benthic components such as corals, sponges, and 

macroalgae, 10 m transect tapes were positioned randomly within each study site. 

Conducted at random locations, the transect surveys were used to compare habitat types 

and provide information to document the benthic reef community of EFGB and WFGB in 

2011 and 2012. 

3.2. RANDOM TRANSECT METHODS

3.2.1. Random Transect Field Methods 

Four random transects within each quadrant of each study site, totaling 16 transects, were 

completed. For each quadrant, a random number between 0 and 50 was generated to 

indicate the starting location along the perimeter boundary line in the designated quadrant 

(e.g., if the random number is 27 and the corner of the transect tape is 0, the transect is 

started at 27 m along the transect tape, and if the lowest corner of the transect tape is 50, 

the transect is started at 77 m along the transect tape). A second random number was 

generated between 0 and 40 to determine the number of fin kicks perpendicular from the 

boundary line into the study site, as it takes approximately 40 fin kicks to swim 50 m, 

assuming no opposing current. This randomly generated number of kicks provides the start 

location for the first transect. A random number between 0° and 359° was also generated 

for the direction of the 10 m transect from the starting point. 

The subsequent survey starting point was determined with a second set of randomly 

generated numbers. First, the number of fin kicks, between 12 and 40, was determined to 

ensure the starting point was at least 15 m away from the previous location. Second, the 

compass heading, between 0° and 359°, was established for the direction of the next 10 m 

transect. If a quadrant boundary was encountered, the line was reflected at a 90° angle back 

into the quadrant. Random numbers and headings were given to divers before each survey. 

Each transect was designed to capture approximately 8 m2

 of benthic habitat. A still 

camera, mounted on a 0.65 m t-frame with bubble level and strobes, was used to capture 

non-overlapping images above the reef (Figure 3.2.1). The bubble level mounted to the 

center of the t-frame ensured images were taken in a vertical orientation to standardize the 

area captured. 

A Canon Power Shot® G11 digital camera was used in an Ikelite® housing with a 28 mm 

equivalent wet mount lens adaptor with two Inon® Z240 strobes set 1.2 m apart on the tframe. The mounted camera was placed at intervals marked on the spooled, fiberglass, 

measuring tape at 55.88 cm apart producing 19 non-overlapping images along the 10 m 

transect. Each still frame image captured an 80 x 55 cm area. This produced a total 

photographed area of 8.36 m2

 per transect, or a minimum of 117.04 m2 photographed per 

study site per year. 
20 

Figure 3.2.1. NOAA scientific diver with camera and strobes mounted on aluminum 

t-frame taking random transect photographs (NOAA/FGBNMS). 

3.2.2. Random Transect Data Processing 

Mean percent cover in the random transect images was analyzed using Coral Point Count 

with Microsoft® Excel® extensions (CPCe). CPCe is Microsoft® Windows®-based software 

that provides a tool for the determination of coral cover using transect photographs (Kohler 

and Gill 2006). A total of 500 points was distributed evenly between all the photos that 

were within a transect. Points were randomly overlaid on each image and benthic species 

lying under these points were identified. Microsoft® Excel® spreadsheets were created 

automatically in the program using customized code files pertinent to the cover of coral and 

other benthic species in the region. CPCe is provided by the National Coral Reef Institute 

as freeware to researchers from scientific institutions and government agencies. 

Organisms positioned beneath each random dot were identified as corals, sponges, or 

macroalgae and all were identified to the lowest possible taxonomic group. The macroalgae 

group included algae longer than approximately 3 mm and thick algal turfs. Crustose 

coralline algae, fine turfs, and bare rock were collectively identified as “CTB” (Aronson 

and Precht 2000). The components of the CTB group were combined for analysis because 

they represent potential habitat where settlement of coral or other organisms could occur. 

Macroalgae is not included in this category since settlement has already occurred. 

Additional categories included other live components (ascidians, fish, serpulids, etc.), sand, 

rubble, and unknown (Volume II Appendix 1). 
21 

The coverages of coral bleaching, paling, concentrated and isolated fish biting, and disease 

were recorded as “notes,” providing additional information for each random point. Any point 

that landed on a portion of coral that was white with no visible zooxanthallae was 

characterized as “bleached.” Any point that landed on coral that was pale relative to what was 

considered “normal” for the species, was characterized as “paling” coral (AGRRA 2010). If 

the colony displayed some bleaching or paling, but the point landed on a healthy area of the 

organism, the point was “healthy” and no bleaching or paling was noted in CPCe. To 

classify fish biting, any point that landed where fish biting occurred on a coral head more 

than once was classified as concentrated fish biting, and any point where there was only 

one occurance of fish biting was classified as isolated fish biting. Fish biting that results in 

the removal of coral polyps from an affected area is due primarily to stoplight parrotfish 

activity (Sparisoma viride) (Bruckner and Bruckner 1998; Bruckner et al. 2000). 

After each image was analyzed, the data were entered into project-specific Microsoft®

Excel® spreadsheets. Quality assurance/quality control (QA/QC) for the photographic 

methods consisted of multiple, scientific divers all trained on the same camera systems for 

correct camera operation. Divers were able to practice camera setup and operation with 

mock corals in a swimming pool before field work began. Statistical comparisons of 

identifications by multiple investigators were conducted to confirm the same identifications 

in the photographs to ensure that they agreed on species identifications within the photo 

frames. Each investigator was given photographs from the same transect from EFGB and 

WFGB and identified all benthic components in each photograph of that transect. 

Identification of benthic components agreed 95% of the time for transects analyzed from 

EFGB and WFGB in 2011 and 2012, with no significant difference (α=0.05) between the 

benthic components identified in the identical transects by different investigators. 

3.2.3. Random Transect Statistical Analyses 

Mean percent cover was calculated for each transect from the 500 analyzed points for each 

of the taxa and benthic categories. Factor plots were produced in CPCe to compare the 

average percent cover of major benthic categories and coral species between banks and 

through time. CPCe spreadsheet contents included header information, statistical 

parameters of each species/substrate type (mean, standard deviation, standard error) and the 

calculation of the Shannon–Weaver diversity index for each species (Kohler and Gill 

2006). Results are presented as mean percent cover ± standard error. Previous 

examination of means and variances, using different numbers of random dots, 

determined that 500 dots per transect provided the required accuracy and precision for 

estimates of the coverage of benthic components, regardless of the transect length (Aronson 

et al. 1994; Murdoch and Aronson 1999; Aronson et al. 2005). 

Analyses of Variance (ANOVA) were performed to test the null hypotheses that the 

response variables of univariate benthic cover did not differ by year (2011 and 2012) and 

bank (EFGB and WFGB). ANOVAs were calculated for each variable with the statistical 

software JMP® version 10.0. Data were tested for normality and square root transformed as 

necessary to assume a normal distribution to meet the assumptions of parametric statistical 

tests (Zimmer et al. 2010). 
22 

Multivariate statistical techniques were used to compare how the two banks may differ in 

benthic composition. Based on benthic mean percent cover, comparisons in community 

differences between the two banks were made using nonparametric analysis for non-normal 

data. Significant dissimilarities were tested using analysis of similarity (ANOSIM) with 

square root transformation and Bray-Curtis similarity resemblance measure (Bray and 

Curtis, 1957). Cluster analyses were performed on similarity matrices, and 

multidimensional scaling (MDS) was used to visualize community dissimilarities by bank 

(Kruskal, 1964). Ordinations were run using 100 random starting configurations to 

determine the best fit model and minimize stress. The R statistic, typically ranging between 

0 and 1, indicates between and within group dissimilarities, where R values less than 0.3 

indicate that similarities between sites and within sites are the same (Clarke & Warwick 

2001). Species contributing to the observed dissimilarities were identified using similarity 

percentages (SIMPER). All analyses were all carried out using Primer® version 6.0. 

For long-term trends (1978-2012), each functional group sample was averaged by year and 

compared using nonparametric analysis for non-normal data. Percent cover data of each 

functional group were used to calculate ecological distance via Bray-Curtis similarity 

matrices. Data were square root transformed to minimize the impacts of extremely 

dominant members of the community. Cluster analyses were performed on similarity 

matrices, and MDS plots were used to visualize community dissimilarities between years, 

with time series trajectory to highlight community shifts over time. SIMPER identified the 

greatest contributors to the observed dissimilarity. 

3.3. RANDOM TRANSECT RESULTS

The point count data from the random transects was expressed as mean percent cover ± 

standard error (SE). The major benthic component of the random transects from 2011 and 

2012 was coral cover (56%), followed by macroalgae cover (32%) and CTB (11%). The 

sponge cover (including encrusting sponges) was very low (0.5%) because not many 

macrosponges are found at the FGB; encrusting sponges are common but rarely seen in 

photographs because they are generally found on the underside of boulders (Figure 3.4.1). 

Volume II Appendix 4 of this report contains the random transect data from 2011 and 2012 

at the FGB. 

At EFGB, mean coral cover remained above 50 percent from 2011–2012 (57.49% ± 2.28 

to 52.49% ± 4.50), and the sponge cover remained extremely low for both years (0.49% ± 

0.17 to 0.62% ± 0.23) (Figure 3.3.1 and Table 3.3.1). Macroalgae cover (mainly fleshy 

algae and Dictyota spp.) increased slightly from 2011–2012 (30.10% ± 1.59 to 37.59% ± 

3.80), and CTB cover decreased (11.53% ± 0.07 to 8.63% ± 0.17). 

At WFGB, coral cover was above 50 percent, consistent with previous monitoring 

periods. The 2011 coral cover was the highest between the two years and banks (59.51% ± 

2.09), and the coral cover decreased in 2012 (54.78% ± 3.41). The sponge cover 

remained extremely low for both years (0.31% ± 0.11 to 0.68% ± 0.24). Macroalgae 

remained stable from 2011–2012 (29.11% ± 1.90 to 31.43% ± 2.48) along with relatively 

stable CTB cover (10.40% ± 0.25 to 12.27% ± 0.26) (Figure 3.3.1 and Table 3.3.1). 
23 

0

10

20

30

40

50

60

70

80

90

100

2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB

Mean Percent Cover

Bank and Year

Mean Percent Cover of Four Functional Catagories at the Flower 

Garden Banks, 2011 - 2012

Coral

Macroalgae

CTB

Sponge

Figure 3.3.1. Mean percent cover + SE of four functional benthic categories from random 

transects at the FGB from 2011–2012. 
24 

Table 3.3.1. 

 

Mean Percent Cover ± SE of Benthic Categories in Random Transects at EFGB and WFGB 

from 2011 and 2012 (listed from most to least abundant). 

Cover Category 2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB 

Coral 

Orbicella franksi 25.53 ± 4.16 25.76 ± 3.96 23.52 ± 3.11 26.06 ± 3.94 

Pseudodiploria strigosa 6.13 ± 1.91 7.65 ± 2.05 12.36 ± 2.62 9.32 ± 1.94 

Orbicella spp. 5.26 ± 1.74 2.65 ± 0.89 6.16 ± 3.06 2.03 ± 0.42 

Montastraea cavernosa 5.25 ± 1.14 3.24 ± 0.77 2.92 ± 0.81 1.89 ± 1.01 

Porites astereoides 4.17 ± 0.74 5.35 ± 0.88 3.60 ± 0.64 4.24 ± 0.55 

Orbicella faveolata 3.86 ± 1.28 2.82 ± 0.66 5.26 ± 1.69 7.33 ± 2.80 

Orbicella annularis 2.93 ± 2.07 0.13 ± 0.06 0.39 ± 0.31 0.20 ± 0.20 

Colpophyllia natans 1.66 ± 0.69 2.54 ± 0.67 0.75 ± 0.25 0.77 ± 0.28 

Siderastrea siderea 0.93 ± 0.31 0.19 ± 0.19 2.56 ± 1.87 0.60 ± 0.41 

Unidentified coral 0.57 ± 0.26 0.98 ± 0.30 0.64 ± 0.28 0.51 ± 0.18 

Stephanocoenia intersepta 0.38 ± 0.23 0.60 ± 0.22 0.69 ± 0.27 0.88 ± 0.24 

Scolymia cubensis 0.17 ± 0.14 0.00 0.00 0.00 

Madracis decactis 0.15 ± 0.09 0.14 ± 0.09 0.03 ± 0.02 0.11 ± 0.09 

Siderastrea spp. 0.13 ± 0.05 0.06 ± 0.06 0.01 ± 0.01 0.00 

Agaricia agaricites 0.13 ± 0.05 0.15 ± 0.05 0.25 ± 0.09 0.14 ± 0.05 

Millepora alcicornis 0.11 ± 0.07 0.14 ± 0.05 0.21 ± 0.13 0.15 ± 0.06 

Mussa angulosa 0.08 ± 0.05 0.07 ± 0.04 0.03 ± 0.02 0.02 ± 0.02 

Colpophyllia amaranthus 0.02 ± 0.02 0.00 0.01 ± 0.01 0.00 

Scolymia spp. 0.01 ± 0.01 0.00 0.00 0.00 

Agaricia spp. 0.01 ± 0.01 0.00 0.01 ± 0.01 0.00 

Porites furcata 0.00 0.03 ± 0.02 0.01 ± 0.01 0.00 

Madrepora spp. 0.00 0.02 ± 0.02 0.01 ± 0.01 0.00 

Madracis spp. 0.00 0.01 ± 0.01 0.00 0.08 ± 0.05 

Madracis auretenra 0.00 0.00 0.05 ± 0.02 0.04 ± 0.03 

Colpophyllia spp. 0.00 0.00 0.02 ± 0.02 0.00 

Siderastrea radians 0.00 0.00 0.00 0.39 ± 0.37 

Leptoseris cucullata 0.00 0.00 0.00 0.01 ± 0.01 

Agaricia fragilis 0.00 0.00 0.00 0.01 ± 0.01 

Total Mean Coral Cover 57.49 ± 2.28 52.49 ± 4.50 59.51 ± 2.09 54.78 ± 3.41 

Sponge 

Agelas clathrodes 0.16 ± 0.06 0.12 ± 0.05 0.07 ± 0.04 0.10 ± 0.05 

Aiolochroia (Pseudoceratina) crassa 0.04 ± 0.04 0.08 ± 0.07 0.01 ± 0.01 0.05 ± 0.04 

Ircinia strobilina 0.04 ± 0.04 0.03 ± 0.02 0.02 ± 0.02 0.08 ± 0.08 

Unidentifiable sponge 0.04 ± 0.04 0.15 ± 0.08 0.04 ± 0.04 0.06 ± 0.04 

Placospongia melobesioides 0.01 ± 0.01 0.01 ± 0.01 0.00 0.00 

Xestospongia muta 0.00 0.09 ± 0.09 0.01 ± 0.01 0.25 ± 0.17 

Mycale laxissima 0.00 0.04 ± 0.04 0.00 0.00 
25 

Cover Category 2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB 

Ectyoplasia ferox 0.00 0.02 ± 0.02 0.03 ± 0.02 0.00 

Aplysina spp. 0.00 0.01 ± 0.01 0.00 0.00 

Ircinia felix 0.00 0.00 0.00 0.01 ± 0.01 

Encrusting sponge 0.19 ± 0.06 0.03 ± 0.02 0.13 ± 0.05 0.03 ± 0.02 

Unidentifiable encrusting sponge 0.00 0.02 ± 0.02 0.00 0.08 ± 0.05 

Total Mean Sponge Cover 0.49 ± 0.17 0.62 ± 0.23 0.31 ± 0.11 0.68 ± 0.24 

Macroalgae 

Fleshy algae 14.04 ± 1.41 23.36 ± 3.05 13.45 ± 1.48 17.37 ± 2.05 

Dictyota spp. 11.62 ± 1.47 9.60 ± 1.26 1.44 ± 0.30 1.96 ± 0.61 

Lobophora variegata 3.09 ± 0.62 1.23 ± 0.23 11.17 ± 0.98 9.52 ± 1.60 

Thick turf algae 1.32 ± 0.31 3.29 ± 0.78 2.95 ± 0.58 2.43 ± 0.42 

Peysonnelia spp. 0.03 ± 0.02 0.00 0.00 0.00 

Filamentous algae 0.00 0.08 ± 0.05 0.08 ± 0.05 0.01 ± 0.01 

Unidentifiable macroalgae 0.03 ± 0.03 0.00 0.02 ± 0.02 0.13 ± 0.13 

Total Mean Macroalgae Cover 30.10 ± 1.59 37.59 ± 3.80 29.11 ± 1.90 31.43 ± 2.48 

CTB 

Fine turf algae 5.20 ± 1.10 4.11 ± 0.59 4.66 ± 0.56 5.81 ± 1.11 

Bare substrate 3.94 ± 0.76 2.86 ± 0.51 4.33 ± 0.54 3.63 ± 0.34 

Crustose coralline algae 1.89 ± 0.38 1.25 ± 0.28 1.30 ± 0.23 2.71 ± 0.61 

Substrate rubble 0.36 ± 0.15 0.03 ± 0.02 0.07 ± 0.03 0.05 ± 0.04 

Coral rubble 0.15 ± 0.08 0.37 ± 0.27 0.04 ± 0.02 0.07 ± 0.05 

Total Mean CTB Cover 11.53 ± 1.41 8.63 ± 0.96 10.40 ± 0.61 12.27 ± 1.36 

Orbicella franksi was the most abundant coral species observed in 2011 (25.53% ± 4.16) 

and 2012 (25.76% ± 3.96) at EFGB. Pseudodiploria strigosa (6.13% ± 1.91 and 7.65% ± 

2.05 in 2011 and 2012, respectively) was the next most abundant species, followed by 

unidentified Orbicella spp., Montastraea cavernosa, and Porites astreoides (Figure 3.3.2 

and Table 3.3.1). The remaining coral cover was made up of twenty-four species, none 

of which exceeded 4.0% cover individually in either 2011 or 2012 (Table 3.3.1). 

Corals that could not be differentiated (less than 1%) because of camera angle or camera 

distortion were labeled as “unidentified coral.” Shannon-Wiener diversity values remained 

consistent at EFGB (H’=0.95 and H’=0.91 in 2011 and 2012, respectively). 

As with EFGB, Orbicella franksi was the most abundant coral species observed in 2011 

(23.52% ± 3.11) and 2012 (26.06% ± 3.94) at WFGB. Pseudodiploria strigosa (12.36% ± 

2.62 and 9.32% ± 1.94 in 2011 and 2012, respectively) was the next most abundant species, 

followed by Orbicella faveolata (5.26% ± 1.69 to 7.33% ± 2.80). Other abundant species 

included Porites astreoides, unidentified Orbicella spp., and Monastraea cavernosa

(Figure 3.3.3 and Table 3.3.1). The remaining coral cover was made up of twenty-five 

species, none of which exceeded 3.0% individually in either 2011 or 2012 (Table 

3.3.1). Corals that could not be differentiated (less then 1%) because of camera angle or 

camera distortion were labeled as “unidentified coral.” Shannon-Wiener diversity values 

were higher at WFGB in 2011 than in 2012 (H’=0.93 and H’=0.98 in 2011 and 2012, 

respectively). 
26 

0 5 10 15 20 25 30 35

Orbicella franksi

Pseudodiploria strigosa

Orbicella spp.

Montastraea cavernosa

Porites astereoides

Orbicella faveolata

Orbicella annularis

Colpophyllia natans

Siderastrea siderea

Unidentified coral

Stephanocoenia intersepta

Mean Percent Cover 

Coral Species

Mean Percent Cover of the Dominant Coral Species at 

East Flower Garden Bank, 2011-2012

2011

2012

Figure 3.3.2. Mean percent cover + SE of observed dominant coral species from 

random transect photographs at EFGB in 2011 and 2012. 

0 5 10 15 20 25 30 35

Orbicella franksi

Pseudodiploria strigosa

Orbicella spp.

Montastraea cavernosa

Porites astereoides

Orbicella faveolata

Orbicella annularis

Colpophyllia natans

Siderastrea siderea

Unidentified coral

Stephanocoenia intersepta

Mean Percent Cover

Coral Species

Mean Percent Cover of the Dominant Coral Species at 

West Flower Garden Bank, 2011-2012

2011

2012

Figure 3.3.3. Mean percent cover + SE of observed dominant coral species from 

random transect photographs at WFGB in 2011 and 2012. 
27 

The Montastraea annularis species complex (MASC), containing Montastraea annularis, 

Montastraea faveolata, and Montastraea franksi, has now been taxonomically reclassified 

as the Orbicella annularis species complex (OASC), containing Orbicella annularis, 

Orbicella faveolata, and Orbicella franksi (Budd et al. 2012). Diploria strigosa has also 

been reclassified as Pseudodiploria strigosa. The Orbicella annularis species complex was 

grouped together throughout the monitoring program until 2008; after that time individual 

species within the complex were identified. In past monitoring years, the OASC has been 

difficult to differentiate using the photographic techniques employed in this study 

(primarily because the scale of the photograph does not allow visualization of the entire 

colony formation, which is sometimes essential for identification). However, with 

improved digital photography resolution and the FGBNMS staff’s familiarity with the 

species in the study site, most components of the OASC were individually indentified. Still, 

the use of OASC remains relevant when comparing historical data before separation. 

Approximately 16% of the OASC components were unable to be differentiated during the 

monitoring period, which may be due to OASC hybridization or genotypic variation. These 

were referred to as unidentified OASC, or Orbicella spp. (Table 3.3.1). 

In the 2011 and 2012 random transects, the incidences of bleaching, paling, and fish biting 

were low at each bank and coral disease was absent (Table 3.3.2). The mean percentage of 

corals impacted by isolated/concentrated fish biting was 0.00–0.07%. Less than 1% of the 

coral cover analyzed in the random transects was diseased or bleached in 2011 and 2012. 

It is important to note that bleaching as determined by the long-term monitoring 

methodology may be incomplete, as surveys usually occur when weather is optimal (e.g., 

before hurricane season) in earlier summer months before signs of bleaching occur. 

Table 3.3.2. 

 

Mean Percent Cover ± SE of Coral Condition Categories in Random 

Transects at EFGB and WFGB from 2011 and 2012. 

Cover Category 2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB 

Coral Condition (occurrences in coral) 

Bleached Coral 0.00 0.00 0.07 ± 0.05 0.02 ± 0.02 

Paling Coral 0.37 ± 0.14 0.18 ± 0.14 0.31 ± 0.12 0.11 ± 0.06 

Concentrated Fish Biting 0.06 ± 0.04 0.00 0.05 ± 0.03 0.00 

Isolated Fish Biting 0.00 0.02 ± 0.02 0.07 ± 0.05 0.00 

Disease 0.00 0.00 0.00 0.00 

In summary, combined mean percent coral cover averaged approximately 56% at EFGB 

and WFGB in the period 2011 through 2012. These values were consistent with 

measurements of coral cover above 50% at the FGB in previous years (Dokken et al. 2003; 

Precht et al. 2006; Johnston et al. 2013) and they are high compared to other western 

Atlantic reefs (Aronson et al. 1994; Gardner et al. 2003). Macroalgae ranked second behind 

the corals, and sponge cover was below one percent each year. This pattern was consistent 

with previous monitoring from EFGB and WFGB (Aronson et al. 2005; Precht et al. 2006; 

Zimmer et al. 2010; Johnston et al. 2013) and previous work in the Caribbean (Aronson 

and Precht 2000). 
28 

3.3.1. Random Transect Univariate Analysis 

The random transect point count data expressed as mean percent cover was analyzed by 

one-way ANOVA, with bank and year as fixed factors with an experimentwise error rate of 

α=0.05. The data on proportional cover of sponges were non-normal, so categories were 

square root transformed. The one-way ANOVA on the proportional cover of all observed 

corals, sponge, macroalgae, and CTB showed no significant difference between bank or 

year. A two-way ANOVA displaying the bank by year interaction was also not significant 

(Table 3.3.3). 

Table 3.3.3. 

 

Results of ANOVA on Mean Percent Cover Estimates from Random Transects in 

2011 and 2012 

Source Sum of Squares df Mean Square F-ratio P-value 

(A) Corals 

Bank 2.46 1 2.46 2.97 0.09 

Year 0.50 1 0.50 0.58 0.45 

Bank*Year 2.96 2 1.48 1.77 0.18 

Error 50.74 61 0.83 

Total 53.70 63 

(B) Sponges 

Bank 0.66 1 0.66 3.25 0.08 

Year 0.01 1 0.01 0.05 0.82 

Bank*Year 0.67 2 0.34 1.63 0.21 

Error 12.66 61 0.21 

Total 13.34 63 

(C) Macroalgae 

Bank 2.18 1 2.18 2.66 0.11 

Year 1.37 1 1.37 1.65 0.20 

Bank*Year 3.55 2 1.77 2.19 0.12 

Error 49.33 61 0.02 

Total 52.88 63 

(D) CTB 

Bank 0.16 1 0.16 0.31 0.58 

Year 0.90 1 0.90 1.79 0.19 

Bank*Year 1.06 2 0.53 1.04 0.36 

Error 31.15 61 0.51 

Total 32.22 63 
29 

3.3.2. Random Transect Multivariate Analysis 

The point counts for the random transects were further analyzed by using multivariate 

techniques. Multivariate cover analysis was compared between bank and year using 

ANOSIM. There were no significant differences between years. ANOSIM results indicate 

a biologically significant, but small spatial variation, with dissimilarities between banks 

(Global R=0.05, p<4.6%). Though differences are detected, the very small R value 

indicates that the dissimilarities between groups are less than some of the within-group 

dissimilarities. In most cases, a small R value with significant P-value is uninformative. 

Cluster analysis and MDS plot placed the benthic cover between bank and year in one 

cluster (80% similarity), with the exception of one outlier from WFGB. The stress level of 

the MDS was low at 0.1, indicating good goodness-of-fit in a two-dimensional scale, 

suggesting high confidence in the pattern displayed (Figure 3.3.4). These results agree with 

both the ANOVA and ANOSIM that no significant differences of bank or year occur 

between EFGB and WFGB, making the banks similar in terms of benthic composition. 

Figure 3.3.4. Two-dimensional MDS plot based on Bray-Curtis similarities 

showing the spatial representation of benthic community 

similarities between EFGB and WFGB in 2011 and 2012. 

The green circle groups surveys that are 80% similar. 
30 

3.3.3. Historical Comparison of Random Transect Benthic Cover 

A historical comparison of dominant benthic cover components is an important part of 

monitoring to measure changes over long time periods. Therefore, the mean percent 

benthic cover from the four functional random transect categories were analyzed. 

Mean percent coral cover was first collected in 1978; however, data for the remaining three 

categories (sponge, macroalgae, and CTB) did not begin until 1992. No data were collected 

in 1993 due to poor weather, and in 1996 and 1997 no data were recorded for the CTB 

category (known as reef rock from previous monitoring periods). 

Mean percent coral cover showed an overall increase during the period from 1992–2012 

at WFGB; the highest cover recorded was in 2010 and a mean of approximately 52% cover 

over time. Estimates varied at EFGB but remained consistently at or above 52% (Figure 

3.3.5 and Table 3.3.4). Periods of lower coral cover generally coincided with increases in 

the algal component and decreases in the CTB category. 

 

Multivariate historical mean percent cover analysis from EFGB and WFGB was compared 

among years (1994 to 2012) to calculate benthic cover change over a large time scale. 

SIMPER analysis indicated that for most comparisons between 1994 and 2012, the greatest 

contributors to the observed dissimilarity were CTB and macroalgae. Cluster analysis and 

MDS plot placed the mean percent cover from 1994–2012 in two clusters (80% similarity). 

The stress level of the MDS was low at 0.03, indicating good goodness-of-fit in a twodimensional scale, suggesting high confidence in the pattern displayed (Figure 3.3.6). The 

data suggests communities were similar between 1994 and 1998; a significant shift in 

community composition occurred between 1999 and 2002, then similar again between 

2003 and 2012. 

The macroalgae increases generally coincided with lower CTB cover (Figure 3.3.5. and 

Table 3.3.4). In 1999, a sudden increase in macroalgae cover was observed, leading to a 

reciprocal relationship between macroalgae and CTB cover until 2008. After 2008, 

macroalgae dominated CTB cover, as macroalgae cover continued to increase. These trends 

correspond to SIMPER results, suggesting that the greatest contributors to the observed 

dissimilarity over time were CTB and macroalgae. This also corresponds to the MDS plot, 

suggesting that from 1994–1998 the community was stable, and starting in 1999 there was 

a shift due to changes in the CTB and macroalgae cover, causing the community to 

stabilize once again from 2009–2012, but with higher macroalgae percent cover than ever 

recorded on both banks (Figure 3.3.6). 
31 

0

10

20

30

40

50

60

70

80

Mean Percent Cover

Year

Mean Percent Cover of Four Functional Categories at

East Flower Garden Bank, 1992-2012 Coral

Macroalgae

CTB

Sponge

a. TAMU, b. CSA, c. TAMU-CC, d. PBSJ, e. FGBNMS

0

10

20

30

40

50

60

70

80

Mean Percent Cover

Year

Mean Percent Cover of Four Functional Categories at 

West Flower Garden Bank, 1992-2012 Coral

Macroalgae

CTB

Sponge

a. TAMU, b. CSA, c. TAMU-CC, d. PBSJ, e. FGBNMS

Figure 3.3.5. Historical representation of mean percent cover of coral, sponge, 

macroalgae, and CTB at (A) EFGB and (B) WFGB. 

No m e a n percent cover data were reported in 1993. Data for 1978–1982 from 

Gittings et al. (1992), who reported data from Kraemer (1982); for 1988–1991 from 

Gittings et al. (1992); for 1992–1995 from Continental Shelf Associates, Inc. (CSA) (1996); 

for 1996–2001 from Dokken et al. (2003); 2002–2008 from PBS&J (Precht et al. 2006, 

2008b); and FGBNMS for 2009–2012 (Johnston et al. 2013). 

(A) 

(B) 
32 

Table 3.3.4. 

 

EFGB and WFGB Random Transect Data for Dominant Cover Categories. 

EFGB Random Transect Data 

Year Coral Macroalgae CTB Sponge 

1978-1982 50.40 NA NA NA 

1988-1991 46.00 NA NA NA 

1992 40.15 4.78 54.46 0.74 

1994 49.30 0.29 47.31 1.23 

1995 50.20 0.57 42.15 0.67 

1996 43.70 ± 12.0 6.10 ± 5.20 NA 0.90 ± 1.00 

1997 41.6 ± 8.30 0.50 ± 0.60 NA 1.10 ± 1.70 

1998 51.60 ± 8.30 3.20 ± 2.60 27.60 ± 5.90 0.50 ± 0.90 

1999 53.0 ± 9.00 24.70 ± 13.20 11.10 ± 8.20 0.70 ± 0.90 

2000 58.30 ± 6.70 17.30 ± 4.90 4.30 ± 1.70 0.70 ± 0.80 

2001 61.80 ± 10.0 14.90 ± 5.60 5.70 ± 3.60 0.80 ± 1.00 

2002 56.43 ± 2.36 4.06 ± 0.75 37.07 ± 2.69 0.79 ± 0.36 

2003 53.2 ± 3.01 16.74 ± 2.05 28.12 ± 2.05 1.54 ± 0.40 

2004 64.13 ± 2.70 12.03 ± 2.77 20.89 ± 3.08 0.31 ± 0.24 

2005 49.55 ± 3.01 34.03 ± 2.58 11.96 ± 1.49 0.48 ± 0.26 

2006 52.26 ± 3.50 21.10 ± 2.32 23.15 ± 1.94 0.83 ± 0.33 

2007 51.93 ± 4.46 21.73 ± 2.28 24.43 ± 2.11 0.56 ± 0.22 

2008 56.37 ± 3.62 24.06 ± 2.16 17.64 ± 1.77 0.40 ± 0.15 

2009 53.35 ± 4.17 31.85 ± 3.49 13.32 ± 1.07 0.13 ± 0.05 

2010 54.49 ± 3.69 32.94 ± 3.05 11.15 ± 0.86 0.25 ± 0.13 

2011 57.49 ± 2.28 30.10 ± 1.59 11.53 ± 0.07 0.49 ± 0.17 

2012 52.49 ± 4.50 37.59 ± 3.80 8.63 ± 0.17 0.62 ± 0.23 
33 

WFGB Random Transect Data 

Year Coral Macroalgae CTB Sponge 

1978-1982 55.20 NA NA NA 

1988-1991 46.50 NA NA NA 

1992 37.20 4.45 56.56 1.53 

1994 45.10 0.42 51.08 1.58 

1995 47.40 2.70 45.85 0.27 

1996 46.50 ± 12.30 4.50 ± 5.20 NA 1.00 ± 1.00 

1997 47.90 ± 13.90 0.10 ± 0.60 NA 0.90 ± 1.30 

1998 48.50 ± 12.70 2.30 ± 2.60 20.70 ± 5.90 0.60 ± 0.60 

1999 51.50 ± 8.10 18.80 ± 13.20 21.10 ± 8.20 0.60 ± 0.70 

2000 51.60 ± 13.70 22.60 ± 14.00 8.50 ± 3.70 0.60 ± 0.80 

2001 53.10 ± 11.40 25.40 ± 7.30 4.60 ± 2.90 1.00 ± 1.10 

2002 49.70 ± 3.35 19.14 ± 1.40 27.63 ± 3.14 1.31 ± 0.32 

2003 57.10 ± 3.81 8.41 ± 1.41 31.63 ± 3.04 1.56 ± 0.38 

2004 60.41 ± 2.94 14.75 ± 1.50 20.85 ± 2.11 0.40 ± 0.15 

2005 54.41 ± 3.13 18.35 ± 1.44 18.27 ± 1.67 0.25 ± 0.11 

2006 58.28 ± 2.88 12.38 ± 1.34 25.64 ± 2.06 0.46 ± 0.12 

2007 56.58 ± 3.28 17.64 ± 2.44 24.27 ± 1.89 0.35 ± 0.10 

2008 59.27 ± 3.40 12.06 ± 1.31 26.74 ± 2.41 1.00 ± 0.47 

2009 53.84 ± 3.73 30.03 ± 2.63 14.93 ± 1.52 0.10 ± 0.05 

2010 65.95 ± 2.85 22.03 ± 2.00 10.20 ± 1.03 0.25 ± 0.10 

2011 59.51 ± 2.09 29.11 ± 1.90 10.40 ± 0.25 0.31 ± 0.11 

2012 54.78 ± 3.41 31.43 ± 2.48 12.27 ± 0.26 0.68 ± 0.24 

Values listed in table are the mean percent covers. Standard deviations are shown for 

1996 to 2001 based on analysis by Dokken et al. (2003) and standard errors (± SE) are 

reported from 2002–2012. Data for 1978–1982 from Gittings et al. (1992), who 

reported data from Kraemer (1982); for 1988–1991 from Gittings et al. (1992); for 

1992–1995 from Continental Shelf Associates, Inc. (CSA) (1996); for 1996–2001 from 

Dokken et al. (2003); 2002–2008 from PBS&J (Precht et al. 2006, 2008b); and FGBNMS 

for 2009–2012 (Johnston et al. 2013). 
34 

Figure 3.3.6. Two-dimensional MDS plot based on Bray-Curtis similarities 

comparing benthic cover analysis from 1994–2012 at EFGB and 

WFGB. 

The green circles group years that are 80% similar. 
35 

3.4. RANDOM TRANSECT DISCUSSION

In a global trend of declining coral reef health and cover, the FGB continues to support 

high coral cover compared to other reefs of the western Atlantic and Caribbean region 

(Aronson et al. 1994, 2005; Gardner et al. 2003; AGRRA 2003; Pina Amargós et al. 

2008; ONMS 2011; Steneck et al. 2011; Johnston et al. 2013) (Table 3.4.1). Gardner et al. 

(2003) reported the regional decline of corals across the Caribbean basin over the last 

three decades, with the average hard coral cover on reefs decreasing from approximately 

50% to 10%. Natural and anthropogenic factors, including storm events, temperature 

stress, disease, predation, overfishing, sedimentation, eutrophication, and habitat 

destruction have all played a part in the decline (Aronson and Precht 2001; Rogers and 

Beets 2001; Gardner et al. 2003). 

Caribbean reefs that have historically displayed high coral cover are showing declines, 

mainly due to algae competition, and bleaching or coral disease, or both. Bonaire reported a 

decrease in coral cover from 38% to 10% in 2011 (Steneck et al. 2011). Mean coral cover 

in Florida Keys National Marine Sanctuary decreased from 13% to approximately 7% with 

ranges from approximately 3% to 20% (ONMS 2011). The Cuban reefs within Jardin de la 

Reina range from 7% to 9% cover (Pina Amargós et al. 2008). In contrast, coral cover at 

the FGB has remained relatively stable throughout the monitoring program, and is between 

6 to 11 times higher than cover values estimated for other locations in the Caribbean region 

(Caldow et al. 2009) (Figure 3.5.1). Analysis of the random transect data revealed that the 

mean percent coral cover at EFGB and WFGB was 56.07% from 2011–2012. Coral cover 

was also similar to values from earlier studies, (Dokken et al. 1999, 2001; CSA 1996; 

Gittings et al. 1992), highlighting the stability of the coral assemblage at the FGB (Figure 

3.4.1). 

Table 3.4.1. 

 

Percentage of Coral Cover on Living Reefs in the Western Atlantic and Caribbean Region

Location Percent Coral Cover Source 

Flower Garden Banks 56 this report 

Netherlands Antilles 10–47 AGRRA 2003 

St. Vincent Grenadines 29–44 AGRRA 2003 

Bonaire 38 Steneck et al. 2011 

Puerto Rico 7-36 Waddell and Clark 2008 

Navassa Island 10-25 Waddell and Clark 2008 

Cayman Islands 21 AGRRA 2003 

Florida Keys NMS 3–20 ONMS 2011 

Jardin de la Reina, Cuba 7–19 Pina Amargós et al. 2008 

Pedro Bank, Jamaica 5-19 Bruckner 2013 

Akumal, Mexico 17 AGRRA 2003 

Cay Sal Bank, Bahamas 7-9 Bruckner 2011 

St. Kitts and Nevis 6-13 Bruckner and Willams 2012 

U.S. Virgin Islands 5-7 Caldow et al. 2009 
36 

0

10

20

30

40

50

60

70

80

90

100 Mean Percent Cover

Year

Mean Percent Coral Cover at the 

Flower Garden Banks, 1978 - 2012

East Bank

West Bank

a. TAMU, b. CSA, c. TAMU-CC, d. PBSJ, e. FGBNMS

Film Photography Video Digital 

Photography

LPI

Figure 3.4.1. Random transect mean percent coral cover + SE at EFGB and WFGB over 

time. 

