Office of Research and Development

National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division

 

EPA/600/R-13/350 | December 2014 

www.epa.gov/ord 

Workshop on 

Biological Integrity 

of Coral Reefs 

Caribbean Coral Reef Institute
 

Isla Magueyes, La Parguera, Puerto Rico
 

August 21-22, 2012
 

Office of Research and Development

National Health and Environmental Effects Research Laboratory 

 

 

 

 

EPA/600/R-13/350 

December 2014 

www.epa.gov/ord 

Workshop on Biological Integrity of Coral Reefs
 

August 21-22, 2012
 

Caribbean Coral Reef Institute
 

Isla Magueyes, La Parguera, Puerto Rico
 

by 

Patricia Bradley 

US EPA 

Atlantic Ecology Division 

NHEERL, ORD 

33 East Quay Road 

Key West, FL 33040 

Deborah L. Santavy 

US EPA 

Gulf Ecology Division 

NHEERL, ORD 

1 Sabine Island Drive 

Gulf Breeze, FL 32561 

Jeroen Gerritsen 

Tetra Tech Inc. 

400 Red Brook Boulevard 

Suite 200 

Owings Mills, MD 21117 

Contract No. EP-C-09-001
 

Work Assignment 3-01 

Great Lakes Environmental Center, Inc.
 

Project Officer: 

Shirley Harrison 

US EPA 

Office of Water 

Office of Science and Technology 

Washington, DC 20460 

Work Assignment Manager: 

Susan K. Jackson 

US EPA 

Office of Water 

Office of Science and Technology 

Washington, DC 20460 

National Health and Environmental Effects Research Laboratory
 

Office of Research and Development
 

Washington, DC 20460
 

Printed on chlorine free 100% recycled paper 

with 50% post-consumer fiber using vegetable-based ink. 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Notice and Disclaimer 

The US Environmental Protection Agency (EPA) through its Office of Research and Development and 

Office of Water funded and collaborated in the research described here under EP-C-09-001,
 

Work Assignment #3-01, to Great Lakes Environmental Center, Inc. It has been subjected to the
 

Agency’s peer and administrative review and has been approved for publication as an EPA
 

document. Mention of trade names or commercial products does not constitute endorsement or
 

recommendation for use.
 

Under authority of the Clean Water Act (CWA), EPA is committed to protecting the biological 

integrity of the Nation’s waters, including marine coastal habitats such as mangroves, seagrasses
 

and coral reefs that lie within the 3-mile territorial waters.
 

This report summarizes an EPA-sponsored workshop on coral reef biological integrity held at the
 

Caribbean Coral Reef Institute in La Parguera, Puerto Rico, on August 21-22, 2012. The workshop
 

brought together scientists with expertise in coral reef taxonomic groups (e.g., stony corals, fishes,
 

sponges, gorgonians, algae, seagrasses and macroinvertebrates), specializing in community
 

structure, organism condition, ecosystem function and ecosystem connectivity.
 

The experts evaluated photos and videos for 12 stations collected during EPA coral reef surveys 

(2010 and 2011) from Puerto Rico coral reefs exhibiting a wide range of conditions. The experts
 

individually rated each station as to observed condition (good, fair or poor) and documented their
 

rationale for the assignment. The group discussed the reef attributes that characterize biological
 

integrity (or the natural condition) for Puerto Rico’s coral reefs, which will serve as the baseline
 

condition, since the CWA is grounded in the concept of natural, undisturbed conditions.
 

The long-term goal is to derive scientifically defensible thresholds for different levels of coral reef
 

condition with a well-defined narrative for each level. Managers will be able to use the narratives to
 

determine which level most appropriately describes the current condition of their coral reefs and
 

which level is the desired condition. From this, managers can set easily communicated, quantitative
 

goals for achieving those conditions. The conceptual model will serve as an interpretative
 

framework to explicitly link science and monitoring information to management and decisionmaking.
 

This is a contribution to the EPA Office of Research and Development’s Safe and Sustainable Waters
 

Research Program, characterizing the effects of land use on estuarine and coastal resources.
 

