Integration of fisheries acoustics surveys and bathymetric

mapping to characterize midwater-seafloor habitats of 

US Virgin Islands and Puerto Rico (2008–2010) 

NOAA Technical Memorandum NOS NCCOS 130
This report has been reviewed by the National Ocean Service of the National 

Oceanic and Atmospheric Administration (NOAA) and approved for publication. 

Such approval does not signify that the contents necessarily represent the official 

position of NOAA or of the Government of the United States, nor does mention of 

trade names or commercial products constitute endorsement or recommendation 

for their use. Furthermore, this report is intended to serve as a record of cruise 

activities and preliminary observations during a field survey in support of an 

ongoing research study, and thus does not represent a final analysis or 

interpretation of project results. 

This work is part of NOAA’s Coral Reef Conservation Program. For more 

information about this report or to request a copy, please contact the NOAA 

National Center for Coastal Ocean Science – CCEHBR at 843-762-8511 or write 

to: NOAA NCCOS CCEHBR, 219 Fort Johnson Road, Charleston, SC 29412

We appreciate the contribution of the officers and crew of the NOAA ship Nancy 

Foster. They provided safe sailing and many hours of diving and engineering 

support to make these deployments possible. Lance Horn and Glenn Taylor of 

NOAA’s Undersea Research Center at the University of North Carolina 

Wilmington provided ROV and DIDSON support. Len Balthis provided 

programming support for processing the acoustics data. Stephen Roth reviewed 

and documented ROV video data collected in 2010. Special thanks to Len 

Balthis, Peter Etnoyer and Todd Kellison for their helpful review of this document.

Kracker, L.M., J.C. Taylor, E. F. Ebert, T.A. Battista, and C. Menza. 2011. 

Integration of fisheries acoustics surveys and bathymetric mapping to 

characterize midwater-seafloor habitats of US Virgin Islands and Puerto Rico 

(2008–2010). NOAA Technical Memorandum NOS NCCOS 130. 44 pp.

Citation for this Report 

Disclaimer 

For more information

Acknowledgements
Integration of fisheries acoustics surveys 

and bathymetric mapping to characterize 

midwater-seafloor habitats of US Virgin 

Islands and Puerto Rico (2008–2010)

Kracker, L.M.1, J.C. Taylor2, E.F. Ebert2, T.A. Battista3

, 

and C. Menza3 

1NOAA/National Ocean Service/National Centers for Coastal Ocean 

Science/Center for Coastal Environmental Health and Biomolecular Research, 

Charleston, SC

2NOAA/National Ocean Service/National Centers for Coastal Ocean 

Science/Center for Coastal Fisheries and Habitat Research, Beaufort, NC 

3NOAA/National Ocean Service/National Centers for Coastal Ocean 

Science/Center for Coastal Monitoring and Assessment, Silver Spring, MD.

NOAA, National Ocean Service 

National Centers for Coastal Ocean Science 

Center for Coastal Environmental Health and Biomolecular Research 

219 Fort Johnson Road 

Charleston, South Carolina 29412-9110 

NOAA Technical Memorandum NOS NCCOS 130 

May 2011

 

 United States Department of National Oceanic and National Ocean Service

 Commerce Atmospheric Administration

 Gary Locke Jane Lubchenco David Kennedy

 Secretary Administrator Assistant Administrator

 

1 

NOAA’s Coral Reef Conservation program (CRCP) develops coral reef management priorities by 

bringing together various partners to better understand threats to coral reef ecosystems with the 

goal of conserving, protecting and restoring these resources. Place-based and ecosystem-based 

management approaches employed by CRCP require that spatially explicit information about 

benthic habitats and fish utilization are available to characterize coral reef ecosystems and set 

conservation priorities. To accomplish this, seafloor habitat mapping of coral reefs around the 

U.S. Virgin Islands (USVI) and Puerto Rico has been ongoing since 2004. In 2008, fishery 

acoustics surveys were added to NOAA survey missions in the USVI and Puerto Rico to assess 

fish distribution and abundance in relation to benthic habitats in high priority conservation areas. 

NOAA’s National Centers for Coastal Ocean Science (NCCOS) have developed fisheries

acoustics survey capabilities onboard the NOAA ship Nancy Foster to complement the CRCP

seafloor habitat mapping effort spearheaded by the Center for Coastal Monitoring and 

Assessment Biogeography Branch (CCMA-BB). The integration of these activities has evolved 

on the Nancy Foster over the three years summarized in this report. A strategy for improved

operations and products has emerged over that time. Not only has the concurrent operation of 

multibeam and fisheries acoustics surveys been beneficial in terms of optimizing ship time and 

resources, this joint effort has advanced an integrated approach to characterizing bottom and 

mid-water habitats and the fishes associated with them. 

CCMA conducts multibeam surveys to systematically map and characterize coral reef 

ecosystems, resulting in products such as high resolution bathymetric maps, backscatter 

information, and benthic habitat classification maps. These products focus on benthic features 

and live bottom habitats associated with them. NCCOS Centers (the Center for Coastal Fisheries 

and Habitat Research and the Center for Coastal Environmental Health and Biomolecular 

Research) characterize coral reef ecosystems by using fisheries acoustics methods to capture 

biological information through the entire water column. Spatially-explicit information on marine 

resources derived from fisheries acoustics surveys, such as maps of fish density, supports 

marine spatial planning strategies and decision making by providing a biological metric for

evaluating coral reef ecosystems and assessing impacts from pollution, fishing pressure, and 

climate change. 

Data from fisheries acoustics surveys address management needs by providing a measure of 

biomass in management areas, detecting spatial and temporal responses in distribution relative 

to natural and anthropogenic impacts, and identifying hotspots that support high fish abundance 

or fish aggregations. Fisheries acoustics surveys conducted alongside multibeam mapping efforts 

inherently couple water column data with information on benthic habitats and provide information 

on the heterogeneity of both benthic habitats and biota in the water column. Building on this 

information serves to inform resource managers regarding how fishes are organized around 

habitat structure and the scale at which these relationships are important. Where resource 

managers require place-based assessments regarding the location of critical habitats along with 

high abundances of fish, concurrent multibeam and fisheries acoustics surveys serve as an 

important tool for characterizing and prioritizing coral reef ecosystems. 

This report summarizes the evolution of fisheries acoustics surveys onboard the NOAA ship 

Nancy Foster from 2008 to 2010, in conjunction with multibeam data collection, aimed at 

characterizing benthic and mid-water habitats in high priority conservation areas around the USVI 

and Puerto Rico. It also serves as a resource for the continued development of consistent data 

products derived from acoustic surveys. By focusing on the activities of 2010, this report

highlights the progress made to date and illustrates the potential application of fisheries data 

derived from acoustic surveys to the management of coral reef ecosystems. 

Executive Summary
2 
3 

1. Introduction ............................................................................................................................... 5

1.1 NOAA’s Coral Reef Conservation Program benthic habitat mapping ...................... 6

1.2 Fisheries acoustics surveys of water column and seafloor habitats ......................... 7

1.3 Integration of multibeam bathymetric mapping and fisheries acoustics ................ 12

2. Fisheries acoustics surveys ................................................................................................. 13

2.1 Western Puerto Rico (NF-08-04-USVI) ....................................................................... 13

2.1.1 Methods ..................................................................................................................... 13

2.1.2 Analysis and products ............................................................................................. 15

2.2 Vieques and El Seco, Puerto Rico (NF-08-06-SEAS, NF-09-01-USVI) ................ 18

2.2.1 Methods ..................................................................................................................... 18

2.2.2 Analysis and products ............................................................................................. 20

2.3 Virgin Passage and St. John Shelf (NF-10-03-USVI) ............................................... 25

2.3.1 Methods ..................................................................................................................... 25

2.3.2 Analysis and products ............................................................................................. 27

3. Summary ................................................................................................................................ 40

4. References ............................................................................................................................. 41

Appendix A Data acquisition and processing .................................................................... 42

Appendix B Links to cruise summaries ............................................................................. 44

Table 1. Cruise numbers, dates and locations of joint fisheries acoustics and multibeam 

mapping missions on the NOAA ship Nancy Foster. 