Values calculated from random transect photographs. SE not available from 1978-2001. No 

m e a n percent cover data were reported in 1993. Data for 1978–1982 from Gittings et 

al. (1992), who reported data from Kraemer (1982); for 1988–1991 from Gittings et al. 

(1992); for 1992–1995 from Continental Shelf Associates, Inc. (CSA) (1996); for 1996–2001 

from Dokken et al. (2003); 2002–2008 from PBS&J (Precht et al. 2006, 2008b); and FGBNMS 

for 2009–2010 (Johnston et al. 2013). 

Some reasons for the exceptional condition of the FGB include 1) water depth of the 

reefs, which buffers the reef cap from the effects of storm waves and variable 

seasurface temperatures; 2) the remote offshore location, which limits human access and 

exposes these reefs consistently to oligotrophic, oceanic waters; 3) healthy grazer 

populations; and 4) protective federal regulations, which prevent direct hydrocarbon-related 

impacts, as well as effects from anchoring and certain fishing methods (Aronson et al. 

2005). The importance of the FGB, in terms of the Atlantic coral reef system as a whole, 

has been substantially elevated because of the regional decline of corals. On August 27, 

2014, NOAA Fisheries listed 22 corals as threatened under the Endangered Species Act 

(ESA). The listing classifies the Orbicella annularis species complex and Acropora 

palmata as threatened. 
37 

3.4.1. Historical Comparison of Random Transect Benthic Cover 

Changes in the frequency and severity of the El Niño–Southern Oscillation (ENSO) have 

been partially responsible for transitions from coral-dominated communities to algaedominated reef systems in the Caribbean (Glynn 1984, 1993; Goreau and Hayes 1994; 

Wilkinson and Souter 2008), and these local and regional weather patterns may also affect 

benthic communities like those at the FGB. In 1987, 1995, and 1998, severe ENSO 

fluctuations affected the western Atlantic, causing large-scale coral bleaching, subsequent 

coral mortality, and colonization of substrate by algae (Glynn 1984; McField 1999; 

Aronson et al. 2000). Widespread and severe coral bleaching also occurred in the 

Caribbean in 2005, but in the absence of an El Niño event (Wilkinson and Souter 2008). 

Macroalgae cover has increased since the beginning of the monitoring program (Figure 

3.3.5). Algae cover at the FGB, represented primarily within the macroalgae category, 

remained relatively low until 1999, a n d never reached greater than 6.1% at either bank. 

It increased dramatically in 1999 and, while fluctuating, has remained comparatively high 

ever since when compared to previous years. Historically, macroalgae mean cover has 

been approximately 17% at EFGB and 15% at WFGB (Table 3.3.4). Concurrent with 

high algae cover, the CTB category was lower at EFGB in 1999, 2004, and 2012 and at 

WFGB in 2000, 2004, and 2010. Overall, the most noticeable pattern was the inverse 

relationship between macroalgae and CTB cover. Macroalgae tend to be ephemeral, with 

different species becoming abundant under certain seasonal conditions (Diaz-Pulido and 

Garzon-Ferreira 2002). The results suggest that algal overgrowth can significantly affect 

estimates of underlying benthic cover (since coral does not grow/die at the same rate as 

algae), but due to the ephemeral nature of algae blooms, does not necessarily lead to 

longer, reductions in those populations. Macroalgae cover is a highly dynamic component 

of the ecosystem, varying in relation to seasonal eutrophication caused by up upwelling and 

nutrient availability, and in relation to grazer community composition in reef habitats. In 

some areas within the region, increased algae cover has driven coral decline; however, this 

has not yet happened at the FGB (ONMS 2011). 

Despite increasing algal cover, coral cover remains greater than 50% at the FGB. Dominant 

coral cover at the FGB from 1992 to 2012 included the Orbicella spp., Pseudodiploria 

strigosa, Montastraea cavernosa, Porites astereoides, and Colpophyllia natans. These 

major reef building corals have remained stable since the beginning of the monitoring 

program. The Orbicella annularis species complex, dominanted by Orbicella franksi, 

showed an overall increase in b e n t h i c cover during the period from 1992–2012 at 

the FGB (Table 3.4.2 and Figure 3.4.2). It should be noted that before 2002, species of 

Orbicella were not individually analyzed, so for historical comparison they are grouped 

together. The highest OASC cover at EFGB was recorded in 2001, an average of 

approximately 45% cover. The highest OASC cover at WFGB was recorded in 2010, an 

average of approximately 46% cover. From 2011–2012 at the FGB, Pseudodiploria 

strigosa coral cover averaged 8%, Porites astereoides averaged 4%, Montastraea 

cavernosa averaged 3%, Colpophyllia natans averaged 2%. This suggests that coral health 

at the FGB has remained stable throughout the monitoring program, a trend of increasing 

growth from 1978–2012. 
38 

Table 3.4.2. 

 

EFGB and WFGB Random Transect Data for Dominant Coral Cover 

EFGB Random Transect Data

Year OASC Pseudodiploria 

strigosa 

Montastraea 

cavernosa 

Porites 

astereoides 

Colpophyllia 

natans 

1978-1982 NA NA NA NA NA 

1988-1991 NA NA NA NA NA 

1992 24.12 4.69 1.49 4.57 2.14 

 1993 NA NA NA NA NA 

1994 26.93 8.92 4.80 3.89 1.59 

1995 35.65 7.92 3.20 2.71 3.78 

1996 21.30 10.10 3.70 3.60 0.80 

1997 21.60 5.10 4.70 5.30 0.80 

1998 30.40 8.30 3.50 4.20 2.10 

1999 28.20 12.40 2.40 3.40 3.60 

2000 39.50 6.20 4.80 2.60 2.60 

2001 44.80 3.90 3.60 4.60 2.60 

2002 33.59 ± 3.86 6.96 ± 1.69 3.90 ± 1.08 6.79 ± 0.83 0.57 ± 0.39 

2003 28.47 ± 2.98 6.19 ± 1.55 4.24 ± 1.41 5.69 ± 0.98 3.29 ± 1.40 

2004 30.14 ± 4.76 12.13 ± 2.82 7.73 ± 1.94 8.19 ± 0.99 2.81 ± 1.28 

2005 26.80 ± 4.09 5.95 ± 1.26 3.40 ± 1.14 7.55 ± 1.19 1.77 ± 1.08 

2006 31.45 ± 4.09 10.25 ± 1.52 2.48 ± 0.67 4.91 ± 0.83 1.73 ± 1.06 

2007 32.44 ± 4.62 5.82 ± 1.11 3.74 ± 0.94 5.81 ± 0.88 1.56 ± 0.85 

2008 33.58 ± 4.52 7.69 ± 2.00 2.84 ± 0.92 7.27 ± 1.19 1.65 ± 0.58 

2009 29.52 ± 12.99 10.08 ± 2.54 3.58 ± 1.22 4.93 ± 1.29 3.21 ± 1.00 

2010 33.89 ± 3.84 9.38 ± 1.72 3.71 ± 1.46 5.11 ± 0.69 2.45 ± 0.63 

2011 37.58 ± 9.25 6.13 ± 1.91 5.25 ± 1.14 4.17 ± 0.74 1.66 ± 0.69 

2012 31.36 ± 5.58 7.65 ± 2.05 3.24 ± 0.77 5.35 ± 0.88 2.54 ± 0.67 
39 

WFGB Random Transect Data

Year OASC Pseudodiploria 

strigosa 

Montastraea 

cavernosa 

Porites 

astereoides 

Colpophyllia 

natans 

1978-1982 NA NA NA NA NA 

1988-1991 NA NA NA NA NA 

1992 23.02 6.15 0.87 1.49 3.11 

 1993 NA NA NA NA NA 

1994 24.95 10.15 3.15 2.55 2.82 

1995 31.00 6.66 2.33 2.44 0.97 

1996 27.20 7.90 1.50 2.50 1.30 

1997 27.70 9.10 4.30 2.70 1.30 

1998 28.40 9.60 2.60 2.40 1.70 

1999 31.70 10.90 2.40 2.70 0.70 

2000 30.90 8.10 5.80 2.50 3.60 

2001 35.10 9.50 2.10 2.00 2.80 

2002 31.73 ± 3.57 3.20 ± 0.91 2.74 ± 1.16 3.44 ± 0.74 1.67 ± 1.21 

2003 33.80 ± 4.31 9.04 ± 2.68 2.67 ± 1.10 3.77 ± 0.46 2.17 ± 0.84 

2004 31.70 ± 2.70 13.41 ± 1.74 3.70 ± 1.02 5.19 ± 0.62 3.48 ± 1.56 

2005 36.20 ± 3.50 6.68 ± 1.29 2.43 ± 0.69 4.04 ± 0.46 1.40 ± 0.54 

2006 40.13 ± 3.29 10.14 ± 1.64 2.25 ± 0.84 3.39 ± 0.57 0.55 ± 0.28 

2007 35.50 ± 3.81 9.56 ± 1.85 1.84 ± 0.53 3.61 ± 0.44 3.35 ± 1.24 

2008 37.01 ± 4.65 8.98 ± 2.43 2.81 ± 1.05 3.62 ± 0.64 1.14 ± 0.45 

2009 27.25 ± 3.32 10.84 ± 2.70 4.03 ± 0.97 3.85 ± 0.64 4.26 ± 1.38 

2010 45.98 ± 3.68 5.39 ± 0.94 5.09 ± 1.12 3.20 ± 0.62 1.45 ± 0.42 

2011 35.34 ± 8.18 12.36 ± 2.62 2.92 ± 0.81 3.60 ± 0.64 0.75 ± 0.25 

2012 35.62 ± 7.35 9.32 ± 1.94 1.89 ± 1.01 4.24 ± 0.55 0.77 ± 0.28 

Values listed in the table are mean percent coral cover. Standard errors (± SE) are 

reported from 2002–2012. Data for 1978–1982 from Gittings et al. (1992), who 

reported data from Kraemer (1982); for 1988–1991 from Gittings et al. (1992); for 

1992–1995 from Continental Shelf Associates, Inc. (CSA) (1996); for 1996–2001 from 

Dokken et al. (2003); 2002–2008 from PBS&J (Precht et al. 2006, 2008b); and FGBNMS 

for 2009–2012 (Johnston et al. 2013). 
40 

0

5

10

15

20

25

30

35

40

45

50

Mean Percent Cover

Year

Dominant Coral Cover Change at East Flower Garden Bank, 

1978-2012 OASC

Pseudodiploria strigosa

Montastraea cavernosa

Porites astereoides

Colpophyllia natans

a. TAMU, b. CSA, c. TAMU-CC, d. PBSJ, e. FGBNMS

0

5

10

15

20

25

30

35

40

45

50

Mean Percent Cover

Year

Dominant Coral Cover Change at West Flower Garden Bank, 

1978-2012 OASC

Pseudodiploria strigosa

Montastraea cavernosa

Porites astereoides

Colpophyllia natans

a. TAMU, b. CSA, c. TAMU-CC, d. PBSJ, e. FGBNMS

Figure 3.4.2. Historical representation of mean percent d o m i n a n t c o r a l cover at (A) 

EFGB and (B) WFGB. 

No m e a n percent cover data were reported in 1993. Data for 1978–1982 from Gittings 

et al. (1992), who reported data from Kraemer (1982); for 1988–1991 from Gittings et al. 

(1992); for 1992–1995 from Continental Shelf Associates, Inc. (CSA) (1996); for 1996–2001 

from Dokken et al. (2003); 2002–2008 from PBS&J (Precht et al. 2006, 2008b); and FGBNMS 

for 2009–2010 (Johnston et al. 2013). 

(B)

(A)
41 

CHAPTER 4.0: REPETITIVE QUADRATS 

4.1. REPETITIVE QUADRAT METHODOLOGICAL RATIONALE

Permanent photostation quadrats were used to monitor changes in the composition of 

benthic assemblages in repetitive sites and individual colonies at the FGB. The repetitive 

quadrats were located within the EFGB and WFGB study sites, except for the deep stations 

at EFGB and WFGB. The photographs were analyzed in two ways. The first method 

measured percent benthic cover components in 2011 and 2012 using random-dot analysis. 

For the second method, selected corals within the repetitive quadrats were analyzed using 

planimetry to measure gain or loss of planar tissue area in individual colonies. 

4.2. REPETITIVE QUADRAT METHODS

4.2.1. Repetitive Quadrat Field Methods 

Repetitive quadrats are located and marked by SCUBA divers using underwater maps 

(Volume II, Appendix 2), and then divers photograph each station. In 2011, thirty-five and 

forty 5 m2

 repetitive quadrats were photographed at EFGB and WFGB, respectively. In 2012, 

thirty-seven and forty-one 5 m2

 quadrats were photographed at EFGB and WFGB respectively 

(Figure 4.2.1). All nine EFGB deep photostations were photographed in 2011, and a total of 

twelve were photographed in 2012 after two were added during site refurbishment. Twelve 

WFGB deep photostations were installed and photographed in 2012. 

Figure 4.2.1. Repetitive quadrat station #761 at EFGB in 2012 (NOAA/FGBNMS). 
42 

In 2011 and 2012, stations were photographed using a Nikon® D300® SLR camera with 

16 mm lens in Sea&Sea® housing with small dome port. The camera was mounted in the 

center of a T-shaped camera frame, at a distance of 2 m from the substrate. Two strobes 

(Inon Z240®) were mounted 1.2 m apart on the ends of the T-frame and set on TTL. This 

set-up produced images with a coverage of 5 m2. A compass and bubble level mounted to 

the center of the t-frame ensured images were taken in a vertical and northward orientation 

to standardize the area captured, ensuring that the same quadrats were photographed in the 

same manner each year. 

4.2.2. Repetitive Quadrat Data Processing 

4.2.2.1. Percent Cover Analysis of Benthic Components 

Mean percent cover in the repetitive quadrat images was analyzed using Coral Point Count 

with Microsoft® Excel® extensions (CPCe). The percent cover was determined by overlaying 

100 random dots on each photograph, then benthic species lying under these points were 

identified. Microsoft® Excel® spreadsheets were created automatically in the program using 

customized code files pertinent to the cover of coral and other benthic species in the region. 

Organisms positioned beneath each random dot were identified as corals, sponges, 

macroalgae, or CTB, as described in section 3.2. Additional categories included other live 

components (ascidians, fish, serpulids, etc.), sand, rubble, and unknown (Volume II 

Appendix 4). After each image was analyzed, the data were entered into project-specific 

Microsoft® Excel® spreadsheets. QA/QC for the photographic methods consisted of 

multiple, scientific divers all trained on the same camera systems for correct camera 

operation. Divers were able to practice camera setup and operation with mock corals in a 

swimming pool before field work began. Statistical comparisons of identifications by 

multiple investigators were conducted to confirm the same identifications in the 

photographs to ensure that they agreed on species identifications within the frames. Each 

investigator was given sample photographs from EFGB and WFGB and identified all 

benthic components in each photograph. We found that identification of benthic 

components agreed 95% of the time with no significant difference (α=0.05) between the 

benthic components identified in the identical photographs by different investigators. 

4.2.2.2. Planimetry Analysis 

Planimetry was used to measure percent change in area of living tissue of selected coral 

colonies (i.e., Orbicella spp., Pseudodiploria strigosa, Colpophyllia natans, Montastraea 

cavernosa, Porites astreoides, Siderastrea siderea, and Stephanocoenia intersepta) at 

repetitive quadrat stations in successive years. For the 2011–2012 interval, it was possible 

to compare 32 quadrat photographs at EFGB and 39 quadrat photographs at WFGB. For 

EFGB deep stations, all nine quadrats were compared for the interval. 

Planimetry results were calculated by taking areal measurements of some coral colonies 

whose lateral margins were contained entirely within the image frame from 2011 and 2012. 

Colonies close to the center of the image, with a complete lateral margin, were selected. 

The live tissue cover of each colony was traced in Adobe® Illustrator® CS2 using a 

Wacom® Cintiq® 12WX Tablet. A mask was then created of the live tissue and areal 
43 

measurements were calculated using ImageJ®. The percent change in area for each colony 

was calculated by comparing the area of 2011 to the area of 2012. The change 

(positive=growth, or negative=retreat) in pixels was divided by the area (pixels) from 2011 

to determine proportional growth or loss of tissue area. 

4.2.3. Repetitive Quadrat Statistical Analyses 

Mean percent cover was calculated for each photo from the 100 analyzed points for each of 

the taxa and four benthic categories. Factor plots were produced in CPCe to compare the 

mean percent cover of major benthic categories and coral species between banks and 

through time. CPCe spreadsheet contents included header information, statistical 

parameters of each species/substrate type (mean, standard deviation, standard error) and the 

calculation of the Shannon–Weaver diversity index for each species (Kohler and Gill 

2006). Results are presented as mean percent cover ± standard error. 

ANOVA was performed to test the null hypotheses that the response variables of 

univariate benthic cover did not differ by year (2011 and 2012) and bank (EFGB and 

WFGB). ANOVAs were calculated for each variable with the statistical software JMP®

version 10.0. Data were tested for normality and square root transformed as necessary to 

assume a normal distribution to meet the assumptions of parametric statistical tests 

(Zimmer et al. 2010). However, the ANOVA procedure is robust enough to perform 

calculations on data that deviate from normal assumptions (Zar 1984). 

A two-tailed t-test was performed to test the null hypotheses that the response variables of 

univariate margin cover did not differ between banks for the planimtery analysis. T-tests 

were calculated to identify differences in marginal percent change of dominant corals with 

the statistical software JMP® version 10.0. Data were tested for normality to meet the 

assumptions of parametric statistical tests. 

Multivariate statistical techniques were used to compare how the two banks may differ in 

benthic composition. Based on benthic mean percent cover, comparisons in community 

differences between the two banks were made using nonparametric analysis for non-normal 

data. Significant dissimilarities were tested using ANOSIM with square root transformation 

and Bray-Curtis similarity resemblance measure. Cluster analyses were performed on 

similarity matrices, and MDS was used to visualize community dissimilarities by bank. 

Ordinations were run using 100 random starting configurations to determine the best fit 

model and minimize stress. SIMPER was used to analyze community dissimilarity between 

year and bank and highlight species that contributed to the observed dissimilarity. The R 

statistic, typically ranging between 0 and 1, indicates between and within group 

dissimilarities, where R values less than 0.3 indicate that similarities between sites and 

within sites are the same (Clarke & Warwick 2001). All analyses were all carried out using 

Primer® version 6.0. 

For long-term trends, each functional group sample was averaged by year and compared 

using nonparametric analysis for non-normal data. Mean percent cover data of each 

functional group were used to calculate ecological distance via Bray-Curtis similarity 

matrices. Data were square root transformed to minimize the impacts of extremely 

dominant members of the community. Cluster analyses were performed on similarity 
44 

matrices, and MDS plots were used to visualize community dissimilarities between years, 

with time series trajectory to highlight community shifts over time. SIMPER identified the 

greatest contributors to the observed dissimilarity. 

4.3. REPETITIVE QUADRAT RESULTS

4.3.1. Repetitive Quadrat Analysis

4.3.1.1. Repetitive Quadrat Percent Cover 

The point count data from the repetitive quadrats in the 10,000 m2

 study sites were 

expressed as mean percent cover ± standard error (SE), the same way the random transect 

data were displayed in section 3.4. In general, repetitive quadrat results from 2011 and 

2012 revealed higher mean percent coral cover (63%) than random transects (56%), 

followed by macroalgae cover (24%), CTB cover (11%), and very low coverage of sponges 

(including encrusting sponges) (0.3%) (Figure 4.3.1). Macroalgae cover increased at both 

banks over both years. The higher mean coral cover at repetitive stations, when compared 

to random transect coral cover (56%) was to be expected, because the stations were 

originally selected as premium monitoring sites with high coral cover to track individual 

sites and colonies over time. They were not selected to be representative of average benthic 

percent cover. Volume II Appendix 8 of this report contains the repetitive quadrat data for 

2011 and 2012 at the FGB. 

At EFGB, mean coral cover remained above 60 percent from 2011–2012 (63.29% ± 2.97 

to 63.29% ± 2.83), while the sponge cover remained extremely low for both years (0.46% 

± 0.18 to 0.47% ± 0.22) (Figure 4.3.1 and Table 4.3.1). Macroalgae cover (mainly 

Dictyota spp. and fleshy algae) increased from 2011–2012 (24.85% ± 2.40 to 26.27% ± 

2.53), and CTB cover remained stable (10.83% ± 0.91 to 9.02% ± 0.82) as well. 

In quadrats at WFGB, mean coral cover remained above 60% from 2011 (63.54% ± 2.30) 

to 2012 (63.50% ± 2.09). The sponge cover remained extremely low for both years at 

WFGB (0.11% ± 0.09 to 0.22% ± 0.15) (Figure 4.3.1 and Table 4.3.1). Macroalgae cover 

increased from 2011–2012 (20.90% ± 1.76 to 22.54% ± 1.80) and CTB cover remained 

stable (13.79% ± 1.12 to 11.98% ± 1.08) between both years. 
45 

0

10

20

30

40

50

60

70

80

90

100

2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB

Mean Percent Cover

Bank and Year

Mean Percent Cover of Repetitive Quadrat Functional Catagories 

at the Flower Garden Banks, 2011-2012

Coral

Macroalgae

CTB

Sponge

Figure 4.3.1. Mean percent cover + SE of four functional benthic categories at the 

FGB in 2011 and 2012. 

Values calculated from repetitive quadrat photographs. 
46 

Table 4.3.1. 

 

Mean Percent Cover ± SE of Benthic Categories in Repetitive Quadrats at EFGB and WFGB in 

2011 and 2012 (listed from most to least abundant). 

Cover Category 2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB 

Coral 

Orbicella franksi 30.72 ± 3.11 30.94 ± 3.11 28.81 ± 2.62 29.35 ± 2.49 

Pseudodiploria strigosa 11.39 ± 1.82 9.95 ± 1.60 9.87 ± 1.66 8.42 ± 1.42 

Unidentified OASC (Orbicella spp.) 5.95 ± 1.40 4.92 ± 1.55 7.92 ± 2.31 7.25 ± 1.90 

Orbicella faveolata 4.48 ± 1.42 5.73 ± 1.51 3.41 ± 1.39 1.72 ± 0.92 

Porites astereoides 3.72 ± 0.48 4.35 ± 0.54 4.36 ± 0.59 3.71 ± 0.44 

Montastraea cavernosa 3.52 ± 1.05 3.75 ± 1.05 3.40 ± 1.02 3.37 ± 0.93 

Colpophyllia natans 0.91 ± 0.29 1.78 ± 0.48 1.20 ± 0.46 3.33 ± 0.71 

Unidentified Coral 1.53 ± 0.48 0.85 ± 0.25 0.91 ± 0.22 1.68 ± 0.38 

Agaricia agaricites 0.10 ± 0.07 0.09 ± 0.07 0.08 ± 0.05 0.05 ± 0.04 

Orbicella annularis 0.31 ± 0.18 0.18 ± 0.18 1.77 ± 0.87 2.63 ± 1.14 

Millepora alcicornis 0.23 ± 0.09 0.21 ± 0.08 0.17 ± 0.08 0.18 ± 0.09 

Stephanocoenia intersepta 0.19 ± 0.08 0.13 ± 0.08 0.66 ± 0.24 0.46 ± 0.16 

Madracis decactis 0.07 ± 0.07 0.07 ± 0.05 0.16 ± 0.09 0.17 ± 0.10 

Mussa angulosa 0.06 ± 0.04 0.03 ± 0.03 0.08 ± 0.05 0.11 ± 0.07 

Porites furcata 0.06 ± 0.04 0.00 0.03 ± 0.03 0.00 

Leptoseris cucullata 0.03 ± 0.03 0.00 0.00 0.00 

Siderastrea siderea 0.03 ± 0.03 0.32 ± 0.29 0.56 ± 0.44 1.00 ± 0.85 

Madracis auretenra 0.00 0.00 0.06 ± 0.04 0.03 ± 0.03 

Agaricia spp. 0.00 0.00 0.00 0.00 

Scolymia cubensis 0.00 0.00 0.00 0.03 ± 0.03 

Total Mean Coral 63.29 ± 2.97 63.29 ± 2.83 63.54 ± 2.30 63.50 ± 2.09 

Sponge 

Unknown Sponge 0.22 ± 0.16 0.12 ± 0.09 0.03 ± 0.03 0.03 ± 0.03 

Aiolochroia (Pseudoceratina) crassa 0.13 ± 0.07 0.03 ± 0.03 0.00 0.00 

Ircinia felix 0.06 ± 0.06 0.06 ± 0.04 0.06 ± 0.04 0.00 

Xestospongia muta 0.03 ± 0.03 0.00 0.00 0.03 ± 0.03 

Encrusting sponge 0.03 ± 0.03 0.25 ± 0.18 0.03 ± 0.03 0.08 ± 0.06 

Agelas clathrodes 0.00 0.00 0.00 0.08 ± 0.06 

Total Mean Sponge 0.46 ± 0.18 0.47 ± 0.22 0.11 ± 0.09 0.22 ± 0.15 

CTB 

Bare Substrate 4.99 ± 0.51 3.12 ± 0.38 7.30 ± 0.62 4.89 ± 0.49 

Fine Turf 3.96 ± 0.63 4.93 ± 0.63 3.04 ± 0.49 5.39 ± 0.76 

Crustose Coralline Algae 1.75 ± 0.38 0.90 ± 0.24 2.93 ± 0.58 1.11 ± 0.23 

Total Mean CTB 10.83 ± 0.91 9.02 ± 0.82 13.79 ± 1.12 11.98 ± 1.08 

Macroalgae 

Dictyota spp. 10.56 ± 1.45 12.25 ± 1.60 1.39 ± 0.40 1.96 ± 0.39 

Fleshy Algae 9.05 ± 1.00 8.87 ± 1.00 9.10 ± 0.93 9.76 ± 1.15 
47 

Cover Category 2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB 

Lobophora variegata 3.66 ± 0.66 2.21 ± 0.41 8.24 ± 1.06 6.84 ± 0.90 

Thick Turf Algae 1.58 ± 0.29 2.68 ± 0.53 2.06 ± 0.28 3.97 ± 0.49 

Filamentous Algae 0.00 0.26 ± 0.15 0.11 ± 0.07 0.00 

Total Mean Macroalgae 24.85 ± 2.40 26.27 ± 2.53 20.90 ± 1.76 22.54 ± 1.80 

Orbicella franksi was the dominant coral cover component at the EFGB repetitive stations 

in 2011 (30.72% ± 3.11) and 2012 (30.94% ± 3.11). Pseudodiploria strigosa (11.39% ± 

1.82 and 9.95% ± 1.60 in 2011 and 2012, respectively) and Orbicella spp. that could not be 

differentiated were the next most abundant taxa (5.95% ± 1.40 in 2011 and 4.92% ± 1.55 in 

2012), followed by Orbicella faveolata, Porites astereodes, and Montastrea cavernosa

(Figure 4.3.2 and Table 4.3.1). The remaining coral cover was made up of thirteen 

species, none of which exceeded 2.0% in either year (Table 4.3.1). Corals that could 

not be differentiated (less then 2%) because of camera angle or camera distortion were 

labeled as “unidentified coral.” Shannon-Wiener diversity values remained consistent at 

EFGB (H’= 0.84 and H’= 0.83 in 2011 and 2012, respectively). 

As with EFGB, Orbicella franksi was the dominant coral cover component at WFGB 

repetitive stations in 2011 (28.81% ± 2.62) and 2012 (29.35% ± 2.49). Pseudodiploria 

strigosa (9.87% ± 1.66 and 8.42% ± 1.42 in 2011 and 2012, respectively) and Orbicella 

spp. that could not be differentiated (7.92% ± 2.31 in 2011 and 7.25% ± 1.90 in 2012) were 

the next most abundant taxa, followed by Porites astereodes, Montastrea cavernosa, and 

Orbicella faveolata (Figure 4.3.3 and Table 4.3.1). The remaining coral cover was made 

up of thirteen species, none of which exceeded 4.0% in either year (Table 4.3.1). 

Corals that could not be differentiated (less then 2%) because of camera angle or camera 

distortion were labeled as “unidentified coral.” Shannon-Wiener diversity values remained 

consistent at WFGB (H’=0.86 and H’=0.87 in 2011 and 2012, respectively). 

In the repetitive quadrats in 2011 and 2012, the incidences of bleaching, paling, disease, and 

fish biting were extremely low at both banks (Table 4.3.2). The mean percentage of corals 

impacted by isolated or concentrated fish biting at EFGB and WFGB ranged from 0.00 to 

0.17%. Less than 0.3% of the coral cover analyzed in the repetitive quadrats exhibited 

signs of disease, and less than 1% of the coral cover analyzed showed signs of bleaching or 

paling at EFGB and WFGB in either year. It is important to note that bleaching as 

determined by the long-term monitoring methodology may be incomplete, as surveys 

usually occur when weather is optimal (e.g., before hurricane season) in earlier summer 

months before signs of bleaching occur. 
48 

0 5 10 15 20 25 30 35

Orbicella franksi

Psuedodiploria strigosa

Orbicella spp.

Orbicella faveolata

Porites astreoides

Montastraea cavernosa

Unidentified Coral

Colpophyllia natans

Millepora alcicornis

Siderastrea siderea

Orbicella annularis

Mean Percent Cover

Coral Species

Mean Percent Cover of Dominant Coral Species at

East Flower Garden Bank, 2011-2012

2011

2012

Figure 4.3.2. Mean percent cover + SE of dominant observed coral species in 

repetitive quadrats at EFGB in 2011 and 2012. 

0 5 10 15 20 25 30 35

Orbicella franksi

Psuedodiploria strigosa

Orbicella spp.

Orbicella faveolata

Porites astreoides

Montastraea cavernosa

Colpophyllia natans

Orbicella annularis

Unidentified Coral

Millepora alcicornis

Siderastrea siderea

Mean Percent Cover

Coral Species

Mean Percent Cover of Dominant Coral Species at 

West Flower Garden Bank, 2011-2012

2011

2012

Figure 4.3.3. Mean percent cover + SE of dominant observed coral species 

in repetitive quadrats at WFGB in 2011 and 2012. 
49 

Table 4.3.2. 

 

Mean Percent Cover ± SE of Coral Condition Categories in Repetitive Quadrats at EFGB 

and WFGB from 2011 and 2012. 

Cover Category 2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB 

Coral Condition (occurrences in coral) 

Bleached Coral 0.00 0.05 ± 0.04 0.00 0.00 

Paling Coral 0.20 ± 0.11 0.22 ± 0.10 0.63 ± 0.26 0.00 

Isolated Fish Biting 0.00 0.03 ± 0.03 0.03 ± 0.03 0.00 

Concentrated Fish Biting 0.00 0.11 ± 0.08 0.00 0.17 ± 0.10 

Disease 0.00 0.14 ± 0.10 0.00 0.02 ± 0.02 

In summary, the combined data collected in 2011 and 2012 showed persistence of 

Orbicella franksi as the dominant coral species in the repetitive quadrats at EFGB and 

WFGB (Table 4.3.1). Pseudodiploria strigosa was the second-most prevalent coral 

species during this time period. Orbicella spp. corals that could not be differentiated, along 

with Orbicella faveolata, Porites astreoides, and Montastraea cavernosa were 

consistently the third, fourth, and fifth most abundant corals observed. The mean percent 

coral cover in the repetitive quadrats at both banks was 63.41 ± 2.55 for the reporting 

period. This was higher than the random transect mean percent cover for both banks 

(56.07%), but, as explained previously, the coral in the repetitive stations were selected 

partly because of their high coral cover. 

4.3.1.2. Repetitive Quadrat Univariate Analysis 

The repetitive quadrat point count data expressed as mean percent cover was analyzed by 

one-way ANOVA, with bank and year as fixed factors with an experimentwise error rate of 

α=0.05. The data on proportional cover were non-normal, so categories were square root 

transformed. The one-way ANOVA showed no significant difference between bank or year 

for coral or macroalgae. A two-way ANOVA displaying the bank by year interaction was 

also not significant for coral and macroalgae (Table 4.3.3). 

A one-way ANOVA on the proportional cover of CTB a n d s p o n g e s showed no 

significant difference between years; however, the effects of bank on sponges (Pvalue=0.02) and CTB (P-value=0.01) were significant. The two-way ANOVA displaying 

the bank by year interaction were significant for sponges (P-value=0.04) and CTB (Pvalue=0.02) as well in the repetitive quadrats (Table 4.3.3). Overall, CTB cover was higher 

at WFGB than EFGB during the study period, and sponge cover was higher at EFGB. 

Tukey–Kramer a posteriori comparisons showed that CTB cover was significantly higher 

(P-value=0.03) at WFGB than EFGB, and sponge cover was significantly higher at EFGB 

(P-value=0.03). 
50 

Table 4.3.3. 

 

Results of ANOVA on Mean Percent Cover Estimates from Repetitive Quadrats 

from 2011 and 2012 

Source Sum of Squares df Mean Square F-ratio P-value 

(A) Corals 

Bank 0.16 1 0.16 0.07 0.79 

Year 0.01 1 0.01 0.01 0.98 

Bank*Year 0.17 2 0.08 0.03 0.97 

Error 382.85 162 2.36 

Total 383.01 164 

(B) Sponges 

Bank 1.07 1 1.07 5.88 0.02 

Year 0.09 1 0.09 0.51 0.47 

Bank*Year 1.17 2 0.58 3.20 0.04 

Error 29.48 162 0.05 

Total 30.65 164 

(C) Macroalgae 

Bank 4.77 1 4.77 2.50 0.12 

Year 1.32 1 1.32 0.69 0.41 

Bank*Year 6.06 2 3.03 1.59 0.21 

Error 309.07 162 0.09 1.27 0.28 

Total 315.13 164 

(D) CTB 

Bank 7.45 1 7.45 8.52 0.01 

Year 3.14 1 3.14 3.49 0.06 

Bank*Year 10.53 2 5.26 6.12 0.02 

Error 139.45 162 0.08 

Total 149.98 164 

Comparisons of groups where ANOVA was performed are in bold with 

appropriate P values where significant. 

4.3.1.3. Repetitive Quadrat Multivariate Analysis 

The point counts for the repetitive quadrats were further analyzed by using multivariate 

techniques. Multivariate cover analysis was compared between bank and year using 

ANOSIM. There were no significant differences between years, and there were no 

significant differences between banks, resulting in no multivariate interaction. These results 

differ from the ANOVA, which detected individually significant sponge and CTB 

differences. However, these within group dissimilarities may not have been significant 

enough to detect an overall community difference between banks in the ANOSIM analysis. 
51 

Cluster analysis and MDS plot placed the repetitive quadrat cover between bank and year 

in two tight clusters trending to the right of the ordination (80% similarity), with three 

outlier groups. The stress level of the MDS was 0.07, indicating good goodness-of-fit in a 

two-dimensional scale, suggesting high confidence in the pattern displayed (Figure 4.3.4). 

These results agree with the ANOSIM quadrats were similar between years and banks. 

Figure 4.3.4. Two-dimensional MDS plot based on Bray-Curtis similarities 

showing the spatial representation of repetitive quadrat 

benthic community cover similarities between EFGB and 

WFGB for 2011 and 2012. 

The green circles group surveys that are 80% similar. 

4.3.1.4. Historical Comparison of Repetitive Quadrat Benthic Cover 

The mean percent benthic cover from the four functional categories from the repetitive 

quadrats was analyzed to measure changes over time at the repetitive quadrat 

photostations. Mean percent coral cover was not collected at the repetitive quadrat stations 

until 1992, and the remaining three categories did not begin until 2002. No data were 

collected in 1993 due to poor weather, and cover data were not calculated in 1998 or 1999. 

Mean percent coral cover i n t h e r e p e t i t i v e q u a d r a t s showed an overall increase 

in b e n t h i c cover during the period from 1992–2012 at EFGB; highest cover was 

recorded in 2002 and the mean was of approximately 61% cover over time. Coral cover in 

the repetitive quadrats at WFGB showed an overall increase from 1992–2012; the highest 

cover was recorded in 2010 and the mean was of approximately 60% overtime (Figure 

4.3.5 and Table 4.3.4). Periods of lower CTB cover generally coincided with increases in 

the algal component, and led to a reciprocal relationship between macroalgae and CTB 

cover. 
52 

The increase in coral cover at both banks from 2001–2002 may be a result of the 

monitoring program being awarded to a different contract company in 2002, with new staff 

and different expertise analyzing the monitoring data. It should also be noted that slight 

increases in coral cover from 2009–2010 most likely were due to changing camera systems. 

The camera system from 2009 captured a smaller area than the system in 2010, resulting in 

the necessary cropping of 2010 photos for comparison. This resulted in coral colonies in 

the center of the photostations comprising a larger percentage of the captured photos than 

in past monitoring periods, inflating coral cover for both years in CPCe (Johnston et al. 

2013). Updated camera systems corrected for this in 2011 and 2012, and captured an area 

of 5 m2

. 

The historical cover from repetitive quadrats was further analyzed by using multivariate 

techniques. Multivariate historical cover analysis from EFGB and WFGB was compared 

between years (complete dataset from 2002–2012) to calculate mean benthic cover change 

over a large time scale. SIMPER analysis identified that, for most comparisons between 

2002 and 2012, the greatest contributors to the observed dissimilarity were CTB and 

macroalgae. 
53 

0

10

20

30

40

50

60

70

80

Mean Percent Cover

Year

Mean Percent Cover of Repetitive Quadrat Four Functional 

Categories at East Flower Garden Bank, 1992-2012

Coral

Sponge

Macroalgae

CTB

b. CSA, c. TAMU-CC, d. PBSJ, e. FGBNMS

0

10

20

30

40

50

60

70

80

Mean Percent Cover

Year

Mean Percent Cover of Repetitive Quadrat Four Functional 

Categories at West Flower Garden Bank, 1992-2012

Coral

Sponge

Macroalgae

CTB

b. CSA, c. TAMU-CC, d. PBSJ, e. FGBNMS

Figure 4.3.5. Historical representation of mean percent cover of coral, sponge, 

macroalgae, and CTB in repetitive quadrats at (A) EFGB and (B) WFGB. 