The appropriate citation for this report is:
 

Bradley P, Santavy DL and Gerritsen J. 2014. Workshop on Biological Integrity of Coral Reefs,
 

August 21-22, 2012, Caribbean Coral Reef Institute, Isla Magueyes, La Parguera, Puerto Rico. 

US Environmental Protection Agency, Office of Research and Development, Atlantic Ecology
 

Division, Narragansett, RI. EPA/600/R-13/350.
 

This document can be downloaded from:
 

http://water.epa.gov/scitech/swguidance/standards/criteria/aqlife/biocriteria/technical_index.cfm
 

ii Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table of Contents 

Figures and Tables ...........................................................................................................................................

....................................................................................................................................... 

...................................................................................................................................... 

..................................................................................................................... 

v
 

Acknowledgements vii
 

Executive Summary viii
 

Chapter 1. Introduction 

1.1 Coral Reef Ecosystems 1-2
 

1.2 Puerto Rico’s Coral Reef Ecosystems ............................................................................................... 

.......................................................................................................................................... 

................................................................................................................. 

............................................................................................ 

............................................................................................................... 

...................................................................................................................... 

1-2
 

1.3 Timelines 1-4
 

1.3.1 Condition Timeline 1-4
 

1.3.2 Anthropogenic Activity Timeline 1-7
 

1.4 Southwestern Puerto Rico 1-9
 

1.5 The Clean Water Act 1-10
 

1.6 Why a Coral Reef Ecosystem Conceptual Model is Needed .......................................................... 

........................................................... 

.............................................................................................. 

........................................................................................................... 

......................................................................................................................... 

......................................................................................................... 

.................................................................................................... 

................................................................................................................. 

................................................................................................................. 

1-11
 

1.7 The Framework: The Biological Condition Gradient (BCG) 1-11
 

1.7.1 How is the BCG Constructed? 1-12
 

Chapter 2. Approach 

2.1 Video and Photo Evaluations 2-2
 

2.2 Summary of Ratings 2-5
 

2.2.1 Best Station, Ranked #1 2-5
 

2.2.2 Worst Station, Ranked #12 2-6
 

2.2.3 Stations Rated Fair 2-7
 

2.2.4 Station Rated Poor 2-8
 

2.3 Summary of Attributes .................................................................................................................... 

................................................................................... 

..................................... 

............................................................................................................ 

............................................................................. 

....................................................................... 

.......................................................................................................... 

........................................................................................................... 

2-8
 

2.4 Reference Condition for Biological Integrity 2-9
 

2.4.1 Experts’ Examples of Reference Condition for Biological Integrity 2-10
 

2.4.2 Summary Discussion 2-14
 

2.5 Attributes of a Very Good to Excellent Station 2-14
 

2.5.1 Three-dimensional Topographic Complexity 2-14
 

2.5.2 Stony Coral Attributes 2-19
 

2.5.3 Gorgonian Attributes 2-19
 

2.5.4 Sponge Attributes ................................................................................................................ 

...................................................................................................................... 

................................................................................................. 

.............................................................................................. 

................................................................................................................... 

.............................................................................................................................. 

...................................................................................................................................... 

...................................................................................................................................... 

2-20
 

2.5.5 Fish Attributes 2-20
 

2.5.6 Large Vertebrate Attributes 2-20
 

2.5.7 Other Invertebrate Attributes 2-21
 

2.5.8 Algae Attributes 2-21
 

2.5.9 Condition 2-21
 

Chapter 3. Discussion and Next Steps 

3.1 Discussion 3-1
 

3.2 Next Steps 3-1
 

3.2.1 Second Workshop ................................................................................................................ 

................................................................................................. 

......................................................................................... 

.............................................................................................................. 

............................................................. 

................................................................................................................................ 

3-1
 

3.2.2 Species Tolerance Database 3-2
 

3.2.3 Assembling the Monitoring Data 3-2
 

3.2.4 Calibrating the BCG 3-3
 

3.2.5 Economic Valuation of Coastal Ecosystem Services 3-4
 

3.3 Final Thoughts 3-6
 

Table of Contents iii 
 

 

 

 

 

 

 

 

 

 

Appendices 

A. References ...................................................................................................................................... 

.................................................................................................................... 

.......................................................................................................................... 