Table 2. Description of echograms based on raw variables collected. 

Table 3. Fisheries acoustics surveys analyzed 2008. 

Figure 1. Priority benthic habitats mapped in 2008, 2009, and 2010.

Figure 2. Echogram depicting water column features detected by acoustic surveys.

Figure 3. Template that contains properties for platform, sensors, echograms, lines 

and virtual variables in Echoview.

Figure 4. Flow diagram showing data processing steps from Echoview to ArcGIS. 

List of Figures

Table of Contents

List of Tables
4 

Figure 5. Result of bottom detection, virtual lines, and fish tracking algorithm applied 

to mid-water targets.

Figure 6. Western Puerto Rico priority mapping areas as identified in the NF-08-04-

USVI Cruise Instructions.

Figure 7. Maps of Mona Island and Tourmaline Bank showing simultaneous fisheries 

acoustics and multibeam transects, as well as ROV transects. 

Figure 8. Mean volume backscatter (Sv_mean) integrated at 100m intervals and 

interpolated across survey area at Tourmaline Bank to depict the distribution 

of fish biomass.

Figure 9. Fish density at Tourmaline Bank based on single target detection where 

target strength >-50dB. 

Figure 10. Location of small, medium, and large fish at Tourmaline Bank. 

Figure 11. Vieques priority areas for benthic habitat characterization as identified in the 

NF-09-01-USVI Cruise Instructions. 

Figure 12. Deployment of Simrad EK-60 120 kHz transducer for fisheries acoustic 

surveys in 2008 and 2009.

Figure 13. Areas surveyed at Vieques, PR 2008 and El Seco, PR 2009. 

Figure 14. Cumulative distribution of fish targets by depth at Vieques 2008. 

Figure 15. Fish density at Vieques of medium and large fish for the entire water 

column. 

Figure 16. Fish density at Vieques of medium and large fish for the portion of the water 

column within 10m from the bottom. 

Figure 17. Fish density at El Seco of medium and large fish for the entire water column. 

Figure 18. Fish density at El Seco of medium and large fish for the portion of the water 

column within 10m from the bottom. 

Figure 19. St. Thomas and St. John priority areas for benthic habitat characterization 

as identified in the NF-10-03-USVI Cruise Instructions.

Figure 20. Simrad 38/120 kHz system deployed alongside Reson 7125 on the NOAA 

ship Nancy Foster. Phantom 2 ROV with video camera and DIDSON high 

resolution sonar. 

Figure 21. Areas mapped for benthic habitat classification using multibeam at Virgin 

Passage southwest of St. Thomas and St. John shelf. 

Figure 22. Dedicated fish surveys conducted at Grammanik Bank and Tampo.

Figure 23. Fish density at Virgin Passage and St. John shelf.

Figure 24. Fish density by size class at Virgin Passage.

Figure 25. Fish density by size class at St. John shelf. 

Figure 26. Diel patterns of fish density at Virgin Passage and St. John shelf. 

Figure 27. Fish density derived from acoustic surveys targeting fish aggregations sites 

at Grammanik Bank. 

Figure 28. Mean length of large fish (>29cm) at Grammanik Bank. 

Figure 29. Cluster analysis of large fish from acoustic survey with observations of 

yellowfin grouper (Mycteroperca venenosa) along ROV track and fish 

aggregation on echogram.

Figure 30. Acoustic surveys targeting fish aggregation sites at Tampo with ROV track. 

Figure 31. Fish density at Tampo April 4-5, 2010.

Figure 32. Temporal changes in fish density at Tampo near shelf edge. 

Figure 33. Echograms related to areas of highest fish density along the near-edge 

transect at Tampo showing variation in the arrangement of fish in the water 

column at various times of day.

Figure 34. School of Carangidae observed on ROV video between the first and second 

dedicated fish acoustic surveys at Tampo. 
5 

1. Introduction

Through NOAA’s Coral Reef Conservation Program, the Center for Coastal Monitoring 

and Assessment (CCMA) Biogeography Branch has conducted surveys on board the 

NOAA ship Nancy Foster since 2004 as part of an ongoing effort to produce 

comprehensive digital coral reef ecosystem maps for all U.S. States, Territories and 

Commonwealths. The primary objective of CCMA’s benthic habitat mapping effort is to 

collect high resolution multibeam bathymetric and acoustic backscatter data to produce 

accurate information on marine resources in high priority conservation areas in support 

of coral reef research, monitoring, and management needs. This effort focuses on 

bathymetry and the classification of benthic habitats, as well as the utilization of these 

habitats by important marine species. 

Methods for quantifying and classifying benthic habitats have been successfully 

developed and implemented in Puerto Rico and U.S. Caribbean (Kendall et al.2001, 

Costa et al.2009). In addition, long term monitoring of reef fishes conducted throughout 

the USVI documented the changing trophic structure of reef fish assemblages. An 

increase in herbivorous fish and macroalgae, a decline in large predators such as 

groupers and snappers, and the decimation of some spawning aggregations has 

resulted from overfishing in spite of existing management strategies (Friedlander and 

Beets 2008). Recently, priority areas have been established through the Coral Reef 

Conservation Program and CCMA in collaboration with the Caribbean Fishery 

Management Council and other partners to conduct additional mapping to better 

understand benthic resources and species utilization of these habitats. 

Data from fisheries acoustic surveys using spilt-beam echo-sounding systems support 

these resource management needs and offer several advantages over diver based 

surveys and other methods of assessing fisheries resources. For instance, while 

monitoring programs that rely on diving to census fish are valuable in providing a high 

level of detail on fish and invertebrate communities, as well as monitoring trends in fish

communities at specific locations, there are limitations in terms of level of effort required

and the area that can be covered. Ship-board fisheries acoustics surveys provide 

information on abundance and location of individual fish and fish aggregations 

throughout the water column, from small planktivores to large predators, allowing for 

estimation of fish density at nearly any spatial resolution. This results in spatially-explicit 

data on fish distribution at resolutions and extents comparable to habitat maps, allowing 

for examination of benthic features as a driver of reef fish habitat use (Ross and 

Quattrini 2007). Furthermore, this sampling strategy is non-destructive compared to 

other methods such as trawling. 

One limitation of acoustic surveys is the lack of explicit information on fish species. 

However, in many cases, size-specific (rather than species-specific) data may be 

sufficient to address management needs such as increasing biomass in management 

areas and detecting spatial and temporal responses in distribution relative to natural and 

anthropogenic impacts. Size-specific data can also be used to identify functional groups 

such as mature snapper-grouper and rule out smaller species. By mapping the spatial 

distribution of fish across broad areas, hotspots supporting high abundance or fish 

aggregations can be identified and assessed for their biological value. Fisheries 

acoustics surveys conducted alongside multibeam mapping efforts inherently couple 

water column data with information on benthic habitats and provide information on the 
6 

heterogeneity of both benthic habitats and biota in the water column. Building on this 

information serves to inform resource managers regarding physical and biological 

relationships within coral reef ecosystems, how fishes are organized around habitat 

structure, and the scale at which these relationships are important (Kracker et al.2008). 

In addition, the changing temporal and spatial patterns indicative of fish behavior can be 

observed, for instance, as fish move off the reef or up into the water column at night and 

return during the day. Where resource managers require place-based assessments 

regarding the location of critical habitats and

high abundance of fish, concurrent multibeam 

and fisheries acoustics surveys serve as an 

important tool for characterizing and prioritizing 

coral reef ecosystems. 