No percent cover data were reported in 1993. Data for 1992–1995 was reported from 

Continental Shelf Associates, Inc. (CSA) (1996); for 1996–2001 from Dokken et al. (2003); 

2002–2008 from PBS&J (Precht et al. 2006, 2008b); and FGBNMS for 2009–2010 (Johnston 

et al. 2013). 

(A) 

(B) 
54 

Table 4.3.4. 

 

EFGB and WFGB Repetitive Quadrat Data for Dominant Cover Categories from 1992–2012. 

EFGB Repetitive Quadrat Data 

Year Coral Sponge Macroalgae CTB 

1992 50.6 NA NA NA 

1994 49.3 NA NA NA 

1995 50.2 NA NA NA 

1996 58.2 NA NA NA 

1997 57 NA NA NA 

2000 53.1 NA NA NA 

2001 51.6 NA NA NA 

2002 72.9 NA 10.7 14.9 

2003 71.1 NA 19.6 5.8 

2004 62.98 ± 2.72 0.09 ± 0.04 3.00 ± 0.58 30.83 ± 2.52 

2005 62.78 ± 2.60 0.12 ± 0.06 23.78 ± 2.13 10.39 ± 1.16 

2006 62.87 ± 2.32 0.26 ± 0.13 18.45 ± 1.36 16.91 ± 1.24 

2007 61.43 ± 2.64 0.42 ± 0.13 20.04 ± 1.62 16.21 ± 1.10 

2008 61.46 ± 2.82 0.16 ± 0.08 18.92 ± 1.69 17.89 ± 1.52 

2009 69.27 ± 2.69 0.24 ± 0.11 19.27 ± 1.98 10.83 ± 0.94 

2010 72.41 ± 2.56 0.19 ± 0.08 15.37 ± 1.71 11.69 ± 1.14 

2011 63.29 ± 2.97 0.46 ± 0.18 24.85 ± 2.40 10.83 ± 0.91 

2012 63.29 ± 2.83 0.47 ± 0.22 26.27 ± 2.53 9.02 ± 0.82 
55 

WFGB Repetitive Quadrat Data 

Year Coral Sponge Macroalgae CTB 

1992 48 NA NA NA 

1994 45.1 NA NA NA 

1995 47.4 NA NA NA 

1996 56.6 NA NA NA 

1997 56.5 NA NA NA 

2000 50 NA NA NA 

2001 48.3 NA NA NA 

2002 70.3 NA 13.5 15.4 

2003 68.6 NA 9.6 20.1 

2004 65.68 ± 3.09 0.08 ± 0.09 2.23 ± 0.66 24.54 ± 3.04 

2005 65.57 ± 3.38 0.16 ± 0.12 10.04 ± 2.36 17.91 ± 1.86 

2006 66.17 ± 1.98 0.42 ± 0.12 11.45 ± 1.00 18.97 ± 1.41 

2007 62.47 ± 2.06 0.45 ± 0.15 10.54 ± 0.97 22.91 ± 1.55 

2008 63.86 ± 1.86 0.19 ± 0.08 9.92 ± 1.02 22.07 ± 1.35 

2009 72.19 ± 2.49 0.03 ± 0.03 11.65 ± 1.53 15.41 ± 1.51 

2010 74.19 ± 2.07 0.11 ± 0.06 7.46 ± 1.01 14.69 ± 1.21 

2011 63.54 ± 2.30 0.11 ± 0.09 20.90 ± 1.76 13.79 ± 1.12 

2012 63.50 ± 2.09 0.22 ± 0.15 22.54 ± 1.80 11.98 ± 1.08 

Values listed in the table are mean percent covers. Standard errors (± SE) are reported 

from 2002–2012. Data for 1978–1982 from Gittings et al. (1992), who reported data 

from Kraemer (1982); for 1988–1991 from Gittings et al. (1992); for 1992–1995 from 

Continental Shelf Associates, Inc. (CSA) (1996); for 1996–2001 from Dokken et al. 

(2003); 2002–2008 from PBS&J (Precht et al. 2006, 2008b); and FGBNMS for 2009–

2012 (Johnston et al. 2013). 

Cluster analysis and MDS plot placed the cover analysis from 2002–2012 in one tight 

cluster (90% similarity), with the year 2004 as an outlier. The low stress level (0.01) 

indicated good goodness-of-fit in a 2-dimensional scale, suggesting high confidence in the 

pattern displayed (Figure 4.3.6). Overall, these results agree with the ANOSIM (no 

significant differences of bank or year occur between EFGB and WFGB), and make the 

banks similar in terms of benthic composition for the repetitive quadrats. 
56 

Figure 4.3.6. Two-dimensional MDS plot based on Bray-Curtis similarities 

comparing benthic cover analysis from 2002–2012 in repetitive 

quadrats at EFGB and WFGB. 

The green circle groups years that are 90% similar. 

The coral cover increases generally coincided with lower macroalgal cover, and periods 

of lower coral cover generally coincided with increases in the algal component and 

decreases in the CTB category (Figure 4.3.5. and Table 4.3.4). In 2004 macroalgae cover 

decreased, but in 2005, macroalgae cover was observed to increase, which led to a 

reciprocal relationship between macroalgae and CTB cover until 2010. After 2010, 

macroalgae was greater than CTB cover, as macroalgae cover continued to increase. These 

trends correspond to SIMPER results, and suggest that the greatest contributors to the 

observed dissimilarity over time were CTB and macroalgae. This also corresponds to the 

MDS analysis, and suggests that 2002–2012 the community was stable, with the exception 

of 2004 when algae declined. These results are similar to the random transects: stable coral 

cover but with increasing macroalgae percent cover throughout the monitoring program. 

4.3.2. Repetitive Deep Station Percent Cover 

All EFGB deep photostations were photographed in 2011 (nine stations) and 2012 (twelve 

stations) and analyzed for benthic cover using random dot analysis. Twelve WFGB deep 

photostations were installed and photographed in 2012. The point count data were grouped 

into four functional categories and expressed as mean percent covers, the same way the 

random transect point counts and repetitive quadrats were displayed. Mean percent coral 

cover ranged from 72–77% between 2011 and 2012, and sponge cover was extremely low 

(0.00–0.93%). Mean coral cover was followed by macroalgae (19%) and CTB cover (7%) 

(Figure 4.3.7). Volume II Appendix 8 of this report contains the repetitive deep station data 

for 2011 and 2012. 
57 

At WFGB, 2012 was the first year deep repetitive photographs were taken and analyzed. 

Coral cover (76.96% ± 4.77) was above 70 percent in 2012 and sponge cover was very 

low (0.93% ± 0.49). Macroalgae cover was lower at WFGB (13.87% ± 3.00) while CTB 

cover (7.29% ± 2.09) was comparable to EFGB (Figure 4.3.7 and Table 4.3.5). 

At EFGB, mean coral cover remained above 70 percent from 2011–2012 (72.81% ± 3.99 

to 72.22% ± 4.43). Sponge cover was very low in 2011 (0.12% ± 0.12) and not detected in 

2012. Macroalgae cover (mainly fleshy algae, Lobophora variegata, and Dictyota spp.) 

remained stable from 2011–2012 (20.66% ± 3.99 to 20.97% ± 3.52), as did CTB cover 

(5.54% ± 0.93 to 6.70% ± 1.09) (Figure 4.3.7 and Table 4.3.5). 

0

10

20

30

40

50

60

70

80

90

100

2011 EFGB 2012 EFGB 2012 WFGB

Mean Percent Cover

Bank and Year

Mean Percent Cover of Repetitive Deep Station Functional 

Categories at the Flower Garden Banks, 2011-2012 

Coral

Macroalgae

CTB

Sponge

Figure 4.3.7. Mean percent cover + SE of four functional benthic categories at the 

FGB repetitive deep stations in 2011 and 2012. 
58 

Table 4.3.5. 

 

Mean Percent Cover ± SE of Benthic Categories in Repetitive Deep Stations at EFGB 

from 2011 and 2012, and at WFGB in 2012 (listed from most to least abundant). 

Cover Category 2011 EFGB 

Deep Stations 

2012 EFGB 

Deep Stations 

2012 WFGB 

Deep Stations 

Coral 

Orbicella franksi 34.82 ± 4.77 38.79 ± 5.14 30.00 ± 6.19 

Montastraea cavernosa 14.44 ± 3.54 17.68 ± 4.78 17.13 ± 4.43 

Orbicella spp. 7.07 ± 3.85 3.35 ± 1.12 4.44 ± 2.78 

Colpophyllia natans 5.22 ± 2.89 4.56 ± 1.85 0.94 ± 0.54 

Pseudodiploria strigosa 2.29 ± 1.52 1.85 ± 0.83 2.41 ± 1.27 

Unidentified Coral 2.44 ± 0.92 0.57 ± 0.46 3.68 ± 0.81 

Millepora alcicornis 2.07 ± 1.27 1.15 ± 0.80 0.66 ± 0.28 

Stephanocoenia intersepta 1.86 ± 0.95 1.27 ± 0.63 8.91 ± 3.63 

Mussa angulosa 1.28 ± 0.70 1.15 ± 0.63 0.00 

Porites astereoides 0.64 ± 0.52 0.81 ± 0.68 2.53 ± 1.15 

Orbicella faveolata 0.34 ± 0.34 0.58 ± 0.35 1.15 ± 0.62 

Agaricia spp. 0.23 ± 0.23 0.11 ± 0.11 0.09 ± 0.09 

Madracis decactis 0.00 0.00 1.54 ± 1.16 

Madracis auretenra 0.12 ± 0.12 0.00 3.26 ± 2.31 

Madracis spp. 0.00 0.00 0.12 ± 0.12 

Orbicella annularis 0.00 0.00 0.10 ± 0.10 

Scolymia cubensis 0.00 0.35 ± 0.25 0.00 

Total Coral 72.81 ± 3.99 72.22 ± 4.43 76.96 ± 4.77 

Sponge 

Encructing sponge 0.00 0.00 0.19 ± 0.13 

Ircinia strobilina 0.00 0.00 0.10 ± 0.10 

Agelas clathrodes 0.00 0.00 0.09 ± 0.09 

Total Sponge 0.12 ± 0.12 0.00 0.93 ± 0.49 

Macroalgae 

Fleshy algae 10.71 ± 2.46 14.01 ± 2.27 9.09 ± 1.87 

Lobophora variegata 6.90 ± 1.48 5.12 ± 1.52 1.42 ± 0.54 

Dictyota spp. 2.19 ± 0.80 1.27 ± 0.51 1.15 ± 0.35 

Thick turf algae 0.73 ± 0.36 0.57 ± 0.35 2.21 ± 1.21 

Filamentous Algae 0.13 ± 0.13 0.00 0.00 

Total Macroalgae 20.66 ± 4.00 20.97 ± 3.52 13.87 ± 3.00 

CTB 

Bare Substrate 2.29 ± 0.57 3.34 ± 0.78 1.51 ± 0.51 

Fine Turf 1.68 ± 0.56 2.07 ± 0.79 3.92 ± 1.65 
59 

Cover Category 2011 EFGB 

Deep Stations 

2012 EFGB 

Deep Stations 

2012 WFGB 

Deep Stations 

Crustose Coralline Algae 1.09 ± 0.18 1.17 ± 0.60 1.07 ± 0.53 

Total CTB 5.54 ± 0.93 6.70 ± 1.09 7.29 ± 2.09 

Other 

Shadow 7.78 ± 1.62 2.11 ± 0.72 10.83 ± 1.65 

Wand 1.22 ± 0.43 1.44 ± 0.41 2.17 ± 0.42 

Sand 0.48 ± 0.36 0.00 0.56 ± 0.29 

Fish 0.26 ± 0.17 0.00 0.00 

Invertebrate 0.12 ± 0.12 0.11 ± 0.11 0.19 ± 0.13 

Tag 0.11 ± 0.11 0.11 ± 0.11 0.00 

Consistent with past monitoring results, Orbicella franksi continued to dominate the EFGB 

repetitive deep stations in 2011 and 2012; it increased from 2011–2012 (34.82% ± 4.77 to 

38.79% ± 5.14). Different from the shallower repetitive quadrats and random transects, 

Montastraea cavernosa (14.44% ± 3.54 and 17.68% ± 4.78 in 2011and 2012) was the next 

dominant deep station coral at EFGB. This was followed by Orbicella spp. that could not 

be differentiated (7.07% ± 3.85 to 3.34% ± 1.12), Colpophyllia natans (5.22% ± 2.89 to 

4.56% ± 1.85), and Pseudodiploria strigosa (2.29% ± 1.52 to 1.85% ± 0.82) in 2011 and 

2012. The remaining coral cover was made up of 10 species, none of which exceeded 

m o r e than 3.0% in either year (Table 4.3.5). Corals that could not be differentiated 

due to camera angle or camera distortion were labeled as “unidentified coral” (Figure 

4.3.8). 

At WFGB in 2012, Orbicella franksi was the main component (30.00% ± 6.19). 

Montastraea cavernosa (17.13% ± 4.43) was the next dominate deep station coral at 

WFGB. This was followed by Stephanocoenia intersepta (8.91% ± 3.63) and Orbicella 

spp. components that could not be differentiated (4.44% ± 2.78). The remaining coral 

cover was made up of 10 species, none of which exceeded m o r e than 4% of the 

total cover (Table 4.3.5). Corals that could not be differentiated due to camera angle or 

camera distortion were labeled as “unidentified coral” (Figure 4.3.9). 
60 

0 10 20 30 40 50

Orbicella franksi

Montastraea cavernosa

Orbicella spp.

Colpophyllia natans

Pseudodiploria strigosa

Millepora alcicornis

Unidentified Coral

Stephanocoenia intersepta

Mussa angulosa

Porites astereoides

Orbicella faveolata

Mean Percent Cover

Coral Species

Mean Percent Cover of Dominant Coral Species at East Flower 

Garden Bank Repetitive Deep Stations, 2011-2012

2011

2012

Figure 4.3.8. Mean percent cover + SE of the observed dominant coral species at 

EFGB repetitive deep stations in 2011 and 2012. 

 

0 10 20 30 40 50

Orbicella franksi

Montastraea cavernosa

Stephanocoenia intersepta

Orbicella spp.

Unidentified Coral

Madracis mirabilis

Porites astereoides

Pseudodiploria strigosa

Madracis decactis

Orbicella faveolata

Colpophyllia natans

Millepora alcicornis

Mean Percent Cover

Coral Species

Mean Percent Cover of Dominant Coral Species at West Flower 

Garden Bank Repetitive Deep Stations, 2012

2012

Figure 4.3.9. Mean percent cover + SE of the observed dominant coral species at 

WFGB repetitive deep stations in 2012. 
61 

In EFGB repetitive deep stations in 2011 and 2012, the incidences of bleaching, paling, 

disease, and fish biting were extremely low. The percentage of corals impacted by isolated 

or concentrated fish biting ranged from 0.00 to 0.11%. The coral cover analyzed in the 

deep repetitive quadrats exhibited no signs of disease or bleaching; only 2% of the mean 

coral cover analyzed showed signs of paling at EFGB in 2011 and 0.11% in 2012. There were 

no signs of bleaching, paling, disease, or fish biting at WFGB deep stations (Table 4.3.6). 

Table 4.3.6. 

 

Mean Percent Cover ± SE of Coral Condition Categories in Repetitive Deep Stations 

at EFGB from 2011 and 2012, and at WFGB in 2012. 

Cover Category 2011 EFGB 

Deep Stations 

2012 EFGB 

Deep Stations 

2012 WFGB 

Deep Stations 

Coral Condition (occurrences in coral) 

Bleached Coral 0.00 0.00 0.00 

Paling Coral 2.00 ± 1.76 0.11 ± 0.11 0.00 

Concentrated Fish Biting 0.11 ± 0.11 0.00 0.00 

Isolated Fish Biting 0.00 0.00 0.00 

Other Disease 0.00 0.00 0.00 

4.3.2.1. Repetitive Deep Station Univariate Analysis 

EFGB deep repetitive station point count data grouped into four major functional 

categories and expressed as mean percent covers were analyzed by one-way ANOVA with 

year as a fixed factor and an experimentwise error rate of α=0.05. The 2012 EFGB and 

WFGB deep station point count mean percent cover data were analyzed by one-way 

ANOVA, with bank as a fixed factor. The data on proportional cover for sponges and CTB 

were non-normal, so categories were square root transformed. 

A one-way ANOVA on the proportional cover of all observed corals, sponge, macroalgae, 

and CTB at EFGB deep stations showed no significant difference between years (Table 

4.3.7). A one-way ANOVA on the proportional cover of all observed corals, sponge, 

macroalgae, and CTB between EFGB and WFGB deep stations showed no significant 

difference between banks (Table 4.3.8). 
62 

Table 4.3.7. 

 

Results of ANOVA on Mean Percent Cover Estimates from EFGB Repetitive 

Deep Stations from 2011 and 2012 

Source Sum of Squares df Mean Square F-ratio P-value 

(A) Corals 

Year 0.01 1 0.01 0.01 0.90 

Error 9.62 16 0.60 

(B) Sponges 

Year 0.06 1 0.06 1.00 0.33 

Error 0.96 16 0.06 

(C) Macroalgae 

Year 0.05 1 0.05 0.03 0.85 

Error 24.19 16 1.51 

(D) CTB 

Year 0.22 1 0.22 0.61 0.45 

Error 5.74 16 0.36 

Table 4.3.8. 

 

Results of ANOVA on Mean Percent Cover Estimates between EFGB 

and WFGB Repetitive Deep Stations from 2012 

Source Sum of Squares df Mean Square F-ratio P-value 

(A) Corals 

Bank 0.33 1 0.33 0.37 0.55 

Error 17.21 19 0.91 

(B) Sponges 

Bank 1.47 1 1.47 3.60 0.07 

Error 7.75 19 0.41 

(C) Macroalgae 

Bank 5.17 1 5.17 3.10 0.09 

Error 31.73 19 1.67 

(D) CTB 

Bank 0.08 1 0.08 0.07 0.80 

Error 22.03 19 1.16 

4.3.2.2. Repetitive Deep Station Multivariate Analysis 

The point counts for the deep stations were further analyzed by using multivariate 

techinques. Multivariate cover analysis was compared between bank and year using 

ANOSIM. There were no significant differences between years, and there were no 

significant differences between banks, which resulted in no multivariate interaction. 
63 

Cluster analysis and MDS plot placed EFGB deep station cover in a loosely clustered 

group (80% similarity), while WFGB 2012 stations appeared to be more varied. However, 

the stress level of the MDS was low at 0.05, which indicates good goodness-of-fit in a twodimensional scale, which suggests high confidence in the pattern displayed (Figure 4.3.10). 

These results agree with both the ANOVA and ANOSIM that no significant differences of 

bank or year occur between EFGB and WFGB deep stations; this makes the banks similar 

in terms of deep repetitive photostation composition. 

Figure 4.3.10. Two-dimensional MDS plot based on Bray-Curtis similarities 

showing the spatial representation of benthic community 

similarities between the 2011 and 2012 EFGB and 2012 WFGB 

repetitive deep stations. 

The green circle groups surveys that are 80% similar. 

4.3.2.3. Repetitive Deep Station and Shallow Station Comparison 

The point count data from the repetitive deep stations (DS) and the shallow station (SS) 

quadrats in the 10,000 m2

 study sites were compared. The 2011 WFGB shallow station 

repetitive quadrat data were not included in this comparison (deep stations were not 

installed until 2012). The mean percent coral cover was higher in the repetitive deep 

stations when compared to the shallower repetitive quadrats; it averaged 73% from 2011–

2012 at the deep stations and 63% at the shallow repetitive quadrats in the study sites. 

Macroalgae cover for both banks averaged 18% for the deep stations, and the shallow 

stations macroalgae cover was 24% from 2011 and 2012. Mean percent CTB cover at the 

deep stations was 7% and the mean CTB cover at the repetitive shallow stations was 11%. 

Mean percent sponge cover was below 1% for both the deep and shallow repetitive stations 

(Table 4.3.9 and Figure 4.3.11). 
64 

Table 4.3.9. 

 

Mean Percent Cover ± SE of Benthic Categories in Repetitive Deep Stations and Shallow 

Repetitive Quadrats at EFGB and WFGB from 2011 and 2012 

Cover Category 2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB 

Shallow Station Coral 63.29 ± 2.97 63.29 ± 2.83 63.54 ± 2.30 63.50 ± 2.09 

Deep Station Coral 72.81 ± 3.99 72.22 ± 4.43 NA 76.96 ± 4.77 

Shallow Station Macroalgae 24.85 ± 2.40 26.27 ± 2.53 20.90 ± 1.76 22.54 ± 1.80 

Deep Station Macroalgae 20.66 ± 4.00 20.97 ± 3.52 NA 13.87 ± 3.00 

Shallow Station CTB 10.83 ± 0.91 9.02 ± 0.82 13.79 ± 1.12 11.98 ± 1.08 

Deep Station CTB 5.54 ± 0.93 6.70 ± 1.09 NA 7.29 ± 2.09 

Shallow Station Sponge 0.46 ± 0.18 0.47 ± 0.22 0.11 ± 0.09 0.22 ± 0.15 

Deep Station Sponge 0.12 ± 0.12 0.00 NA 0.93 ± 0.49 

0

10

20

30

40

50

60

70

80

90

100

2011 EFGB 2012 EFGB 2012 WFGB

Percent Cover

Bank and Year

Percent Cover of Repetitive Deep Station and Shallow Station 

Functional Categories at the 

Flower Garden Banks, 2011-2012 DS Coral

SS Coral

DS Macroalgae

SS Macroalgae

DS CTB

SS CTB

DS Sponge

SS Sponge

 Figure 4.3.11. Mean percent cover + SE of four functional benthic categories at the FGB 

repetitive deep stations (DS) and shallow station (SS) repetitive quadrats in 

2011 and 2012. 

The deep repetitive station and shallow repetitive quadrat point count data grouped into 

four major functional categories and expressed as mean percent covers were analyzed by 

one-way ANOVA with depth (deep and shallow) as a fixed factor and an experimentwise 

error rate of α=0.05. The data on proportional cover for sponges and CTB were nonnormal, so categories were square root transformed. 
65 

A one-way ANOVA on the proportional cover of all observed sponges and macroalgae 

showed no significant difference between depths; however, corals (P-value>0.01) and CTB 

(P-value>0.01) were significantly different (Table 4.3.10). High error was reported for all 

categories because there were more shallow stations than deep stations in the analysis and 

this resulted in an uneven sample size. 

Table 4.3.10. 

 

Results of ANOVA on Proportional Mean Cover Estimates from Repetitive Deep 

Stations and Shallow Station Repetitive Quadrats from 2011 and 2012 

Source Sum of Squares df Mean Square F-ratio P-value 

(A) Corals 

Depth 22.02 1 22.02 10.50 >0.01 

Error 404.72 193 2.10 

(B) Sponges 

Depth 0.11 1 0.11 0.56 0.45 

Error 41.07 193 0.21 

(C) Macroalgae 

Depth 7.26 1 7.26 3.80 0.06 

Error 368.43 193 1.91 

(D) CTB 

Depth 15.84 1 15.84 17.50 >0.01 

Error 174.69 193 0.91 

Comparisons of groups where ANOVA was performed are in bold with 

appropriate P-values where significant. 

4.3.2.4. Historical Comparison of Repetitive Deep Station Benthic Cover 

Mean percent coral cover i n t h e r e p e t i t i v e d e e p p h o t o s t a t i o n s was 77% 

during the period from 2003–2012 at EFGB; the highest cover was recorded in 2004 with 

a mean of approximately 86% (Table 4.3.11). In 2003, the mean coral cover in EFGB deep 

stations was 76.5% Data from 2003–2008 was collected by Precht et al (2006 and 2008b). 

From 2004–2010, the mean ranged from 72–86%. In 2012, twelve deep stations were 

established at WFGB. The mean coral cover in WFGB deep station quadrats was 77% in 

2012. 

Periods of lower coral cover generally coincided with increases in the algal component 

and decreases in the CTB category. Coral and CTB cover increases generally coincided 

with lower macroalgal cover (Figure 4.4.12). At this time, the results suggest that algal 

overgrowth is not affecting estimates of underlying benthic coral cover. Overall, the most 

noticeable pattern was the inverse relationship between coral and CTB components and the 

macroalgae cover, with an increasing trend in algae cover, similar to the random transects 

and repetitive quadrats in the study sites on the shallower portion of the reef cap. However, 

this is a general observation, because coral does not grow and die at the same rate as algae. 
66 

Table 4.3.11. 

 

EFGB and WFGB Repetitive Deep Station Data for Dominant Cover Categories 

from 2003–2012. 

EFGB Repetitive Deep Stations 

Year Coral Sponge Macroalgae CTB 

2003 76.00 ± 4.00 1.00 ± 0.20 0.50 ± 0.10 12.00 ± 1.00 

2004 86.20 ± 5.18 0.00 0.57 ± 0.62 13.18 ± 4.62 

2005 77.51 ± 3.77 0.00 10.82 ± 1.89 8.84 ± 1.85 

2006 72.00 ± 4.60 1.02 ± 0.46 7.77 ± 2.07 15.76 ± 2.75 

2007 73.80 ± 4.09 0.51 ± 0.25 14.67 ± 2.62 8.90 ± 1.66 

2008 74.52 ± 3.14 0.13 ± 0.09 10.11 ± 1.47 13.92 ± 2.42 

2009 81.73 ± 3.90 0.00 10.56 ± 3.12 7.72 ± 1.39 

2010 82.18 ± 3.01 0.25 ± 0.25 10.28 ± 2.06 6.98 ± 1.53 

2011 72.81 ± 3.99 0.12 ± 0.12 20.66 ± 4.00 5.54 ± 0.93 

2012 72.22 ± 4.43 0.00 20.97 ± 3.52 6.70 ± 1.09 

WFGB Repetitive Deep Stations 

Year Coral Sponge Macroalgae CTB 

2012 76.96 ± 4.77 0.93 ± 0.49 13.87 ± 3.00 7.29 ± 2.09 

Values listed in table are mean percent covers. Standard errors (± SE) are reported 

from 2003–2012. Data for 2003–2008 from PBS&J (Precht et al. 2006, 2008b); and 

FGBNMS for 2009–2012 (Johnston et al. 2013). 

0

10

20

30

40

50

60

70

80

90

100

Mean Percent Cover

Year

Mean Percent Cover of Four Functional Categories at 

East Flower Garden Bank Repetitive Deep Stations, 

2003-2012

Coral

Sponge

Macroalgae

CTB

Figure 4.3.12. Repetitive deep station mean percent cover from 2003–2012 of 

coral, sponge, macroalgae, and CTB at EFGB. 
67 

4.3.3. Repetitive Quadrat Planimetric Analysis 

Selected corals in repetitive quadrat photographs were analyzed using planimetry. 

Measurements of the amount of change in living area on selected coral colonies were 

conducted to document the dynamics of particular coral colonies at EFGB repetitive 

quadrats, including EFGB repetitive deep stations and WFGB repetitive quadrats. Colonies 

with discernable margins close to the center of the photograph were measured for planar 

areal change from 2011–2012. In each frame, one to four colonies of framework-building 

corals, where the margins were clearly defined, were chosen for analysis. Orbicella spp., 

the main contributors to coral cover at the FGB, and Pseudodiploria strigosa and Porites 

astreoides colonies were the most common colonies selected. A complete list of repetitive 

quadrat photostation coral colonies selected for planimetric analysis and their percent 

change from 2011 and 2012 are listed in Volume II Appendix 7 of this report. 

On average, coral colonies selected for analysis at EFGB and WFGB were found to 

increase in area from 2011–2012. While retreat in specific colonies was measured, overall 

percent change was positive in the coral colonies measured in EFGB repetitive quadrats 

(13.51%), EFGB repetitive deep stations (9.17%), and WFGB repetitive quadrats (6.42%) 

(Figure 4.3.13). 

0

5

10

15

20

25

30

35

40

45

50

2011-2012

Mean Percent Change

Bank and Year

Planar Mean Percent Change in Coral Colony Areas at the

Flower Garden Banks, 2011 to 2012

EFGB

EFGB Deep

WFGB

Figure 4.3.13. Mean percent change from repetitive quadrat planimetry analysis for 

2011 and 2012 at EFGB and WFGB repetitive quadrats and EFGB 

repetitive deep stations (EFGB Deep). 
68 

When comparing complete individual colonies for planimetry analysis, Porites astreoides

was the dominant coral taxon that exhibited proportional growth from 2011–2012, most 

likely because it is small and fits the criteria for selection. This was followed by 

Colpophylia natans at WFGB repetitive quadrats and EFGB repetitive deep stations, and 

Orbicella franksi at EFGB repetitive quadrats. Several colonies exhibited tissue loss from 

2011–2012, including Stephanocoenia intersepta at EFGB repetitive deep stations, and 

Siderastrea siderea and Montastraea cavernosa at WFGB. The mean percent change in 

tissue results (change in planar area) for coral colonies measured from EFGB was 

approximately 10%, 4% in WFGB repetitive quadrats, and 11% in EFGB repetitive deep 

stations (Figure 4.3.14). 

-20

-10

0

10

20

30

40

50

60

Mean Percent Change

Coral Species

Planar Mean Percent Change in Coral Species from 2011 to 2012 at 

the Flower Garden Banks

EFGB

EFGB Deep

WFGB

Figure 4.3.14. Mean percent change from coral species from repetitive quadrat planimetry 

analysis for 2011 and 2012 at EFGB and WFGB repetitive quadrats and 

EFGB repetitive deep stations (EFGB Deep). 

Sample size for Porites astreoides: EFGB n=30, WFGB n=33, EFGB Deep n=2; Colpophylia 

natans: EFGB n=9, WFGB n=10, EFGB Deep n=4; Pseudodiploria strigosa: EFGB n=29 WFGB 

n=32, EFGB Deep n=1; Orbicella franksi: EFGB n=24, WFGB n=24, EFGB Deep n=9; Orbicella 

faveolata: EFGB n=9, WFGB n=13; Montastraea cavernosa: EFGB n=7, WFGB n=11, EFGB 

Deep n=10; Orbicella spp.: EFGB n=1, EFGB Deep n=2; Stephanocoenia intersepta: WFGB n=1; 

Orbicella annularis: WFGB n=5; Siderastrea siderea: WFGB n=1. 
69 

A two-sample t-test was performed to compare the percent change of dominant coral 

species (Porites astreoides, Colpophylia natans, Orbicella franksi, Orbicella faveolata, and 

Pseudodiploria strigosa) from EFGB to WFGB quadrats to examine variations by bank 

with an experimentwise error rate of α=0.05. The percent change data were non-normal. 

Transformation did not correct for normality, so data were left untransformed. 

The two-tailed t-test revealed that percent colony change differences were not significant 

for Colpophylia natans, Orbicella faveolata, and Pseudodiploria strigosa between the two 

banks. However, percent colony change for Porites astreoides (P-value=0.04) and 

Orbicella franksi (P-value>0.01) were significantly different between WFGB and EFGB 

(Table 4.3.12). Overall, both Porites astreoides and Orbicella franksi percent change was 

higher at EFGB than WFGB from 2011–2012. EFGB repetitive deep stations were not 

included in this analysis due to the small sample size and lack of a WFGB repetitive deep 

station comparison in 2011. 

Table 4.3.12. 

 

Results of t-test on Percent Colony Change for Dominant Coral Species from 

Repetitive Quadrat Planimetry Analysis for 2011 and 2012 at EFGB and WFGB 

Source Difference df Standard Error Difference T-ratio P-value 

(A) Porites astreoides

Bank -10.38 61 5.81 -1.79 0.04 

(B) Colpophylia natans

Bank 0.01 17 5.37 0.002 0.50 

(C) Orbicella franksi

Bank -11.07 46 3.57 -3.10 >0.01 

(D) Orbicella faveolata

Bank -0.33 20 4.66 -0.07 0.47 

(E) Pseudodiploria strigosa

Bank -2.18 59 2.91 -0.76 0.23 
70 

4.4. REPETITIVE QUADRAT DISCUSSION

4.4.1. Study Site Repetitive Quadrats 

Repetitive quadrats were analyzed for mean percent cover of benthic components, including 

coral species, sponge, macroalgae, and CTB, and to identify coral health indicators 

(bleaching, paling, concentrated fish biting, isolated fish biting, and disease) in 2011 and 

2012. Higher coral cover estimates (63%) were obtained from the repetitive quadrats in 

comparison to the random transects (56%) at both EFGB and WFGB. Higher percent coral 

cover in repetitive quadrats relative to random transects has also been documented in 

previous reports (Dokken et al. 2003; Precht et al. 2006, 2008b; Zimmer et al. 2010; 

Johnston et al. 2013). It should be noted that this does not provide a comprehensive view of 

the dominant species at EFGB and WFGB, because repetitive photostations are biasedly 

placed on diverse habitat with high coral cover (large coral colonies). They were not 

intended to be representative of mean benthic cover. 

Repetitive photostations also display a unique time series from 2006–2012 (Figure 4.4.1). 

Like most stations, in the example from EFGB station 102, the overall coral community 

appears to be stable from 2006–2012 and in good health during all years. Some colonies 

may appear paler in certain years due to variations in photographic equipment (e.g., note 

large Montastraea cavernosa in upper right corner in 2010), because all photos are subject 

to varying degrees of differing camera settings, lighting, etc. Small changes include 

concentrated fish biting (bright white patch in the center of the frame) in 2011, and a 

damselfish garden that appeared on a Pseudodiploria strigosa head in the lower left corner 

in 2011 and 2012, affecting approximately 25% of the colony. 

Species composition at repetitive stations was similar to that in the random transects; the 

dominant corals were Orbicella franksi, Pseudodiploria strigosa, Orbicella spp., and 

Orbicella faveolata. Coral disease was virtually absent from analyzed quadrats at both 

banks in 2011 and 2012. Paling and bleaching were also rare, and concentrated and 

isolated fish biting. 

In the repetitive quadrats, mean percent coral cover showed an overall increase in 

b e n t h i c cover during the period from 1992–2012 at EFGB and WFGB. EFGB mean 

coral cover was approximately 61% over time. WFGB mean coral cover was 

approximately 60% over time. Macroalgae mean percent cover at EFGB and WFGB both 

increased in 2011 and 2012 when compared to previous years (Figure 4.3.5.). 

A similar pattern was observed in the random transects in section 3.4, where coral cover 

showed an overall increase from 1992–2012. At EFGB and WFGB, coral cover 

averaged approximately 52% cover over time. Macrolagae cover in the random transects at 

both EFGB and WFGB increased from 2008 to 2012, when compared to previous years. 
71 

Figure 4.4.1. Repetitive photostation 761 (re-named 102 in 2012) from EFGB in a 

time series from 2006–2012, showing a healthy and stable coral 

community: (A) 2006; (B) 2007; (C) 2008; (D) 2009; (E) 2010; (F) 

2011; (G) 2012 (NOAA/FGBNMS). 

(A) (B) 

(C) (D) 

(E) (F) 

(G) (B) 
72 

In the repetitive quadrats and random transects, periods of lower coral cover generally 

coincided with increases in the algal component and decreases in the CTB category. 

Overall, the most noticeable patterns were: 1) inverse relationship between CTB and the 

macroalgae cover, 2) increasing macroalage cover, and 3) stable coral cover over time. 

Despite the higher coral cover in the repetitive quadrats, these stations showed similar 

trends observed in the random transects, which suggests that monitoring these specific 

stations also gives a representative view of the dynamics of the overall study site, and an 

increasing trend in algal cover. 

4.4.2. Repetitive Deep Stations 

At EFGB, nine deep stations located at 32–40 m depths were established in April of 2003 

to monitor the deeper benthic coral community, and two more stations were added in 2012. 

The coral cover was significantly higher in the deep stations, and averaged 74% in 2011 

and 2012, when compared to the shallower repetitive quadrats (63%). 

Higher percent coral cover in the deep station quadrats relative to random transects has also 

been documented in previous reports (Precht et al. 2006, 2008b; Zimmer et al. 2010; 

Johnston et al. 2013). The deep stations were dominated by Orbicella franksi; 

Montastraea cavernosa was the second-most dominant coral species, unlike the 

shallower study sites. A noticeable difference between EFGB and WFGB deep repetitive 

stations and the shallow repetitive quadrat stations was the lack of Orbicella annularis

cover at the deep stations and decreased occurrence of Pseudodiploria strigosa. The coral 

community observed in the deep station photographs appears to be both healthy and stable 

from 2003 to 2012, with consistent percent cover above 70% when compared to past 

monitoring periods. 

4.4.3. Planimetry 

To document the growth dynamics of particular coral colonies at the FGB, repetitive 

quadrats were analyzed using planimetry by taking areal measurements of coral colonies 

whose lateral margins were contained entirely within the image frame from 2011 and 2012. 

Planimetric analysis at repetitive stations generally revealed tissue growth with limited 

living tissue loss. 

Orbicella franksi, followed by Pseudodiploria strigosa, were the dominant coral cover 

species in the repetitive quadrats. However, even though Orbicella franksi and 

Pseudodiploria strigosa were the dominant frame building corals in the repetitive quadrat 

percent cover analysis, Porites astreoides was the dominant coral to exhibit proportional 

growth from selected corals analyzed from 2011–2012. It should be noted that Porites 

astreoides colonies were not the dominant corals in the repetitive quadrats, but were 

selected because of their clearly defined margins. For example, even though large 

Orbicella franksi and Pseudodiploria strigosa colonies dominate the coral cover at EFGB 

repetitive quadrat station #10 (Figure 4.4.2), smaller Colpophylia natans, Porites 

astreoides, and Pseudodiploria strigosa colonies were selected for analysis because their 

lateral margins were within the image frame. 
73 

Orbicella franksi and Pseudodiploria strigosa also exhibited tissue growth, but many of 

these colonies contained margins outside of the photographs, and their large size most 

likely exhibits slower growth rates than smaller colonies, such as Porites astreoides. 