............................................................... 

.............................................................. 

......................................................................

........................................................... 

......................................................................................................................... 

.......................................................................................... 

A-1
 

B. Workshop Participants B-1
 

C. Workshop Agenda C-1
 

D. Tally Sheet - Rating Condition of Coral Reef Videos (1st) D-1
 

E. Tally Sheet - Rating Condition of Coral Reef Videos (2nd) E-1
 

F. Notes Sheet - Rating Condition of Coral Reef Videos F-1
 

G. Supporting Photos - Rating Condition of Coral Reef Videos G-1
 

H. Workshop Glossary H-1
 

I. Summary Data Results for BCG Stations I-1
 

J. Formulas Used for Calculating Condition Metrics ........................................................................... J-1
 

iv Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figures
 

1-1. The Biological Condition Gradient (BCG) ......................................................................................... 

....................... 

.............................................................. 

............................................................................................................ 

......................................................................................................................... 

.................... 

.................................................. 

....... 

......................................... 

........................................ 

................................................................................................................................. 

1-13
 

2-1. Map with locations of the 12 EPA stations along the southern coast of Puerto Rico 2-2
 

2-2. Recent changes from 2009 to 2012 in Montastraea populations on a coral reef in Curaçao
 

(Watamula) that were caused by a 2010 bleaching event 2-10
 

2-3. Two experts suggested Cordelia Banks near Roatan, Honduras, as an example of a reference site
 

for excellent coral condition 2-11
 

2-4. Monitoring of massive Acropora cervicornis banks at Cordelia Banks located off a major airport
 

in Roatan, Honduras 2-12
 

2-5. Panoramic view of Acropora cervicornis banks at Cordelia Banks, Roatan, Honduras 2-12
 

2-6. Cover for the book, Beneath the Waves, by Hector J. Ruiz Torres 2-13
 

I-1. Comparison of the density of the major sessile invertebrates assessed in the 12 BCG stations I-2
 

I-2. Comparison of density for fish carnivores vs. herbivores at BCG stations I-3
 

I-3. Comparison of biomass for fish carnivores vs. herbivores at BCG stations I-3
 

I-4. Percentages of stony coral species, gorgonian morphologies and sponge morphologies
 

for BCG Station 1 I-4
 

I-5. Percentages of stony coral species and sponge morphologies for BCG Station 2 .............................. 

................................................................................................................................. 

............................ 

............................ 

............................................................................................................................... 

....................... 

....................... 

............................................................................................................................... 

............................................................................................................................. 

............................................................................................................................. 

............................................................................................................................. 

................ 

I-6
 

I-6. Percentages of stony coral species, gorgonian morphologies and sponge morphologies
 

for BCG Station 3 I-8
 

I-7. Percentages of stony coral species and sponge morphologies for BCG Station 4 I-10
 

I-8. Percentages of stony coral species and sponge morphologies for BCG Station 5 I-12
 

I-9. Percentages of stony coral species, gorgonian morphologies and sponge morphologies
 

for BCG Station 6 I-14
 

I-10. Percentages of stony coral species and gorgonian morphologies for BCG Station 7 I-16
 

I-11. Percentages of stony coral species and gorgonian morphologies for BCG Station 8 I-18
 

I-12. Percentages of stony coral species, gorgonian morphologies and sponge morphologies
 

for BCG Station 9 I-20
 

I-13. Percentages of stony coral species, gorgonian morphologies and sponge morphologies
 

for BCG Station 10 I-22
 

I-14. Percentages of stony coral species, gorgonian morphologies and sponge morphologies
 

for BCG Station 11 I-24
 

I-15. Percentages of stony coral species, gorgonian morphologies and sponge morphologies
 

for BCG Station 12 I-26
 

Tables 

1-1. Number of currently reported species in each of the major marine taxa for Puerto Rico 1-3
 

1-2. Complex relationships between stressors exist in southwestern Puerto Rico ................................ 

....... 

......................................................... 

................................................... 