This report details the evolution of surveys 

using spilt-beam echo-sounding systems 

onboard the NOAA ship Nancy Foster in 

conjunction with multibeam data collection

aimed at characterizing benthic and mid-water 

habitats in high-priority conservation areas of 

the USVI and Puerto Rico (Table 1). 

Specifically, this document describes fisheries 

acoustics surveys conducted from 2008 to 

2010, presents data products related to 

fisheries resources that support the 

characterization of marine habitats, and 

outlines procedures for data collection and 

processing of fisheries information derived 

from acoustic surveys (See also Rudstam et 

al.2009 and Simmonds and MacLennan 2005). 

1.1 NOAA’s Coral Reef Conservation Program benthic habitat mapping

NOAA works in partnership with the Caribbean Fisheries Management Council, the 

University of the Virgin Islands, the USVI Department of Fish and Wildlife, and the 

National Park Service to identify and protect coral reef ecosystems throughout the U.S. 

Caribbean, including important fish aggregation sites subject to intense fishing pressure. 

Much of this effort has focused on utilizing multibeam data to map and classify benthic 

habitats. In 2008, CCMA’s coral reef benthic habitat mapping activities were expanded 

to include fisheries acoustics surveys as a technique for quantifying biotic resources 

associated with coral reef habitats and associated waters within coral reef ecosystems. 

Priority coral reef ecosystems, including historic and candidate fish aggregation sites, 

identified for multibeam and fisheries acoustics mapping (Figure 1) consist of waters 

west of Puerto Rico around Tourmaline Bank and Mona Island (2008), nearshore

habitats around Vieques Island (2008) and El Seco (2009) off the east coast of Puerto 

Rico, and Virgin Passage south of St. Thomas and St. John shelf (2010). From 2008-

2010, fisheries acoustics surveys were conducted simultaneously with multibeam 

operations to map the abundance and distribution of biomass in the entire water column

in these priority areas. The Center for Coastal Fisheries and Habitat Research (CCFHR) 

and the Center for Coastal Environmental Health and Biomolecular Research 

Table 1.

Cruise numbers, dates and locations

of joint fisheries acoustics and

multibeam mapping missions on

the NOAA ship Nancy Foster

--

NF-08-04-USVI

February 25-March 8, 2008

Tourmaline Bank, Mona Is., PR

--

NF-08-06-SEAS

March 26-April 4, 2008

Vieques, PR 

---

NF-09-01-USVI

March 21-April 3, 2009

El Seco, PR

---

NF-10-03-USVI

March 18-April 6, 2010

St. Thomas Virgin Passage

St. John shelf
7 

(CCEHBR) have been instrumental in developing the fisheries acoustics component of 

these surveys. 

Multibeam data acquisition capabilities for benthic mapping have become an integral 

component of the NOAA ship Nancy Foster. A Kongsberg/Simrad EM1002 multibeam 

sonar is permanently hull-mounted. The EM1002 is a 95kHz system with a 150o swath 

comprised of 111 individual 2o beams. In 2009 and 2010, a Reson 7125 multibeam 200

and 400 kHz sonar with 512 individual beams and 128o swath was deployed to conduct 

shallow water mapping. On all such missions, an ROV equipped with video and high 

resolution still cameras was deployed using a modified stratified random sampling 

approach to validate the benthic habitat types derived from the multibeam data. These 

survey data are processed to produce high resolution bathymetry, backscatter and 

habitat classification maps (Costa et al.2009). Data and documentation are available at:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/overview.html

Figure 1. Priority benthic habitats mapped in 2008 (Mona Island, Tourmaline Bank, 

Vieques), 2009 (El Seco) and 2010 (St. Thomas, St. John). 

1.2 Fisheries acoustics surveys of water column and seafloor habitats

Fisheries acoustics surveys were conducted in waters around Puerto Rico and the USVI

from the NOAA ship Nancy Foster using hull mounted split-beam echosounders. A 

Biosonics 120 kHz split-beam system was deployed at Tourmaline Bank and Mona 

Island in 2008. A Simrad EK-60 120 kHz system was used at Vieques in 2008 and El

Seco in 2009. A two frequency (38/120 kHz) Simrad EK-60 system was used for St. 

Thomas and St. John priority mapping areas in 2010. These operations were run 

concurrently with multibeam bottom mapping and ROV ground truthing activities. 

Additionally, in 2010, two survey days were dedicated to exploring specific locations 

identified as historic fish spawning sites. Results from acoustic surveys were viewed as 

echograms that capture information on fish size and spatial distribution within the water 

 Tourmaline 

Mona Is. Bank St Thomas St. John

 Puerto Rico 

 Vieques El Seco

 
8 

column along multibeam transects (Figure 2). Fish aggregations were also detected and 

quantified based on the echogram. 

Within the survey area, the crepuscular period was of particular interest in waters that 

are 20-40m deep since there was a high probability of occurrence of spawning 

aggregations of yellowfin grouper (Mycteroperca venenosa), tiger grouper (Mycterperca 

tigris), and red hind (Epinephelus guttatus). Yellowfin grouper spawning aggregations 

may occur at a depth of approximately 25m at the shelf break one half hour after sunset 

(Michelle Scharer pers comm. Feb 2008). Spawning aggregations of tiger grouper have 

been recorded at Vieques, east of Puerto Rico since the late 1980’s (Sadovy et al.1994). 

In 1991, aggregations were observed a few days before full moon and remained for up 

to a week after full moon. Red hind are known to aggregate along the southwest coast of 

Puerto Rico at depths of 20-30m around full moon, typically in January, February or 

March (Shapiro et al.1993). Aggregations that are presumed to consist of spawning red 

hind have been detected using hydroacoustics around the coast of Puerto Rico and 

Mona Island (Johnston et al.2006). This interpretation was based on the unique shape 

of the aggregation (vertically stacked, coherent schools), near-shelf distribution, and 

timing around full moon. Shapiro et al.(1993), on the other hand, describes the spatial 

structure of red hind spawning aggregations based on diver observations in 1986 and 

1987 as primarily horizontal, two-dimensional small clusters of fish. 

 

Figure 2. Echogram depicting water column features detected by acoustic surveys, 

including scattering of zooplankton and aggregations of fish. The thick red line indicates 

the bottom. The color scale represents the strength of the returned echo in decibels 

(dB) with red indicating a strong return and blue a weaker return. 

In 2008, analysis of acoustic survey data focused on depths down to 100m to detect 

possible spawning aggregations at Tourmaline Bank and off the west coast of Mona 

Island. Data were collected using a Biosonics split-beam 120 kHz system. Analysis 
9 

included estimates of biomass and fish density for each 100m segment along survey 

transects. Fish density estimates were binned along 100m segments as a common 

sampling unit for all three years for comparison and to ensure that a sufficient number of 

fish targets were included to constitute a valid sample size. In addition, echograms were 

reviewed for features that may be indicative of spawning or schooling aggregations. 

Similar surveys were conducted along the south shore of Vieques in 2008. Surveys in 

2009 covered waters around El Seco. Acoustic data were collected aboard the NOAA 

Ship Nancy Foster using a Simrad 120 kHz splitbeam transducer. Data were collected 

simultaneously with multibeam data collection. Analysis of the fisheries acoustics data 

from 2008 and 2009 included mapping of fish densities by size class along 100m 

segments of survey transects. 

In 2010, acoustic surveys were conducted using a hull mounted sled with two EK-60 

spilt-beam transducers (38 and 120 kHz). A Reson 7125 multibeam 200 and 400 kHz 

sonar was also attached to the sled. Split-beam transects were analyzed for fish 

density, the spatial distribution of fish sizes across the survey area, and differences in 

spatial patterns from day to night. In addition, ship time was dedicated to exploring 

potential fish spawning sites at Grammanik Bank and Tampo, both potential yellowfin 

grouper spawning sites. Maps of fish densities and temporal changes at these locations 

were mapped. 