A total of 267 colonies were compared between 2011 and 2012 from EFGB, WFGB, and 

EFGB deep stations; only 18% of the colonies exhibited tissue loss. Similar to the 

Pseudodiploria strigosa colonies documented in the lateral growth stations in section 6.1, 

Pseudodiploria strigosa colonies in the planimetric analysis also revealed tissue growth. 

Figure 4.4.2. An example of colonies selected for planimetric analysis 

include 1) Colpophylia natans, 2) Porites astreoides, and 

3) Pseudodiploria strigosa in photo (A), and colony 

planar outlines in (B), at repetitive quadrat station #10 at 

EFGB in 2012. 

(A) 

(B) 
75 

CHAPTER 5.0: LATERAL GROWTH 

5.1. LATERAL GROWTH METHODOLOGICAL RATIONALE

Pseudodiploria strigosa is the second largest contributor to coral cover at the FGB, after 

Orbicella franksi (Bright et al. 1984; USDOI, MMS 1998; Dokken et al. 2003; Gittings et al. 

1992; Precht et al. 2006; Precht et al. 2008b; Zimmer et al. 2010; Johnston et al. 2013). The 

lateral margins of selected Pseudodiploria strigosa colonies were monitored and photographed 

annually to detect any incipient changes over time and space. Pseudodiploria strigosa is more 

suitable for marginal comparisons than other coral species because of the conspicuous patterns 

and grooves that, when photographed, can be matched when repetitive annual photographs are 

overlaid. 

5.2. LATERAL GROWTH METHODS

5.2.1. Lateral Growth Field Methods 

At the beginning of the monitoring program in the late 1980s, sixty lateral growth stations, 

located on the margins of Pseudodiploria strigosa colonies, were established at each bank to 

assess coral margin growth rates. In 2003, 12 new stations at EFGB and 17 new stations at 

WFGB were established to replace old stations that had been lost or were overgrown. With few 

exceptions, this method is not common among coral reef monitoring programs and has proved to 

be extremely problematic throughout the FGB monitoring program (section 5.4). 

Rates of coral advance (tissue gain) and retreat (tissue loss) were determined through 

photographic analysis of these permanent stations. Lateral growth stations are located along a 

margin of live Pseudodiploria strigosa adjacent to bare substrate or reef rock. The stations 

contain two bolts that are embedded into the substrate in such a manner that the growth margin 

of the coral bisects a close-up photograph of the station. Each station is identified by a uniquely 

numbered plastic tag secured to one of the station bolts. 

Lateral growth stations are located and marked by SCUBA divers using underwater maps 

(Volume II, Appendix 2), and then divers photograph each station. Divers were equipped with a 

camera, a close-up framer, and strobe. In 2011 and 2012, a Canon Power Shot G11® in a Fisheye 

Fix® housing with a standard flatport and Inon® strobe was used. The camera was set at auto 

exposure, ISO 200, on macro and autofocus settings, and strobe set to TTL. The framer was 

placed on corner bolts at each station, with the intention to obtain a repeated image of the station 

(Figure 5.2.1). Some stations were missing identification tags. Those stations that did have tags 

were photographed with the tag in the frame. For stations without tags, the current photographs 

were matched with past photographs using the ridge patterns of the Pseudodiploria strigosa 

colonies. 
76 

Figure 5.2.1. Lateral growth station #108 on a Pseudodiploria strigosa colony with 

close-up framer at WFGB in 2011 (NOAA/FGBNMS). 

Note arrows pointing to the coral overgrowth of marker bolts and the approach of the 

advancing edge of the coral to the station boundary, even extending beyond it in some 

places. 

5.2.2. Lateral Growth Data Processing 

Images corresponding to a specific lateral growth station were compared between consecutive 

years (2010–2011 and 2011–2012). Lateral differences in the margins of the Pseudodiploria 

strigosa colonies were evaluated by overlaying the pairs of photographs, using Photoshop CS5®, 

and dividing the lateral growth edge of the colony vertically into areas categorized as “growth,” 

“retreat,” “stable,” and “not available” (for areas that were dark, shadowed, or out of focus). 

Using ImageJ® (a public domain, Java-based image processing program developed at the 

National Institutes of Health), the entire horizontal width of the frame was set to 100 units, then 

the horizontal distances of growth, retreat, and stability were measured (Figure 5.2.2). These 

values were then combined to obtain an overall percentage of growth, retreat, and stability for 

each image. Successive photographs of a given colony were aligned using the colony’s ridge 

patterns. 
77 

Figure 5.2.2. Image analysis of Pseudodiploria strigosa lateral growth margin at EFGB 

(NOAA/FGBNMS). 

The red line is the 2010 margin and the blue line is the 2011 margin demonstrating tissue 

growth from 2010–2011. 

5.2.3. Lateral Growth Data Presentation and Analysis 

Proportional annual change in the lateral margin of individual Pseudodiploria strigosa colonies, 

whether positive or negative, was examined. A percent change value was calculated for each 

comparable image margin, and each image margin was assigned an overall designation category 

of growth, retreat, or stability from 2010–2011 and 2011–2012. Lateral growth data can be found 

in Volume II Appendix 3. 

The growth, retreat, and stability of colony margin tissue were calculated by subtracting the 

linear distance for each category measured for each station margin for the current year from the 

linear distance for each category measured during the previous year. Areas of the image that 

were not distinguishable during analysis were not included in the total percentage. Percent 

changes were calculated by determining the linear margin gained or lost and dividing by the total 

units of the photographed colony margin and multiplying by 100. A two-tailed t-test was 

performed to test the null hypotheses that the marginal growth did not differ between banks 

(EFGB and WFGB) with an experimentwise error rate of α=0.05. All analyses were calculated 

with the statistical software JMP® version 10.0. 
78 

5.3. LATERAL GROWTH RESULTS

In 2011, 29 colonies of Pseudodiploria strigosa were photographed at EFGB and 31 in 2012. In 

2011, 19 lateral growth stations were photographed at WFGB and 40 in 2012. However, as in 

previous years, most of these photographs were not usable for analysis. Of the photographs taken, 

21 photos of the same station were taken in 2010–2011 and 20 photos of the same station from 

2011–2012 for EFGB. However, only four pairs generated successful matches from 2010–2011 and 

only one photo pair generated a successful match from 2011–2012. Of the photos taken at WFGB, 

13 photos from the same station were taken in 2010–2011, and 17 from the same stations were 

taken from 2011–2012. However, only three pairs generated successful matches from 2010–2011 

and no pairs generated a successful match from 2011–2012 (Table 5.3.1). 

Table 5.3.1. 

 

Comparable Lateral Growth Station Photographs from 2009–2012 

Year 

EFGB WFGB 

Number 

of Photos 

Collected 

Photos 

Matched to 

Station from 

Previous Year 

Number of 

Successful 

Photo Matches 

to Station from 

Previous Year 

Number 

of Photos 

Collected 

Photos 

Matched to 

Station from 

Previous 

Year 

Number of 

Successful Photo 

Matches to Station 

from Previous 

Year 

2009 30 0 0 41 0 0 

2010 29 20 5 32 9 9 

2011 29 21 4 19 13 3 

2012 31 20 1 40 17 0 

Lateral growth data was not collected during the 2008 annual monitoring cruise due to the constraints of 

weather; therefore, there was no comparable data from 2009 to 2008. 

Several factors contribute to the great discrepancy in the number of photographs collected 

compared to the number of “successful matches” for analysis. These factors include: 1) some 

stations no longer have margins to measure in a photograph because of colony growth or death and 

2) photographs are not taken in the same position or orientation each year because of bolts 

overgrown by coral, missing bolts, photographer error, and changes in the rugosity of some 

colonies. Though numerous stations may have been photographed in two consecutive years, 

because of the reasons listed above, far fewer photo comparisons were possible. 

The proportion of annual change in marginal tissue growth or retreat was examined by bank 

(EFGB and WFGB) and by year (2010–2011 and 2011–2012). There was a high degree of 

variability between progression/regression percentages among years for both EFGB and WFGB 

(Table 5.3.2). On average, the proportions of marginal growth from 2010–2012 were advancing. 

For each station, a single estimate of each measure (growth, retreat, and stability), was 

calculated, regardless of the number of areas of progression or regression present. Greater than 

33% of all the marginal length analyzed was advancing and exhibiting positive growth. At 

EFGB, there was an overall increase in marginal growth from 2010–2011, and from 2011–2012, the 

marginal growth retreated. WFGB also showed an increase in Pseudodiploria strigosa marginal 

growth from 2010–2011. There were no comparable stations during 2011–2012. Volume II 

Appendix 6 of this report contains the lateral growth data from 2011 and 2012. 
79 

Table 5.3.2. 

 

Pseudodiploria strigosa Lateral Growth Stations and Percent of Margin 

Growing, Retreating, or Remaining Stable of Coral Tissue at EFGB and 

WFGB from 2010–2011 and 2011–2012 

Site Percent Change from 2010–2011 

EFGB Station Growth Retreat Stable 

EFGB 12 100.0 0.0 0.0 

EFGB 13 67.3 8.9 23.8 

EFGB 29 0.0 100.0 0.0 

EFGB 49 53.2 25.6 21.2 

WFGB Station Growth Retreat Stable

WFGB 69 77.4 22.6 0.00

WFGB 73 100.0 0.0 0.0 

WFGB 99 45.1 15.1 39.8 

Site Percent Change from 2011–2012

EFGB Station Growth Retreat Stable 

EFGB 49 12.7 87.3 0.0 

5.3.1. Historical Comparison of Lateral Growth Results 

A historical comparison of percent change in Pseudodiploria strigosa colonies was made 

from year 2001–2012. Although lateral growth measurements have been collected 

since the beginning of the monitoring program, variations in methods over the 

monitoring years only allowed comparisons to be made for this time frame. 

There was a high degree of variability between advance/retreat percentages among all years for both 

EFGB and WFGB (Figure 5.3.1). However, greater than 13% of all the marginal length analyzed 

was advancing and exhibiting positive growth from 2001–2012. At EFGB, there was an overall 

4% increase in marginal growth from 2001–2012. WFGB also showed an increase (23%) in 

Pseudodiploria strigosa marginal growth from 2001–2011 (there were no comparable WFGB 

stations during 2011–2012). A two-tailed t-test revealed no significant difference in Pseudodiploria 

strigosa marginal growth between EFGB and WFGB from 2011–2012 (df=15, Std Error= 15.91, tratio=1.35, P-value=0.90). 
80 

-100

-80

-60

-40

-20

0

20

40

60

80

100

Percent Change

Years

Percent Change in Psuedodiploria strigosa Colony Margins 

at the Flower Garden Banks

EFGB

WFGB

Figure 5.3.1. Percent change ± SE in Pseudodiploria strigosa colonies at EFGB and WFGB 

during intervals from 2001–2012. 

No ± SE value for 2011–2012 at EFGB and no comparison for WFGB from 2011–2012. Sample 

size for each bank in parentheses above corresponding bar on graph. Note declining sample 

size number as photo station matches decline over time. 

 

5.4. LATERAL GROWTH DISCUSSION 

Lateral growth measurements have been used for much of the monitoring history of the FGB. 

However, this is not a common method, and does not allow for comparison to other coral reef 

monitoring programs in the region. 

Many factors have affected the quality of lateral growth data from the long-term monitoring 

study for many years. The stations appear to have a short useful life because the colonies can 

overgrow the small area within the station in a short period of time, causing coral to grow 

beyond the margin and over the station bolts (Figure 5.4.1). It is a laborious task to keep the 

stations maintained, because they have to be re-established or repaired frequently. The stations 

can also retreat or become overgrown with algae (Figure 5.4.2). The margins on many colonies 

can also become irregular by overgrowing on one side, thus making the station no longer usable 

because the margin can no longer be measured and compared to previous photos from past years 

(Figure 5.4.3). Previous researchers have encountered problems with locating overgrown lateral 

growth photostations and photographing the stations in a consistent way (e.g., at the same angle 

every time) due to bolts shifting from coral overgrowth, which results in a different orientation 

from one year to the next (Figure 5.4.4). As of the 2012 research season, few comparable stations 

remained at either bank. 

(18) (11) 

 (8) (4) 

 (24) 

 (21) 

 (30) 

 (25) 

(35) (50) (39) (15) 

 (5) 

 (9) (4) 

 (3) 

 (1) 
81 

Figure 5.4.1. Lateral growth station #10 on a Pseudodiploria strigosa colony 

with close-up framer at EFGB in 2012 displaying an overgrown 

margin and bolts (NOAA/FGBNMS). 

Figure 5.4.2. Lateral growth station #15 on a Pseudodiploria strigosa colony 

with close-up framer at EFGB in 2012 displaying algae 

overgrowth (NOAA/FGBNMS). 
82 

Figure 5.4.3. Lateral growth station #10 on a Pseudodiploria strigosa colony with close-up 

framer at EFGB in (A) 2009 displaying a measurable margin, and (B) in 2012 

displaying an overgrown irregular margin that can no longer provide a 

comparable measurement (NOAA/FGBNMS). 

Figure 5.4.4. Lateral growth station #34 on a Pseudodiploria strigosa colony with close-up 

framer at EFGB in (A) 2011 where the framer was not placed in the correct 

orientation, and (B) in 2012 displaying the correct orientation and bolt 

placement; however, the photo is no longer comparable to the previous year 

(NOAA/FGBNMS). 

In 2012, many of the stations established years ago were completely overgrown by coral 

(Volume II Appendix 6.B.), which resulted in the loss of many stations. When FGBNMS began 

conducting the long-term monitoring in 2009, many of the lateral growth stations could not be 

located because of colony over growth or inaccurate mapping of the stations from previous 

years. Also, the frequent loss of marker pins and great changes in stations resulted in 

photographs being taken in different orientations, which made analysis difficult or impossible. In 

many instances, the framer used in the technique prevents exact replication of the sample area 

because the subject area is not two-dimensional and the framer cannot be laid “flat” on the coral 

surface. Because of the direct contact, the effects of increased rugosity and the changing 

orientation of margins caused by bioerosion, and accretionary growth also hinders repetitive 

photography. 

(A) (B) 

(A) (B) 
83 

In an attempt to summarize the status of the lateral growth stations since FGBNMS began the 

long-term monitoring, lateral growth stations were compared from 2009 to 2012; over time the 

majority of the stations have become overgrown by coral or algae (Volume II Appendix 3B). At 

EFGB, 89% of the stations had been overgrown with coral by 2012, and 84% of the stations at 

WFGB had been overgrown with coral by 2012. Though these stations no longer create 

comparable photos for analysis, it should be noted that they are displaying positive growth. 

This method has proved to be extremely problematic throughout the FGB monitoring program. 

Originally, both Pseudodiploria strigosa and Montastreaea annularis colonies were measured 

for lateral growth. However, Montastreaea annularis stations were eliminated in 1992 after 

stations were unsuitable for analysis. Throughout the years, different methods have been used to 

analyze lateral growth (e.g., cm/6 months, cm/year, cm2

/year, cm2/year percent change, and 

positive or negative percent change), and a variety of analyses have been conducted (net growth, 

advance/retreat rates, advance/retreat ratios, marginal stability, percent change) that are not 

consistent among reporting periods; this makes historical comparisons problematic. A full 

analysis of varying methods used throughout the monitoring program shows inconsistencies 

among techniques and analyses (Table 5.4.1). 

Improvements in methodology and a separate cruise to allow time to establish new stations are 

necessary. A new method, replacing the current framer bolts with a small “key and keyhole” 

plate is currently being tested (Figure 5.4.5). A thick plastic plate bolted to the bare substrate will 

act as a keyhole next to the Pseudodiploria strigosa margin. The new camera “key” pole locks 

into the plate, allowing for precise and consistent photographic repeatability. The “key and 

keyhole” mechanism prevents improper orientation, which has caused issues with data analyses 

in past years. The “key holes” will be plugged to prevent biofouling. Thirty test stations at each 

bank have custom numbers based on bank and quadrant with new Y-Tex tags. The distance and 

heading to each lateral station has been incorporated into a new master map; this gives divers 

more accurate location information for each station from a known location. Comparisons for the 

updated method will be available from 2014–2015. 

Figure 5.4.5. New lateral growth test station on a Pseudodiploria strigosa colony margin 

(A), and lateral photograph taken by placing the framer in the key hole plate 

(B) (NOAA/FGBNMS). 

(A) (B) 
84 

Table 5.4.1. 

Historical Review of Pseudodiploria strigosa Lateral Growth Methods and Analyses 

Throughout the Monitoring Program 

Years 1989–1991 1992, 1994–1995 1996–1997 1998–1999 1998–2001 2002–2003 2004–2005 2004–2008 Report Gittings et al. 

TAMU 1992 

Continental Shelf Associates 1996 

Dokken et al. TAMUCC 1999 

Dokken et al. TAMUCC 2001 

Dokken et al. TAMUCC 2003 

Precht et al. PBS&J 2006 

Precht et al. PBS&J 2008 

Zimmer et al. PBS&J 2010 

Growth Units 

cm/6 months cm/yr cm/yr cm2/station % change: 

cm2/station 

% change - positive/negative 

% change - cm2/station 

% change - cm2/station 

Growth rate 

0.10 EFGB: 0.05, 

WFGB: 0.2 

EFGB: 0.06, WFGB 0.14 

EFGB: -0.14, WFGB: -0.54 

NR NR NR NR 

EFGB Lateral Photos 

60 P. strigosa, 60 M. annularis

60 photographed, number analyzed not reported. 

60 P. strigosa 46 (1998), 

50 (1999) 

13 (2000), 29 (2001) 

54 photographed, 18 "matches" (2002), 62 photographed, 8 "matches" (2003) 

36 photographed, 24 "matches" (2004), 60 photographed, 30 "matches" (2005) 

52 photographed, 35 "matches" (2006), 58 photographed, 39 "matches" (2007) 

WFGB Lateral Photos 

60 P. strigosa, 60 M. annularis

60 photographed, number analyzed not reported. 

60 P. strigosa 1998 not 

recorded, 47 (1999) 

25 (2000), 24 (2001) 

43 photographed, 11 "matches" (2002), 64 photographed, 4 "matches" (2003) 

27 photographed, 21 "matches" (2004), 58 photographed, 25 "matches" (2005) 

60 photographed, 50 "matches" (2006), 18 photographed, 15 "matches" (2007) 

Methods and Analysis 

Nails used to mark stations. Number of stations actually analyzed/sampled throughout study not reported. Variety of analyses conducted (net growth, advance/retreat rates, advance/retreat ratios, marginal stability). 

Previously installed stations unsuitable. New stations established in 1994. Of photographed stations, 60% could not be analyzed.M. annularisstations eliminated after 1992.

Of 60 stations established on each bank, approximately 20 on each bank were suitable. New stations were established in 1996. Ternary diagrams used to display advance/retreat ratios. 

A substantial number of stations were unsutiable for analysis in 1998. Ternary diagrams used to display advance/retreat ratios. 

Data are used for descriptive purposes only because the pins and markers are constantly being lost, rendering data unsuitable for analysis. 

Unusuable photographs in 2002 (too dark). New stations established in 2003, so could not compare with previous year. Very little usable data so only generalizations made. 

Poor weather conditions in 2004 limited sampling. 

Stations not sampled in 2008 due to weather. Digital photography "tested" in 2007. High variability of data over time prevented statistical analysis 

82 
85 

Despite improved methods for collecting comparable lateral stations, it should be evaluated 

whether lateral growth data is a valuable measure for monitoring. These stations have proved to 

be problematic throughout the program history, as stated above and noted in previous reports, 

and lateral growth data is not comparable to other coral reef monitoring programs because other 

programs do not collect this data. 
87 

CHAPTER 6.0: SCLEROCHRONOLOGY 

6.1. SCLEROCHRONOLOGY METHODOLOGICAL RATIONALE

Sclerochronology involves the study of coral growth by the measurement of the 

accretionary growth bands deposited by corals in their calcium carbonate skeletons. One 

commonly measured coral growth parameter is skeletal extension rate. The skeletons of 

many corals, including Orbicella spp., contain a consistent sequence of high- and lowdensity bands, comparable to tree rings. Annual growth is represented by each couplet of 

adjacent high- and low-density bands (Figure 6.1.1). Thus, the rate of skeletal extension 

can be determined by measuring the combined width of two adjacent growth bands along 

the length of a corallite. The skeletons of long-lived corals therefore record the histories 

of coral growth, and it is possible to examine how current rates compare with those of the 

past (Dodge and Kohler 1984). 

Although the method of counting seasonal density bands within a coral skeleton has been 

used for some time (Knutson et al. 1972; Buddemeier et al. 1974), there remains some 

uncertainty as to the exact cause of the density variations. In the case of Orbicella spp. 

living in the Gulf of Mexico and Caribbean region, it is generally believed that annual 

low-density bands are produced during much of the year when favorable growth 

conditions exist, and annual high-density bands are produced in the summer when 

suboptimal growth conditions occur and the coral is putting more energy toward sexual 

reproduction and less into skeletal extension. Variations in several physical 

environmental factors are known to influence coral skeletal density: 1) light (Macintyre 

and Smith 1974; Knutson et al. 1972; Wellington and Glynn 1983); 2) temperature 

(Highsmith 1979; Hudson et al. 1976); and 3) suspended sediment (Dodge et al. 1974; 

Brown; Howard 1985). Salinity and water agitation may also exert some control. Other 

factors that influence the metabolism of the coral may be reflected in skeletal growth, 

including nutrient availability and reproductive activity (Wellington and Glynn 1983; 

Szmant and Gassman 1990). The roles played by symbiotic zooxanthellae in influencing 

calcification, and endolithic algae in modifying density patterns, and the effects of boring 

organisms, are further complications. 

Lack of high-density summer band deposition, or the occurrence of high-density winter 

stress bands may correspond to times during the year when significant coral bleaching or 

other stresses exist, including cold-air outbreaks, pulses of freshwater influx from rivers, 

concentrated parrotfish biting, and damselfish territory effects (Wells 1963; Buddemeier 

et al. 1974; Dodge 1975, 1980; Hudson et al. 1976, 1989; Kaufman 1977; Highsmith 

1979; Hudson 1981a, b; Smith et al. 1989; Leder et al. 1991; Fitt et al. 1993; Heiss and 

Dullo 1995; Insalco 1996). Care must be taken to differentiate between normal, annual 

bands and other bands produced by stressful non-cyclic environmental fluctuations 

(Graus and Macintyre 1982; Leder et al.1991). 
88 

Figure 6.1.1. Example X-radiograph of Orbicella faveolata skeletal 

material from the FGB showing density banding 

(Slowey/TAMU). 

6.2. SCLEROCHRONOLOGY METHODS

6.2.1. Why Orbicella faveolata? 

The determination of coral skeletal extension rate has been identified as one of the 

best quantitative measures of coral stress due to disturbance, because this parameter 

integrates a variety of physiological processes (Brown and Howard 1985). It is also 

widely accepted that coral growth rates may be inherently variable for a single species 

within a reef zone and even within individual colonies (Buddemeier and Kinzie 1976). 

Gladfelter et al. (1978) described some species as “conservative” in their growth. 

Specifically, they argued that the Orbicella spp. show relatively little response in growth 

rate to varying environmental conditions compared to other species. However, studies 

have shown significant suppression of Orbicella faveolata growth may occur if a coral 

is disturbed, for example, by short-term exposure to high concentrations of drilling 

mud (Hudson and Robbin 1980) or by changes in environmental parameters when a 

coral is transferred from an offshore location to an inshore site (Hudson 1981b). 

A significant feature revealed by X-radiography is the presence of high-density skeletal 

deposits or “stress” bands, which have been observed in sections of Orbicella annularis 

during periods of rapid chilling and mixing of shallow inshore waters (Hudson et al. 

1976; Hudson 1977, 1981a; Shinn et al. 1989) and during periods of increased sea 

surface temperatures and coral bleaching (Leder et al. 1991). 

Previous research on sclerochronology on the Orbicella spp. has been extensive 

(Dustan 1975; Hudson et al. 1976; Emiliani et al. 1978; Foster 1980; Hudson 1981a, 

1981b; Graus and Macintyre 1982; Dodge and Lang 1983; Dodge and Brass 1984; 

Leder et al. 1991; Slowey and Crowley 1995). It has been shown that accelerated 

High-Density 

Annual 

Summer Bands 

High-Density 

Winter 

Stress Bands 
89 

growth in Orbicella spp. occurs seasonally during cooler periods (Leder et al. 1991). 

In Belize, Highsmith (1979) noted that, when compared with Montastraea cavernosa 

and Porites astreoides from the same locality, high- density bands of Orbicella spp. 

appeared to be deposited for only short periods of time, whereas the low-density bands 

were generally produced for a greater part of the year. 

6.2.2. Sclerochronology Field Methods 

Random Orbicella faveolata core samples from each quadrant of EFGB and WFGB 

study sites were collected every two years. In July 2012, four cores were taken from 

robust Orbicella faveolata corals living within the northeast (NE), northwest (NW), 

southeast (SE) and southwest (SW) quadrants of the study site, for a total of eight cores. 

The quality of the initial SW and SE cores recovered from WFGB was not certain, so 

replicate cores were taken. The NW core from EFGB did not produce clearly 

recognizable growth bands and was therefore not used in the analysis. 

A pneumatic drill, fitted with a diamond-tipped 35 mm lapidary bit, was used to extract 

short cores of skeletal material from the apex of the Orbicella faveolata colonies. Corals 

were sampled at their apex because growth rate is known to vary across the surface of an 

individual coral colony and it is at the apex where the maximum rate typically occurs. 

The longitudinal axis of each core was oriented as closely as possible to the direction that 

the corallites appeared to grow, that is, along the main growth axis of the coral. The cores 

were about 30 mm in diameter and their lengths ranged from 5 to 17 cm long. The holes 

left from core extraction were filled with pre-drilled coral skeleton plugs and coral rubble 

(obtained from coral cores extracted previously during mooring drilling) that were fixed 

in place using LiquidRoc 500® adhesive to prevent subsequent bioerosion and mortality 

of the sampled colony. 

The cores were placed in padded sections of plastic pipe that were filled with 95% 

ethanol solution, and refrigerated to preserve the coral skeletal material and reduce 

disturbance during storage and transport. For processing and analysis, the coral cores 

were transferred to the laboratory of Dr. Niall Slowey at the Department of 

Oceanography at Texas A&M University. 

6.2.3. Sclerochronology Data Processing 

Comparable images of the coral cores collected in 2012 were obtained using the 

computerized tomography (CT) scanner approach (Brooks and Hounsfield 1973; DiChiro 

1976; and Wellington and Vinegar 1987). The process of determining the coral extension 

rates involved several steps. First, a Siemens® CT scanner at Texas A&M University’s 

College of Veterinary Medicine and Biomedical Sciences was used to generate a 

three-dimensional matrix of X-ray attenuation coefficients that correspond to adjacent 0.6 

 0.6  0.6 mm volumes of the skeletal material in each coral core section. Matrix values 

were expressed in CT number notation, where variations in CT number largely reflect 

variations in skeletal bulk density. 
90 

To create and analyze digital images of the coral cores, the CT numbers were associated 

with grayscale values where smaller CT values (lower densities) correspond to smaller 

grayscale values (darker gray). Next, the images generated by the CT scanner were 

loaded into OsiriX® medical image processing software (Rosset et al. 2004). For each 

image, the pixel grayscale values of 14 adjacent 0.6 mm thick “slices” of CT scanner data 

were averaged, simulating the image that would have been obtained if an 8.4- mm-thick 

“slab” of skeletal material had actually been cut from the core section and then X-rayed 

in the traditional fashion. The resultant slab images revealed variations in skeletal 

density, and allowed annual bands and stress bands to be identified. Ages for the annual 

band couplets were assigned by counting backwards from the most recently deposited 

colony surface at the top of each core toward older skeletal material at depths within the 

each core. Finally, the slab images were loaded into the ImageJ® software package 

(Schneider et al. 2012). Three straight transect lines were drawn to measure the changes 

of grayscale corresponding to the annual density band couplets, with each transect line 

following the apparent corallite walls while remaining as perpendicular as possible to the 

growth bands. For each transect, pixel grayscale compared with distance was determined 

and the distance between summertime high-density bands indicates the annual extension 

rate of the coral for specific time periods. An average extension rate value for each year 

was obtained by averaging the values from the three transects. 

For each core of Orbicella faveolata skeletal material, slab images were generated at 

three or four different orientations about the core’s longitudinal axis. Results from the 

orientation that yielded the most accurate extension rates for each coral core are 

presented in this report. A thorough analysis of the potential influence of “slab” 

orientation on extension rate values is presented elsewhere (Yudelman 2014). 

6.2.4. Sclerochronology Data Presentation and Analysis 

After the annual accretionary growth (extension) rates were determined for each coral 

core, the means and standard errors were calculated for each bank and year. ANOVA 

was performed to compare differences in extension rates between banks (EFGB and 

WFGB) with an experimentwise error rate of α=0.05. Analyses were calculated with the 

statistical software JMP® version 10.0. 

6.3. SCLEROCHRONOLOGY RESULTS

X-ray images of skeletal material in the Orbicella faveolata coral cores obtained in 2012 

revealed two types of distinct high-density bands: annual bands presumably deposited 

during late summer, and stress bands deposited during periods of otherwise rapid growth. 

The spatial patterns of corallite development within the cores were such that it was 

possible to determine reliable annual extension rates from eight of the cores (Figures 

6.3.1 and 6.3.2; Table 6.3.1). Mean extension rates and standard error values were 

calculated for each bank and year when comparable measurements were available. 

Extension rates were not determined for the time period extending from the summer 

2011–2012 because clearly recognizable high-density growth bands corresponding to the 

summer of 2012 were not evident. The 2012 sclerochronology data is in Volume II 

Appendix 5 of this report. 
91 

Annual extension rate records are presented for three Orbicella faveolata corals at EFGB 

(Table 6.3.1). The longest time period spanned by these records was from 1995 to 2012 

(>16 years). During this period, annual extension rates ranged from 4.6 to 9.6 mm/yr; the 

maximum value occurred from 2004 to 2005, and the minimum value occurred from 

2010 to 2011. From 1996 and 2010, the mean annual extension rate of EFGB corals was 

6.5 mm/yr. 

Annual extension rate records are presented for five Orbicella faveolata corals at WFGB 

(Table 6.3.1). The longest time period spanned by these records was from 1997 to 2012 

(>14 years). WFGB corals displayed a greater range of annual extension rates than the 

corals at EFGB; they ranged from 3.3 to 10.3 mm/yr, with the maximum value occurred 

from 2007 and 2008 and the minimum value occurred from 2010 and 2011. Corals at 

WFGB extended at a mean rate of 5.6 mm/yr during the period from 1997 to 2012. 

Figure 6.3.1. Digitally created slab X-radiographs of Orbicella faveolata

skeletal structure in the plane of corallite growth from coral 

cores taken in EFGB study site quadrants (NE=northeast, 

SE=southeast, SW=southwest) (Yudelman 2014). 

Yellow lines across each image indicate transects along which coral 

extension was measured to obtain values in Table 6.3.1. 
92 

Figure 6.3.2. Digitally created slab X-radiographs of Orbicella faveolata skeletal structure 

in the plane of corallite growth from coral cores taken in WFGB study site 

quadrants (NW=northwest, NE=northeast, SE=southeast, SW=southwest) 

(Yudelman 2014). 

Yellow lines across each image indicate transects along which coral extension was measured 

to obtain values in Table 6.3.1. 
93 

Table 6.3.1. 

Coral Growth at the FGB Determined from Cores Taken in 2012 

Orbicella faveolata Extension Rate (mm/yr) 

Year 

East Flower Garden Bank West Flower Garden Bank

NE SE SW Mean Std. 

Error NE NW SW SEA 

SEB Mean Std. 

Error

2012 - 2011    ۛ ۛ      ۛ ۛ

2011 - 2010 4.6 4.9 6.3 5.3 0.5 6.5 3.3 5.7 8.0 8.4 6.4 0.9 

2010 - 2009 7.6 5.4 6.8 6.6 0.6 5.7 3.9 6.3 9.5 9.0 6.9 1.1 

2009 - 2008 6.8 5.2 7.1 6.4 0.6 5.6 4.6 6.1 9.6 10.0 7.2 1.1 

2008 - 2007 5.1 5.9 7.4 6.1 0.7 6.0 3.5 6.5 7.5 10.3 6.8 1.1 

2007 - 2006 6.4 6.2 6.4 6.3 0.1 6.1 3.7 4.0 8.3 4.4 1.1 

2006 - 2005 8.6 5.7 6.9 7.1 0.8 6.9 5.0 5.1 10.0 5.4 1.2 

2005 - 2004 9.6 5.8 6.8 7.4 1.1 6.0 4.0 6.0 5.4 0.7 

2004 - 2003 7.4 6.5 6.9 7.0 0.3 6.5 4.1 6.1 5.6 0.8 

2003 - 2002 7.5 5.6 7.2 6.8 0.6 7.6 4.4 6.2 6.1 0.9 

2002 - 2001 5.6 6.8 6.2 0.6 7.7 4.2 5.9 1.7 

2001 - 2000 5.4 7.0 6.2 0.8 5.9 5.9 

2000 - 1999 7.0 7.0 5.4 5.4 

1999 - 1998 6.2 6.2 4.2 4.2 

1998 - 1997 6.8 6.8 3.3 3.3 

1997 - 1996 6.2 6.2 

1996 - 1995 6.2 6.2      

 

Mean All 

Years 6.5 0.6 Mean All Years 5.6 1.0 

Each value is an average of measurements made on three transects across digitally created 

slab X-radiographs of coral cores (yellow lines on Figure 6.3.1 and Figure 6.3.2). Extension 

rates were not determined for 2011–2012 because clearly recognizable high-density growth 

bands were not evident. Cores are designated by quadrant in each study site: 

NW=northwest, NE=northeast, SE=southeast, SW=southwest. Data from Yudelman (2014). 

EFGB cores indicate more similar extension rates than WFGB cores (Figure 6.3.3 and 

Figure 6.3.4). No apparent correlation exists between average annual extension rate and 

the water depth where the corals lived (all cores are from water depths between 18 and 22 

m). Other factors may cause the differences in extension rates between the cores (i.e., 

genetic variability, temperature, food availability, surrounding organisms and habitat, 

current locations, predation, etc). 
94 

Extension rates also depend on two other factors: 1) where on the surface of the coral 

head a core is taken, and 2) the overall size and vitality of a coral. When divers sampled 

Orbicella faveolata coral heads for this study in 2012, they chose robust corals for 

sampling and attempted to take the cores from apex of the coral heads where the 

maximum rate typically occurs. Slight variations in the nature of the coral heads and the 

relative positions of the cores could nevertheless introduce biases. 

To determine if the growth rates differed significantly between banks, a simple one-way 

ANOVA was performed to compare extension rates between EFGB and WFGB from 

2012-1995 with an experimentwise error rate of α=0.05. The data were normally 

distributed, so no transformation was necessary. The extension rates for the period of 

comparison were not significantly different between EFGB and WFGB (df=1, SS=1.67, 

F-ratio=0.65, P-value=0.42). 

0.0

2.0

4.0

6.0

8.0

10.0

12.0

Extension Rate (mm/yr)

Year

Mean Annual Extension from 2012 Coral Cores

at East Flower Garden Bank

NE

SW

SE

Figure 6.3.3. Mean annual extension rates determined from cores collected in 

2012 at EFGB (Yudelman 2014). 
95 

0.0

2.0

4.0

6.0

8.0

10.0

12.0

Extension Rate (mm/yr)

Year

Mean Annual Extension from 2012 Coral Cores 

at West Flower Garden Bank NW

NE

SW

SE-A

SE-B

Figure 6.3.4. Mean annual extension rates determined from cores collected in 

2012 at WFGB (Yudelman 2014). 

6.4. SCLEROCHRONOLOGY DISCUSSION

Many factors can affect coral growth rate: depth, salinity, temperature, light, genetic 

factors, and relative position on the colony (Knutson et al. 1972; Bak 1974; Weber and 

White 1977; Highsmith 1979; Hudson 1981a; Hudson et al. 1989; Smith et al. 1989). 

Accretionary rates of Orbicella annularis documented over a wide geographic range 

throughout the Caribbean vary from 3.0 to 12.0 mm/yr (Weber and White 1977). 

Growth rates have been shown to vary with depth, with faster growth rates generally 

occurring in shallower water (Weber and White 1977). Hudson (1981a) reported 

growth rates of Orbicella annularis in the Florida Keys to be 6.3 mm/yr on offshore 

reefs and 8.2 mm/yr on mid-shelf reefs from 1928–1978. Hudson and Robbin (1980) and 

Deslarzes (1992) reported annual growth rates for 16 colonies of Orbicella annularis at 

the FGB. The mean was 7.9 mm/yr from 1886–1907, 8.8 mm/yr from 1907–1957, 7.0 

mm/yr from 1957–1988, and 9.0 mm/yr during 1988–1989 (the last year they had data). 

Dokken et al. (2001) reported a lower growth rate for 1985–1999, and an average of 6.80 

mm/yr at EFGB and 5.13 mm/yr at WFGB. The shorter sampling period was offered as a 

possible explanation for the observed differences. Alternative explanations are that the 

cores analyzed by Dokken et al. were not taken from the apex of the coral head, were 

taken from smaller coral heads than those analyzed by Hudson and Robbin (1980) and 

Deslarzes (1992), or that Orbicella franksi may have been mistakenly sampled instead of 

Orbicella faveolata. Each possibility would result in lower estimates that are not readily 

comparable with the Hudson and Robbin (1980) and Deslarzes (1992) data. 
96 

Cores taken during the 2012 sampling period indicate that, for at least the decade leading 

up to and including the summer of 2011, Orbicella faveolata extension rates ranged from 

4.6 to 9.6 mm/yr at EFGB and 3.3 to 10.3 mm/yr at WFGB. These ranges are quite 

similar to those found from cores taken during the 2009–2010 sampling period (3.0 to 

7.6 mm/yr at EFGB and 3.3 to 9.7 mm/yr at WFGB) and the growth rates reported by 

Zimmer et al. (2010) for the 2004–2008 long-term monitoring reporting period, but 

differed slightly from the growth rates reported by Precht et al. (2006) and the past 

work by Dokken et al. (2003), who reported a wider range of growth rates at EFGB 

and WFGB. Growth rates for Orbicella faveolata at WFGB, and less so at EFGB, 

continued to be in the middle to upper range of FGB growth rates as recorded by 

Hudson and Robbin (1980). 