1-10
 

1-3. Biological and other ecological attributes used to characterize the freshwater streams BCG 1-14
 

1-4. Ecological attributes used to characterize the estuarine BCG 1-16
 

2-1. Shallow inshore linear reefs used for BCG workshop stations that correspond to
 

US EPA stations sampled along the southern coast of Puerto Rico 2-2
 

Figures and Tables v 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

2-2. Coral reef condition evaluated by the experts .................................................................................. 

... 

.................................................................................................................... 

....................................................................................... 

...................................................................................... 

............................................................................ 

..................................................................... 

.................................................................................. 

....................................................................................... 

..................................................................... 

2-4
 

2-3. Rankings given by experts after visually evaluating videos and photographs for 12 EPA stations 2-4
 

2-4. Summary of attributes and their relationships for assessing coral reef condition
 

from station evaluations 2-8
 

2-5. Summary of descriptions of four condition categories (very good to poor) based on
 

expert assessments of individual stations 2-15
 

2-6. Condition levels and associated attributes 2-17
 

3-1. Coral reef ecosystem services and reef attributes 3-5
 

I-1. Scleractinian coral summary statistics for BCG stations I-1
 

I-2. Gorgonian summary statistics for BCG stations I-1
 

I-3. Sponge summary statistics for BCG stations I-2
 

I-4. BCG Station 1 data summary for corals and subgroups I-4
 

I-5. Fish species found in BCG Station 1, with density and biomass for 100m2 transect .......................... 

..................................................................... 

.......................... 

..................................................................... 

.......................... 

................................................................... 

........................ 

................................................................... 

........................ 

................................................................... 

........................ 

................................................................... 

........................ 

I-5
 

I-6. BCG Station 2 data summary for corals and subgroups I-6
 

I-7. Fish species found in BCG Station 2, with density and biomass for 100m2 transect I-7
 

I-8. BCG Station 3 data summary for corals and subgroups I-8
 

I-9. Fish species found in BCG Station 3, with density and biomass for 100m2 transect I-9
 

I-10. BCG Station 4 data summary for corals and subgroups I-10
 

I-11. Fish species found in BCG Station 4, with density and biomass for 100m2 transect I-11
 

I-12. BCG Station 5 data summary for corals and subgroups I-12
 

I-13. Fish species found in BCG Station 5, with density and biomass for 100m2 transect I-13
 

I-14. BCG Station 6 data summary for corals and subgroups I-14
 

I-15. Fish species found in BCG Station 6, with density and biomass for 100m2 transect I-15
 

I-16. BCG Station 7 data summary for corals and subgroups I-16
 

I-17. Fish species found in BCG Station 7, with density and biomass for 100m2 transect I-17
 

I-18. BCG Station 8 data summary for corals and subgroups ................................................................... 

........................ 

................................................................... 

........................ 

................................................................. 

...................... 

................................................................. 

...................... 

................................................................. 

...................... 

........ 

........................................................ 

....................................................................................... 

I-18
 

I-19. Fish species found in BCG Station 8, with density and biomass for 100m2 transect I-19
 

I-20. BCG Station 9 data summary for corals and subgroups I-20
 

I-21. Fish species found in BCG Station 9, with density and biomass for 100m2 transect I-21
 

I-22. BCG Station 10 data summary for corals and subgroups I-22
 

I-23. Fish species found in BCG Station 10, with density and biomass for 100m2 transect I-23
 

I-24. BCG Station 11 data summary for corals and subgroups I-24
 

I-25. Fish species found in BCG Station 11, with density and biomass for 100m2 transect I-25
 

I-26. BCG Station 12 data summary for corals and subgroups I-26
 

I-27. Fish species found in BCG Station 12, with density and biomass for 100m2 transect I-27
 

J-1. Stony corals included in Western Atlantic and Caribbean assessments with the three-letter
 

identification code and the morphological conversion factor for calculating 3-D surface area J-2
 

J-2. Gorgonian morphological shapes, abbreviations, simulated model, in situ example and
 

regression models to estimate three-dimensional surface area J-6
 

J-3. Sponge morphological shapes, abbreviations, simulated model, in situ example and
 

regression models to estimate surface area J-8
 

vi Workshop on Biological Integrity of Coral Reefs 
 

 

Acknowledgements 

The US Environmental Protection Agency (EPA) Office of Research and Development (ORD) 

prepared this coral reefs report. 