Fisheries acoustics survey data were analyzed using Myriax Echoview software. 

Echograms were produced based on the raw variables: backscatter of pings (Sv), 

angular position of pings, and target strength (TS) of pings (Table 2). Split beam 

echosounding systems are capable of determining the location of single targets within 

the beam. The amount of time is takes for a sonar ping to reach a target in the water 

column and return an echo to the transducer is indicative of the depth of the target. The 

strength of the returned echo is related to the size of the target. Since the echo returns 

from off axis targets are diminished compared to targets located directly on the center 

axis of the beam, an off-axis beam angle compensation algorithm uses the angular 

position echogram to provide more accurate estimates of target strength, measured in 

decibels (dB). Therefore, each fish detected by the splitbeam sonar has three spatial 

dimensions (x, y, depth) calculated relative to the acoustic beam and in real-world 

coordinates when coupled with the ship’s navigation system, as well as an associated 

target strength relative to fish size. 

Table 2. Description of echograms based on raw variables collected

Myriax Echoview 4.6. Hobart, Tasmania.

Sv echogram - Each data point on an Sv echogram represents a volume backscattering 

coefficient measured in decibels referenced to 1 m2

/m3. It is possible to integrate Sv data. 

Indeed Sv data are considered by many to have meaning only when they are integrated.

Angular position echogram - Each data point on an angular position echogram represents a 

position within the transducer beam, measured by a pair of angles, one in the direction of 

the minor axis, and the other in the direction of the major axis of the transducer.

TS echogram - Each data point on a TS echogram represents a Target Strength measured in 

decibels referenced to 1m2

. 

Single target echograms are distinct from ordinary echograms in that they do not consist of a 

grid of data points. Pings are displayed left to right as usual, but each single target in the 

data file (or detected by Echoview) is displayed at its depth.
10 

Post processing of data involved applying a bottom detection algorithm to the echo 

return to create a line representing the sea floor. Edits were made to the bottom 

detection line where it was necessary to better define the separation between bottom 

and fish returns to ensure that the bottom signature was not included in the water 

column analysis and fish targets were not associated with the bottom signal 

inadvertently. Bad data regions (for example, when ship speeds were too fast or too

slow, or ship turns created bubbles in the water column) were identified and excluded 

from analysis. ‘Virtual’ and fixed lines were created at various depth strata to partition the 

water column horizontally. An analysis grid was applied to partition the water column 

vertically, every 100m along the transect. Offsets were included to account for the 

configuration of transducers and GPS relative to the ship. These settings were saved in 

a template to ensure that all processing parameters were applied consistently. The 

variables created in Echoview (Figure 3) and the data processing procedures (Figure 4) 

are outlined here. Fish tracks detected within the single target echogram (Figure 5) form 

the basis of fish density maps. Target strength is the measure of the reflected acoustic 

energy from the transmitted pulse or ping, is proportional to the size of the fish, and 

relates primarily to the size and morphology of the fish’s swim bladder. The equation 

used here to convert target strength to fish length was based on the general equation of 

Love (1977): Total Length (cm) = 10^((TS_mean+64.0035)/19.2)

Figure 3. Template that contains properties for platform, sensors, echograms, lines 

and virtual variables in Echoview.

 Single target detection echogram export  analysis by cells  fish tracks
11 

Figure 4. Flow diagram showing data processing steps from Echoview to ArcGIS. 

 

Figure 5. Result of bottom detection, virtual line 5m from bottom, and fish tracking 

algorithm applied to mid-water targets.
12 

1.3 Integration of multibeam bathymetric mapping and fisheries acoustics

The mission plan for these surveys focused first on multibeam mapping as a priority in 

terms of ship operations, with fisheries acoustics intended to complement that effort. 

Therefore, fisheries acoustics survey data were collected along planned night time 

multibeam lines. The spacing of multibeam tracklines is dependent on water depth and 

beam width. Generally, tracklines are run parallel to bathymetric contours to provide full 

coverage for bottom mapping. By comparison, swath coverage of the acoustic beam is 

only 5% of multibeam coverage. Surveys are typically conducted at ship speeds of 4-10 

knots. 

Typically, daily ship operations for multibeam surveys utilize daytime hours for ROV 

transects to ground truth the multibeam data. While fisheries acoustics data can be 

collected during ROV transects, these surveys are conducted at very slow speeds (less 

than 1 knot) which are not conducive to acoustic data collection unless a truly stationary 

deployment is designed. However, observations from ROV operations are useful for 

determining fish species within the survey area. 

The following section describes the methods and results of fisheries acoustics surveys 

conducted in 2008, 2009 and 2010, concurrent with multibeam mapping efforts. 
13 

2. Fisheries acoustics surveys

 

2.1 Western Puerto Rico (NF-08-04-USVI)

In 2008, the waters around Mona Island and Tourmaline Bank were identified as priority 

areas for benthic habitat mapping (Figure 6). Acoustic surveys were conducted to 

characterize potential yellowfin grouper, tiger grouper and red hind spawning sites. 

 

Figure 6. Western Puerto Rico priority mapping areas (blue outline) as identified in the 

NF-08-04-USVI Cruise Instructions.

2.1.1 Methods

A 120 kHz Biosonics split beam transducer was mounted on the hull of the ship and 

transmitted at 6 pings per second with a pulse width of 0.4 msec to a depth of 100m (see 

Appendix A for details on system configuration). Acoustic survey lines followed 

multibeam track lines.

Transects were reviewed to identify bad data regions. A threshold of -70dB was used to 

examine the raw data variable Sv (volume backscattering) while synchronized with the 

cruise track. The threshold for viewing single target detection echograms was set at -

55dB while each transect was examined for evidence of red hind columns (Johnston et 

al.2006) and other features indicative of spawning aggregations. Volume backscattering 

was echo-integrated for each 100m segment of transect and at various depth intervals. 

Mean volume backscatter (Sv_mean) and individual fish tracks were exported for further 

analysis and mapping.
14 

After reviewing all fisheries acoustics transects for appropriate depth ranges, time 

frames and continuous, reliable data, survey transects were chosen for further analysis 

(Table 3). Three nights of transecting at Tourmaline Bank (February 26-27; February 29-

March 1; March 1-2) spanned roughly the same time period and collectively provided 

extensive coverage of Tourmaline Bank (Figure 7, right). Due to an equipment failure on

March 3, 2008, only one hour of useable data from Mona Island was collected and 

analyzed (Figure 7, left). A full moon occurred on February 20, 2008. Sunset was at 

1830 on February 29, 2008. 

 

Table 3. Fisheries acoustics surveys analyzed 2008

Location Start date End date Start 

time

End 

time

Approx. 

duration 

(hr)

Survey 

length

(nmi)

Tourmaline Bank_1 2/26/08 2/27/08 16:30 05:45 11 70

Tourmaline Bank_2 2/29/08 3/1/08 23:00 07:30 8.5 46.5

Tourmaline Bank_3 3/1/08 3/2/08 23:00 05:00 6 31

Mona Island 3/3/08 3/3/08 20:45 21:35 0.8 6 

Mona Island Tourmaline Bank

Figure 7. Maps of Mona Island and Tourmaline Bank showing simultaneous fisheries 

acoustics and multibeam transects (yellow), as well as ROV transects (blue). Survey 

track lines are overlaid on NOAA nautical charts, along with bathymetric data. Unless 

otherwise noted, the bathymetric color scale used in this document shows warmer colors 

for shallower depths. http://ccma.nos.noaa.gov/products/biogeography/benthic/htm/data.htm

 1

 2 

 3 
15 

2.1.2 Analysis and products

Acoustic backscatter data were analyzed in Echoview using echo integration based on 

the Sv echogram. In addition, single target detection algorithms, using both the TS splitbeam and angular position echograms, were applied to generate fish tracks. Water 

column backscatter data were integrated using a minimum Sv threshold of -66dB and an 

uncompensated target strength threshold of -60dB (Rudstram et al.2009), then analyzed 

for each 100m segment of transect. For fish track detection, a threshold of -50dB was 

used to eliminate very small fish and noise. Various depth strata grids are used to 

partition the water column. For Tourmaline Bank, transect data were summarized at 

100m intervals along the transect for various depth strata. In addition, targets were 

divided into size classes and mapped.