The fact that the range of values found during the past three monitoring efforts displays a 

decrease in range of values, when compared to previous monitoring efforts, may reflect 

two factors. First, the divers collecting the monitoring cores have greater awareness of 

the need to consistently take cores from the apexes of similarly-sized, robust coral heads, 

reducing variability associated with differences in coral growth associated with coral 

head geometry and coral head vitality. Second, natural interdecadal variations in 

environmental factors do occur. Because coral cores taken for monitoring purposes are 

relatively short, the effects of interdecadal variations in environmental conditions on 

coral extension become more apparent when data from monitoring efforts associated with 

different time periods are compared. 

For example, of long-term growth studies of Orbicella faveolata corals at the FGB, 

Hudson and Robbin (1980) and Deslarzes (1992) observed that a late 1950s growth 

decline is a prominent feature of the records. Studies first hypothesized this decline could 

be caused by lower light levels due to bank subsidence that resulted from salt dome 

dissolution (Rezak and Bright 1981), or local variations in water temperature or outflow 

from the Atchafalaya River (Dodge and Lang 1983; Szmant-Froelich 1984) with a 

positive correlation between and winter/spring temperature and growth, and a negative 

correlation between Atchafalaya River discharge and growth. The analysis by Slowey 

and Crowley (1995) supported the temperature explanation and fit it into a large-scale 

climatic context. They compared meteorologic and coral growth records and found that 

during the past century changes in coral growth at the FGB correspond to changes in the 

winter climate of the Gulf of Mexico and southeastern U.S. Slowey and Crowley (1995) 

found that recent decadal scale variability in both coral growth and regional wintertime 

climate are closely linked to changes to the orientation of the mid-latitude atmospheric jet 

stream over North America. When the jet stream has a more north-south orientation, 

wintertime temperatures in the Gulf of Mexico and southeastern U.S. are colder and the 

corals exhibit slower growth and possess more winter stress bands. Variations in the 

orientation of the jet stream and wintertime climate are among the dominant modes of 

extratropical climate variability in the Northern Hemisphere (Wallace and Gutzler 1981; 

Simmons et al. 1983; Wallace et al. 1993). 
97 

Hudson (1981a, 1984) observed that Orbicella faveolata corals within the Florida Keys 

National Marine Sanctuary (FKNMS) show a decline in growth rates and deposited 

abundant winter stress bands during the late 1950s and early 1960s. Fluctuations in river 

discharge cannot account for changes in Florida Keys coral growth. The similarity in 

temporal variations in extension rate changes and stress banding displayed by both FGB 

and FKNMS corals supports the contention that coral growth in both locations is most 

likely impacted by regional changes of wintertime climate (Slowey and Crowley 1995). 

In the summer of 2010, the FGB experienced an unusual warming of the water column 

and coral bleaching, which were reflected in the data at WFGB. As described in the 

random transect data, approximately 7% of the corals at WFGB were bleached and 11% 

were paling. Seven of the eight coral cores collected during 2012 do indicate a slight 

decline in extension rate from about 2008–2009 to 2010–2011. However, though this 

correspondence is intriguing, the available environmental and coral skeletal information 

is insufficient to ascertain whether this decline is statistically significant and a 

consequence of bleaching and paling. Though valuable growth rate information is 

collected from cores, it should be evaluated whether coral cores should be taken every 

two years during monitoring periods. Due to the slow nature of coral growth rates, it may 

be more appropriate to take longer cores once every five years. 
99 

CHAPTER 7.0: PERIMETER VIDEOGRAPHY 

7.1. PERIMETER VIDEOGRAPHY METHODOLOGICAL RATIONALE

Portions of the perimeter lines were videotaped each year at EFGB and WFGB to 

document change at known locations along the perimeter of the study sites. General 

aspects of coral condition were documented and compared year to year. The perimeter 

surveys are intended to provide a visual long-term dataset and general overview of coral 

reef health and are particiularly useful for documenting effects from natural events, such 

as bleaching and hurricanes on large areas of the reef. 

7.2. PERIMETER VIDEOGRAPHY METHODS

Divers videotaped two 100 m segments of the perimeter lines at EFGB (north and east 

margins) and WFGB (south and west margins) in 2011 and 2012. At EFGB, divers began 

at the northwest corner of the 10,000 m2 study site and videotaped the north line to the 

northeast corner, then the east line to the southeast corner. At WFGB, divers captured 

footage of the south and west lines, beginning at the southeast corner and ending at the 

northwest corner. The videographer maintained an approximate 2.0 m distance above the 

bottom by attaching a weighted 2 m line to the bottom of the camera housing to assist 

with consistency of distance from the substrate. The line was kept to the left of the 

perimeter. The camera was aimed downward at a 45 angle to capture the substratum. In 

both years, a 360 panoramic view of the reef was videotaped at the three corners 

documented during the perimeter video. In 2011, a Sony® Handicam® DCR-TRV950 

video camera in a Light and Motion® Bluefin® housing with Light and Motion® Sunray®

video lights was used with a red filter for color correction. In 2012, a Canon® VIXIA®

HF G10 HD video camera in a Light and Motion® Stingray® housing with Light and 

Motion® SOLA® 4000 lights was used with a red filter for color correction. 

The video footage was reviewed to record the general condition of corals along the 

perimeter of the study sites. Individual coral colonies displaying possible disease, 

bleaching, paling, or other notable conditions on the reef were identified and recorded. 

Affected coral colonies were compared in 2011 and 2012. Changes in coral colony 

condition were recorded. The perimeter surveys are intended to provide a visual longterm dataset and general overview of coral reef health. Because the analyses were 

qualitative, no statistical analyses were conducted. 

7.3. PERIMETER VIDEOGRAPHY RESULTS

The perimeter video was reviewed for a qualitative analysis of the general condition of 

corals along the perimeter of the study sites. The review of the 2011 and 2012 

perimeter videos suggests that, in general, the coral community along the perimeter 

lines at EFGB and WFGB study sites displayed low levels of stress and healthy corals. 

The limited bleaching and paling observed were similar to random transect and repetitive 

quadrat data. Furthermore, no evidence of disease was observed at either bank. The use 

of the HD video camera in 2012 greatly improved the quality of the video and ability to 

differentiate coral species and conditions. 
100 

7.3.1. EFGB Perimeter Lines 

In 2011, the perimeter video was taken at 1800 CDT; in 2012, it was taken at 1700 CDT. 

Three incidences of paling were observed at EFGB in 2011. Two were Montastraea 

cavernosa colonies and the other was an Orbicella spp. colony. In 2012, one Montastraea 

cavernosa colony displayed signs of paling. No bleaching was observed in 2011 or 2012 

at EFGB. 

A seismic cable used for oil and gas exploration penetrates part of the EFGB study site 

boundary. In 2011 it was observed to scour and create a scar on a Pseudodiploria strigosa

colony, but in 2012, the cable had shifted and the scar on the colony had healed (Figure 

7.3.1). Seismic cables had been observed on both EFGB and WFGB before the banks 

were designated a national marine sanctuary. These seismic cables may be left over from 

surveys decades ago. The cables have been observed to be degrading over time, and are 

now considered marine debris. 

7.3.2. EFGB 360 Panoramic Views 

At the northwest corner, corals appeared to be healthy in both 2011 and 2012. In 2011, 

there was a paling Porites astreoides colony. In 2012, it appeared there was higher turf 

algal cover than in 2011; however, this may have been more visible due to the HD 

camera used in 2012. At the northeast and southeast corners, the corals appeared to be in 

good condition, with no evidence of bleaching stress or disease in 2011 or 2012. 

7.3.3. WFGB Perimeter Lines 

In 2011, the perimeter video was taken at 0800 CDT; in 2012, it was taken at 1000 CDT. 

In 2011, bleaching occurred on two colonies (Montastraea cavernosa and Porites 

astreoides). In 2012 at WFGB, one Pseudodiploria strigosa colony was covered with 

algal over growth. No signs of disease were observed in either year. The Montastraea 

cavernosa colony that was observed to bleach in 2011 was recovered by 2012 (Figure 

7.3.2). Along the south line in 2011, a cleaning station was observed that included a tiger 

grouper (Mycteroperca tigri) with neon gobies (Elacatinus oceanops) and Spanish 

hogfish (Bodianus rufus). 

7.3.4. WFGB 360 Panoramic Views 

Corals in the southeast corner showed no signs of bleaching, paling, or fish biting in 2011 

and 2012. In 2012, it appeared there was higher turf algal cover than in 2011; however, 

this may have been more visible due to the HD camera used in 2012. At the southwest 

and northwest corners, the corals appeared to be in good condition, with no evidence of 

bleaching stress or fish biting. 
101 

Figure 7.3.1. A seismic cable drapped over a Colpophyllia natans coral head in 2011 

(A), the cable and scar in 2011 (B), and the recovered colony and shifted 

cable in 2012 (C) at EFGB (NOAA/FGBNMS). 

(A) 

 

 Cable

 

(B) 

 Cable 

 Scar 

(C) 

 Recovered 

 Coral 

 

 Cable 
102 

Figure 7.3.2. A bleached Montastraea cavernosa colony in 2011 (A), and the same 

recovered colony in 2012 (B) at WFGB (note shift in line between years) 

(NOAA/FGBNMS). 

7.4. PERIMETER VIDEOGRAPHY DISCUSSION

Videography of the perimeter lines and 360° panoramic views of the corner markers at 

EFGB and WFGB provided a general overview of coral condition at the study sites from 

2011–2012. Similar to the findings from the random transects, in both years coral 

condition appeared to be in relatively good health at both banks and there were no 

signs of coral disease. There were few incidences of bleaching and paling. The use of the 

HD camera in 2012 made corals and fish much easier to discern, due to the higher 

resolution and sharper image of the upgraded system, which provided clear images of 

both the perimeter lines and 360° panoramic views of the reef at each corner marker. 

(A) 

 

 Bleached 

 Colony 

(B) 

 Recovered 

 Colony 
103 

It is important to note that the perimeter lines did shift between years on both banks 

(Figure 7.4.1), as the study sites were refurbished in 2012. Due to the effect of currents 

and surge on the flexible perimeter lines between the fixed corner markers, which are 

100-m apart, mid-transect eye bolts were installed in 2012 to help improve repeatability 

so that transect lines can be attached to eye bolts to avoid shifting lines with the current. 

Missing corner markers were also replaced with permanent eyebolts, and installed to 

make the study site a 10,000 m2

 area. In the past, shifting perimeter lines and corner 

marker positions resulted in a lack of overlapping video footage and fewer available coral 

comparisons. Now that corner markers and mid transect eyebolts are permanent, transect 

lines should be repeatable and allow for more coral colony comparisons. 
105 

CHAPTER 8.0: DIVER OBSERVATIONS 

8.1. DIVER OBSERVATIONS METHODOLOGICAL RATIONALE

In addition to the annual data collection protocol, other biologically relevant information 

is documented within the study sites at EFGB and WFGB. During each annual 

monitoring cruise, observations of general coral reef health and notable biological and 

oceanographic events (e.g., spawning, animal behavior) were qualitatively assessed. 

8.2. DIVER OBSERVATIONS METHODS 

As divers traversed the FGB study sites during the 2011 and 2012 annual monitoring 

cruises, they noted and photographically documented any biologically relevant 

observations and events. 

8.3. DIVER OBSERVATION RESULTS

8.3.1. Wildlife Observations 

8.3.1.1. Elasmobranch Sightings 

During the 2011 EFGB annual monitoring cruise, two mantas (Manta spp.) were sighted 

during diving operations. Each manta has a unique set of markings and color patterns on 

its ventral side. These can be used to identify individual rays. The two sighted were newly 

recorded mantas and were added to the FGBNMS manta sighting catalog. A Caribbean reef 

shark (Carcharhinus perezi) and dusky shark (Carcharhinus obscurus) were also 

observed in the EFGB study site. Mantas were not sighted at WFGB in 2011 during the 

monitoring period, however a sicklefin devil ray (Mobula tarapacana) was observed in the 

study site. In 2012, no mantas were observed at EFGB. At WFGB, two mantas and a devil 

ray were observed within the study site. 

8.3.1.2. Fish Sightings 

In 2011 at WFGB, a marbled grouper (Dermatolepis inermis) visited divers on a sand flat 

near the water quality instrumentation (Figure 8.3.1) and a large loggerhead sea turtle 

(Caretta caretta) was observed surfacing near the R/V Manta. A large green moray 

(Gymnothorax funebris), a rarely seen species at the FGB, was observed in the study site, 

and several queen conch (Lobatus gigas) were observed in the sand flat. 

At EFGB repetitive deep stations in 2012, a rare barred hamlet (Hypoplectrus puella) was 

seen by divers. This was the first documented sighting of this species within sanctuary 

boundaries. Divers also observed a lionfish (Pterios spp.), and an adult female loggerhead 

sea turtle at the EFGB repetitive deep stations. In 2012 at WFGB, a yellowmouth grouper 

(Mycteroperca interstitiali) was seen at a cleaning station, and a large loggerhead sea turtle 

was observed in the study site. A nesting sergeant major (Abudeduf saxatilis) damselfish 

with eggs was observed by divers. At the WFGB repetitive deep stations, a lionfish and 

hawksbill sea turtle (Eretmochelys imbricata) were also observed at WFGB (Figure 8.3.2). 

These observations are anecdotal and quantitative fish surveys are reported in Chapter 10. 
106 

Figure 8.3.1. Marbled grouper (Dermatolepis inermis) visits diver at WFGB 

(NOAA/FGBNMS). 

Figure 8.3.2. Hawksbill sea turtle (Eretmochelys imbricata) at WFGB 

(NOAA/FGBNMS). 
107 

8.3.2. Coral Health Observations 

During the 2011 and 2012 annual monitoring cruises, scientific divers made qualitative 

observations of coral colonies exhibiting signs of disease or other coral health issues. During 

the 2011 and 2012 monitoring cruises, divers experienced 30 m visibility and water 

temperatures near 29°C. There were no unusual observations at EFGB in 2011; however, 

Xestospongia “wasting disease” was observed in a giant barrel sponge (Xestospongia 

muta) and “false bleaching” was observed at WFGB in 2011 (Figure 8.3.3). 

Occasionally, a syndrome that has been called “false bleaching” is seen in coral colonies at 

the FGB, especially in large polyped coral species, such as Monastraea cavernosa (Figure 

8.3.3). This syndrome appears very similar to that reported by Kramarsky-Winter et al. 

(2006), and is not bleaching at all, but coral surfaces covered by a layer of aggregate-like 

protist microorganisms embedded in the mucus and surface coral tissue in patchy 

distributions. The role of protists in the marine environment is not well understood, but it 

is thought that corals may benefit from the protist association through protist nutrient 

production, actually helping massive corals survive bleaching events better than 

branching corals. Further study of this syndrome at the FGB should be conducted. 

Figure 8.3.3. Monastraea cavernosa “false bleaching” at WFGB 

(NOAA/FGBNMS). 
108 

In 2012, divers observed fluorescent orange algae growth at EFGB (Figure 8.3.4). This 

was also observed in 2010 in the previous reporting period. The orange alga was very 

noticeable in the crevices of the reef, and has been identified as Martensia pavonia, a 

delicate net-forming alga that is a member of the Delesseriaceae family and exhibits a 

bright orange color in its deteriorating state (Fredericq, University of Louisiana at 

Lafayette, pers. comm.). Algal blooms are classic indicators of high nutrient levels on coral 

reefs, and tend to expand in the warm season and during the rainy season when more 

nutrients are flushed offshore from land. 

Figure 8.3.4. Fluorescent orange algae, Martensia pavonia, 

observed at EFGB in 2012 (NOAA/FGBNMS). 

There were no unusual observations at WFGB in 2012, but divers did observe sponge 

spawning in the northwest corner of the study site at 0911 CDT on 27 July 2012 (Figure 

8.3.5). 

Figure 8.3.5. Arrow points to spawn leaving the barrel of the sponge 

at WFGB in 2012 (NOAA/FGBNMS). 
109 

8.3.3. Invasive Species Sightings 

In 2002, orange cup coral (Tubastraea coccinea) was first documented at EFGB. It is 

native to the Indo-Pacific and may have entered the South Atlantic and Caribbean by 

attaching to a ship’s hull, having its larvae discharged in ballast water, or being 

transported on reused structures such as drilling rigs or production platforms. This 

species is now common on oil and gas platforms in the Gulf of Mexico, and it is 

suspected that platforms played a role in the spread of this species (Fenner and Banks 

2004). It is the most common coral species on High Island A389A, the only oil and gas 

production platform inside sanctuary boundaries. This platform is located about one mile 

from the coral cap at EFGB. In 2011 and 2012, sporadic colonies were observed on the 

reefs near the EFGB and WFGB study sites, and were also observed in previous 

monitoring periods (Figure 8.3.8). As of this time, Tubastraea coccinea has been 

documented along the south perimeter line near the southwest corner of the WFGB study 

site. 

Figure 8.3.6. Patches of orange cup coral (Tubastraea coccinea), an invasive species 

from the Pacific, at WFGB (NOAA/FGBNMS). 
110 

Lionfish (Pterois miles/volitans), an invasive species known for their voracious appetites, 

venomous spines and rapid reproduction, first invaded in the southern Gulf of Mexico off 

the northern Yucatan Peninsula in December 2009. In September 2010, two lionfish were 

sighted at Sonnier Bank by Texas A&M University Galveston researcher divers. These 

were the first confirmed sightings of lionfish at the natural banks in the northwestern Gulf 

of Mexico, about 60 miles east of EFGB. In July 2011, no lionfish were observed in the 

long-term monitoring study site, but in 2012, Lionfish were observed at EFGB and 

WFGB repetitive deep stations and within the WFGB study site (Figure 8.3.9). Overall, a 

total of four were observed at EFGB and two at WFGB in 2011. In 2012, lionfish 

sightings increased, with 40 observed at EFGB and 105 at WFGB. Reported sightings are 

from recreational and FGBNMS divers. 

Figure 8.3.7. Invasive lionfish (Pterois spp.) at WFGB in 2012 (NOAA/FGBNMS). 

8.4. DIVER OBSERVATIONS DISCUSSION

8.4.1. Wildlife Observations 

8.4.1.1. Elasmobranch Sightings 

Sanctuary staff and volunteers have been collecting photos and videos of mantas sighted 

in the sanctuary over many years. These photos are the basis of a FGBNMS Manta Photo 

Catalog, identifying each of the known individuals and the additional of new individuals. 

The catalog can be viewed on the FGBNMS website and downloaded as a poster. Of the 

four mantas observed during 2011 and 2012, one could be positively identified as having 

been seen in the past. 
111 

8.4.2. Coral Health Observations 

In 2011 and 2012, divers observed minimal bleaching in the FGB study sites. This varied 

from the previous monitoring period, where divers observed a higher than normal number 

of bleached coral colonies (primarily Montastraea cavernosa and Millepora alcicornis) at 

WFGB in 2010. 

It should be noted that monitoring at EFGB and WFGB was conducted in July in both 

2011 and 2012, before signs of bleaching are normally observed. In the Gulf of Mexico 

region, bleaching tends to occur in the late fall after sustained peak temperatures and 

beaching is significantly visible. In July of 2011 and 2012, NOAA's Coral Reef Watch 

Program's satellite data provided near-real time data on the reef environmental conditions 

in the Gulf of Mexico to quickly identify areas at risk for coral bleaching. Areas near and 

inside FGBNMS boundaries were coded at bleaching alert “No Stress” levels and 

“Watch” in July of 2011. Areas near and inside FGBNMS boundaries were coded at 

bleaching alert “Watch” in July of 2012. In September of 2011 and 2012, there was no 

risk of bleaching near the FGB. Therefore, even though monitoring was not done in the 

late fall when signs of bleaching peak from warm sea surface water temperatures exceed 

the 30°C coral bleaching threshold, the temperatures were not sustained in the 2011 and 

2012 monitoring seasons to create a bleaching threat. 

In 2012, divers also observed the fluorescent orange algae, Martensia pavonia, at EFGB. 

Algal growth often indicates excessive levels of nutrients moving from the coastal zone into 

offshore habitats, stimulating production. Coral reef ecosystems are sensitive to high 

concentrations of nitrogen and phosphorus, which promote algal overgrowth. Besides algal 

cover, reefs with high levels of nutrients in the water may be more susceptible to coral 

diseases. Along developed coastlines excess nutrients come from human sources, such as 

human sewage, livestock manures, and agricultural runoff. Nutrients carried offshore act as 

fertilizers for marine plants growth. Algae can be considered an early warning of changes in 

water quality and potential impacts to coral health. 

8.4.3. Invasive Species Sightings 

Invasive species have recently become a concern for marine resource managers because 

of the inherent potential negative impacts that they can cause. Tubastraea coccinea was 

first documented within FGBNMS boundaries in 2002 (Fenner and Banks 2004) and has 

further established itself on nearby oil and gas infrastructure, as well as in discrete 

locations within the sanctuary. Tubastraea coccinea began to colonize Geyer Bank, 

which is located 52 km east of EFGB, and approximately 50 colonies of Tubastraea 

coccinea were removed by sanctuary divers in 2004. Since that time, Tubastraea 

coccinea has become well established at Geyer Bank, and has also been documented near 

or in, or both, EFGB and WFGB study sites. 

Tubastraea coccinea is a zooxanthellate scleractinian coral that is an exotic, invasive 

species within the Caribbean and western Atlantic (Fenner 1999, 2001; Fenner and Banks 

2004). Native to the tropical Indo-Pacific and the eastern Atlantic (Cairns 2000), 

Tubastraea coccinea was first reported in the Caribbean in 1943 (Fenner and Banks 

2004). No fossil evidence of this species has been found within the Caribbean (Cairns 
112 

1999). Tubastraea coccinea is typically located on the undersides of rocks or massive 

corals, in caves, and on rock walls (Glynn et al. 2008). It appears to compete particularly 

well on artificial substrates, which may account for its widespread dispersal. It is a 

hermaphroditic brooding coral that releases planula larvae year round (Cairns 2000; 

Glynn et al. 2008) and has a mean growth rate of approximately 3 cm2/year (Vermeij 

2006). This species reaches reproductive maturity at a small size (from as small as 2–10 

polyps; Glynn et al. 2008) and at an early age (reproductively viable at approximately 1.5 

years; Vermeij 2006). Tubastraea coccinea has the ability to compete effectively by 

forming thin tissue outgrowths (“runners”) that extend over the substrate until suitable 

substrate is encountered, at which time a new polyp forms (Vermeij 2005). These 

competitive mechanisms may put native benthos at risk. 

This species was first observed in the Caribbean in 1943 by Vaughn and Wells, and has 

since spread throughout the Caribbean and Bahamas (IUCN 2007; Glynn et al. 2008), 

Gulf of Mexico (Fenner and Banks 2004), and Brazil (Figueira de Paula and Creed 2004). 

Possible mechanisms of introduction to these regions include boat and ship hulls, ballast 

water, transport of marine structures and machinery (e.g., oil platforms; Ferriera 2003; 

Fenner and Banks 2004). Tubastraea coccinea has colonized many of the oil and gas 

platforms in the northwestern Gulf of Mexico (Sammarco et al. 2006). The probability 

that oil and gas platforms are playing a role in the colonization of this invasive species 

should be of interest to BOEM. 

Over the last five years, one of the world’s most popular ornamental aquarium fish, the 

native Indo-Pacific lionfish (Pterios spp.), has invaded much of the western Atlantic and 

Caribbean region (Morris and Whitfield 2009) (Figure 8.4.2). The proliferation of this 

species has occurred quickly due to early sexual maturation, high fecundity, ability to 

invade many habitats, and effectiveness in competing for food (they are voracious 

predators that have no known predators in the region) (Mumby et al. 2011). Lionfish 

subject small-bodied and juvenile reef fish to greatly elevated predation, and coral reefs 

are at risk of phase shifts mediated by secondary effects of changes in fish trophic 

structure (e.g. increasing algal cover caused by the loss of herbivores). The long-term 

consequences on reef biodiversity and function are not yet clear, but are a matter of grave 

concern to resource managers. 

The FGBNMS will continue to monitor the sanctuary for this invasive species. FGBNMS 

staff has worked with other staff at sanctuary sites to develop a National Marine 

Sanctuary Lionfish Response Plan (Johnston et al. 2015). Though there is little scientific 

evidence to support using biocontrol as a natural means to slow the lionfish invasion, 

EFGB and WFGB provides a unique opportunity to conduct an experiment to measure 

the effectiveness of natural predation, and the influence of fishing on this natural control 

mechanism. The managers of FGBNMS are currently in the process of investigating the 

use of an experimental research area to assess these questions. 
113 

Figure 8.4.1. Lionfish sightings from 1985–2012 (USGS). 
115 

CHAPTER 9.0: WATER QUALITY 

9.1. WATER QUALITY METHODOLOGICAL RATIONALE

During the reporting period, Sea-Bird and HoboTemp dataloggers deployed at EFGB and 

WFGB recorded variations of temperature and salinity. Temperature and salinity depth 

profiles were also collected opportunistically throughout the field season using an YSI 

probe. Water samples collected quarterly from the sea surface to the reef cap at EFGB 

and WFGB were analyzed for chlorophyll a (Chl-a) and nutrients (ammonia, nitrate, 

nitrite, soluble reactive phosphorous and total Kjeldahl nitrogen [TKN]). 

Hereafter, “water quality” will refer to the physical (temperature) and biological (Chl-a), 

and chemical (salinity and nutrients) characteristics of the seawater overlying the FGB. 

This report presents the results of the water quality monitoring at EFGB and WFGB 

conducted from February 2011 to November 2012, and temperature and salinity profiles 

collected from January 2011 to December 2012. 

9.2. WATER QUALITY METHODS

9.2.1. Sea-Bird Conductivity and Temperature Recorder 

The Sea-Bird Electronics, Inc. (SBE) 37-SMP MicroCAT with RS-232 serial interface is 

a conductivity and temperature recorder designed for long-term oceanographic 

deployment (www.seabird.com). The MicroCATs used at the FGB included pressure and 

sound velocity sensors. The primary role of the MicroCAT in this study was to accurately 

record temperature and salinity. The specifications (and typical stability) of the 

MicroCAT indicate an initial accuracy of 0.003 mS/cm (conductivity) and 0.002°C 

(temperature). The resolution of the instrument is 0.0001 mS/cm and 0.0001°C (Figure 

9.2.1). 

One Sea-Bird datasonde was deployed at EFGB (23 m) near buoy number two and one at 

WFGB (27 m) near buoy number two. Sand flats were used as deployment locations to 

accommodate the secure attachment of the datasondes to galvanized train wheels. Water 

quality data were recorded every 30 min. These instruments are returned to Sea-Bird 

Electronics, Inc., in Bellevue, Washington for annual calibration and maintenance. 

9.2.1.1. Specific Conductance (Salinity) 

Datasondes used a cell with four nickel electrodes to measure solution-conductance. 

Two of the electrodes were current driven, and two were used to measure the drop in 

voltage. Differences were converted into a specific conductance value and reported in 

milli-Siemens (milliohms). Salinity was later derived from the conductivity and 

temperature readings according to accepted algorithms and reported as practical salinity 

units (PSU). 
116 

Figure 9.2.1. Sea-Bird 37-SMP MicroCAT water quality instrument at 

EFGB (NOAA/FGBNMS). 

9.2.1.2. Temperature 

The datasondes used a thermistor of sintered metallic oxide that changed predictably in 

resistance with variation in temperature. The algorithm for conversion of resistance to 

temperature was built into the datasonde software, and accurate temperature readings in 

degrees Celsius (°C), Kelvin (°K), or Fahrenheit (°F) were provided automatically. No 

user calibration or maintenance of the temperature sensor was necessary. 

9.2.2. HoboTemp Thermographs 

One HOBO Pro v2 Water Temperature Data Logger (HoboTemp) was attached to each 

of the Sea-Bird instruments as backup recorders of seawater temperature. HoboTemp 

recorders have an accuracy of ± 0.2°C and resolution is 0.02°C at 25°C. They are 

designed with a durable streamlined case for extended deployment in fresh or salt water, 

and equipped with an Optic USB interface for data offload in the field. The data loggers 

were deployed in a water depth of 23 m at EFGB and in at 27 m at WFGB and recorded 

every 30 min. Recorders were also located at EFGB and WFGB deep stations at 30.5 m 

and 39.6 m. 

9.2.3. YSI Probe 

During each cruise, opportunistic temperature profiles were measured by researchers 

using an YSI water quality sensor deployed by hand. Temperature and salinity were 

recorded at 20 m, 15 m, 10 m, 5 m, 4 m, 3 m, 2 m, 1 m, and the surface. These data 

complement the data collected by the stationary water quality instruments on the sea floor 

by providing additional information about the conditions throughout the water column. 
117 

9.2.4. Chlorophyll a and Nutrients 

Surface (<1 m), midwater (10 m), and near bottom (20 m) water samples were acquired 

eight different times at EFGB and WFGB between February 2011 and November 2012 

(Table 9.2.1). During each sampling event, water was collected twice at each depth using 

a vertical 10 liter sampling bottle (Niskin®). Water samples were immediately transferred 

into pre-cleaned polyethylene and glass containers (tested monthly using nanopure water) 

provided by an independent, U.S. Environmental Protection Agency (USEPA) certified 

analytical laboratory (Anacon, Inc. in Houston, TX). Water samples were analyzed for 

Chl-a, ammonia, nitrate, nitrite, TKN, and soluble reactive phosphorous. Water samples 

for Chl-a analyses were collected in 1000 ml glass containers with no preservatives. 

Samples for reactive soluble phosphorous were placed in 250 ml bottles with no 

preservatives. Ammonia, nitrate, nitrite, and TKN samples were collected in 1000 ml 

bottles with sulphuric acid (H2SO4) as a preservative. One blind duplicate seawater 

sample was taken at one of the sampling depths on one of the banks for each sampling 

period. Within minutes of sampling, labeled sample containers were stored on ice at 4°C 

and a chain of custody was initiated. Once back onshore, the samples were sent to 

Anacon, Inc. for analysis using standard USEPA methods (Table 9.2.2) to assess 

concentrations of Chl-a and nutrients (ammonia, nitrate and nitrite, TKN, soluble reactive 

phosphorous). 

Table 9.2.1. 

 

Water Sampling Schedule, Depth, and Number of Samples Taken at EFGB and WFGB in 2011 

and 2012 

EFGB WFGB 

Sampling Date Depth Samples Sampling Date Depth Samples 

02/15/2011 1, 10, 20 m 6 02/15/2011 1, 10, 20 m 6 

05/15/2011 1, 10, 20 m 6 05/17/2011 1, 10, 20 m 6 

08/20/2011 1, 10, 20 m 6 08/21/2011 1, 10, 20 m 6 

10/24/2011 1, 10, 20 m 6 10/25/2011 1, 10, 20 m 6 

03/25/2012 1, 10, 20 m 6 03/25/2012 1, 10, 20 m 6 

05/29/2012 1, 10, 20 m 6 05/29/2012 1, 10, 20 m 6 

08/09/2012 1, 10, 20 m 6 08/09/2012 1, 10, 20 m 6 

11/09/2012 1, 10, 20 m 6 11/09/2012 1, 10, 20 m 6 

Dates represent month/day/year.
118 

Table 9.2.2. 

 

Standard USEPA Methods Used to Analyze Water Samples Taken at the FGB 

Parameter Method Detection Limit 

Chlorophyll-a 10200HPLC 1-mg/m3 

Ammonia M4500 NH3 D 0.10–mg/l 

Nitrate E353.3 0.15–mg/l 

Nitrite E353.2 0.15–mg/l 

Soluble reactive phosphorous SM 4500 P E 0.02–mg/l 

Total Kjeldahl nitrogen (TKN) SM 4500 NH3 C 0.55–mg/l 

 mg/m3 = milligrams per cubic meter; mg/l = milligrams per liter 

9.3. WATER QUALITY RESULTS

9.3.1. Sea-Bird Temperature and Salinity 

9.3.1.1. Temperature 

Seawater temperature was simultaneously measured at EFGB (23 m) and WFGB (27 m) 

using a Sea-Bird 37-SMP MicroCAT datasonde from January 2011 to December 2012. 

The seawater temperature records were complete, with the exception of a gap from 08 

November 2012 to 31 December 2012 at EFGB and 9 August 2012 to 31 December 2012 

at WFGB due to a sensor malfunction. The gaps in these Sea-Bird records were 

supplemented with backup HoboTemp logger data. The temperature records include the 

winter minimum and summer maximum, and daily average temperatures were calculated. 

Water quality data from 2011 and 2012 at the FGB is found in Volume II Appendix 9 of 

this report. 

At EFGB, temperature ranged from a minimum of 18.62°C to a maximum of 30.30°C in 

2011. The annual mean temperature was 24.85°C. In 2012, the temperature ranged from 

20.41°C to 30.49°C. The 2012 mean temperature was 25.50°C (Table 9.3.1). 

Overall, 2012 was a warmer year than 2011; however, several thermal anomalies were 

recorded at EFGB. There were episodes of low temperature in the summer (June) of 2012 

ranging from 24.91–25.20°C on the reef cap of the EFGB study site, as well as a 

decreases in temperature (to 28.51°C) in late August 2011 at EFGB, with a spike in 

temperature in September 2011 (to 29.93°C). Winter and early spring temperatures in 

2011 (January–April) were lower than in 2012, and the temperatures on the reef cap in 

late summer through early winter in 2011 (September–December) were also lower than in 

2012. Both the maximum temperatures in 2011 and 2012 exceeded 30°C. In 2011, 

temperature exceeded 30°C for eight days, and in 2012, temperature exceeded 30°C for 

23 days. This is considered the coral bleaching threshold for the FGB (Hagman and 

Gittings 1992); however, because only limited time was spent above this temperature, the 

risk of bleaching was low (Figure 9.3.1). 
119 

Table 9.3.1. 

 

Summary of Sea-Bird Seawater Temperature Parameters from 2011–2012 

Measurement 

2011 2012 

EFGB WFGB EFGB WFGB 

Annual Mean 

Temperature (°C) 24.85 24.84 25.50 25.49 

Annual Minimum 

Temperature (°C) 18.62 17.92 20.41 20.41 

Annual Maximum 

Temperature (°C) 30.30 30.44 30.49 30.55 

16

18

20

22

24

26

28

30

32

1-Jan

13-Jan25-Jan

6-Feb

18-Feb

1-Mar

13-Mar25-Mar

6-Apr

18-Apr30-Apr

12-May24-May

5-Jun

17-Jun29-Jun

11-Jul23-Jul

4-Aug

16-Aug28-Aug

9-Sep

21-Sep

3-Oct

15-Oct27-Oct

8-Nov

20-Nov

2-Dec

14-Dec26-Dec

Temperature (°C)

Date

Sea-Bird Annual Temperature Variation at East Flower 

Garden Bank, 2011-2012

2011

2012

Figure 9.3.1. Sea-bird datasonde daily mean seawater temperature measured near the 

reef cap at EFGB from 2011–2012. 

At WFGB, the annual daily mean temperature ranged from a minimum of 17.92°C to a 

maximum of 30.44°C in 2011. The annual mean temperature was 24.84°C. In 2012, 

temperature ranged from 20.41°C to 30.55°C. The annual mean temperature was 25.49°C 

(Table 9.3.1). 
120 

Overall, 2012 was a warmer year than 2011; however, several thermal anomalies were 

recorded at WFGB. Winter and early spring temperatures in 2011 (January–April) were 

lower than in 2012, and the temperatures on the reef cap in the fall through early winter 

in 2011 (October–December) were also lower than in 2012. In September 2011, a sharp 

temperature decline was recorded (24.31°C), beginning September 22, 2011 and ending 

September 24, 2011. The temperature stayed below 27°C for 40 hours. Like EFGB, both 

the maximum temperatures in 2011 and 2012 exceeded 30°C. In 2011, temperature 

exceeded 30°C for 12 days and in 2012, temperature exceeded 30°C for 24 days. 

However, only limited time was spent above this temperature, reducing the risk of 

bleaching (Figure 9.3.2). 

16

18

20

22

24

26

28

30

32

1-Jan

13-Jan25-Jan

6-Feb

18-Feb

1-Mar

13-Mar25-Mar

6-Apr

18-Apr30-Apr

12-May24-May

5-Jun

17-Jun29-Jun

11-Jul23-Jul

4-Aug

16-Aug28-Aug

9-Sep

21-Sep

3-Oct

15-Oct27-Oct

8-Nov

20-Nov

2-Dec

14-Dec26-Dec

Temperature (°C)

Date

Sea-Bird Annual Temperature Variation at 

West Flower Garden Bank, 2011-2012

2011

2012

Figure 9.3.2. Sea-bird datasonde daily mean seawater temperature measured near the 

reef cap at WFGB from 2011–2012. 

9.3.1.2. Salinity 

Salinity records at EFGB and WFGB were complete between January 2011 and 

December 2011. At EFGB, there were data gaps from 08 November 2012 to 31 

December 2012 and 9 August 2012 to 31 December 2012 at WFGB due to a sensor 

malfunctions. The annual daily mean salinity ranged from 35.02 PSU to 36.66 PSU in 

2011 at EFGB. The annual mean salinity was 36.27 PSU. In 2012, salinity ranged from 

34.58 PSU to 36.65 PSU. The annual mean salinity was 36.09 PSU (Table 9.3.2). At 

WFGB, the annual range was 34.76 to 37.80 PSU in 2011. The annual mean salinity was 

36.51 PSU. In 2012, salinity ranged from 34.58 to 36.65 PSU. The annual mean was 

36.14 PSU (Table 9.3.2). 
121 

Table 9.3.2. 