This is ORD tracking number ORD-007028, Atlantic Ecology Division, Narragansett, RI. EPA was 

supported in the development of this report by the Great Lakes Environmental Center, Inc., 

through contract EP-C-09-001. 

The production of this report would not have been possible without the workshop participants. 

Photos from: Charles LoBue, Peggy Harris, Mel Parsons, Alan Humphries, Scott Grossman, 

Richard Henry, Alina Szmant and Melanie McField. 

The report was peer reviewed by Dr. Ku’ulei Rogers (University of Hawaii), Dr. Wendy Wiltse 

(US EPA, Region 9), Ms. Susan K. Jackson (US EPA, Office of Water), and Dr. Giancarlo Cicchetti 

and Dr. Marguerite (Peg) Pelletier (US EPA, Office of Research and Development). 

We would like to thank the Caribbean Coral Reef Institute, and Drs. Richard Appeldoorn and 

Francisco Pagan for hosting the workshop and providing the conference facilities on Magueyes 

Island. 

We would also like to thank Mr. Roberto Viquiera (Protectores de Cuencas) for assisting with the 

logistics, including providing the dormitory facilities in Yauco for visiting scientists. 

Acknowledgements vii 
 

 

 

 

 

 

Executive Summary 

EPA’s Office of Research and Development (ORD) and Office of Water (OW) hosted a workshop on 

coral reef biological integrity that brought together scientists with expertise in coral reef taxonomic 

groups (e.g., stony corals, fishes, sponges, gorgonians, algae, seagrasses and macroinvertebrates), 

specializing in community structure, organism condition, ecosystem function and ecosystem 

connectivity. The goals of this first workshop were to: 

•	 Identify key qualitative and quantitative ecological characteristics (reef attributes) that 

determine the condition of linear coral reefs inhabiting shallow waters (<12 m) in 

southwestern Puerto Rico.
 

•	 Use those reef attributes to recommend categorical condition rankings for establishing a 

biological condition gradient. 

•	 Ascertain through expert consensus those reef attributes that characterize biological integrity 

(a natural, fully-functioning system of organisms and communities) for coral reefs. 

•	 Develop a conceptual, narrative model that describes how biological attributes of coral reefs 

change along a gradient of increasing anthropogenic (human-generated) stress. 

The long-term goal is to derive scientifically defensible thresholds for different levels of coral reef 

condition that can be coupled with management objectives and used to evaluate alternative decision 

options. 

The experts evaluated photos and videos for 12 stations collected in 2010 and 2011 during EPA coral 

reef surveys from Puerto Rico coral reefs exhibiting a wide range of conditions. The experts 

individually rated each station as to observed condition (good, fair or poor) and documented their 

rationale for the assignment. The group discussed the reef attributes that characterize biological 

integrity (or the natural condition) for Puerto Rico’s coral reefs. These attributes will be further 

developed to characterize the baseline condition, an important concept for achieving Clean Water 

Act goals. 

The attributes and thresholds will be organized into a conceptual, narrative model that describes 

how biological attributes of coral reefs change along a gradient of increasing anthropogenic stress. 

By providing the explicit characterization of how attributes of the biological system change as human 

disturbance increases, decision-makers will be able to use the narratives to determine which level 

most appropriately describes the current condition of their coral reefs and which level is the desired 

condition. From this, managers can set easily communicated, quantitative goals for achieving those 

conditions. 

This is the first in a series of facilitated workshops and webinars with this group of coral reef experts. 

viii Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

Chapter 1. Introduction 

The approach described in this report will assist in developing a conceptual, narrative model that 

describes how biological attributes of coral reefs change along a gradient of increasing 

anthropogenic stress. The framework is expected to serve multiple purposes. 

•	 It will assist decision-makers in understanding the current conditions of the Puerto Rico coral 

reefs relative to natural, undisturbed conditions, the critical attributes of the coral reefs and 

how each attribute changes in response to stress. Through this framework, decision-makers can 

set realistic goals for their coral reefs and establish monitoring (measurement) endpoints that 

are meaningful based upon the attributes identified by the scientific community. 