Information derived from acoustic surveys conducted at Mona Island and Tourmaline 

Bank: 

• Interpolated maps of mean volume backscatter integrated through the water 

column, inclusive of 20m below the surface to the bottom, for each 100m section 

of transect at Tourmaline Bank (Figure 8). An interpolated surface resulting from 

kriging depicts the distribution of biomass as a continuous surface. Darker areas 

indicate higher estimates of biomass. Geostatistical approaches can be helpful in 

further defining the patchy nature of fish distributions depending on spacing 

between transects and the size of the aggregations being targeted (Taylor et 

al.2006). 

• Fish density (fish/100m2

) at Tourmaline Bank based on single target detection 

(Figure 9). This map of fish density illustrates the spatial distribution of fish in the 

water column from 10m below the surface to the bottom with mean target 

strength > -50dB. 

• Location of small (<11cm), medium (11-29cm), and large fish (>29cm) at 

Tourmaline Bank based on single target detection from 10m below surface to the 

bottom (Figure 10). The distribution of fish by size indicates that small and 

medium size fish are distributed throughout the survey area, whereas, large fish 

are found at fewer, specific locations.

• Potential spawning aggregations and other water column features. A qualitative 

visual examination of echograms from Mona Island and Tourmaline Bank

indicate variation in marine seascapes with location and time of day. While some 

features within the water column were notable, there were no features that had 

definitive characteristics resembling those expected from spawning aggregations. 

However, the configuration of fishes in the water column and the spatial 

characteristics that result from various schooling, dispersion, or refuge behaviors 

may have ecological and bioenergetic implications (Kracker 2004) and may be 

indicative of the association between biomass and benthic features or habitat 

types (Kracker et al.2008).

 

 

 
16 

 

Figure 8. Mean volume backscatter (Sv_mean) is proportional to biomass. Sv_mean 

was integrated at 100m intervals and interpolated across the survey area at Tourmaline 

Bank to depict the distribution of biomass in the water column from 20m below surface to 

the bottom. [Ordinary kriging, exponential variogram model, lags = 12, lag size = 400m, 

nugget = 24.4882; range = 3567m, mean std error = 0.00028, RMSE = 0.9728].

 

Figure 9. Fish density (fish/100m2

) at Tourmaline Bank based on single target detection 

where target strength > -50dB from 10m below surface to the bottom. 
17 

 

 

 

Figure 10. Location of small (< 11cm, top), medium (11-29cm, middle), and large fish 

(> 29cm, bottom) at Tourmaline Bank based on single target detection from 10m below 

the surface to the bottom. Love equation (1977) for target strength-length relationship 

was used to estimate fish size.
18 

2.2 Vieques and El Seco, Puerto Rico (NF-08-06-SEAS, NF-09-01-USVI) 

In 2008 and 2009, areas around Vieques were identified as priority areas for benthic 

habitat mapping based on historic spawning sites and the location of the Red Hind 

Conservation Area (Figure 11). Acoustic surveys targeted yellowfin grouper, tiger 

grouper and red hind aggregations. Split-beam acoustics were run simultaneously with 

multibeam operations. 

 

 

Figure 11. Vieques priority areas for benthic habitat characterization as identified in the 

NF-09-01-USVI Cruise Instructions. Green dots indicate known spawning aggregation 

sites. 

2.2.1 Methods

A Simrad EK-60 120 kHz split beam transducer was pole mounted and attached to the 

moon pool on the hull of the NOAA ship Nancy Foster in 2008 (Figure 12 – left). In 2009, 

the EK-60 120kHz transducer was attached to a flange alongside a Reson 7125 

multibeam system (200,400 kHz) and attached to the moon pool (Figure 12 – right). 

2009 was the first year of operation with the 7125 system. A hydrographic survey report 

entitled Report on Benthic Habitat and Hydrographic Survey Project is available at:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/pdf/NF-09-01_DAPR.pdf

This system did not perform as expected; therefore, multibeam mapping was 

accomplished using the Simrad EM 1002 system on board as in previous years. 
19 

Acoustic survey lines followed multibeam track lines at Vieques and El Seco. Areas 

surveyed are shown in Figure 13. Details on the configuration of the split-beam system 

used in 2008 and 2009 are provided in Appendix A. 

 

Figure 12. Deployment of Simrad EK-60 120 kHz transducer for fisheries acoustic 

surveys in 2008 (left) and 2009 (right).

Figure 13. Areas surveyed at Vieques, PR March 26 through April 3, 2008 (left) and El 

Seco, PR March 26 through April 2, 2009 (right). 
20 

2.2.2 Analysis and products

 

Acoustic backscatter data were analyzed in Echoview, which included editing bottom 

lines and identifying bad data regions. Single target detection algorithms were applied to 

the TS split-beam and angular position echograms to generate fish tracks. Fish density 

(fish/100m2

) was calculated at 100m intervals along the transect. An examination of fish 

distribution from survey data collected at Vieques in 2008 indicated that 90% of fish were 

found within 10m of the bottom (Figure 14). Therefore, the water column was partitioned 

horizontally and fish density was mapped for both the entire water column (Figure 15) 

and for the portion of the water column within 10m of the bottom (Figure 16) for medium

(11-29cm) and large (>29cm) fish. Estimates of fish density derived from acoustic 

surveys conducted near El Seco in 2009 were mapped similarly (Figure 17-18).

 

Figure 14. Cumulative distribution of fish targets by depth at Vieques in 2008. 
21 

Figure 15. Fish density at Vieques of medium (11-29cm) and large fish (>29cm) 

for the entire water column. 

Vieques, Puerto Rico 2008

Medium fish 11-29 cm

Vieques, Puerto Rico 2008

Large fish >29 cm
22 

Figure 16. Fish density at Vieques of medium (11-29cm) and large fish (>29cm) 

for the portion of the water column within 10m from the bottom. 

Vieques, Puerto Rico 2008

Medium demersal fish 11-29 cm

Vieques, Puerto Rico 2008

Large demersal fish >29 cm
23 

Figure 17. Fish density at Vieques El Seco of medium (11-29cm) and large fish 

(>29cm) for the entire water column. 

Vieques, Puerto Rico 2009 (El Seco)

Medium fish 11-29 cm

Vieques, Puerto Rico 2009 (El Seco)

Large fish >29 cm
24 

Figure 18. Fish density at Vieques El Seco of medium (11-29cm) and large fish 

(>29cm) for the portion of the water column within 10m from the bottom. 

Vieques, Puerto Rico 2009 (El Seco)

Medium demersal fish 11-29 cm

Vieques, Puerto Rico 2009 (El Seco)

Large demersal fish >29 cm
25 

2.3 Virgin Passage and St. John Shelf (NF-10-03-USVI) 

In 2010, two locations in the USVI were identified as priority areas for benthic habitat 

mapping - Virgin Passage near St. Thomas and the St. John Shelf (Figure 19 – black 

polygons). Acoustic surveys targeted known grouper spawning sites, including yellowfin 

grouper. Two operating days were dedicated to known and candidate fish aggregation 

sites at Grammanik Bank and Tampo. 