 

Summary of Sea-Bird Salinity Parameters from 2011–2012 

Measurement 

2011 2012 

EFGB WFGB EFGB WFGB 

Annual Mean PSU 36.27 36.51 36.09 36.14 

Annual Minimum PSU 35.02 34.76 34.58 34.58 

Annual Maximum PSU 36.66 37.80 36.65 36.65 

 Practical salinity unit (PSU)

EFGB and WFGB experienced periods of salinity in July of 2011 averaging 

approximately 35 PSU. WFGB exhibited sharp salinity declines in May 2011 (34.76 

PSU) and June 2012 (34.58 PSU). Salinity at WFGB in January and February of 2011 

averaged 37.7 PSU, and then experienced a sharp decline in March 2011. This may have 

been a sensor malfunction. For the remainder of the 2011–2012 monitoring period, 

salinity remained stable at approximately 36 PSU (Figure 9.3.3). 

34

35

35

36

36

37

37

38

38

1-Jan-11

1-Feb-11

1-Mar-11

1-Apr-11

1-May-11

1-Jun-11

1-Jul-11

1-Aug-11

1-Sep-11

1-Oct-11

1-Nov-11

1-Dec-11

1-Jan-12

1-Feb-12

1-Mar-12

1-Apr-12

1-May-12

1-Jun-12

1-Jul-12

1-Aug-12

1-Sep-12

1-Oct-12

1-Nov-12

1-Dec-12

Practical salinity unit (PSU)

Date

Sea-Bird Annual Salinity Variation at East and West Flower 

Garden Banks, 2011-2012 

EFGB

WFGB

Figure 9.3.3. Sea-bird datasonde daily mean salinity measured near the reef cap at 

EFGB and WFGB from 2011 and 2012. 

9.3.2. HoboTemp Thermograph Data 

HoboTemp thermographs were attached to each of the Sea-Bird instruments at both 

banks from January 2011 through December 2012. The HoboTemp record provided 

similar data to that captured by the Sea-Bird datasondes: low average temperatures in 

2011, and higher fall temperatures in 2012 (Table 9.3.3). 
122 

At EFGB, the HoboTemp temperature ranged from 17.85°C to 30.65°C in 2011. The 

annual mean was 24.78°C. In 2012, the annual mean ranged from 20.37°C to 30.21°C. 

The annual mean was 25.35°C. At WFGB, it ranged from 18.63°C to 30.32°C in 2011, 

with a mean of 24.91°C. In 2012, the range was 19.96°C to 30.55°C. The mean was 

25.45°C (Table 9.3.3). 

Table 9.3.3. 

 

Summary of HoboTemp Seawater Temperature Parameters from 2011–2012 

Measurement 

2011 2012 

EFGB WFGB EFGB WFGB 

Annual Mean 

Temperature (°C) 24.78 24.91 25.35 25.45 

Annual Minimum 

Temperature (°C) 17.85 18.63 20.37 19.96 

Annual Maximum 

Temperature (°C) 30.65 30.32 30.21 30.55 

HoboTemp thermographs were also located at the EFGB repetitive deep stations at 30.5 

m and 40 m from July 2011 through December 2012; however, due to a lost logger at the 

30.5 m depth, there was a data gap from 20 August 2011 to 24 July 2012. HoboTemp 

thermographs were also placed at WFGB deep stations at 30.5 m and 40 m when they 

were installed in 2012, for a short data record from November through December 2012. 

In a similar trend, when compared to the shallower temperature records, temperatures 

peaked in late summer (August-September) and were lowest in the winter (JanuaryFebruary). At EFGB, the HoboTemp temperature ranged from 28.34°C to 30.38°C in 

2011 at the 30.5 m depth, and 22.04°C to 30.27°C at the 40 m depth. In 2012, 

temperature ranged from 22.38°C to 29.85°C in 2011 at the 30.5 m depth, and 20.41°C to 

29.55°C at the 40 m depth (Table 9.3.4). As expected, the longer, more complete data 

records were lower in temperature when compared to the records on the shallower section 

of the reef, with maximum temperatures not exceeding the 30°C bleaching threshold. 

 Table 9.3.4. 

Summary of HoboTemp Seawater Temperature Parameters from 2011–

2012 at EFGB and WFGB Repetitive Deep Stations 

Measurement 

2011 2012 

EFGB 

30.5 m 

EFGB 

40 m 

EFGB 

30.5 m 

EFGB 

40 m 

WFGB 

30.5 m 

WFGB 

40 m 

Annual Mean 

Temperature (°C) 29.48 26.37 27.35 24.44 25.19 24.73 

Annual Minimum 

Temperature (°C) 28.34 22.04 22.38 20.41 23.11 22.76 

Annual Maximum 

Temperature (°C) 30.38 30.27 29.85 29.55 26.57 26.08 
123 

16

18

20

22

24

26

28

30

32

1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-Sep 1-Oct 1-Nov 1-Dec

Temperature (°C)

Date

HOBO Annual Temperature Variation at Flower Garden 

Banks Repetitive Deep Stations, 2011-2012

2011 EFGB 30.5 m

2011 EFGB 40 m

2012 EFGB 30.5 m

2012 EFGB 40 m

2012 WFGB 30.5 m

2012 WFGB 40 m

Figure 9.3.4. HoboTemp thermographs daily mean seawater temperature measured 

at the EFGB and WFGB repetitive deep stations from 2011–2012. 

9.3.3. YSI Vertical Profiles 

During each cruise, opportunistic seawater temperature profiles were measured using an 

YSI probe deployed by hand. Temperature and salinity were recorded at 20 m, 15 m, 10 

m, 5 m, 4 m, 3 m, 2 m, and 1 m increments, as well as at the water surface (Table 9.3.5). 

These data complement the data collected by the stationary water quality instruments on 

the sea floor at each bank by giving additional information, if needed, about the 

conditions at the surface and throughout the water column. YSI profiles corroborated the 

high water temperatures in the summer of 2011 and 2012. They also indicate the lack of a 

pronounced thermocline between the surface and 20 m during any times of the year. The 

majority of the time, there was less than one degree difference (°C) between the 

temperature on the surface and the temperature on the reef. 
124 

Table 9.3.5. 

 

Summary of Opportunistic YSI Seawater Temperature Vertical Profiles from 2011–2012 at EFGB 

and WFGB. 

Temperature (°C) 

Depth (m) 

Bank Buoy Date Time 0.0 1.0 2.0 3.0 4.0 5.0 10.0 15.0 20.0 

EFGB 2 5/15/2011 19:50 24.7 24.7 24.7 24.7 24.7 24.7 24.7 24.7 24.6 

EFGB 2 5/16/2011 19:03 24.8 24.8 24.8 24.8 24.8 24.7 24.6 24.6 24.6 

WFGB 2 5/17/2011 20:19 24.7 24.7 24.7 24.7 24.7 24.8 24.8 24.9 24.9 

EFGB 2 7/11/2011 14:05 30.4 30.4 30.4 30.3 30.3 30.2 30.1 29.9 29.7 

EFGB 2 7/12/2011 10:30 30.4 30.3 30.2 30.2 30.1 30.1 30.1 30.1 30.1 

WFGB 5 7/13/2011 10:13 30.2 30.2 30.2 30.2 30.2 30.2 30.0 29.9 29.8 

WFGB 5 7/14/2011 9:25 29.8 29.8 29.8 29.8 29.8 29.8 29.8 29.8 29.9 

EFGB 2 7/21/2011 19:18 30.3 30.3 30.2 30.2 30.2 30.2 29.8 29.8 29.3 

EFGB 2 7/22/2011 8:42 29.8 29.8 29.8 29.8 29.8 29.8 29.8 29.8 29.7 

EFGB 3 8/3/2011 6:58 30.1 30.1 30.1 30.1 30.1 30.1 30.1 30.0 29.7 

EFGB 5 8/19/2011 16:43 31.2 31.2 31.2 31.1 31.0 30.9 30.4 30.1 30.1 

EFGB 4 8/20/2011 19:03 30.9 30.9 30.9 30.8 30.8 30.8 30.4 30.2 30.1 

WFGB 2 8/21/2011 8:49 30.3 30.3 30.3 30.3 30.3 30.3 30.3 30.3 30.3 

EFGB 1 9/15/2011 17:40 29.5 29.5 29.4 29.4 29.4 29.2 29.2 29.2 29.1 

WFGB 4 9/16/2011 12:35 29.9 29.7 29.7 29.7 29.7 29.6 29.6 29.6 29.0 

EFGB 3 10/24/2011 20:30 26.7 26.7 26.8 26.7 26.7 26.7 26.7 26.7 26.7 

WFGB 2 10/25/2011 20:10 26.5 26.5 26.5 26.5 26.5 26.5 26.4 26.4 26.4 

EFGB 5 3/25/2012 17:25 23.2 23.1 22.5 22.3 22.3 22.3 22.1 22.1 22.1 

WFGB 2 3/25/2012 19:30 23.0 23.3 23.1 23.1 22.8 22.7 22.6 22.6 21.8 

EFGB 5 5/29/2012 11:00 27.0 26.9 26.9 26.9 26.9 26.8 26.6 26.3 26.1 

WFGB 2 5/29/2012 12:47 27.7 27.7 27.7 27.7 27.5 27.2 26.8 26.6 25.6 

WFGB 5 6/27/2012 19:25 30.0 30.0 29.9 29.9 29.8 29.6 28.8 28.7 27.8 

WFGB 5 6/28/2012 14:45 30.2 30.2 30.1 30.0 29.8 29.7 28.9 28.7 27.7 

WFGB 5 6/29/2012 20:08 29.3 29.3 29.3 29.3 29.3 29.3 29.0 28.6 28.0 

EFGB 3 7/18/2012 20:20 30.0 30.0 30.0 30.0 29.9 29.7 29.3 29.3 28.8 

EFGB 3 7/19/2012 6:30 29.6 29.5 29.5 29.5 29.6 29.7 29.9 29.4 29.2 

WFGB 2 7/19/2012 11:27 29.9 29.9 29.9 29.9 29.9 29.8 29.7 29.3 27.6 

EFGB 6 9/3/2012 16:20 30.2 30.2 30.1 30.0 29.7 29.7 29.6 29.6 29.6 

EFGB 6 9/4/2012 18:50 30.5 30.4 30.4 30.2 30.0 29.7 29.7 29.7 29.7 

WFGB 2 9/6/2012 18:00 30.5 30.5 30.4 30.0 29.9 30.0 30.0 29.9 29.8 

EFGB 3 9/21/2012 20:10 29.1 29.1 29.1 29.1 29.1 29.1 29.1 28.9 28.9 

EFGB 1 11/9/2012 6:40 26.6 26.6 26.6 26.6 26.6 26.6 26.6 26.6 26.6 

WFGB 2 11/9/2012 10:20 26.4 26.4 26.4 26.4 26.4 26.4 26.4 26.4 26.4 

 

Rows in bold highlight more than one degree difference from top to bottom 
125 

9.3.4. Water Samples 

9.3.4.1 Chlorophyll a and Nutrients 

Surface (<1 m), midwater (10 m), and near bottom (20 m) water samples were acquired 

at 8 different times at both EFGB and WFGB for the 2011 and 2012 monitoring periods. 

Water samples were analyzed for Chl-a and nutrients (ammonia, nitrate, nitrite, soluble 

reactive phosphorous, and TKN). Nitrite and soluble reactive phosphorus were not 

detected in any of the tested samples.

Approximately 3% of the water samples collected contained concentrations of Chl-a that 

were above detectable limits (>1 mg/m3). These samples were collected in February 

2011, specifically those from the surface and at the reef cap at EFGB. The highest 

concentration detected was 2.94 mg/m3 of Chl-a (Table 9.3.6). 

Table 9.3.6. 

 

Chl-a Concentrations (mg/m3) in Water Samples at EFGB and WFGB from 2011–2012 

Chl-a 

(Detection 

limit: 

1 mg/m3) 

2011 2012 

 

2/15/11

–

2/16/11 

5/15/11

–

5/17/11 

8/20/11

–

8/21/11 

10/24/11

–

10/25/11 

3/25/12 5/29/12 8/9/12 11/9/12 

EFGB 

Surface A 2.94 ND ND ND ND 0.2 ND ND 

EFGB 

Surface B ND ND ND ND ND 0.1 ND ND 

EFGB 

Midwater A 2.14 ND ND ND ND ND ND ND 

EFGB 

Midwater B ND ND ND ND ND 0.2 ND ND 

EFGB Reef 

Cap A 2.94 ND ND ND ND 0.1 ND ND 

EFGB Reef 

Cap B ND ND ND ND ND 0.1 ND ND 

WFGB 

Surface A ND ND ND ND ND 0.1 ND ND 

WFGB 

Surface B ND ND ND ND ND ND ND ND 

WFGB 

Midwater A ND ND ND ND ND ND ND ND 

WFGB 

Midwater B ND ND ND ND ND 0.1 ND ND 

WFGB Reef 

Cap A ND ND ND ND ND 0.1 ND ND 

WFGB Reef 

Cap B ND ND ND ND ND ND ND ND 

ND=Not detected at reporting limit. Concentrations above detectable limits (>1 mg/m3) in bold. 

Dates represent month/day/year. 
126 

Approximately 38% of water samples contained concentrations of ammonia above 

detectable limits. Ammonia was detected in all samples taken from 15-17 May 2011, 20-

21 August 2011, and 25 March 2012 at EFGB and WFGB. Ammonia concentrations 

ranged from 0.10 to 0.34 mg/l (Table 9.3.7). The modal value for ammonia levels was 

0.10 mg/l. Samples containing the greatest amount of ammonia were obtained at EFGB 

on 25 March 2012. 

Table 9.3.7. 

 

Concentrations of Ammonia (mg/l) in Water Samples at EFGB and WFGB from 2011–2012 

Ammonia 

 (Detection 

limit: 

0.10 mg/l) 

2011 2012 

 

2/15/11

–

2/16/11 

5/15/11

–

5/17/11 

8/20/11

–

8/21/11 

10/24/11

–

10/25/11 

3/25/12 5/29/12 8/9/12 11/9/12 

EFGB 

Surface A ND 0.10 0.20 ND 0.26 ND ND ND 

EFGB 

Surface B ND 0.20 0.30 ND 0.25 ND ND ND 

EFGB 

Midwater A ND 0.20 0.30 ND 0.34 ND ND ND 

EFGB 

Midwater B ND 0.10 0.20 ND 0.28 ND ND ND 

EFGB Reef 

Cap A ND 0.20 0.20 ND 0.19 ND ND ND 

EFGB Reef 

Cap B ND 0.10 0.30 ND 0.24 ND ND ND 

WFGB 

Surface A ND 0.10 0.30 ND 0.21 ND ND ND 

WFGB 

Surface B ND 0.20 0.30 ND 0.24 ND ND ND 

WFGB 

Midwater A ND 0.10 0.30 ND 0.22 ND ND ND 

WFGB 

Midwater B ND 0.10 0.30 ND 0.23 ND ND ND 

WFGB Reef 

Cap A ND 0.10 0.20 ND 0.19 ND ND ND 

WFGB Reef 

Cap B ND 0.30 0.10 ND 0.20 ND ND ND 

ND=Not detected at reporting limit. Concentrations at or above detectable limits 

(>0.10 mg/l) in bold. Dates represent month/day/year. 
127 

In approximately 2% of water samples, the nitrate concentrations were above detection 

limits (0.15 mg/l). The only samples that contained detectable levels were those collected 

on the EFGB reef cap in February 2011 and October 2011 (Table 9.3.8). 

Table 9.3.8. 

 

Concentrations of Nitrate in Water Samples at EFGB and WFGB from 2011–2012 

Nitrate 

(Detection 

limit: 

0.15 mg/l) 

2011 2012 

 

2/15/11

–

2/16/11 

5/15/11

–

5/17/11 

8/20/11

–

8/21/11 

10/24/11

–

10/25/11 

3/25/12 5/29/12 8/9/12 11/9/12 

EFGB 

Surface A ND ND ND ND ND ND ND ND 

EFGB 

Surface B ND ND ND ND ND ND ND ND 

EFGB 

Midwater A ND ND ND ND ND ND ND ND 

EFGB 

Midwater B ND ND ND ND ND ND ND ND 

EFGB Reef 

Cap A ND ND ND ND ND ND ND ND 

EFGB Reef 

Cap B 0.31 ND ND 0.31 ND ND ND ND 

WFGB 

Surface A ND ND ND ND ND ND ND ND 

WFGB 

Surface B ND ND ND ND ND ND ND ND 

WFGB 

Midwater A ND ND ND ND ND ND ND ND 

WFGB 

Midwater B ND ND ND ND ND ND ND ND 

WFGB Reef 

Cap A ND ND ND ND ND ND ND ND 

WFGB Reef 

Cap B ND ND ND ND ND ND ND ND 

ND=Not detected at reporting limit. Concentrations above detectable limits (>0.15 mg/l) in bold. 

Dates represent month/day/year. 
128 

TKN was detectable in 75% of all water samples collected at EFGB and WFGB. It was 

detected in all of the 2011 samples, and half of the 2012 samples. Concentrations ranged 

from 0.60 to 45.20 mg/l, both of which were collected at EFGB on 09 November 2012 

and 21 August 2011, respectively (Table 9.3.9). 

Table 9.3.9. 

 

Concentrations of TKN in Water Samples at EFGB and WFGB from 2011–2012 

TKN 

(Detection 

limit: 

0.55 mg/l) 

2011 2012 

 

2/15/11

–

2/16/11 

5/15/11

–

5/17/11 

8/20/11

–

8/21/11 

10/24/11

–

10/25/11 

3/25/12 5/29/12 8/9/12 11/9/12 

EFGB 

Surface A 2.90 4.60 15.20 4.40 7.90 ND ND 0.60 

EFGB 

Surface B 7.30 2.30 7.60 9.30 9.40 ND ND 0.90 

EFGB 

Midwater A 7.90 2.10 34.10 8.10 6.80 ND ND 1.00 

EFGB 

Midwater B 6.40 6.50 45.20 17.4 8.70 ND ND 1.10 

EFGB Reef 

Cap A 7.60 3.60 15.90 2.20 5.30 ND ND 0.80 

EFGB Reef 

Cap B 4.40 1.90 36.40 24.0 6.30 ND ND 0.90 

WFGB 

Surface A 6.90 1.30 38.90 20.70 4.80 ND ND 1.00 

WFGB 

Surface B 4.30 6.80 34.30 1.80 7.50 ND ND 0.70 

WFGB 

Midwater A 5.70 2.10 15.40 14.70 8.10 ND ND 0.70 

WFGB 

Midwater B 5.70 2.70 31.60 18.60 9.90 ND ND 0.70 

WFGB Reef 

Cap A 5.80 2.50 8.40 30.40 3.80 ND ND 0.60 

WFGB Reef 

Cap B 5.00 2.00 13.10 20.60 5.70 ND ND 0.70 

ND=Not detected at reporting limit. Concentrations above detectable limits (>0.55–mg/l) in bold. 

Dates represent month/day/year. 
129 

9.4. WATER QUALITY DISCUSSION

9.4.1. Water Quality Parameters 

Water quality parameters investigated at EFGB and WFGB from January 2011 through 

December 2012 were temperature, salinity, Chl-a, and nutrients (ammonia, nitrate, 

nitrite, soluble reactive phosphorous, and TKN). 

9.4.1.1. Sea-Bird versus Hobo Temperature Records 

HoboTemp thermographs were attached to each of the Sea-Bird 37-SMP MicroCAT 

datasondes as backup records of seawater temperature, and data were acquired at the both 

banks from January 2011 through December 2012. Concurrent Sea-Bird and Hobo data 

could be compared to evaluate accuracy. Overall, both methods provided reliable 

temperature records. Statistical comparisons were conducted to compare daily means 

from 2011–2012 using a two-sample t-test with an experimentwise error rate of α=0.05. 

Although differences were seen in July and August in 2012, potentially due to 

uncalibrated instruments, overall no significant differences were found. However, one or 

both of the sensors at EFGB began to provide slightly different readings during mid-June 

through July of 2012, as the Sea-Bird datasonde recorded higher temperatures than the 

HoboTemp thermographs (Figure 9.4.1). WFGB Sea-Bird and Hobo temperature data 

had only slight differences at WFGB (Figure 9.4.2). Interestingly, the HoboTemp 

thermograph at WFGB and the Sea-Bird datasonde at WFGB both recorded the low 

temperature drop below 27°C in late September of 2011. Both instruments were 

functioning properly, so it is unknown what caused this sudden decrease in temperature. 

Both the Sea-Bird and Hobo Temp thermographs will continue to be used at the FGB to 

enhance long-term monitoring of temperature on the reef cap, as well as provide reliable 

backup records if one sensor fails. 
130 

16

18

20

22

24

26

28

30

32

1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-Sep 1-Oct 1-Nov 1-Dec

Temperature (°C)

Date

Comparison of Sea-Bird and Hobo Annual Temperature 

Variation Readings at East Flower Garden Bank, 2011-2012

2011 Sea-Bird

2011 HOBO

2012 Sea-Bird

2012 HOBO

Figure 9.4.1. Comparison of Sea-Bird and Hobo daily mean seawater temperature 

readings measured near the reef cap at EFGB from 2011–2012. 

16

18

20

22

24

26

28

30

32

1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-Sep 1-Oct 1-Nov 1-Dec

Temperature (°C)

Date

Comparison of Sea-Bird and Hobo Annual Temperature 

Variation Readings at West Flower Garden Bank, 2011-2012

2011 Sea-Bird

2011 HOBO

2012 Sea-Bird

2012 HOBO

Figure 9.4.2. Comparison of Sea-Bird and Hobo daily mean seawater temperature 

readings measured near the reef cap at the WFGB from 2011–2012. 
131 

9.4.1.2. Temperature 

Historical long-term averages derived from past monitoring periods show that the 

temperature minimum on the reef cap typically occurs from January to mid-March and 

the temperature maximum from mid-August through mid-September (Figures 9.4.3 and 

9.4.4). The temperature on the EFGB reef cap was typically warmer than that on WFGB, 

especially during the summer months. This may be due to WFGB proximity to the shelf 

edge, which is more likely to subject the reef cap to cooler water. EFGB is slightly farther 

up on the continental shelf, perhaps subjecting it more regularly to warmer water masses. 

The mean daily temperature range on the EFGB reef cap from 1990 to 2012 was 20.0 to 

29.8°C. The mean daily temperature range on the WFGB reef cap from 1990 to 2012 was 

19.8 to 29.5°C. 

Trends in seasonal thermal changes over the reef caps of EFGB and WFGB are 

apparent (Figures 9.4.3 and 9.4.4). From a winter minimum, the temperature gradually 

rises through the end of March and reaches a maximum during mid-August through 

mid-September. The temperature decreases gradually starting around October and 

reaches an annual minimum by mid-February through mid-March. During the 2011–

2012 monitoring period, there were several thermal anomalies (both positive and 

negative). The most notable was temperature dips below the mean in June of 2012 at 

EFGB and temperature dips below the mean at WFGB in February and September of 

2011. Overall, both EFGB and WFGB show warming trends of temperatures above the 

historical mean temperatures. 

As expected, the mean temperatures recorded within the study site were warmer than the 

temperatures recorded at the repetitive deep stations. At EFGB, the annual mean 

temperature was 24.85°C in 2011 and 25.50°C in 2012. At WFGB, the annual mean 

temperature was 24.84°C and 25.49°C in 2012. At the deepest 40 m depth, the annual 

mean temperature was 24.44°C at EFGB and 24.73°C at WFGB in 2012. 
132 

16

18

20

22

24

26

28

30

32

1-Jan 1-Mar 1-May 1-Jul 1-Sep 1-Nov

Temperature (°C)

Date

Sea-Bird Annual Temperature Variation at East Flower 

Garden Bank, 2011-2012

1990-2012 Mean

Temp

2011

2012

Figure 9.4.3. Seawater temperature measured using Sea-Bird datasonde near the reef 

cap at EFGB in 2011 and 2012, and the historical long-term mean 

temperature from past monitoring periods. 

16

18

20

22

24

26

28

30

32

1-Jan 1-Mar 1-May 1-Jul 1-Sep 1-Nov

Temperature (°C)

Date

Sea-Bird Annual Temperature Variation at West Flower 

Garden Bank, 2011-2012

1990-2012 Mean

2011

2012

Figure 9.4.4. Seawater temperature measured using Sea-Bird datasonde near the reef 

cap at WFGB in 2011 and 2012, and the historical long-term mean 

temperature from past monitoring periods. 
133 

9.4.1.3. Salinity 

Salinity data were obtained from the Sea-Bird MicroCAT for January 2011 to 

December 2012, ranging from approximately 34.6 to 37.8 PSU at EFGB and WFGB with 

a mean of approximately 36 PSU. The data indicated lower salinity in summer months, a 

pattern consistent on both banks. During 2011, there were two events of low salinity on 

the reef caps of the FGB: one in May and another, more pronounced event from July 

through August. During 2012, there were also two events of low salinity: one in July 

and another, less pronounced event in August at EFGB. The data collected appear to be 

within the accepted limits of salinity for coral reefs located in the Western Atlantic (31–

38 PSU; Coles and Jokiel 1992). 

Future salinity data collected by the Sea-Bird MicroCAT conductivity recorder 

should elucidate the occurrence and intensity of low salinity events on the reef cap of 

the FGB. For now, independent measurements of salinity at and near the FGB point 

to the occurrence of substantial changes of salinity. The most probable source of low 

salinity water at the FGB is a nearshore river-seawater mix that reaches the outer 

continental shelf, eminating principally from the Mississippi and Atchafalaya River 

watersheds, and subjecting the FGB occasionally to nearshore processes and to regional 

river runoff. 

9.4.2. Chlorophyll a and Nutrients 

Chl-a concentrations in 2011 and 2012 revealed that the water column overlying the FGB 

reef caps could occasionally contain as much as 2.94 mg/m3. Not all water samples 

contained detectable levels of Chl-a (>1 mg/m3), and concentrations at the shelf edge in 

the northwestern Gulf of Mexico typically range from 0.1–0.3 mg/m3 (Nowlin et al. 

1998). The highest values for surface Chl-a are typically expected in the summer 

(July–August; Nowlin et al. 1998). The relatively high values of Chl-a (by FGB 

standards) observed on 15 February 2011 may be indicative of an algal bloom, or a pulse 

of inshore water rapidly pushed offshore. 

In a recent study, Bell et al. (2013) suggest that coral cover reduction on the Great Barrier 

Reef is attributable largely to chronic eutrophication, and that threshold Chl-a values 

need to be decreased to 0.2 mg/m3 to sustain healthy reef communities. Though most 

FGB values were below this range, some water samples contained values above this 

threshold. Unfortunately no oceanographic satellite data were available through 

NOAA’s CoastWatch Program to examine the occurrence of an algal bloom at the FGB 

in February 2011, because the use of CoastWatch to monitor changes in Chl-a in the 

area of the FGB is certainly more useful than spot checks alone. 

Ammonia values were typically less than 1 mg/l from the sea surface to the reef cap, 

with the exception of samples taken on 15–17 May 2011, 20–21 August 2011, and 25 

March 2012 at EFGB and WFGB. While high levels of ammonia can be toxic to aquatic 

life and indicate pollution, the levels of ammonia reported ranged between 0.10–0.34 

mg/l, just above the 0.10 mg/l reporting limit. Seasonal fluctuations in ammonia 

concentrations are natural due to varying rates of organic loading and biological decay. 
134 

Nitrate levels were not detected, with the exception of two samples above the reporting 

limit (0.15 mg/l). Nitrite and soluble reactive phosphorus were not detected in any of the 

samples. 

TKN (organic nitrogen and ammonia) was detected in all water samples collected at the 

banks in 2011, with concentrations ranging from 1.3–45.2 mg/l (above the 0.55 mg/l 

detection threshold). In 2012, 50% of the samples contained TKN concentrations above 

the detectable threshold ranging from 0.6–9.9 mg/l. TKN is a portion of the total nitrogen 

measurement and tests for the presence of nitrogen through the subtraction of ammonia 

nitrogen to give organic nitrogen. Organic nitrogen consists mainly of protein substances 

and their byproducts. The presence of nitrogenous compounds at abnormal levels in 

surface water generally indicates pollution and can lead to excess algae growth. 

The first Chl-a and and nutrient concentration samples were taken at the FGB as part of 

the long-term monitoring program in 2002. Since that time, most nutrients have been 

recorded below detectable limits, with the exception of the occasional spike in Chl-a and 

ammonia (Figure 9.4.5 and Figure 9.4.6). However, the one historical trend that is 

apparent at EFGB and WFGB is the increase in TKN since the first measurements were 

made in 2002. Organic nitrogen and ammonia that contributes to TKN is typically formed 

within the water column by phytoplankton and bacteria and cycled within the food chain, 

and is subject to seasonal fluctuations in the biological community, but can be affected by 

both point and non-point sources. It is possible that high levels of TKN may be correlated 

with the increased levels of macroaglae cover at both banks. Nowlin et al. (1998) 

showed that shelf edge waters in the northwestern Gulf of Mexico are typically 

stripped of nutrients. When present, the probable sources of nutrients in the water 

column at the FGB are nearshore waters (Nowlin et al. 1998), sediments (Entsch et al. 

1983), or benthic and planktonic organisms (D’Elia and Wiebe 1990). More frequent 

sampling is required to understand nutrient dynamics over the reef caps. 
135 

0

5

10

15

20

25

30

35

40 EFGB Surface Water Samples, 2002-2012

Ammonia mg/L

Chl-a mg/m3

Nitrate mg/L

Nitrite mg/L

Phosphorus mg/L

TKN mg/L

0

5

10

15

20

25

30

35

40 EFGB Midwater Water Samples, 2002-2012

0

5

10

15

20

25

30

35

40

Concentration

Year

EFGB Reef Cap Water Samples, 2002-2012

Figure 9.4.5. Water samples taken at the surface, midwater, and on the reef cap at 

EFGB from 2002–2012. 
136 

0

5

10

15

20

25

30

35

40 WFGB Surface Water Samples, 2002-2012

Ammonia mg/L

Chl-a mg/m3

Nitrate mg/L

Nitrite mg/L

Phosphorus mg/L

TKN mg/L

0

5

10

15

20

25

30

35

40 WFGB Midwater Water Samples, 2002-2012

0

5

10

15

20

25

30

35

40

Concentration

Year

WFGB Reef Cap Water Samples, 2002-2012

Figure 9.4.6. Water samples taken at the surface, midwater, and on the reef cap at 

WFGB from 2002–2012. 
137 

9.4.3. Sea State 

During the 2011–2012 monitoring period, three tropical storms and one hurricane 

occurred in the Northern Gulf of Mexico. In the past, up to 11 tropical cyclones have 

affected the Gulf of Mexico in one year (Precht et al. 2006). In 2008, Hurricane Ike 

crossed over EFGB (eventually making landfall in Galveston, Texas), damaging coral in 

the long-term monitoring study site. However, the 2011 and 2012 storms were located in 

other areas of the Gulf of Mexico and did not impact the FGB. Tropical Storm Lee in 

2011 and Hurricane and Tropical Storm Isaac in 2012 were the two cyclones that came 

closest to the FGB during the monitoring period; however, both storms were still over 

200 km east of the FGB. A list of all tropical cyclones that have occurred in the Northern 

Gulf of Mexico since 2002 can be found in Volume II Appendix 11. 
139 

CHAPTER 10.0: FISH SURVEYS 

10.1. FISH SURVEYS METHODOLOGICAL RATIONALE

Surveys of fish assemblages have been conducted at the FGB since the early 1980s; 

however, these surveys have not been part of the long-term monitoring study (Boland et al. 

1983; Rezak et al. 1985; Dennis and Bright 1988; Pattengill 1998). Fish surveys were 

officially added to the long-term monitoring protocol in 2002. The fish assemblages of the 

coral reef zone at EFGB and WFGB are composed of Caribbean reef species; however, the 

total number of species is lower in comparison (Jones and Clark 1981; Lukens 1981; Rezak 

et al. 1985; Mumby et al. 2004). The influence of nearby offshore gas and petroleum 

production platforms on fish assemblages at the FGB has also been investigated (Rooker et 

al. 1997). Continued monitoring of the FGB is vital to increasing the understanding of this 

unique habitat in light of the ongoing, as well as the changing, natural and anthropogenic 

pressures on fish populations. 

10.2. FISH SURVEYS METHODS

Twenty-four stationary visual fish surveys were conducted at both EFGB and WFGB in 

2011 and 2012, six surveys in each quadrant of the study sites. Fishes were visually assessed 

by SCUBA divers using a modified Bohnsack and Bannerot (1986) stationary visual fish 

census technique. Observations of fishes were restricted to an imaginary cylinder with a 

radius 7.5 m from the diver, extending to the surface. All fish species observed within the 

first five minutes of the survey were recorded while the diver slowly rotated in place. 

Immediately following this five minute observation period, one rotation was conducted for 

each species noted in the original five minute period to record abundance (number of 

individuals per species) and total length (within eight categories). Each survey required 10 

to 15 minutes. Transitory or schooling species were counted and measured at the time the 

individuals moved through the cylinder during the initial five-minute period. After the 

initial five-minute period, additional species were recorded but marked as observed after the 

official survey period. These observations were excluded from the analysis, unless otherwise 

stated. 

For each quadrant, a random number between 0 and 50 was generated to indicate the 

starting location along the first boundary line encountered (e.g., if the random number is 27 

m and the corner of the transect tape is 0, the transect is started at 27 m along the transect 

tape, and if the lowest corner of the transect tape is 50 m, the transect is started at 77 m 

along the transect tape). A second random number was generated between 0 and 40 to 

determine the number of fin kicks perpendicular from the boundary line into the study site. 

It takes approximately 40 fin kicks to swim 50 m, the length of the quadrant, if there is not a 

strong current. A third random number was generated to provide a random heading, between 

0° and 359°, providing a direction to swim the random distance. Those criteria provided the 

starting location for the first fish count, with a fourth number to provide a random heading, 

between 0° and 359°, along which to lay the tape marking the radius of the survey. 
140 

Subsequent survey starting points were determined with a second set of randomly generated 

numbers with the first number providing a heading, between 0° and 359°, and the second 

providing the number of fin kicks, between 12 and 40, to ensure the starting point was at 

least 15 m away from the previous location. A third number was generated to provide a 

random heading, between 0° and 359°, in which to lay the tape marking the 7.5 m radius of 

the survey. 

Fish survey dives began in the early morning (0700 CDT), and were repeated throughout the 

day until dusk. Surveys were binned into five time groupings: early morning (0700 to 0900), 

later morning (0901 to 1200), early afternoon (1201 to 1500), late afternoon (1501 to 1800), 

and early evening (1801 to dusk) to document differences throughout the day. Survey 

locations stratified randomly within the 10,000 m2

 study site, and occurred within depths of 

20–24 m. 

10.3. FISH SURVEYS DATA AND STATISTICAL ANALYSIS

Summary statistics of fish census data include abundance, density, sighting frequency, 

richness, diversity, and evenness. Fish densities are expressed as the number of fish per 

100 m2, where densities were calculated by dividing the number of individuals per 

survey by the horizontal area of the survey cylinder (176.7 m2), then multiplying by 100 

to provide fish densities per 100 m2. Sighting frequency for each species is expressed as 

the percentage of the total number of times the species was recorded out of the total 

number of surveys for the site (Bank and Year). Relative abundance is expressed as the 

number of individuals of one species divided by the total number of all species observed. 

Species richness is the total number of species for each site (Bank and Year). Diversity 

was calculated using the Shannon-Wiener diversity index, H': 

 k

H '  pi log pi

i1 

where k is the number of species present and pi is the relative abundance of each 

species, calculated as the proportion of individuals of a given species to the total number 

of individuals observed. 

Species evenness (J') was determined for each site and year using the following 

calculation: 

J ' H '

 H 'max 

where H'max was the maximum possible diversity (H'max = log k). 

Species accumulation curves were generated in PRIMER-E®, showing species 

accumulation as the increasing total number of species observed (Sobs) and Chao’s 

estimator, based on the number of rare species (Chao1). 
141 

Fish total length was recorded as size-classes: <5 cm, 5-10 cm, 10-15 cm, 15-20 cm, 

20-25 cm, 25-30 cm, 30-35 cm and >35 cm. Species were classified into four trophic 

guilds: herbivores, piscivores, invertivores, and planktivores. Size-frequency distributions 

for the four trophic guilds were calculated for each bank and year by dividing the number 

of herbivores, piscivores, invertivores, and planktivores in each size class by the total 

number observed in each trophic guild. 

Fish biomass, an important aspect of coral reef ecology, was computed by converting 

length data to weights using the allometric length-weight conversion formula: 

W = α*Lβ

where W = individual weight (grams), L = length of fish (cm), and α and β are constants 

for each species generated from the regression of its length and weight, derived from 

Froese and Pauly (2009) and Bohnsack and Harper (1988). Mean length for each species 

(to the nearest 5 cm) was used to estimate size. A mean species-biomass per unit area 

estimate (g/m2) was calculated by dividing the mean biomass for a species across all 

surveys by the area of a diver survey (176.7 m2). Biomass and species accumulation plots 

were generated to make overall assessments of the fish community at EFGB and WFGB. 

Observations of mantas and sting rays were removed from all biomass analyses due to 

their rare nature and large size. 

The software package Primer® version 6.0 was used to conduct statistical analyses on 

square root transformed density and biomass data. Species composition changes between 

years and banks were analyzed by converting to ecological distance using Bray-Curtis 

similarity matrices (Bray and Curtis, 1957): 

S’jk = 1 – (Σni=1 Xij - Xik) / (Σni=1 Xij + Xik) 

where n is the number of species and Xij is the abundance of the ith species in the jth sample 

and where there are n species overall. Where required, a dummy variable (value=1) was 

included in the analysis. SIMPER were used to analyze community dissimilarity between 

year and bank and highlight species that contributed greatly to the observed dissimilarity. 

MDS plots, 100 random starting configurations to minimize stress, were generated to 

examine for evidence of community differences by year and bank (EFGB and WFGB). 

Community differences were then compared for significant differences using nonparametric ANOSIM. The R statistic, typically ranging between 0 and 1, indicates 

between and within group dissimilarities, where small R values (<0.3) indicate that 

similarities between sites and within sites are the same (Clarke & Warwick 2001). 

Dominance plots were generated for species abundance and biomass. W-values 

(difference between the biomass and abundance) were calculated for each survey. The 

difference between abundance and biomass curves, w, can range between -1<w>1. 