•	 It will be used to support the development of an economic survey of Puerto Rico’s
 

coral reefs (another project being conducted in collaboration with the National Oceanic
 

and Atmospheric Administration’s Office of National Marine Sanctuaries).
 

•	 It will inform the Bayesian Belief Network (BBN) and Dynamic Systems Models being developed 

by the EPA modelers. 

•	 It will contribute to the development of coral reef biological criteria for water quality standards 

under the Clean Water Act (CWA) for Puerto Rico. 

To initiate the process, scientists with expertise in coral reef taxonomy, ecology, and management 

of stony corals, fishes, sponges, gorgonians, algae, seagrasses, and macroinvertebrates, specializing 

in community structure, organism condition, ecosystem function and ecosystem connectivity were 

brought together. These experts participated in the first workshop, held August 21-22, 2012, in 

La Parguera, Puerto Rico. (See Appendix B for a list of workshop participants.) 

The goals of this first workshop were to: 

•	 Identify key qualitative and quantitative ecological characteristics (reef attributes) that 

determine the condition of linear coral reefs inhabiting shallow waters (< 12 m) in
 

southwestern Puerto Rico.
 

•	 Use those reef attributes to recommend categorical condition rankings for establishing
 

a biological condition gradient.
 

•	 Ascertain through expert consensus those reef attributes that characterize biological integrity 

(a natural, fully-functioning system of organisms and communities) for coral reefs. 

•	 Develop a conceptual, narrative model that describes how biological attributes of coral reefs
 

change along a gradient of increasing anthropogenic stress.
 

The long-term goal is to derive scientifically defensible thresholds for different levels of coral reef 

condition that can be coupled with management objectives and used to evaluate alternative decision 

options. 

Chapter 1. Introduction 1-1 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1.1 Coral Reef Ecosystems 

Coral reefs are the earth’s most biologically diverse marine ecosystems (Sebens 1994; Odum 1997). 

Scleractinian (stony) corals, octocorals and sponges provide structural habitat that supports 

harvestable fish species and attracts tourists (Bradley et al. 2008). Stony corals also protect 

shorelines from erosion by physically blocking current and wave energy (Wilkinson 1996), and 

coral reefs provide food and income for 500 million people globally (TNC 2006). 

Corals are generally found in clear, shallow tropical oceans, and their growth is limited by 

temperature, salinity, light intensity, water clarity, and other chemical and water quality 

characteristics (Wells 1957; Brown and Howard 1985; Hubbard 1997; Ogden 1997; Hoegh-Guldberg 

1999). Coral reefs are sensitive to relatively small changes in the environment (Richmond 1993) and 

their lack of resilience to environmental change has led some to regard coral reefs as sentinels of 

oceanic environmental quality (Hatcher et al. 1987; Andrews and Pickard 1990; Barber et al. 2001). 

Healthy stony corals appear to be critical for fish productivity, species richness and fish biomass, all 

of which have been reported to decrease with a decline in stony coral health (Warren-Rhodes et al. 

2003). Additionally, there appears to be a strong positive correlation of habitat complexity to the 

biodiversity and ecosystem functions of a reef community (Alvarez-Filip et al. 2009), including fish 

species richness (Walker et al. 2009; Pittman et al. 2007a, b). The rich diversity of coral reefs is partly 

dependent on the provision of habitable surface area and partly on the variability of that surface 

area (Principe et al. 2012). 

The adjacent habitats of seagrass meadows and mangrove forests are linked with coral reefs to form 

a complex dynamic mosaic that provides critical nurseries, foraging areas, and refugia for fish and 

invertebrates (Christensen et al. 2003; Mumby et al. 2004, 2008; Aguilar-Perera and Appeldoorn 

2007; McField and Kramer 2007; Meynecke et al. 2008). Mangroves and seagrasses can also trap 

sediments, nutrients, and pollutants, which can improve the water quality on nearby reefs 

(Grimsditch and Salm 2006). Many juvenile fishes occupy shallow-water habitats such as mangroves 

and seagrasses, while the adult forms are found in adjacent coral reefs (Nagelkerken et al. 2000; 

Adams et al. 2006; Cerveny 2006; Dahlgren et al. 2006; Clark et al. 2009; Pittman et al. 2010). 