Figure 19. St. Thomas and St. John priority areas (black polygons) for benthic habitat 

characterization as identified in the NF-10-03-USVI Cruise Instructions. The blue regions 

indicate areas mapped prior to 2010.

2.3.1 Methods

A split-beam, two frequency (38/120 kHz) Simrad system was attached to a sled 

alongside the Reson 7125 multibeam system and mounted on the hull of the NOAA ship 

Nancy Foster (Figure 20 - left). Spilt-beam data acquisition was handled through Simrad 

ER-60 software. Both the 38kHz and 120kHz were set at a ping interval of 0.12 or

approximately 8 pings per second when the multibeam was not operating (See Appendix 

A for details on system configuration). When the multibeam was operating, an inline 

switch triggered ping control from the Reson to the Simrad transceivers to alternate 

pings between systems. Survey lines followed planned multibeam track lines. During the 

day, ROV surveys were conducted to validate benthic habitat types derived from 

multibeam data. 

Split-beam and multibeam surveys were conducted from March 18, 2010 to April 5, 2010 

covering Virgin Passage and St. John shelf (Figure 21). Split-beam surveys conducted 

on April 4-5, 2010 focused on expected fish aggregation locations at Grammanik Bank 
26 

and Tampo (Figure 22). ROV surveys at these sites included the deployment of a video 

camera and DIDSON high resolution sonar attached to the ROV (Figure 20 – right) to 

provide complementary data at Tampo and Grammanik Bank.

 

Figure 20. Simrad 38/120 kHz system deployed alongside Reson 7125 prior to mounting 

on the hull of the NOAA ship Nancy Foster (left). Phantom 2 ROV with video camera and 

DIDSON high resolution sonar as deployed at dedicated fish survey sites (right).

Figure 21. Areas mapped for benthic habitat classification using multibeam at Virgin 

Passage southwest of St. Thomas (left) and St. John shelf (right). 

Targeted fish acoustics surveys at Grammanik Bank and Tampo consisted of several 

passes over the area (Figure 22). Video ROV and high resolution sonar surveys were 

also conducted at these locations to provide insight into species present at the time. An 

acoustic survey was conducted at Grammanik Bank from 12:25 to 20:40 on April 3, 2010

followed by a high resolution sonar and video ROV survey from 20:45 to 23:25. Acoustic 

surveys at Tampo were run in the afternoon and evening of April 4, as well as the early 

morning of April 5, 2010, allowing for temporal comparisons to be made. High resolution 

sonar data and video were collected during an ROV survey at Tampo on April 4, 2010 

from 18:50 to 20:45. 
27 

 

Figure 22. Location of dedicated fish surveys conducted at Grammanik Bank and 

Tampo in 2010.

2.3.2 Analysis and products

Acoustic backscatter data from surveys conducted in 2010 were processed in Echoview 

and converted to fish densities as outlined in Figures 3 and 4. Several approaches for

examining the spatial and temporal distribution of fish throughout the survey area were 

applied. 

• Fish density (fish/100m2

) was calculated every 100m along all transects at Virgin 

Passage and St. John shelf (Figure 23). Fish density mapped at Virgin Passage 

appears to show a rather consistent spatial distribution with a few spots of high 

density; whereas, the map of St. John shelf shows large, localized areas of high 

fish density, particularly in the north-central part of the shelf and near the shelf 

ledge toward the southwest. 

• Fish density was also mapped by size class at Virgin Passage (Figure 24) and 

St. John shelf (Figure 25). Size classes were divided into small (<11cm, top), 

medium (11-29cm, middle), and large (>29cm, bottom) fish. The general 

equation of Love (1977) for target strength-length relationship was used to 

estimate fish size. At Virgin Passage, patterns in fish density of small and 

medium fish may be related to time of survey (see Figure 26). High densities of 

 St. John shelf

 Tampo

 Grammanik Bank
28 

large fish are located at specific locations across the region. At St. John shelf, 

high fish densities of small and medium fish were found primarily in the northcentral region and near the ledge along the southwest. High densities of large 

fish were primarily found near the shelf edge and the promontory at Tampo. 

• Diel patterns (dawn/dusk versus nighttime) were examined in each of the two 

survey areas (Figure 26). Daylight hours (08:00-16:00) were typically dedicated 

to ROV surveys to validate the multibeam data. Therefore, dawn and dusk 

acoustic surveys conducted before and after daytime ROV operations are 

considered daytime transects. These time periods include acoustic transects run 

between 05:00-08:00 and 16:00-19:00. Night time densities are based on 

transects run from 19:00 to 05:00. Sunrise occurred at 06:20 and sunset was at 

18:38 local time on March 31, 2010. While observed patterns of fish density 

mapped across the region are due, in part, to the time of survey at any given 

location, these patterns suggest that areas of higher fish density at Virgin 

Passage occur during the daytime or crepuscular periods. Maps of temporal 

patterns at St. John shelf indicate that areas of high fish density occur in the 

same southwest region during both daytime and nighttime surveys.
29 

Figure 23. Fish density (fish/100m2

) at Virgin Passage (upper) and St. John shelf (lower).
30 

Figure 24. Fish density by size class at Virgin Passage. Size classes are: small (< 11cm, 

top), medium (11-29cm, middle), and large fish (>29cm, bottom). The general equation 

of Love (1977) for TS-length relationship was used to estimate fish size.
31 

Figure 25. Fish density by size class at St. John shelf. Size classes are: small (< 11cm, 

top), medium (11-29cm, middle), and large fish (> 29cm, bottom). The general equation 

of Love (1977) for target strength-length relationship was used to estimate fish size.
32 

Figure 26. Diel patterns (dawn/dusk versus nighttime) of fish density at Virgin Passage 

(upper) and St. John shelf (lower). Day or dawn/dusk hours include acoustic transects 

run between 05:00-08:00 and 16:00-19:00. Nighttime densities are from transects run 

from 19:00 to 05:00. Sunrise was at 06:20; sunset at 18:38 local time on 31 March 2010.
33 

Targeted split-beam acoustic surveys were conducted at two specific locations - 

Grammanik Bank which previously had been identified as a historic fish spawning 

location and Tampo which was identified as a potential new fish spawning aggregation 

site. Split-beam acoustic surveys at Grammanik Bank were run on 3 April 2010 from 

12:25 into the night, followed by an ROV survey with video and DIDSON high resolution 

sonar. Survey results from Grammanik Bank are presented as fish density (fish per 

100m2

) mapped over three time periods. In addition, large fish (>29cm) were mapped 

and spatial analysis applied to detect aggregations of large fish. Further, ROV video was 

reviewed for targeted species and echograms examined for indications of fish 

aggregations in the water column. 

• Maps of fish density derived from acoustic surveys conducted throughout the day 

and into the night at Grammanik Bank indicate rather persistent areas of high fish 

density, especially near the shelf edge (Figure 27). 

• Maps depicting the size-specific distribution of large fish (>29 cm) were produced 

to assess patterns of large fish abundance and possible locations of spawning 

aggregations at Grammanik (Figure 28). A cluster statistic was applied in 

ArcMap (Anselin 1995, local Moran’s I, IDW2

, 250m threshold, alpha=.05) to test 

the degree of spatial similarity of fish lengths using transect intervals of 100m 

where large fish (>29cm) were found. Locations that indicate significant 

clustering of large fish length were identified and mapped (Figure 29). 

Furthermore, an examination of echograms from acoustic surveys and video 

from the ROV survey conducted on the same day resulted in evidence of fish 

aggregations on the echogram and video identification of yellowfin grouper

(Mycteroperca venenosa), both within 500m of where spatial pattern analysis 

indicated significant clustering (Figure 29).