Where w=1 indicates that the population has an evenly distributed abundance, but that 

biomass is dominated by few species, and where w=-1 indicates that the converse is true. 
142 

Two-sample t-tests (two-tailed) were used to analyze parametric data, including diversity 

indices and w-values. Students t-test were used for pair-wise comparisons with the 

statistical software JMP® version 10.0. 

Trend analysis of biomass and density data over time was conducted using the 

nonparametric Mann-Kendall trend test. This analysis was conducted using R (R 

Developent Core Team 2012), with the Kendall package (McLeod 2011). 

10.4. FISH SURVEYS RESULTS

Fish surveys were conducted at both banks during July 2011 and 2012 monitoring 

cruises. During this monitoring period, a total of 96 surveys were conducted, with 24 

surveys conducted at each bank. Each survey represents one sample. Each sample 

covered 176.7 m2

, resulting in a coverage of 42% of the 10,000 m2 study sites during 

2011 and 2012. A complete list of species observed and their abundance per 100 m2

 by 

year and bank is seen in Table 10.4.1. All fish survey data from 2011 and 2012 can be 

found in Volume II Appendix 10 of this report. 

Table 10.4.1. 

 

Complete Species List for 2011 and 2012 at EFGB and WFGB Showing Abundance per 

100 m2

 by Year and Bank 

 

Species ID: EFGB WFGB 

(Family Name: Species Name (Common Name - Trophic 

Guild) 2011 2012 2011 2012 

Pomacentridae: Chromis multilineata (brown chromis - I) 88.24 61.69 108.05 169.14 

Serranidae: Paranthias furcifer (creolefish - PL) 14.88 10.33 7.45 6.11 

Labridae: Thalassoma bifasciatum (bluehead - I) 9.48 10.78 12.31 13.30 

Labridae: Clepticus parrae (creole wrasse - PL) 4.86 6.74 4.53 36.22 

Labridae: Bodianus rufus (Spanish hogfish - I) 2.95 1.89 2.59 3.09 

Tetraodontidae: Canthigaster rostrata (sharpnose puffer - I) 2.57 2.08 1.98 4.17 

Pomacentridae: Stegastes partitus (bi-color damselfish - H) 2.36 7.31 2.69 15.35 

Pomacentridae: Stegastes planifrons (threespot damselfish - I) 2.24 2.52 2.99 3.09 

Acanthuridae: Acanthurus coeruleus (blue tang - H) 2.12 2.19 1.30 2.15 

Kyphosidae: Kyphosus sectatrix (chub [Bermuda/yellow] - H) 1.96 3.65 4.41 7.29 

Pomacentridae: Chromis cyanea (blue chromis - PL) 1.56 2.66 2.50 3.80 

Pomacentridae: Stegastes variabilis (cocoa damselfish - H) 1.56 4.98 1.23 5.05 

Sphyraenidae: Sphyraena barracuda (barracuda - P) 1.39 3.25 2.95 1.89 

Labridae: Sparisoma atomarium (greenblotch parrotfish - H) 1.27 0.38 0.17 0.38 

Belonidae: Belonidae spp. (needlefish spp. - P) 1.18 0.00 0.00 0.00 

Labridae: Scarus taeniopterus (princess parrotfish - H) 1.18 2.15 0.19 5.35 

Balistidae: Melichthys niger (black durgon - H) 0.97 1.11 0.66 1.63 

Labridae: Scarus vetula (queen parrotfish - H) 0.97 2.62 1.20 1.96 

Gobiidae: Elacatinus oceanops (neon goby - I) 0.92 1.11 0.28 2.59 

Labridae: Sparisoma aurofrenatum (redband parrotfish - H) 0.68 1.84 0.42 2.10 
143 

Species ID: EFGB WFGB 

(Family Name: Species Name (Common Name - Trophic 

Guild) 2011 2012 2011 2012 

Pomacentridae: Microspathodon chrysurus (yellowtail damselfish 

- H) 0.66 0.52 0.59 0.33 

Labridae: Sparisoma viride (stoplight parrotfish - H) 0.61 1.13 0.83 1.41 

Carangidae: Caranx latus (horse-eye jack - P) 0.57 0.14 0.14 0.05 

Blenniidae: Ophioblennius macclurei (redlip blenny - H) 0.54 0.19 0.17 0.40 

Chaetodontidae: Chaetodon sedentarius (reef butterflyfish - I) 0.42 0.85 0.71 0.85 

Serranidae: Cephalopholis cruentata (graysby - P) 0.40 0.52 0.26 0.57 

Carangidae: Carangoides ruber (bar jack - P) 0.31 6.91 0.28 1.72 

Pomacentridae: Abudefduf saxatilis (sergeant major - I) 0.28 0.12 0.24 0.17 

Pomacentridae: Stegastes adustus (dusky damselfish - H) 0.28 0.47 0.05 3.16 

Serranidae: Mycteroperca interstitialis (yellowmouth grouper - P) 0.28 0.33 0.05 0.09 

Pomacentridae: Chromis scotti (purple reeffish - PL) 0.26 1.27 0.83 5.54 

Acanthuridae: Acanthurus chirurgus (doctorfish - H) 0.24 0.61 0.07 0.26 

Blenniidae: Parablennius marmoreus (seaweed blenny - I) 0.24 2.05 0.00 3.44 

Chaetodontidae: Prognathodes aculeatus (Longsnout butterflyfish 

- I) 0.24 0.14 0.33 0.33 

Acanthuridae: Acanthurus bahianus (ocean surgeonfish - H) 0.21 0.73 0.02 0.85 

Pomacanthidae: Holacanthus tricolor (rock beauty - I) 0.21 0.31 0.07 0.75 

Labridae: Halichoeres garnoti (yellowhead wrasse - I) 0.19 1.44 0.09 0.97 

Mullidae: Mulloidichthys martinicus (yellow goatfish - I) 0.19 0.73 0.17 0.07 

Chaetodontidae: Chaetodon ocellatus (spotfin butterflyfish - I) 0.17 0.38 0.00 0.07 

Lutjanidae: Lutjanus griseus (gray snapper - I) 0.17 0.14 0.14 0.14 

Pomacentridae: Chromis insolata (sunshinefish - PL) 0.17 0.35 0.26 1.23 

Ostraciidae: Lactophrys triqueter (smooth trunkfish - I) 0.12 0.14 0.19 0.24 

Acanthuridae: Acanthurus spp. (surgeonfish spp. - H) 0.09 0.00 0.00 0.00 

Holocentridae: Holocentrus adscensionis (squirrelfish - I) 0.09 0.05 0.00 0.00 

Serranidae: Cephalopholis fulva (coney - I) 0.09 0.07 0.00 0.00 

Serranidae: Epinephelus adscensionis (rock hind - I) 0.09 0.21 0.00 0.02 

Balistidae: Canthidermis sufflamen (ocean triggerfish- I) 0.07 0.14 0.09 0.02 

Chaetodontidae: Chaetodon striatus (banded butterflyfish - I) 0.07 0.00 0.02 0.05 

Cirrhitidae: Amblycirrhitus pinos (redspotted hawkfish - I) 0.07 0.02 0.09 0.09 

Apogonidae: Apogon maculatus (flamefish - I) 0.05 0.00 0.00 0.00 

Balistidae: Balistes vetula (queen triggerfish - I) 0.05 0.00 0.00 0.00 

Carangidae: Caranx lugubris (black jack - P) 0.05 0.02 0.00 0.00 

Lutjanidae: Lutjanus jocu (dog snapper - P) 0.05 0.12 0.12 0.28 

Pomacanthidae: Pomacanthus paru (French angelfish - I) 0.05 0.00 0.05 0.05 

Labridae: Scarus iseri (striped parrotfish - H) 0.05 0.42 0.12 1.23 

Tetraodontidae: Sphoeroides spengleri (bandtail puffer - I) 0.05 0.00 0.00 0.00 

Carangidae: Caranx hippos (Crevalle jack - P) 0.02 0.00 0.00 0.00 

Labridae: Bodianus pulchellus (spotfin hogfish - I) 0.02 0.00 0.02 0.00 
144 

Species ID: EFGB WFGB 

(Family Name: Species Name (Common Name - Trophic 

Guild) 2011 2012 2011 2012 

Lutjanidae: Ocyurus chrysurus (yellowtail snapper - PL) 0.02 0.00 0.00 0.00 

Monacanthidae: Cantherhines macrocerus (whitespotted filefish - 

I) 0.02 0.00 0.02 0.00 

Monacanthidae: Cantherhines pullus (orange spotted filefish - I) 0.02 0.12 0.02 0.07 

Serranidae: Mycteroperca bonaci (black grouper - P) 0.02 0.00 0.00 0.09 

Serranidae: Mycteroperca phenax (scamp - P) 0.02 0.02 0.00 0.00 

Serranidae: Mycteroperca tigris (tiger grouper - P) 0.02 0.05 0.09 0.05 

Carangidae: Caranx crysos (blue runner - P) 0.00 0.00 0.00 0.54 

Carangidae: Seriola dumerili (greater amberjack - P) 0.00 0.00 0.00 0.07 

Chaenopsidae: Acanthemblemaria aspera (roughhead blenny - PL) 0.00 0.00 0.00 0.02 

Diodontidae: Diodon hystrix (porcupinefish - I) 0.00 0.00 0.00 0.07 

Gobiidae: Gnatholepis thompsoni (goldspot goby - H) 0.00 0.02 0.00 0.00 

Holocentridae: Holocentrus rufus (longspine squirrelfish - I) 0.00 0.05 0.05 0.05 

Labridae: Halichoeres bivittatus (slippery dick - I) 0.00 0.02 0.14 0.00 

Labridae: Halichoeres maculipinna (clown wrasse - I) 0.00 0.09 0.00 1.98 

Labridae: Halichoeres radiatus (pudding wife - I) 0.00 0.05 0.00 0.12 

Lutjanidae: Lutjanus cyanopterus (Cubera snapper - P) 0.00 0.00 0.00 0.05 

Mullidae: Pseudupeneus maculatus (spotted goatfish - I) 0.00 0.00 0.12 0.00 

Muraenidae: Gymnothorax miliaris (goldentail moray - I) 0.00 0.02 0.02 0.05 

Muraenidae: Gymnothorax moringa (spotted moray - P) 0.00 0.00 0.05 0.00 

Ostraciidae: Acanthostracion polygonius (honeycomb cowfish - I) 0.00 0.00 0.05 0.07 

Ostraciidae: Lactophrys bicaudalis (spotted trunkfish - I) 0.00 0.00 0.02 0.00 

Pomacanthidae: Holacanthus bermudensis (blue angelfish - I) 0.00 0.02 0.02 0.02 

Pomacanthidae: Holacanthus ciliaris (queen angelfish - I) 0.00 0.07 0.05 0.07 

Pomacanthidae: Holacanthus townsendi (townsend angelfish - I) 0.00 0.00 0.02 0.00 

Pomacentridae: Stegastes leucostictus (beaugregory - I) 0.00 0.00 0.00 1.04 

Labridae: Sparisoma radians (bucktooth parrotfish - H) 0.00 0.00 0.00 0.05 

P=Piscivore, I=Invertivore, PL=Planktivore, and H=Herbivore 

Total fish abundance at EFGB in 2011 and 2012 was 6,411 and 6,376, respectively. At 

WFGB, total fish abundance in 2011 and 2012 was 6,979 and 12,556, respectively. 

Species accumulation curves indicate that current sample size adequately captures species 

richness for the study period (Figure 10.4.1). 
145 

Figure 10.4.1. Tropical species accumulation curve. 

Sobs represents species accumulation with increasing total number of 

species observed and Chao1 represents Chao’s estimator accounting 

for the number of rare species. 

10.4.1. Population Diversity 

A total of 26 families and 84 species were recorded during this survey period for all 

samples combined. Family richness ranged between 21 (EFGB 2012 and WFGB 2011) 

and 24 (WFGB 2012). Species richness varied between 59 (WFGB 2011) and 65 (WFGB 

2012) (Table 10.4.2). In 2011, an average of 11 ± 2 fish families per sample was recorded 

at EFGB and 11 ± 2 at WFGB. In 2012, an average of 11 ± 2 fish families per sample 

was recorded at EFGB and 13 ± 2 at WFGB. For species richness in 2011, an average of 

20 ± 4 fish species per sample was recorded at EFGB, and 19 ± 3 at WFGB. In 2012, an 

average of 22 ± 4 fish species per sample was recorded at EFGB, and 23 ± 5 at WFGB. 

Table 10.4.2. 

 

Species and Family Richness by Year and Bank 

 EFGB WFGB 

 2011 2012 2011 2012 

Species Richness 64 60 59 65 

Mean Species Richness/Survey 20±4 22±4 19±3 23±5 

Family Richness 22 21 21 24 

Mean Family Richness/Survey 11±2 11±2 11±2 13±2 

 

Values expressed as richness ± SD 
146 

When species richness was compared using a two-way ANOVA with an experimentwise 

error rate of α=0.05, a significant difference was observed between 2011 and 2012 (Pvalue=0.0006), but not between banks. The interaction of year and bank was also not 

significant. Analysis of each pair using a Students t-test showed a significant difference 

in species richness between 2011 and 2012 at WFGB (P-value=0.0009), but not at EFGB. 

No significant difference was seen in species richness between EFGB and WFGB in 

2011 or 2012. 

Species richness within families was calculated overall and between years and banks. 

Overall, the families containing the greatest number of species were the wrasses and 

parrotfishes (Labridae), damselfishes (Pomacentridae), and groupers and seabasses 

(Serranidae), represented by 15, 11, and 8 species, respectively (Table 10.4.3). 

Table 10.4.3. 

 

Species Richness within Families between Years and Banks, and between all Surveys 

Family 

EFGB WFGB 

All Surveys 2011 2012 2011 2012 

Labridae 11 13 11 13 15 

Pomacentridae 10 10 10 11 11 

Serranidae 8 7 7 6 8 

Pomacanthidae 2 3 2 4 5 

Carangidae 4 3 2 3 5 

Acanthuridae 4 3 3 3 4 

Lutjanidae 3 2 3 3 4 

Chaetodontidae 4 3 4 4 4 

Balistidae 3 2 3 2 3 

Ostraciidae 1 1 1 2 3 

Tetraodontidae 2 1 2 1 2 

Gobiidae 1 2 1 1 2 

Blenniidae 2 2 2 2 2 

Mullidae 1 1 1 1 2 

Holocentridae 1 2 1 1 2 

Monacanthidae 2 1 1 1 2 

Muraenidae 0 1 0 1 2 

Sphyraenidae 1 1 1 1 1 

Kyphosidae 1 1 1 1 1 

Belonidae 1 0 1 0 1 

Cirrhitidae 1 1 1 1 1 

Apogonidae 1 0 1 0 1 

Chaenopsidae 0 0 0 1 1 

Diodontidae 0 0 0 1 1 
147 

Diversity and evenness was measured between banks and years by calculating ShannonWiener diversity indices (Table 10.4.4). Diversity varied between banks and years; the 

greatest diversity occurred at WFGB in 2012. The lowest diversity was calculated for 

WFGB in 2011. Evenness between banks and years remained relatively stable; the least 

variation in communities occurred at EFGB in 2012. 

Table 10.4.4. 

 

Shannon-Wiener Diversity and Evenness Indices for Each Bank and Year 

 EFGB WFGB 

 2011 2012 2011 2012 

Diversity (H’) 0.83 1.11 0.71 0.89 

Evenness (J’) 0.46 0.62 0.40 0.49 

When compared between banks using a two-way ANOVA, a significant difference was 

only observed between 2011 and 2012 for species diversity (P-value=0.0083). In pairwise Students t-tests, only the comparison of species diversity between WFGB in 2011 

and EFGB in 2012 were found to be significantly different (P-value=0.0165), suggesting 

a significantly greater species diversity at EFGB in 2012 than WFGB in 2011. 

10.4.2. Sighting Frequency and Occurrence 

The most frequently sighted species from all years and locations was the brown chromis 

(Chromis multilineata), observed in 91% of all surveys. Other frequently sighted species 

included Spanish hogfish (Bodianus rufus), bluehead (Thalassoma bifasciatum), sharpnose 

puffer (Canthigaster rostrata), blue tang (Acanthurus coeruleus), bi-color damselfish 

(Stegastes partitus), and great barracuda (Sphyraena barracuda), with sighting 

frequencies of 90%, 90%, 88%, 85%, 83%, and 80%, respectively (Table 10.4.5) 

Table 10.4.5. 

 

Percent Sighting Frequency for Species by Year and Bank, Including Sighting Frequency for All 

Surveys Conducted during the 2011–2012 Reporting Period 

Species ID: EFGB WFGB 

All 

Surveys 

(Family Name: Species Name (Common Name - Trophic 

Guild) 2011 2012 2011 2012 

Acanthuridae: Acanthurus bahianus (ocean surgeonfish) 20.8 20.8 4.2 29.2 18.0 

Acanthuridae: Acanthurus chirurgus (doctorfish) 20.8 45.8 8.3 20.8 23.0 

Acanthuridae: Acanthurus coeruleus (blue tang) 95.8 79.2 91.7 87.5 85.0 

Acanthuridae: Acanthurus spp. (surgeonfish spp.) 4.2 0.0 0.0 0.0 1.0 

Apogonidae: Apogon maculatus (flamefish) 4.2 0.0 0.0 0.0 1.0 

Balistidae: Balistes vetula (queen triggerfish) 8.3 0.0 0.0 0.0 2.0 

Balistidae: Canthidermis sufflamen (ocean triggerfish) 8.3 20.8 16.7 4.2 12.0 

Balistidae: Melichthys niger (black durgon) 58.3 66.7 58.3 62.5 59.0 

Belonidae: Belonidae spp. (needlefish spp.) 4.2 0.0 0.0 0.0 1.0 
148 

Species ID: EFGB WFGB 

All 

Surveys 

(Family Name: Species Name (Common Name - Trophic 

Guild) 2011 2012 2011 2012 

Blenniidae: Ophioblennius macclurei (redlip blenny) 41.7 16.7 25.0 29.2 27.0 

Blenniidae: Parablennius marmoreus (seaweed blenny) 20.8 25.0 0.0 45.8 22.0 

Carangidae: Carangoides ruber (bar jack) 29.2 45.8 16.7 12.5 25.0 

Carangidae: Caranx crysos (blue runner) 0.0 0.0 0.0 4.2 1.0 

Carangidae: Caranx hippos (Crevalle jack) 4.2 0.0 0.0 0.0 1.0 

Carangidae: Caranx latus (horse-eye jack) 12.5 16.7 16.7 8.3 13.0 

Carangidae: Caranx lugubris (black jack) 4.2 4.2 0.0 0.0 2.0 

Carangidae: Seriola dumerili (greater amberjack) 0.0 0.0 0.0 4.2 1.0 

Chaenopsidae: Acanthemblemaria aspera (roughhead blenny) 0.0 0.0 0.0 4.2 1.0 

Chaetodontidae: Chaetodon ocellatus (spotfin butterflyfish) 12.5 20.8 0.0 8.3 10.0 

Chaetodontidae: Chaetodon sedentarius (reef butterflyfish) 33.3 62.5 54.2 58.3 50.0 

Chaetodontidae: Chaetodon striatus (banded butterflyfish) 8.3 0.0 4.2 4.2 4.0 

Chaetodontidae: Prognathodes aculeatus (longsnout 

butterflyfish) 25.0 20.8 37.5 41.7 30.0 

Cirrhitidae: Amblycirrhitus pinos (redspotted hawkfish) 8.3 4.2 16.7 16.7 11.0 

Diodontidae: Diodon hystrix (porcupinefish) 0.0 0.0 0.0 12.5 3.0 

Gobiidae: Elacatinus oceanops (neon goby) 33.3 54.2 20.8 62.5 41.0 

Gobiidae: Gnatholepis thompsoni (goldspot goby) 0.0 4.2 0.0 0.0 1.0 

Holocentridae: Holocentrus adscensionis (squirrelfish) 12.5 8.3 0.0 0.0 5.0 

Holocentridae: Holocentrus rufus (longspine squirrelfish) 0.0 8.3 4.2 8.3 5.0 

Kyphosidae: Kyphosus sectatrix (chub (Bermuda/yellow)) 70.8 54.2 70.8 79.2 66.0 

Labridae: Bodianus pulchellus (spotfin hogfish) 4.2 0.0 4.2 0.0 2.0 

Labridae: Bodianus rufus (Spanish hogfish) 95.8 91.7 91.7 95.8 90.0 

Labridae: Clepticus parrae (creole wrasse) 66.7 50.0 54.2 75.0 59.0 

Labridae: Halichoeres bivittatus (slippery dick) 0.0 4.2 20.8 0.0 6.0 

Labridae: Halichoeres garnoti (yellowhead wrasse) 25.0 16.7 8.3 12.5 15.0 

Labridae: Halichoeres maculipinna (clown wrasse) 0.0 8.3 0.0 50.0 14.0 

Labridae: Halichoeres radiatus (pudding wife) 0.0 8.3 0.0 12.5 5.0 

Labridae: Thalassoma bifasciatum (bluehead ) 87.5 100.0 87.5 100.0 90.0 

Labridae: Scarus iseri (striped parrotfish) 4.2 16.7 8.3 12.5 10.0 

Labridae: Scarus taeniopterus (princess parrotfish) 41.7 37.5 16.7 45.8 34.0 

Labridae: Scarus vetula (queen parrotfish) 58.3 95.8 66.7 75.0 71.0 

Labridae: Sparisoma atomarium (greenblotch parrotfish) 70.8 29.2 20.8 25.0 35.0 

Labridae: Sparisoma aurofrenatum (redband parrotfish) 41.7 54.2 29.2 58.3 44.0 

Labridae: Sparisoma radians (bucktooth parrotfish) 0.0 0.0 0.0 8.3 2.0 

Labridae: Sparisoma viride (stoplight parrotfish) 45.8 62.5 66.7 58.3 56.0 

Lutjanidae: Ocyurus chrysurus (yellowtail snapper) 4.2 0.0 0.0 0.0 1.0 

Lutjanidae: Lutjanus cyanopterus (Cubera snapper) 0.0 0.0 0.0 4.2 1.0 

Lutjanidae: Lutjanus griseus (gray snapper) 20.8 4.2 16.7 12.5 13.0 
149 

Species ID: EFGB WFGB 

All 

Surveys 

(Family Name: Species Name (Common Name - Trophic 

Guild) 2011 2012 2011 2012 

Lutjanidae: Lutjanus jocu (dog snapper) 8.3 12.5 20.8 37.5 19.0 

Monacanthidae: Cantherhines macrocerus (whitespotted 

filefish) 4.2 0.0 4.2 0.0 2.0 

Monacanthidae: Cantherhines pullus (orange spotted filefish) 4.2 12.5 4.2 8.3 7.0 

Mullidae: Mulloidichthys martinicus (yellow goatfish) 12.5 20.8 20.8 12.5 16.0 

Mullidae: Pseudupeneus maculatus (spotted goatfish) 0.0 0.0 16.7 0.0 4.0 

Muraenidae: Gymnothorax moringa (spotted moray) 0.0 0.0 8.3 0.0 2.0 

Muraenidae: Gymnothorax miliaris (goldentail moray) 0.0 4.2 4.2 4.2 3.0 

Ostraciidae: Acanthostracion polygonius (honeycomb cowfish) 0.0 0.0 8.3 12.5 5.0 

Ostraciidae: Lactophrys bicaudalis (spotted trunkfish) 0.0 0.0 4.2 0.0 1.0 

Ostraciidae: Lactophrys triqueter (smooth trunkfish) 16.7 20.8 25.0 33.3 23.0 

Pomacanthidae: Holacanthus bermudensis (blue angelfish) 0.0 4.2 4.2 4.2 3.0 

Pomacanthidae: Holacanthus ciliaris (queen angelfish) 0.0 12.5 8.3 12.5 8.0 

Pomacanthidae: Holacanthus townsendi (townsend angelfish) 0.0 0.0 4.2 0.0 1.0 

Pomacanthidae: Holacanthus tricolor (rock beauty) 20.8 33.3 12.5 50.0 28.0 

Pomacanthidae: Pomacanthus paru (French angelfish) 8.3 0.0 8.3 8.3 6.0 

Pomacentridae: Abudefduf saxatilis (sergeant major) 12.5 12.5 20.8 16.7 15.0 

Pomacentridae: Chromis cyanea (blue chromis) 29.2 70.8 54.2 70.8 54.0 

Pomacentridae: Chromis insolata (sunshinefish) 12.5 16.7 20.8 37.5 21.0 

Pomacentridae: Chromis multilineata (brown chromis) 95.8 100.0 95.8 87.5 91.0 

Pomacentridae: Chromis scotti (purple reeffish) 16.7 41.7 29.2 62.5 36.0 

Pomacentridae: Microspathodon chrysurus (yellowtail 

damselfish) 54.2 37.5 33.3 20.8 35.0 

Pomacentridae: Stegastes adustus (dusky damselfish) 20.8 33.3 8.3 45.8 26.0 

Pomacentridae: Stegastes leucostictus (beaugregory) 0.0 0.0 0.0 20.8 5.0 

Pomacentridae: Stegastes partitus (bi-color damselfish) 75.0 95.8 87.5 87.5 83.0 

Pomacentridae: Stegastes planifrons (threespot damselfish) 66.7 54.2 83.3 50.0 61.0 

Pomacentridae: Stegastes variabilis (cocoa damselfish) 58.3 75.0 45.8 58.3 57.0 

Serranidae: Cephalopholis cruentata (graysby) 50.0 45.8 25.0 41.7 39.0 

Serranidae: Cephalopholis fulva (coney) 8.3 8.3 0.0 0.0 4.0 

Serranidae: Epinephelus adscensionis (rock hind) 12.5 16.7 0.0 4.2 8.0 

Serranidae: Mycteroperca bonaci (black grouper) 4.2 0.0 0.0 16.7 5.0 

Serranidae: Mycteroperca interstitialis (yellowmouth grouper) 41.7 33.3 8.3 8.3 22.0 

Serranidae: Mycteroperca phenax (scamp) 4.2 4.2 0.0 0.0 2.0 

Serranidae: Mycteroperca tigris (tiger grouper) 4.2 8.3 12.5 8.3 8.0 

Serranidae: Paranthias furcifer (creolefish) 83.3 70.8 100.0 58.3 75.0 

Sphyraenidae: Sphyraena barracuda (barracuda) 66.7 83.3 95.8 87.5 80.0 

Tetraodontidae: Canthigaster rostrata (sharpnose puffer) 100.0 83.3 87.5 95.8 88.0 

Tetraodontidae: Sphoeroides spengleri (bandtail puffer) 4.2 0.0 0.0 0.0 1.0 
150 

Species were considered “rare” if they were recorded in less than 20% of all surveys. 

“Prevalent” species were recorded in ≥20% of surveys. A total of 50 species were 

characterized as “rare” and 34 species were characterized as “prevalent.” 

 

Each survey was transformed to presence/absence for each species, and analyzed for 

differences in community composition based on species occurrence between years and 

banks. The greatest dissimilarity was observed between EFGB in 2011 and WFGB in 

2012 (46.82%); the smallest dissimilarity was seen between EFGB in 2012 and WFGB in 

2012 (43.66%). No single species was identified as contributing predominately to the 

observed dissimilarity; all species made small, incremental contributions. 

MDS ordination had a high 2-dimenstional stress value (0.3), indicating poor goodnessof-fit in a 2-dimensional scale (Figure 10.4.2). A slight data cluster was observed, with 

2011 data trending more to the left of the ordination and 2012 data to the right. 

Figure 10.4.2. MDS plot displaying two-dimensional fish occurrence 

similarity between years and banks. 

ANOSIM results indicate a significant, but small, spatial and temporal variations are 

occurring, with significant differences between year (Global R=0.15, p<0.1%) and bank 

(Global R=0.094, p<0.1%). While these differences are biologically significant, the very 

small R values indicate that the dissimilarities between groups are less than some of the 

within-group dissimilarities and are therefore uninformative. 
151 

10.4.3. Species Density 

Mean fish density (abundance 100 m-2) was highest at WFGB in 2012 (313 ± 318 SD) and 

lowest at EFGB in 2012 (150 ± 75 SD). The high fish density at WFGB in 2012 was 

caused by high local abundance of brown chromis, with an average density of 169 ± 233 

SD individuals per 100 m2

. Brown chromis were the most abundant fish recorded at both 

banks for both years. Variations in fish densities between years and banks are 

predominantly attributed to the presence or absence of dense schooling fish species, 

including brown chromis, creolefish (Paranthias furcifer), and creole wrasse (Clepticus 

parrae). 

Using SIMPER, greatest dissimilarity was observed between EFGB in 2011 and EFGB in 

2012 (54.61%), while the smallest dissimilarity was observed between EFGB in 2012 and 

WFGB in 2012 (46.99%). The greatest contributor of dissimilarity for all comparisons 

was the density of brown chromis. The final MDS ordination had a moderate stress value 

(0.24), indicating moderate goodness-of-fit in a two-dimensional scale (Figure 10.4.3), 

with no apparent data clusters. 

Figure 10.4.3. MDS plot displaying two-dimensional fish density similarity 

between years and banks. 

ANOSIM results indicate a significant, but small, spatial and temporal variations are 

occurring, with significant differences between year (Global R=0.196, p<0.1%) and bank 

(Global R=0.115, p<0.1%). Though these differences are biologically significant, the 

small R values indicate that the dissimilarities between groups are less than some of the 

within-group dissimilarities and are therefore uninformative. 
152 

10.4.4. Trophic Group Analysis 

Species were grouped by trophic guild into four major categories: herbivores, piscivores, 

invertivores, and planktivores. It should be noted that parrotfish, once belonging to the 

Scaridae family, have been reclassified and are part of the Labridae family (Westneat and 

Alfaro 2005; AFS 2013). Volume II Appendix 11 of this report contains all species 

groupings by trophic guild, as defined by NOAA’s Center for Coastal Monitoring and 

Assessment (CCMA) BioGeography Branch fish-trophic level database. 

Species richness and family richness within trophic guilds was calculated between years 

and banks (Table 10.4.6). Overall, the trophic guild containing the greatest number of 

species was the invertivores, with 42 species and 18 families, and the guild containing the 

fewest number of species was the planktivores, with 7 species and 5 families. 

Table 10.4.6. 

 

Species Richness within Trophic Guilds between Years and Banks, and between all Surveys 

Trophic Group 

EFGB WFGB 

All Surveys 2011 2012 2011 2012 

Herbivore 17 (6) 17 (7) 16 (6) 17 (6) 19 (7) 

Invertivore 29 (16) 29 (17) 30 (14) 31 (17) 42 (18) 

Planktivore 6 (4) 5 (3) 5 (3) 6 (4) 7 (5) 

Piscivore 13 (5) 9 (4) 8 (5) 11 (5) 16 (7) 

The number in parenthesis represents family richness 

The density was greatest for the invertivore guild, with an average of 133 individuals per 

100 m2, while the density was smallest for the piscivore guild, with an average of 6 

individuals per 100 m2 (Table 10.4.7). 

Table 10.4.7. 

 

Average Density per 100 m2 of Individuals from each Trophic Guild by Year and Bank, 

± Standard Deviation 

Trophic Group 

EFGB WFGB 

All Surveys 2011 2012 2011 2012 

Herbivore 16±1 30±2 14±1 49±3 27±2 

Invertivore 109±4 87±3 131±6 206±7 133±5 

Planktivore 22±2 21±2 16±2 53±4 28±3 

Piscivore 4±1 11±2 4±1 5±1 6±1 
153 

SIMPER analysis identified the greatest dissimilarity was between 2011 and 2012 at 

WFGB (31.89%), and the smallest dissimilarity was observed between 2011 and 2012 at 

EFGB (22.82%). For all comparisons, the greatest contributor to the observed 

dissimilarity was the invertivore trophic guild. The MDS ordination had a low stress 

value (0.13), indicating good goodness-of-fit in a two-dimensional scale (Figure 10.4.4). 

No clusters were apparent. 

Figure 10.4.4. MDS plot displaying two-dimensional trophic guild density 

similarity between years and banks. 

ANOSIM results indicate a significant, but small, spatial and temporal variations are 

occurring, with significant differences between year (Global R=0.12, p<0.1%) and bank 

(Global R=0.066, p<0.4%). All R statistic values were small, indicating that the 

dissimilarities between groups are less than some of the within-group dissimilarities and 

are therefore uninformative. 

Size-frequency distributions, using the relative abundance of species for each trophic 

guild, were graphed for each trophic guild by year and bank. At both EFGB and WFGB, 

herbivores, invertivores, and planktivores were dominated by smaller individuals, 

whereas piscivores were dominated by larger individuals (Figures 10.4.5 and 10.4.6). 
154 

Figure 10.4.5. EFGB size distribution by trophic guild. 

Blue columns represent year 2011 and red columns represent year 2012, (A) Herbivores, (B) 

Invertivores, (C) Piscivores, and (D) Planktivores. 

(A) (B)

(C) (D)
155 

Figure 10.4.6. WFGB size distribution by trophic guild. 

Blue columns represent year 2011 and red columns represent year 2012, (A) Herbivores, (B) 

Invertivores, (C) Piscivores, and (D) Planktivores. 

10.4.5. Biomass Analysis 

Average biomass for all surveys was calculated to be 118.18 g/m2

 ±233.07 SD). The 

greatest average biomass was seen at WFGB in 2011 (162.58 g/m2

 ±360.08 SD), while 

the lowest average biomass was seen at WFGB in 2012 (24.58 g/m2

 ± 22.58 SD) (Table 

10.4.8). 

Table 10.4.8. 

 

Total and Average Biomass, in g/m2, by Year and Bank, ± Standard Deviation 

 EFGB WFGB 

 2011 2012 2011 2012 

Total Biomass (g/m2) 2357.63 1234.58 3901.63 590.03 

Average Biomass/Survey (g/m2) 98.23±172.02 51.44±51.16 162.57±360.08 24.58±22.58 

(A) (B)

(C) (D)
156 

SIMPER analysis identified the greatest dissimilarity was between 2011 and 2012 at 

WFGB (68.08%); the smallest dissimilarity was observed between WFGB in 2011 and 

EFGB in 2012 (62.62%). For all comparisons, the greatest contributor to the observed 

dissimilarity was great barracuda, except for the comparison between EFGB in 2011 and 

WFGB in 2012, in which the greatest contributor to the observed dissimilarity was 

creolefish. 

The MDS ordination had a moderate stress value (0.25), indicating moderate goodnessof-fit in a two-dimensional scale (Figure 10.4.7). A slight data cluster was observed, with 

2011 data trending more to the left of the ordination and 2012 data to the right. 

Figure 10.4.7. MDS plot displaying two-dimensional biomass similarity between 

years and banks. 

ANOSIM results indicate a significant, but small, spatial and temporal variations are 

occurring, with significant differences between year (Global R=0.178, p<0.1%) and bank 

(Global R=0.126, p<0.1%). All R statistic values were small, indicating that the 

dissimilarities between groups are less than some of the within-group dissimilarities are 

therefore uninformative. 

When summed into trophic guilds, the piscivores possessed the highest average biomass 

for all surveys, with 45.73 g/m2

 (±186.51 SD), over 50% of total biomass. However, 

when averaged between year and bank, the piscivores represented the only greatest 

average biomass at EFGB and WFGB in 2011. In 2012, at both EFGB and WFGB, the 

herbivores represented the greatest average biomass. The lowest average biomass from 

all surveys was represented by the invertivores with 7.46 g/m2 (±11.25 SD). However, 

when averaged between year and bank, the invertivores represented the only lowest 
157 

average biomass at EFGB and WFGB in 2011. In 2012, the lowest average biomass for 

both EFGB and WFGB was the planktivores (Table 10.4.9 and Figure 10.4.8). The 

reduced biomass of piscivores between 2011 and 2012 is primarily due to fewer horseeye jack (Caranx latus) recorded during the 2012 study period. 

 Table 10.4.9. 

 

Average Biomass, in g/m2, for each Trophic Guild by Year and Bank and between all Surveys, 

± Standard Deviation 

Trophic 

Guild 

EFGB WFGB 

All Surveys 2011 2012 2011 2012 

H 23.07 ± 20.61 20.30 ± 37.18 34.45 ± 39.91 16.97 ± 38.16 22.67 ± 30.98 

I 13.81 ± 18.66 3.64 ± 4.43 8.67 ± 6.86 3.28 ± 5.36 7.46 ± 11.25 

PL 15.63 ± 22.93 3.53 ± 5.28 11.25 ± 21.96 2.34 ± 4.94 8.34 ± 16.94 

P 45.72 ± 155.70 17.42 ± 29.10 108.20 ± 334.97 8.34 ± 10.99 45.73 ± 186.51 

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

2011 EFGB 2012 EFGB 2011 WFGB 2012 WFGB

Percent Composition (%)

Planktivore Biomass

Invertivore Biomass

Piscivore Biomass

Herbivore Biomass

Figure 10.4.8. FGB size distribution by trophic guild: (A) herbivores, (B) invertivores, (C) 

piscivores, and (D) planktivores. 

SIMPER analysis identified the greatest dissimilarity was between EFGB in 2011 and 

WFGB in 2012 (44.32%) and the smallest dissimilarity was observed between WFGB in 

2011 and EFGB in 2012 (38.20%). For all comparisons, the greatest contributor to the 

observed dissimilarity was the piscivore guild. 

The MDS ordination had a low stress value (0.14), which indicates good goodness-of-fit 

in a two-dimensional scale (Figure 10.4.9). No clusters were observed. 
158 

Figure 10.4.9. MDS plot displaying two-dimensional trophic guild similarity between 

years and banks. 

ANOSIM results indicate a significant, but small, spatial, and temporal variations are 

occurring, with significant differences between year (Global R=0.156, p<0.1%) and bank 

(Global R=0.063, p<0.6%). All R statistic values were small, indicating that the 

dissimilarities between groups are less than some of the within-group dissimilarities. 

For each trophic guild, the percent contribution each species made to the total biomass 

was calculated (Table 10.4.10). For the herbivore guild, 53.8% of the biomass was 

contributed by Bermuda chub (Kyphosus sectatrix). For the invertivore guild, the greatest 

contribution was brown chromis, contributing 59.5% of all biomass. For the piscivore 

guild, great barracuda contributed the greatest biomass to all surveys, 85.9%. For the 

planktivore guild, the greatest contribution was creolefish, contribution 78.5% of all 

biomass. 
159 

Table 10.4.10. 