1.2 Puerto Rico’s Coral Reef Ecosystems 

The US territory of Puerto Rico encompasses the main island of Puerto Rico, two inhabited islands 

(Culebra and Vieques) and three uninhabited islands (Mona, Monito and Desecheo). Puerto Rico has 

an estimated coastline of 930 km, a land area of 8,950 km2 and fringing coral reefs with a total area 

of 3,370 km2 off the east, south and west coasts (Wilkinson 2004; Burke and Maidens 2004). 

The coral reef ecosystem in Puerto Rico is a complex mosaic of interrelated habitats, including 

mangrove forests, seagrass beds and coral reefs, as well as other coral communities (Garcia-Sais 

et al. 2008). Ballantine et al. (2008) listed 69 shallow-water (<40 m) scleractinian species, 260 fish 

species, 46 shallow-water alcyonarian species and 500 species of benthic marine algal flora, 

excluding cyanobacteria (Table 1-1). 

1-2 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

Table 1-1. Number of currently reported species in each of the major marine taxa for Puerto Rico 

(adapted from Weil 2005). 

Taxon # Species Source 

Algae (diatoms; red, green, 

blue-green and brown algae) 

492 Ballantine and Aponte 1997a, b; Ballantine and 

Aponte 2002 

Mangroves 5 Cerame-Vivas 2001 

Seagrasses (Marine Phanerogams) 7 Vicente 1992 

Sponges (Phylum Porifera) 61 Wilson 1902; Weil 2005 

Corals, anemones, jellyfish 

(Phylum Cnidaria) 

171 Vaughan 1902; Hargitt and Rogers 1902; Almy and 

Carrion-Torres 1963; Garcia et al. 2003; Weil 2005 

Unsegmented worms 

(Phylum Nemertea) 

8 Coe 1902 

Bivalves, snails, octopus, mollusks, 

nudibranchs (Phylum Mollusca) 

1,176 Dall and Simpson 1902; Grana 1993; Ortiz 1998; 

Garcia-Rios 2003 

Segmented worms, polychaetes 

(Phylum Annelida) 

129 Treadwell 1902, 1939; Long 1975 

Ostracods, crabs, shrimp 

(Phylum Arthropoda) 

342 Benedict 1902; Bigelow 1902; Moore 1902; 

Rathbun 1902; Menzies and Glynn 1968 

Starfish, sea urchins, brittle stars 

(Phylum Echinodermata) 

165 Clark 1902, 1933 

Bryozoans (Phylum Ectoprocta) 131 Osburn 1940 

Fishes (Superclass Osteichthyes), 

sharks, rays (Class Chondrichthyes) 

677 Dennis 2000; Dennis et al. 2004 

Reptiles (turtles, snakes) 5 Rivero 1978 

Mammals 18 Beller et al. 1999 

While over 60 species of scleractinian corals inhabit the Western Caribbean, reefs in Puerto Rico 

were historically dominated by the reef-building coral taxa Montastraea annularis complex1 

, 

Agaricia agaricites, Montastraea cavernosa, Porites astreoides and Colpophyllia natans. Additionally, 

Acropora palmata and Acropora cervicornis often formed dense, high-relief monospecific thickets; 

A. palmata in shallow exposed fore-reef habitats and A. cervicornis on fore-reefs and in shallow, 

protected back-reefs (Morelock et al. 2001). 

Recent studies in Puerto Rico show that large corals of the genus Montastraea are critical for the 

biodiversity of fish and invertebrates and for maintaining the structure, function, and flow of reef 

ecosystem services (Beets and Friedlander 1998; Mumby et al. 2008). Mumby et al. (2008) found 

that one-fourth to one-third of benthic invertebrates and fish occurred in the Montastraeadominated fore-reefs in the Caribbean. A. palmata and A. cervicornis, which have recently been 

listed as threatened species in the Caribbean, also significantly contribute to reef growth and 

development and provide essential fish habitat (NOAA 2012a; Principe et al. 2012). 

1 This report does not adopt the new classifications for the Montastraea annularis species complex (Montastraea 

annularis, Montastraea faveolata and Montastraea franksi) reclassified as the original genus Orbicella 

(Budd et al. 2012). 