Split-beam acoustic surveys at Tampo were run in the afternoon and evening of April 4 

and early morning on April 5, 2010. ROV surveys with video and DIDSON high 

resolution sonar were conducted between the first and second set of split-beam acoustic 

surveys. Maps and graphs of fish density, as well as corresponding images from ROV 

video and echograms are presented here. 

• Results from surveys targeting aggregations at Tampo (Figure 30) were used to 

map fish density at two different time periods. Split-beam transects were run in 

afternoon of April 4, 2010 (14:45 to 16:25 – Figure 31, left) and at dawn on April 

5, 2010 (05:45 to 07:45 – Figure 31, right). Mapped results suggest higher fish 

densities in the afternoon surveys compared to surveys conducted at dawn on 

the following day. 

• Temporal changes in fish density were examined at Tampo, specifically near the 

shelf edge (Figure 32). A change in fish density occurs moving from the 

afternoon (17:00) to late evening (23:00) as fish density concentrates near the 

promontory of Tampo. In the pre-dawn hours (05:00) high fish density is also 

observed near the tip of Tampo. 

• Based on patterns of high fish density near the shelf edge, echograms were 

examined for fish aggregations (Figure 33). Echograms associated with the 

highest fish density observed in the Tampo transects illustrate the various 

configurations of fish distribution observed at a scale of 200-300m. These 

echograms can be further analyzed, in conjunction with the ROV data to 

document and compare the characteristics and configuration of fish aggregations 

(Figure 34).
34 

Figure 27. Fish density (fish per 100m2

) derived from acoustic surveys targeting fish 

aggregation sites at Grammanik Bank 3 April 2010.

Fish per 100m2

3 April 2010

17:30-20:50

Grammanik Bank

Fish per 100m2

3 April 2010

12:25 to 14:00

Grammanik Bank

Fish per 100m2

3 April 2010

14:15-17:30

Grammanik Bank
35 

Figure 28. Mean length of large fish (>29cm) at Grammanik Bank

3 April 2010 12:25 to 20:50. 

Figure 29. Cluster analysis (local Moran’s I) of large fish from acoustic survey with fish 

aggregations on echogram and video observations of yellowfin grouper (Mycteroperca 

venenosa ) along ROV track. 

Echogram depicting fish aggregation 

along acoustic survey transect

3 April 2010 13:27

One of many yellowfin grouper Mycteroperca 

venenosa detected along ROV transect

3 April 2010 22:52

Grammanik Bank

Mean length (cm) of large fish (>29cm) 

per 100m survey transect

3 April 2010

12:25-20:50

Cluster analysis

Grammanik Bank

3 April 2010

Significant clustering of large fish

Sighting of yellowfin grouper along ROV track

Location of echogram with fish aggregation
36 

 

Figure 30. Location of acoustic surveys targeting fish aggregation sites at Tampo 

(yellow). The high resolution sonar/ROV track to be used for analysis of fish species 

present at the time of surveys is shown in pink. 

Figure 31. Fish density at Tampo 4 April 2010 14:45 to 16:25 (left) and 5 April 2010 

05:45 to 07:45 (right).
37 

Figure 32. Temporal changes in fish density at Tampo near shelf edge: 4 April late 

afternoon ~17:00 (top), 4 April late evening ~23:00 (middle), and 5 April pre-dawn 

~05:00 (bottom). matches approximate mapped location with fish density bar on 

graph. See also associated echograms in Figure 33 noted by interval numbers.

198

26-28

23

256

268
38 

 Interval 256 16:57 4 April 2010.

Interval 268 17:02 4 April 2010.

Interval 198 23:19 4 April 2010. 

Figure 33. Echograms related to the areas of highest fish density along the near-edge 

transect at Tampo. These echograms depict variation in the configuration and 

arrangement of fish in the water column at various times of day. Intervals are noted by 

 on graphs in Figure 32. (Figure continues on next page).
39 

Interval 22-23 04:59 5 April 2010.

Interval 26-28 05:00 5 April 2010.

Figure 33. (Figure continued from previous page). Echograms related to the areas of 

highest fish density along the near-edge transect at Tampo. These echograms depict 

variation in the configuration and arrangement of fish in the water column at various 

times of day. Intervals are noted by on graphs in Figure 32. 

Figure 34. School of Carangidae observed on ROV video between the first and second 

dedicated fish acoustic surveys at Tampo (18:57:36 4 April 2010). 
40 

3 Summary 

This report summarizes mapping efforts and results from surveys near Puerto Rico

(southwestern PR, Vieques and El Seco), St. Thomas and St. John, using multibeam 

techniques to classify bottom habitats concurrent with split-beam fisheries acoustics to 

quantify and map biota in the water column. Maps of fish density provide a snapshot in 

time of fish distribution throughout the survey area. Repeated sampling at targeted fish 

aggregation sites, video from ROV surveys, review of echograms, and spatial analysis 

provide further insight into the location, timing and configuration of fishes. 

Technically and logistically, there were no major conflicts between multibeam and 

fisheries acoustics surveys that would preclude running both operations simultaneously. 

Interference between the multibeam and split-beam systems, generally, was not a 

problem. Daytime hours were primarily dedicated to nearly stationary ROV operations 

for ground truthing of multibeam data, limiting the amount of fisheries acoustics data 

obtained during daylight hours. Options should be explored for developing procedures to 

utilize daytime surveys to determine species composition, interpreting the acoustic signal 

in regards to TS-fish length relationships for particular species, and examining fish 

behavior to aid in the interpretation of acoustic surveys. Incorporating ROV operations, 

diver surveys, high resolution sonar imaging, or other methods of ground truthing to 

determine species composition should be given ample consideration in survey planning. 

Regarding survey design, where multibeam mapping is given priority, multibeam 

tracklines are not necessarily the preferred design for fisheries acoustics surveys but still 

provide an excellent platform for mapping biological resources in the water column. 

Fisheries acoustics transects often are run perpendicular to ledges and several passes 

are made over features of interest to detect temporal and spatial patterns related to fish 

utilization of benthic habitats. In spite of these compromises, the ability to efficiently 

capture large amounts of data and produce maps of fish size and distribution concurrent 

with multibeam surveys facilitates the identification of highly productive habitats. Moving 

forward, testing options and developing procedures for incorporating supplemental 

survey techniques to validate the acoustic data is a top priority, as is standardizing 

procedures and documenting all stages of acoustic survey data development.

While limitations such as species identification exist, there are a variety of products that 

can be developed from fisheries acoustics surveys to assist resource managers. This 

document provides examples of the information that can be derived from fisheries 

acoustics surveys to characterize important habitats and points to further analyses that 

can be performed. For example, as habitat classification maps from multibeam become 

available, analyses testing the spatial relationships and scale at which benthic habitats 

are coupled with biology would provide resource managers tools to assist in delineating 

marine protected areas. Furthermore, analysis to quantify the configuration and spatial 

characteristics of fish schools may provide insight into questions of behavior and 

ecological strategies. 

This report continues the discussion regarding the best methods for acquiring, 

processing, interpreting, and reporting data from fisheries acoustic surveys. The use of 

acoustics for mapping fish distributions presents unique challenges; and the 

implementation of these methods changes with the aim of each mission. The integration 

of fisheries acoustics and multibeam missions yields new opportunities when conducting 

concurrent water column and benthic mapping. Not only do integrated surveys leverage 
41 

organizational resources, but they directly tie benthic habitat information with information 

on organisms using those habitats. 

4. References

Anselin, Luc. 1995. Local Indicators of Spatial Association – LISA. Geographical 

Analysis, 27(2): 93–115. 

Costa, B.M., L.J. Bauer, T.A. Battista, P.W. Mueller and M.E. Monaco. 2009. ModerateDepth Benthic Habitats of St. John, U.S. Virgin Islands. NOAA Technical 

Memorandum NOS NCCOS 105. Silver Spring, MD. 57 pp.