 

Percent Contribution of Each Species to the Average Biomass of Each Trophic Guild 

Trophic 

Guild 

Species ID: EFGB WFGB All 

Surveys (Family Name:Species Name 

(Common Name - Trophic Guild)) 2011 2012 2011 2012 

Herbivore 

Kyphosidae: Kyphosus sectatrix 

(chub (bermuda/yellow)) 35.2 54.2 66.0 53.6 53.8 

Labridae: Sparisoma viride 

(stoplight parrotfish) 12.6 21.8 11.1 19.4 15.1 

Labridae: Scarus vetula 

 (queen parrotfish) 8.8 9.2 12.1 10.0 10.3 

Balistidae: Melichthys niger 

(black durgon) 20.5 6.6 4.8 6.2 9.4 

Acanthuridae: Acanthurus coeruleus 

(blue tang) 14.8 3.4 2.8 5.2 6.3 

Labridae: Scarus taeniopterus 

(princess parrotfish) 3.5 0.8 0.7 1.1 1.5 

Labridae: Sparisoma aurofrenatum (redband 

parrotfish) 1.3 1.7 1.4 0.9 1.4 

Acanthuridae: Acanthurus chirurgus

(doctorfish) 0.8 0.9 0.4 1.3 0.7 

Pomacentridae: Microspathodon chrysurus

(yellowtail damselfish) 0.9 0.5 0.6 0.2 0.6 

Acanthuridae: Acanthurus bahianus 

(ocean surgeonfish) 0.4 0.4 <0.1 0.8 0.3 

Pomacentridae: Stegastes partitus 

(bi-color damselfish) 0.3 0.3 0.2 0.7 0.3 

Acanthuridae: Acanthurus spp. 

(surgeonfish spp.) 0.6 0.0 0.0 0.0 0.2 

Pomacentridae: Stegastes variabilis 

(cocoa damselfish) 0.1 0.2 <0.1 0.3 0.1 

Labridae: Sparisoma atomarium

(greenblotch parrotfish) 0.1 0.1 <0.1 <0.1 0.1 

Blenniidae: Ophioblennius macclurei (redlip 

blenny) <0.1 <0.1 <0.1 <0.1 <0.1 

Gobiidae: Gnatholepis thompsoni 

(goldspot goby) 0.0 <0.1 0.0 0.0 <0.1 

Pomacentridae: Stegastes adustus 

(dusky damselfish) 0.1 <0.1 <0.1 0.2 <0.1 

Labridae: Scarus iseri 

(striped parrotfish) <0.1 <0.1 <0.1 <0.1 <0.1 

Labridae: Sparisoma radians 

(bucktooth parrotfish) 0.0 0.0 0.0 <0.1 <0.1 

Invertivore 

Pomacentridae: Chromis multilineata

(brown chromis) 63.6 51.6 56.1 60.8 59.5 

Lutjanidae: Lutjanus griseus 

(gray snapper) 13.2 2.9 4.8 1.7 8.1 

Balistidae: Canthidermis sufflamen 

(ocean triggerfish) 3.8 9.3 10.1 0.8 6.0 

Pomacanthidae: Pomacanthus paru 

(French angelfish) 2.1 0.0 5.9 3.5 3.1 
160 

Trophic 

Guild 

Species ID: EFGB WFGB All 

Surveys (Family Name:Species Name 

(Common Name - Trophic Guild)) 2011 2012 2011 2012 

Mullidae: Mulloidichthys martinicus (yellow 

goatfish) 1.3 10.6 1.0 0.9 2.4 

Pomacentridae: Stegastes planifrons 

(threespot damselfish) 1.4 1.3 3.8 1.8 2.1 

Ostraciidae: Acanthostracion polygonius

(honeycomb cowfish) 0.0 0.0 3.3 8.8 2.0 

Labridae: Bodianus rufus 

(Spanish hogfish) 0.9 4.3 1.9 3.2 1.9 

Chaetodontidae: Chaetodon sedentarius

(reef butterflyfish) 1.5 2.0 2.0 1.2 1.7 

Pomacanthidae: Holacanthus ciliaris 

(queen angelfish) 0.0 2.0 3.0 3.3 1.5 

Pomacanthidae: Holacanthus tricolor 

(rock beauty) 1.9 2.1 0.6 0.6 1.4 

Balistidae: Balistes vetula 

(queen triggerfish) 3.0 0.0 0.0 0.0 1.4 

Serranidae: Epinephelus adscensionis 

(rock hind) 1.5 3.5 0.0 <0.1 1.2 

Labridae: Thalassoma bifasciatum 

(bluehead) 0.6 2.4 1.0 1.1 1.0 

Monacanthidae: Cantherhines macrocerus 

(whitespotted filefish) 0.6 0.0 1.6 0.0 0.7 

Tetraodontidae: Canthigaster rostrata

(sharpnose puffer) 0.5 0.8 1.3 0.4 0.7 

Holocentridae: Holocentrus adscensionis

(squirrelfish) 1.3 0.7 0.0 0.0 0.7 

Diodontidae: Diodon hystrix 

(porcupinefish) 0.0 0.0 0.0 6.2 0.7 

Ostraciidae: Lactophrys triqueter 

(smooth trunkfish) 0.3 1.0 0.5 0.6 0.5 

Serranidae: Cephalopholis fulva (coney) 0.4 1.9 0.0 0.0 0.5 

Chaetodontidae: Chaetodon striatus (banded 

butterflyfish) 0.6 0.0 0.5 0.2 0.4 

Pomacentridae: Abudefduf saxatilis

(sergeant major) 0.2 0.3 0.4 0.4 0.3 

Pomacentridae: Stegastes leucostictus

(beaugregory) 0.0 0.0 0.0 2.6 0.3 

Chaetodontidae: Chaetodon ocellatus

(spotfin butterflyfish) 0.2 1.3 0.0 0.3 0.3 

Holocentridae: Holocentrus rufus (longspine 

squirrelfish) 0.0 0.4 0.5 0.3 0.2 

Chaetodontidae: Prognathodes aculeatus

(longsnout butterflyfish) 0.2 <0.1 0.4 0.2 0.2 

Monacanthidae: Cantherhines pullus

(orange spotted filefish) 0.2 0.5 0.1 0.3 0.2 

Cirrhitidae: Amblycirrhitus pinos (redspotted 

hawkfish) 0.4 <0.1 <0.1 <0.1 0.2 

Pomacanthidae: Holacanthus bermudensis

(blue angelfish) 0.0 0.3 0.3 0.1 0.1 
161 

Trophic 

Guild 

Species ID: EFGB WFGB All 

Surveys (Family Name:Species Name 

(Common Name - Trophic Guild)) 2011 2012 2011 2012 

Labridae: Halichoeres garnoti 

(yellowhead wrasse) 0.1 0.1 0.1 <0.1 0.1 

Blenniidae: Parablennius marmoreus

(seaweed blenny) <0.1 0.3 0.0 0.2 0.1 

Mullidae: Pseudupeneus maculatus 

(spotted goatfish) 0.0 0.0 0.2 0.0 0.1 

Gobiidae: Elacatinus oceanops 

(neon goby) 0.1 <0.1 <0.1 0.1 0.1 

Apogonidae: Apogon maculatus 

(flamefish) <0.1 0.0 0.0 0.0 <0.1 

Labridae: Bodianus pulchellus 

(spotfin hogfish) <0.1 0.0 0.1 0.0 <0.1 

Labridae: Halichoeres bivittatus 

(slippery dick) 0.0 <0.1 0.1 0.0 <0.1 

Labridae: Halichoeres maculipinna 

(clown wrasse) 0.0 0.1 0.0 0.3 <0.1 

Labridae: Halichoeres radiatus 

(pudding wife) 0.0 <0.1 0.0 0.2 <0.1 

Muraenidae: Gymnothorax miliaris

(goldentail moray) 0.0 <0.1 0.1 <0.1 <0.1 

Ostraciidae: Lactophrys bicaudalis 

(spotted trunkfish) 0.0 0.0 0.2 0.0 <0.1 

Pomacanthidae: Holacanthus townsendi 

(townsend angelfish) 0.0 0.0 0.1 0.0 <0.1 

Tetraodontidae: Sphoeroides spengleri 

(bandtail puffer) <0.1 0.0 0.0 0.0 <0.1 

Piscivore 

Sphyraenidae: Sphyraena barracuda (great 

barracuda) 74.2 76.4 94.5 62.5 85.9 

Carangidae: Caranx latus 

(horse-eye jack) 17.3 7.0 3.6 2.0 7.3 

Lutjanidae: Lutjanus jocu 

(dog snapper) 1.9 3.1 1.1 14.0 2.2 

Serranidae: Mycteroperca tigris 

(tiger grouper) 0.2 6.3 0.3 0.2 0.9 

Serranidae: Mycteroperca interstitialis

(yellowmouth grouper) 2.6 1.6 0.1 0.1 0.9 

Carangidae: Carangoides ruber 

(bar jack) 0.2 3.9 <0.1 0.5 0.5 

Serranidae: Cephalopholis cruentata

(graysby) 0.8 0.5 0.3 1.3 0.5 

Carangidae: Seriola dumerili 

(greater amberjack) 0.0 0.0 0.0 8.3 0.4 

Belonidae: Belonidae spp. 

(needlefish spp.) 1.5 0.0 0.0 0.0 0.4 

Carangidae: Caranx crysos 

(blue runner) 0.0 0.0 0.0 7.1 0.3 

Serranidae: Mycteroperca bonaci 

(black grouper) 0.2 0.0 0.0 3.9 0.2 

Carangidae: Caranx lugubris 

(black jack) 0.5 0.6 0.0 0.0 0.2 
162 

Trophic 

Guild 

Species ID: EFGB WFGB All 

Surveys (Family Name:Species Name 

(Common Name - Trophic Guild)) 2011 2012 2011 2012 

Carangidae: Caranx hippos 

(crevalle jack) 0.4 0.0 0.0 0.0 0.1 

Serranidae: Mycteroperca phenax 

(scamp) 0.1 0.5 0.0 0.0 0.1 

Muraenidae: Gymnothorax moringa (spotted 

moray) 0.0 0.0 0.1 0.0 0.1 

Lutjanidae: Lutjanus cyanopterus 

(Cubera snapper) 0.0 0.0 0.0 0.1 <0.1 

Planktivore 

Serranidae: Paranthias furcifer 

(creolefish) 82.1 82.1 68.1 61.0 75.8 

Labridae: Clepticus parrae 

(creole wrasse) 17.6 16.7 31.0 36.8 23.5 

Pomacentridae: Chromis cyanea 

(blue chromis) 0.3 1.1 0.8 0.8 0.6 

Pomacentridae: Chromis scotti 

(purple reeffish) <0.1 0.1 0.1 0.9 0.1 

Pomacentridae: Chromis insolata

(sunshinefish) <0.1 0.1 0.1 0.5 0.1 

Chaenopsidae: Acanthemblemaria aspera

(roughhead blenny) 0.0 0.0 0.0 <0.1 <0.1 

Lutjanidae: Ocyurus chrysurus (yellowtail 

snapper) <0.1 0.0 0.0 0.0 <0.1 

10.4.6. Diurnal Density Patterns 

Fish abundance may change throughout the day due to fish behavior, resulting in 

disparate data on morning dives compared to afternoon dives. Community composition 

was compared for all years and location between five time groups: early morning (0700 

to 0900), later morning (0901 to 1200), early afternoon (1201 to 1500), late afternoon 

(1501 to 1800), and early evening (1801 to dusk). Over all surveys, the most samples 

were collected in the late afternoon (32), while the fewest samples were collected in the 

early evening (12) (Table 10.4.11). 

SIMPER analysis identified that the highest dissimilarity occurred between late morning 

and early evening surveys, with a dissimilarity of 53.64%, and the smallest dissimilarity 

occurred between late afternoon and early evening surveys, with a dissimilarity of 

50.02%. For most comparisons, the greatest contributors to the observed dissimilarity 

were brown chromis, creole wrasse, and creolefish. 
163 

Table 10.4.11. 

 

Number of Surveys Conducted During Various Times of the Day 

Time of Day 

EFGB WFGB All 

2011 2012 2011 2012 Surveys 

Early Morning 

(0700-0900) 4 4 4 8 20 

Late Morning 

(0901-1200) 1 4 8 4 17 

Early Afternoon 

(1201-1500) 7 4 4 0 15 

Late Afternoon 

(1501-1800) 10 6 4 12 32 

Early Evening 

(1801-dusk) 2 6 4 0 12 

The final MDS ordination had a moderate stress value (0.24), indicating moderate 

goodness-of-fit in a two-dimensional scale (Figure 10.4.10). No clusters were observed. 

Figure 10.4.10. MDS plot displaying two-dimensional similarity between morning and 

afternoon surveys. 
164 

ANOSIM results indicate a significant, but small, difference between fish communities 

observed in each time bracket (Global R=0.074, p<2.8%). Pair-wise analysis indicate 

significant differences between early morning and early evening surveys (Global 

R=0.178, p<1.5%), later morning and early evening surveys (Global R=0.197, p<0.1%), 

and early afternoon and early evening surveys (Global R=0.198, p<0.3%). However, all 

significant comparisons possess small R values. 

The top three species contributing to the observed dissimilarity were identified as brown 

chromis, creole wrasse, and creolefish. Comparisons were made between the densities of 

these individual species at each time bracket using ANOSIM. No significant differences 

were observed between creolefish densities or brown chromis densities. However, creole 

wrasse showed a significant difference in density by time of day (Global R=0.202, 

p<0.1%). Pair-wise tests indicate significant differences of density exist between the late 

afternoon and all other time brackets, except the early evening, and significant 

differences exist between the early evening and all other time brackets, except the late 

afternoon (Table 10.4.12). 

Table 10.4.12. 

 

ANOSIM Results for Pair-Wise Comparisons of Creole Wrasse Density in Each Time Bracket 

Pair-Wise Comparisons R Statistic Significance 

Level % 

Late Afternoon (1501-1800), Early Morning (0700-0900) 0.289 0.1 

Late Afternoon (1501-1800), Late Morning (0901-1200) 0.38 0.1 

Late Afternoon (1501-1800), Early Afternoon (1201-1500) 0.443 0.1 

Late Afternoon (1501-1800), Early Evening (1801-dusk) -0.051 72.3 

Early Morning (0700-0900), Late Morning (0901-1200) -0.02 69.1 

Early Morning (0700-0900), Early Afternoon (1201-1500) -0.016 53 

Early Morning (0700-0900), Early Evening (1801-dusk) 0.126 3.7 

Late Morning (0901-1200), Early Afternoon (1201-1500) -0.028 96.8 

Late Morning (0901-1200), Early Evening (1801-dusk) 0.329 0.2 

Early Afternoon (1201-1500), Early Evening (1801-dusk) 0.527 0.1 

10.4.7. Abundance-Biomass Curves 

For all samples, w values remained close to 0, indicating a balanced community of both 

large and small species (Table 10.4.13; Figure 10.4.11). W ranged from a maximum of 

0.121 ± 0.109 SD (EFGB 2012) to a minimum of 0.059 ± 0.089 SD (EFGB 2011). 

Comparisons between year and bank were made using an ANOVA, with no data 

transformation. No significant differences were observed between the abundance and 

biomass dominance plots between years or banks, or their interaction. 
165 

Table 10.4.13. 

 

Average w values by Bank and Year, ± Standard Deviation 

EFGB WFGB 

All Surveys 2011 2012 2011 2012 

0.059 ± 0.089 0.121 ± 0.109 0.087 ± 0.139 0.113 ± 0.161 0.095 ± 0.126 

Figure 10.4.11. Abundance-Biomass curves for (A) EFGB 2011, (B) WFGB 2011, 

(C) EFGB 2012, and (D) WFGB 2012, with average w values for all 

suverys at the year and location. 

 

(A) (B)

(C) (D)
166 

10.4.8. Family Level Analysis 

Due to particular concerns for species from the grouper (including Mycteroperca, 

Cephalopholis and Epinephelus generas only) and snapper (Lutjanidae genus only) 

families, additional analyses, on both density and biomass, were conducted on these 

families. 

The grouper family comprised eight species from the Mycteroperca, Cephalopholis and 

Epinephelus genera: graysby (Cephalopholis cruentata), coney (Cephalopholis fulva), 

rock hind (Epinephelus adscensionis), red hind (Epinephelus guttatus), black grouper 

(Mycteroperca bonaci), yellowmouth grouper (Mycteroperca interstitialis), scamp 

(Mycteroperca phenax), and tiger grouper (Mycteroperca tigris). While ANOSIM results 

indicate no significant temporal differences in community composition based on density 

or biomass, a significant spatial difference, with small R values, was observed in density 

(Global R=0.083, p<0.5%) and biomass (Global R=0.07, p<0.4%). The observed 

dissimilarity between banks (86.31% with density, 91.61% with biomass), was 

contributed to predominantly by graysby. 

Abundance-biomass plots for the grouper family were generated for each year and bank. 

The highest w value was observed in 2012 at WFGB (w=0.214), while the lowest w 

value was observed in 2011 at WFGB (w= -0.071) (Table 10.4.14). 

Table 10.4.14 

 

Average w Values by Bank and Year for the Grouper Family 

EFGB WFGB 

All Surveys 2011 2012 2011 2012 

0.031 -0.007 -0.071 0.214 -0.062 

The snapper family comprised four species from the Lutjanidae genus: yellowtail snapper 

(Ocyurus chrysurus), Cubera snapper (Lutjanus cyanopterus), gray snapper (Lutjanus 

griseus), and dog snapper (Lutjanus jocu). ANOSIM results indicate no significant spatial 

or temporal variations in snapper community composition based on density and biomass. 

Abundance-biomass plots for the grouper family were generated for each year and bank. 

The highest w value was observed in 2012 at WFGB (w=0.214) and the lowest w value 

was observed in 2011 at WFGB (w= -0.071) (Table 10.4.15). 

Table 10.4.15. 

 

Average w Values by Bank and Year for the Snapper Family 

 

EFGB WFGB 

All Surveys 2011 2012 2011 2012 

0.209 0.355 0.21 0.442 0.228 
167 

10.4.9. Long-Term Trends 

To visualize trends in biomass and density over time, yearly means were graphed with 

exponential trends lines. Though biomass showed a declining trend over time at both 

banks, trends were not found to be significant (Figure 10.4.12). Density showed a 

marginally increasing relationship over time at both banks, but only density at WFGB 

was found to be significant (Τ=0.56, P-value=0.019) (Figure 10.4.13). Historical 2002–

2012 fish data at the FGB can be found in Volume II Appendix 12 of this report. 

0

50

100

150

200

250

300

2006 2007 2008 2009 2010 2011 2012

Mean Biomass (g/m2)

Year

Mean Biomass, 2006-2012 EFGB

WFGB

Figure 10.4.12. Mean biomass (g/m2

) of the fish community at EFGB and WFGB from 

2006–2012. 

Biomass not recorded until 2006. No data in 2008. Blue represents EFGB and red WFGB. 

0

50

100

150

200

250

300

350

2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013

Mean Density (g/100m2)

Year

Mean Density, 2002-2012 EFGB

WFGB

Figure 10.4.13. Mean fish density (g/100m2) at EFGB and WFGB from 2002–2012. 

Density first recorded in 2002. No data in 2008. Dots represent actual data points. Blue 

represents EFGB and red WFGB. 
168 

10.5. FISH SURVEYS DISCUSSION

The fish communities at EFGB and WFGB are considered to be low in species diversity 

but high in biomass (Pattengill-Semmens and Gittings 2003; Zimmer et al. 2010); they 

have significantly different fish assemblages compared to other reef systems in the 

Caribbean, primarily due to the limited presence of lutjanids and haemulids (Rooker et al. 

1997). The observed fish assemblages of EFGB and WFGB occur near the northern 

latitudinal limit of coral reefs and are remote from other tropical reefs. The high number 

of oil and gas production platforms in the Gulf of Mexico may have promoted the 

dispersal of additional fish species and allowed some to reach the FGB and establish 

themselves (Boland et al. 1983; Rooker et al. 1997; Gittings 1998). 

Fishing pressure, water quality (including temperature and planktonic composition), 

and current flow patterns also affect fish assemblages at the FGB to varying degrees. 

Since the late 1800s, fishermen have conducted hook and line and long-line fishing 

around the FGB (Scarborough-Bull 1988). Since 1992, fishing with bottom long-lines, 

traps, nets, and bottom trawls has been prohibited within the sanctuary’s boundaries. 

Although hand-line and hook and line fishing, including bandit reels (powered reels), are 

allowed within the boundaries, the distance from shore does reduce fishing pressure to 

some extent. 

Fish surveys conducted during this study period (from 2011–2012) indicate a healthy reef 

fish community at both EFGB and WFGB, as observed in previous annual monitoring 

surveys between years (Precht et al. 2006; Zimmer et al. 2010; Johnston et al. 2013). 

However, this does not include long-term trends. A total of six additional species, and 

two fewer families, were recorded during the 2011–2012 study period in comparison to 

the 2009–2010 study period. Species richness was found to be similar between banks, but 

significantly different between years, with a greater species richness observed in 2012 

than 2011. Similar to findings of previous annual monitoring efforts, these findings 

indicate that three families possessed the greatest species richness, including the 

damselfishes (Pomacentridae), groupers and seabasses (Serranidae), and wrasses and 

parrotfish (Labridae). Diversity and evenness indices were similar between years and 

banks, and to previous annual monitoring efforts, with the exception of a significantly 

lower species diversity observed in 2011 at WFGB in comparison to the diversity in 2012 

at EFGB. 

Numerous other approaches have been used over the years to collect fish data from the 

FGB. Extensive surveys conducted in 1980–1982 by Boland et al. (1983) used, 

among other things, remote video to collect data on fish assemblages. A decade later, 

when the Reef Environmental Education Foundation began surveys at the FGB, the 

roving diver technique (RDT) was used (Pattengill-Semmens and Gittings 2003). 

Rooker et al. (1997) and Pattengill et al. (1998) were the first to use the stationary visual 

census technique of Bohnsack and Bannerot (1986) at the FGB. Each of the techniques 

used have strengths and weaknesses. For example, comparisons of visual census 

techniques (e.g., Bortone et al. 1989) have revealed, that the RDT produces good data 

on diversity and sighting frequency, but is not as well suited as stationary surveys for 

recording fish counts, sizes, or densities. 
169 

Some species were likely underestimated because of the techniques used. Many blenny 

and goby species, for example, are small and cryptic. The stationary counting 

technique used here would underestimate their abundance and perhaps the number of 

species. Furthermore, surveys also intentionally excluded sand-covered bottom areas, so 

diver surveys were less likely to have recorded species associated with that habitat. It is 

suggested that multiple fish survey techniques, including both belt transect and stationary 

counting surveys, should be used to obtain more comprehensive data, particularly 

improving data on richness, cryptic species, and fish biomass. 

The most frequently-sighted species on surveys during this study period were brown 

chromis, closely followed by Spanish hogfish and bluehead. All of these species are 

considered prevalent on other northwestern Caribbean and Gulf of Mexico coral reefs 

(REEF 2014) and have been documented with the highest abundance in other studies 

(Caldow et al. 2009). Most shark and ray species are considered rare (occur in <20% of all 

surveys) (REEF 2014), and none were recorded in fish surveys at the FGB during this 

study period. However, species were observed by divers as noted in the General 

Observations Section of this report. Another species that was frequently sighted was the 

great barracuda, but it is possible that this is an artifact of the proximity of the vessel, as 

these fish tend to aggregate below the vessel or close by. 

One species that was not observed on fish surveys was the invasive Indo-Pacific Lionfish. 

Although they were not recorded on fish surveys, they were first observed by divers in 

FGBNMS in 2011 and seen in the study site in 2012 as stated in Chapter 8. Lionfish have 

become established throughout the southeast U.S., the Caribbean Sea, and much of the 

Gulf of Mexico. The range of these invasive predators is still expanding, and they are 

capable of causing significant impacts to biodiversity and recovery of coral reefs, a result 

of their high densities and predation rates on native fish communities. Lionfish are also 

well-known for their venomous spines, rapid colonization rate, and generalist preferences 

for both habitat and diet. This monitoring report is a milestone, because it documents 

baseline, or at least pre-invasion, ecosystem conditions on the reef. 

Though some results indicate a significant spatial and temporal variation in community 

composition, statistical values indicate that this difference is barely separable, and it is 

therefore considered uninformative. No distinct significant differences were observed 

between years and banks, which suggests that, despite small variations, EFGB and WFGB 

fish communities are similar and stable over time. 

At the FGB, the invertivore guild possessed the greatest species diversity and density, and 

variations in the density of this group contributed greatly to observed differences between 

samples. Data from previous study periods have also indicated that invertivores are the 

dominant trophic guild in terms of species diversity and density (Caldow et al. 2009; 

Johnston et al. 2013). Though the herbivore guild is not the dominant trophic guild in terms 

of density at the FGB, changes occurring in this community are important to the health and 

stability of the reef ecosystem. In this study period, less than 21% of all observed variation 

between banks was due to variations in the herbivore guild, indicting a similar and stable 

herbivore population. Though the FGB is documented to have a lower species richness and 
170 

overall abundance of herbivorous fishes than other Caribbean reefs (Rezak 1985; Dennis 

and Bright 1988), the percentages of acanthurids and scarids is similar to deep and fore 

reefs of far western Cuba and Akumal, Yucatan, Mexico (Table 10.5.1.; Claro and 

Cantelar Ramos 2003; Steneck and Lang 2003). Historically, low algal cover has been 

reported in the annual monitoring, but recent data suggest a gradual increase in algal cover 

over time. This increase in algal cover was not reflected by changes in herbivore density 

during this study period. 

Table 10.5.1. 

 

Percentage of Fishes Observed in the Listed Families at Reefs around the Gulf of 

Mexico and the Caribbean Region 

Family Maria La Gorda, 

Cuba

Akumal, Yucatan, 

Mexico

FGBNMS, 

USA 

Acanthuridae 17% 22% 15%

Balistidae 37% 0% 9%

Chaetodontidae 7% 5% 9%

Lutjanidae 5% 7% 1%

Pomacanthidae 4% 2% 4%

Labridae/Scaridae 25% 58% 24%

Serranidae 6% 6% 8%

During this monitoring period, the piscivore guild possessed the greatest average biomass, 

and was the greatest contributor to the observed variations between samples. This guild 

contributed to over 50% of the total biomass, which indicates a limitedly impacted 

ecosystem where apex predators are dominant (Friedlander and DeMartini 2002). Piscivore 

dominated biomass indicates that the ecosystem maintains an inverted biomass pyramid. 

However, when analyzed by year and bank, this pattern was observed only in 2011, and 

piscivores and herbivores both evenly dominated the biomass pyramid in 2012. 

Traditionally, a stable environment is thought to be dominated by the lowest trophic guild 

(herbivores), the inverted biomass pyramid has been documented in reef ecosystems, where 

piscivore dominance is associated with “pristine” habitats with minimal fishing impacts 

(Friedlander and DeMartini 2002; DeMartini et al. 2008; Knowlton and Jackson 2008; 

Sandin et al. 2008; Singh et al. 2012). Typically, these inverted biomass pyramids are 

associated with healthy reef systems with high coral cover, as observed at the FGBs. 

However, the shift from pisicivore dominated biomass at both EFGB and WFGB in 2011 to 

a more evenly dominated biomass between herbivores and piscivores (each contributing 

approximately 40% of the biomass) in 2012 is of interest and should be monitored for long 

term trends in future reports. 

Great barracuda contributed to over 85% of the total biomass of the piscivore guild, with a 

much greater observed average biomass than the 2009 and 2010 study period. The majority 

of these observed individuals were considered too small to be sexually mature and none 

exceeded the average documented length for the species (Froese and Pauly 2014). 

Though these species are commonly documented as solitary, many of the observations 

made during this study period indicate they were observed in small aggregations of up to 

30 individuals, which again may be an artifact of vessel presence. 
171 

Abundance-biomass curves have historically been used to infer community health, where a 

community dominated by few large species is considered “pristine” and a community 

dominated by many small species is considered “impacted.” Results indicate that the fish 

communities of the FGB are evenly distributed, which means that the population can be 

considered mildly disturbed, and lacking in density of large fishes. 

The grouper community exhibits an even population of grouper abundance to size; the 

average density of small bodied groupers (graysby, rock hind, and coney) double that of 

the large bodied groupers. From the large bodied groupers observed, all black grouper 

and tiger grouper were considered too small to be sexually mature, except for two large 

tiger grouper observed at EFGB in 2012 (Heemstra and Randall 1993; Froese and Pauly 

2014). All black grouper observed were below the minimum recreational and commercial 

catch size limits. A previous report, by Caldow et al. (2009), documented a distinct 

correlation between large-bodied grouper size and proximity to the edge of the reef. The 

apparent predominance of small grouper is likely due to the restricted habitat sampled in 

this study: both study sites are located on the shallower portions of the reef cap and do 

not encompass deeper reef edge habitat. 

In contrast to the grouper population, the snapper community was dominated by few 

large species. The largest snappers seen in the study area were typically smaller than the 

average known size for the species (dog snapper, yellowtail snapper, and Cubera 

snapper). Approximately half of the gray snapper observed, and all of the yellowtail 

snapper observed, were considered too small to be sexually mature (Garcia-Cagide et al. 

1994; Froese and Pauly 2014). It should be noted that at EFGB and WFGB, typical 

recruitment/nursery habitat for snappers (mangroves and sea grasses) are not present, and 

the mechanism for recruitment of this family to the area in unknown. 

As fish behavior changes throughout the day, the density of species may also change. 

When the top three species that contribute to the observed variation (brown chromis, 

creole wrasse, and creolefish) were analyzed individually, Creole wrasse were found to 

have a significantly higher density from 1501 to dusk. This information highlights the 

importance of distributing surveys evenly between times of day to accurately capture the 

fish community. 

When analyzing biomass and density for long term trends, it should be noted that both 

measures show high variability between individual surveys, years, and banks. Historical 

analysis in this report found no significant long-term trends fish biomass (2006 – 2012) 

or density (2001-2012) at EFGB, despite trendline indications. However, density (2002-

2012) at WFGB was found to have a significant trend in increasing density between 

years. While this data supports the finding of a stable fish community over the 

monitoring period at EFGB, it suggests the fish density at WFGB may be increasing. 

Continued monitoring of these trends is warrented, and should be expanded to include 

trends in abundance-biomass curves when additional data points (i.e. years of data) are 

available.
173 

CHAPTER 11.0: SEA URCHIN AND LOBSTER SURVEYS 

11.1. SEA URCHIN AND LOBSTER SURVEYS METHODOLOGICAL RATIONALE

The Long-Spined Sea Urchin, Diadema antillarum, was an important herbivore on coral 

reefs throughout the Caribbean until 1983 and 1984. At that time, an unknown pathogen 

decimated populations throughout the region, including the FGB. Since then, patchy but 

limited recovery has been documented in the region (Edmunds and Carpenter 2001). 

Diadema antillarum populations at the FGB pre-1984 exceeded 1 individual/m2

 (hindcast 

surveys were made from archived transect photos taken during daytime hours, which would 

underestimate densities; Gittings et al. 1992; Aronson et al. 2005). 

Lobsters are commercially important species throughout much of the Caribbean and Gulf of 

Mexico; however, population dynamics of Caribbean Spiny Lobster (Panulirus argus) and

Spotted Spiny Lobster (Panulirus guttatus) in the FGB are not well understood. 

11.2. SEA URCHIN AND LOBSTER SURVEYS METHODS 

Due to the nocturnal nature of these species, visual surveys were conducted at night, a 

minimum of 1.5 hours after sunset. In 2011 and 2012, surveys for Diadema antillarum, 

Panulirus argus, and Panulirus guttatus were conducted along the northern and eastern 

perimeter lines at EFGB and along the southern and western boundaries at WFGB. Two 

belt transects 2 m wide and 100 m long were surveyed by diver teams on each bank, thus 

totaling 400 m2 per bank each year. Surveys began with the northeast corner at the EFGB 

study site and the southeast corner at the WFGB study site. All observed species were 

recorded. 

11.3. STATISTICAL ANALYSES OF THE SEA URCHIN AND LOBSTER DATA

The software package Primer® version 6.0 was used to create similarity matrices and 

MDS plots using square-root transformed data. A SIMPER was conducted on the 

abundance data to determine the differences observed within and among groups. 

11.4. SEA URCHIN AND LOBSTER SURVEYS RESULTS

The number of individuals recorded during each survey in 2011 and 2012 are listed in 

Table 11.4.1. One Panulirus argus was observed at EFGB in 2011 (0.25 per 100 m2). No 

other lobsters were observed in 2011 or 2012. 

At EFGB, no Diadema antillarum were observed in 2011 or 2012 along the selected 

EFGB study site perimeter lines. In 2011, 15 Diadema antillarum (3.75 per 100 m2) were 

documented at WFGB. In 2012, 50 (12.5 per 100 m2) were found along selected study 

site lines. This correlates to higher densities at WFGB in both 2011 and 2012 when 

compared to EFGB (Table 11.4.1). 
174 

Table 11.4.1. 

Number of Individual Sea Urchins and Lobsters Observed During Surveys in 2011 and 2012 

No. of Individuals 

Observed 

Sea Urchins Lobsters 

Diadema antillarum Panulirus argus Panulirus guttatus 

EFGB 2011 0 1 0 

EFGB 2012 0 0 0 

WFGB 2011 15 0 0 

WFGB 2012 50 0 0 

11.4.1. Historical Comparison of Sea Urchin and Lobster Surveys 

Since 2004, lobster counts on surveys have ranged from zero to two. They are, however, 

occasionally encountered by divers at other times, so they do occur on the banks in low 

abundance. Since 2004, sea urchin counts on surveys have ranged from zero to fifty-five. A 

higher number of Diadema antillarum were observed during the surveys at WFGB in 

2004 and 2012 (Figure 11.4.1). 

0

2

4

6

8

10

12

14

16

number/100 m2

Sea Urchin and Lobster per 100m2 at the Flower Garden Banks, 

2004-2012

Diadema antillarum

Panulirus argus

Panulirus guttatus

Figure 11.4.1. Sea urchin and lobster densities at the FGB from 2004–2012. 

Data for 2004 to 2008 from PBS&J (Precht et al. 2006, 2008b); and FGBNMS for 2009 and 

2010 (Johnston et al. 2013). 
175 

MDS analysis was performed on the Diadema antillarum abundance data at EFGB and 

WFGB using the 2004-2012 data. The MDS plot (Figure 11.4.2) highlights the 

dissimilarity between banks with EFGB abundance data clustering differently from 

WFGB abundance data (80% similarity). This dissimilarity was due to the abundance of 

Diadema antillarum. The low stress level indicates a high confidence in the relationships 

displayed. The MDS plot also revealed three outliers obtained at EFGB in 2008, 2011, 

and 2012 when no Diadema antillarum were observed, separating these values from all 

others by bank and year. 

Groups were too small to run an ANOSIM; however, a SIMPER revealed a strong 

average dissimilarity of 68.74% between EFGB and WFGB. Results show that Diadema 

antillarum community composition differed between the banks during 2004 to 2012, and 

Diadema antillarum densities were significantly higher on WFGB than EFGB. Due to 

low sample sizes, no such determinations could be made by year. 

Figure 11.4.2. Two-dimensional MDS plot based on Bray-Curtis similarities 

comparing Diadema antillarum densities from 2004–2012. 

The green circles group years that are 80% similar. 

Inset: 
176 

11.5. SEA URCHIN AND LOBSTER SURVEYS DISCUSSION

After the mass die off in 1983, Diadema antillarum populations have not recovered to 

pre-1983 levels, which were at least 140 individuals/100 m2 at EFGB and 50 

individuals/100 m2 at WFGB (Gittings et al. 1998). Post-1984 sea urchin densities 

dropped to near zero (Gittings and Bright 1987). Diadema antillarum populations at 

EFGB remained low during this monitoring period and were similar to those reported in 

previous studies (Zimmer et al. 2010). Populations at WFGB have been consistently 

higher than EFGB. Both 2009 and 2012 had abundances among the higest recorded at 

WFGB since the die off. The previous fluctuations in annual density estimates suggest 

caution in declaring a recovering Diadema antillarum population on the FGB; continued 

monitoring will be required to track and compare temporal changes at both banks. It is 

suggested that the entire study site (all perimeter lines and crosshairs) be surveyed for 

lobster and Diadema antillarum instead of the same single transect every year. 
177 

CHAPTER 12.0: RECOMMENDATIONS 

The following are recommendations for improving the monitoring protocols and 

increasing the scientific value of the monitoring program, as adjustments would improve 

the efficiency and quality of data collection efforts. 

Operational Changes 

Below are recommendations that should be considered as immediate improvements to the 

monitoring program. Most are recommended because they have been identified as 

deficiencies of the current protocols. 

 Evaluate lateral station methodology to remove comparison inconsistencies from 

year to year (a refurbishment cruise to establish new stations with updated 

methods took place July 2014). Based on updated methods, determine the value of 

lateral growth data as a monitoring tool. 

 Evaluate the frequency of coral coring events and the use of schleronconology as 

a monitoring tool. 

 Use multiple fish survey techniques, including belt transect and stationary 

surveys, to obtain more comprehensive data, particularly improving data on 

richness, cryptic species, and fish biomass. This was implemented during the 2013 

monitoring period. 

 Increase the number of lobster and sea urchin surveys instead of the same single 

transect every year. This was implemented during the 2013 monitoring period. 

 Conduct a separate assessment to complete bleaching surveys in the late fall 

months when bleaching is most likely to occur. 

 Add survey for coral size class distribution and for coral recruits. This was 

implemented during the 2013 monitoring period. 

 Determine if great barracuda aggregations are an artifact of vessel presence. 

Additional Recommendations 

 Continue and increase the number of presentations and peer-reviewed publications 

resulting from this work. 

 Create a monitoring quality assurance/quality control methods and procedures 

manual to ensure consistency in field procedures and data analysis (a procedures 

manual is being compiled). 
179 

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