Friedlander, A.M., and J. Beets. 2008. Temporal Trends in Reef Fish Assemblages 

inside Virgin Islands National Park and around St. John, U.S. Virgin Islands, 

1988-2006. Biogeography Branch, Silver Spring, MD. NOAA Technical 

Memorandum NOS NCCOS 70. 60 pp.

Johnston, S.V., J.A. Rivera, A. Rosario, M.A. Timko, P.A. Nealson, and K.K. Kumagai, 

2006. Hydroacoustic evaluation of spawning red hind (Epinephelus guttatus) 

aggregations along the coast of Puerto Rico in 2002 and 2003. In: Emerging 

technologies for reef fisheries research and management. NOAA Professional 

Paper NMFS (5). NOAA, Seattle, WA, pp. 10-17.

Kendall, M.S., M.E. Monaco, K.R. Buja, J.D. Christensen, C.R. Kruer, M. Finkbeiner, and 

R.A. Warner. 2001. (On-line). Methods Used to Map the Benthic Habitats of 

Puerto Rico and the U.S.Virgin Islands URL: 

http://ccma.nos.noaa.gov/products/biogeography/benthic/htm/manual.pdf

Kracker, L., M. Kendall, and G. McFall. 2008. Benthic features as a determinant for fish 

biomass. Marine Geodesy, 31: 1–14.

Kracker, L.M. 2004. Between SST and bathymetry: spatial techniques for defining the 

aquatic landscape. (147-160). In Nishida, T., Kaiola, P.J. and Hollingworth, C.E. 

(Editors). 2004. GIS/Spatial Analyses in Fishery and Aquatic Sciences (Vol. 2). 

Fishery - Aquatic GIS Research Group, Saitama, Japan. 735pp.

Love, R. H. 1977. Target strength of an individual fish at any aspect. Journal of the 

Acoustical Society of America 62:1397–1403.

Myriax Echoview 4.6. Hobart, Tasmania. 

Ross, S.W. and A.M .Quattrini. 2007. The fish fauna associated with deep coral banks 

off the southeastern United States. Deep-Sea Research I 54 :975–1007. 

Rudstam, L. G., Parker-Stetter, S. L., Sullivan, P. J., and Warner, D. M. 2009. Towards a 

standard operating procedure for fishery acoustic surveys in the Laurentian Great 

Lakes, North America. ICES Journal of Marine Science, 66: 000–000.

Sadovy. Y., P.L. Colin, and M.L. Domeier. 1994. Aggregation and spawning in the tiger 

grouper Myceteroperca tigris (Pices: Serraqnidae). Copeia 2:511-516.

Shapiro, D.Y., Y. Sadovy. and M.A. McGehee. 1993. Size, composition, and spatial 

structure of the annual spawning aggregation of the red hind, Epinephelus 

guttatus (Pices: Serranidae). Copeia 2:399-406.

Simmonds, J. and D. MacLennan. 2005 Fisheries Acoustics: Theory and Practice. 

Blackwell Science, Ltd., Oxford, UK.

Taylor, J. C., Eggleston, D.B. and Rand, P.S.. 2006. Nassau grouper (Epinephelus 

striatus) spawning aggregations: hydroacoustic surveys and geostatistical 

analysis. In: Emerging technologies for reef fisheries research and management. 

NOAA Professional Papers NMFS (5). NOAA, Seattle, WA, pp. 18-25.
42 

Appendix A Data acquisition and processing

There are many steps involved in collecting and interpreting acoustic survey data. 

Options related to data acquisition, processing, mapping and reporting are dependent 

upon the study area, species of interest, operational priorities, and research and 

management questions. The process described in this document should be considered a 

starting point to be modified as conditions warrant. The entire process includes 

equipment preparation and calibration, data acquisition, data review and processing, 

data analysis, and map production and reporting. The survey methods reported here are

suited to fisheries acoustics surveys conducted concurrent with multibeam mapping in 

the USVI and Puerto Rico in support of the Coral Reef Ecosystem benthic habitat 

mapping effort. These procedures can be applied to current and future data collected 

under the Coral Reef Conservation Program in the USVI and Caribbean, as well as other 

surveys conducted on the NOAA ship Nancy Foster, with regard for the needs and 

objectives of future missions. 

Environmental and system configuration parameters

2008

NF-08-01-

USVI

2008

NF-08-06-

SEAS

2009

NF09-01-

USVI

2010

NF-10-03-USVI

Acoustic split-beam 

system 

Biosonics 

DT-X 

Simrad 

ES60 GPT; 

ES120-7C 

transducer

Simrad 

ES60 GPT; 

ES120-7C 

transducer

Simrad EK-60

Frequencies (kHz) 120 120 120 38//120

Calibration offset 0 0 0 0

Sound velocity (m/s) 1536.59 1540.73 1536.7 1541.0

Absorption (dB/m) 0.04924 0.0455984 0.0365207 0.0059821/0.446234

Threshold (dB) for 

collection (min/max) -75/99 -70/99 -70/99 -70/99//-70/99

Pulse duration (ms) .4 0.256 0.128 0.128 / 0.256

Ping per second repeat 6 8 8 8

Stop depth (m) 100 60 60 100

Beam width (deg) 7.4 7.0 7.0 7.0//7.0

Transmit power (W) 1000 500 500 600 / 500
43 

Data processing parameters used to create Sv echograms, bottom detect algorithms

and fish tracks in Echoview. 

Parameters used in bottom 

detect algorithm

Algorithm best bottom candidate

Start/Stop depth (m) 5/100 5/60 5/60 5/100

Minimum Sv for good pick 

(dB) -70 -60 -60 -70

Backstep discrimination 

level (dB) -50 -45 -45 -45

Backstep range (m) -0.50 -0.01 -0.01 -0.01

Peak threshold (dB) -50 -50 -50 -50

Maximum dropouts 

(samples) 2 2 2 2 

Window radius (samples) 8 8 8 8

Minimum peak asymmetry -1.0 -1.0 -1.0 -1.0

Parameters used to create 

fish tracks

Algorithm 2D (range and time)

Alpha 0.7

Beta 0.5

Exclusion distance (m) 0.1

Missed ping expansion 0

Range 40

TS 0

Ping gap 0

Minimum number of single 

targets in a track 3 

Minimum number of pings 

in track (pings) 3 

Maximum gap between 

single targets (pings) 1 

2008

Biosonics

2008

Simrad

2009 

Simrad

2010

Simrad

Parameters used to create 

Sv echograms

Minimum Threshold (dB) -66 -60 -60 -77

Maximum threshold (dB) 99 99 99 99

Minimum TS threshold (dB) -60 -70 -70 -70
44 

Appendix B Links to cruise summaries

2010. NF-10-03 USVI. Characterization of Seafloor Habitats of the U.S. Caribbean

Cruise instructions:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/pdf/nf2010_cruise_plan.pdf

Mission webpage:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/nf2010.html

2009. NF-09-01-USVI. Characterization of seafloor habitats of Vieques, Puerto Rico

Cruise instructions:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/pdf/NF-09-01-

USVI_Cruise_Plan.pdf

Mission summary:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/pdf/NF2009.pdf

Hydro survey report:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/pdf/NF-09-01_DAPR.pdf

2008. NF-08-04-USVI. Characterization of midwater seafloor habitats of western Puerto 

Rico

Cruise instructions:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/pdf/NF-08-04-USVICruise.pdf

Mission summary:

http://ccma.nos.noaa.gov/products/biogeography/usvi_nps/pdf/NF2008.pdf
45 
46 

United States Department of Commerce

Gary F. Locke

 Secretary

National Oceanic and Atmospheric Administration

Jane Lubchenco

Under Secretary of 

Commerce for Oceans and Atmosphere, 

NOAA Administrator 

National Ocean Service

 David Kennedy

Assistant Administrator