Chapter 1. Introduction 1-3 
 

 

 

 

 

 

 

1.3 Timelines 

1.3.1 Condition Timeline 

1000: Coral reefs would have been regarded as mostly pristine by current standards with healthy 

corals, large, well-structured fish and invertebrate communities, with probably only a

depletion of some of the larger fauna (Wilkinson 2004). 

1800: Large vertebrates such as the green turtle, hawksbill turtle, manatee and Caribbean monk seal 

were decimated in the central and northern Caribbean Sea (Jackson 1997). 

1880s: Early taxonomic studies of reefs on Puerto Rico (e.g., mollusks [Gundlach 1883]; crustaceans 

[Gundlach 1887]; fishes [Poey 1881]; polyps, worms, fishes and crustaceans [Stahl 1883]; 

algae [Hauck 1888]; and coral [Vaughn 1902]). 

1900: Most coral reefs were healthy and dominated by healthy branching corals, urchins, large 

schools of game fish, sharks and algal grazers. Waters were clear with low nutrient levels 

(Wilkinson 2004). 

1952: The last confirmed sighting of the Caribbean monk seal was at Serranilla Bank between 

Jamaica and Nicaragua (Debrot 2000). 

Late 1950s and early 1960s: Massive fishing pressure began in Puerto Rico (Appeldoorn personal 

communication). Herbivores and predators were reduced to very small fishes and sea urchins 

(Jackson 1997). 

1969: An intensive and extensive coral bleaching event occurred on coral reefs of southwestern 

Puerto Rico. The bleaching was probably caused by 38.1 cm of rain during a hurricane that 

preceded the bleaching (Williams and Bunkley-Williams 1990). 

Late 1970s: Extensive thickets of Acropora palmata were present in 40% of locations surveyed 

around Puerto Rico; 20% of these reefs had dense A. palmata patches and abundant colonies 

of A. cervicornis (Weil et al. 2003). 

Late 1970s and early 1980s: A white-band disease (WBD) epizootic event caused extensive mass 

mortality of Acroporid corals throughout their range in the Caribbean with losses up to 95% 

(Gladfelter 1982; Weil et al. 2003, 2009; Weil and Rogers 2011). 

1981: Minor but widespread bleaching caused by elevated sea surface temperatures (SST) occurred 

in southwestern and western Puerto Rico (Williams and Bunkley-Williams 1989, 1990). 

1983: Diadema antillarum mass mortality, with 85-100% population declines (Bak et al. 1983; Lessios 

et al. 1984; Lessios 1988, 2005; Osborne 2000). The Diadema antillarum mortality was first 

observed in Puerto Rico in January 1984 in the coral reefs off La Parguera (Vicente and 

Goenega 1984b). 

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Late 1980s: Massive coral bleaching and mortality caused by elevated SST. Extensive partial coral 

colony mortalities and some total mortalities of coral reef organisms, including death of some 

400-500 year-old coral colonies (Velazco-Dominguez et al. 2003; Burke and Maidens 2004). 

Massive coral bleaching events in Puerto Rico were first reported by Williams et al. 1987 and 

Goenega et al. 1989. 

1990: Severe bleaching in the western north Atlantic caused by elevated SST and doldrum surface 

waters (from Bermuda, Texas, Florida, throughout the Caribbean, south to Brazil). High 

mortalities of fire corals, scleractinian corals, gorgonians, sponges and other coral reef 

organisms (Velazco-Dominguez et al. 2003). 

1994: Cumulative impacts of disease, coastal development, coral bleaching and over-fishing have 

resulted in heavily damaged reefs. The more isolated reefs were in better condition because 

they were not affected by land-based stressors (Wilkinson 2004). 

1996: Caribbean yellow-band disease (YBD) first observed in Puerto Rico with very low prevalence 

(Bruckner and Bruckner 1997, 2006; Weil et al. 2009). The disease was highly seasonal 

(summer-fall). YBD affects three species of the former Montastraea annularis species-complex 

(M. faveolata, M. annularis and M. franksi), the most important reef-building corals for this 

area (Bruckner and Bruckner 2006; Cróquer and Weil 2009; Harvell et al. 2009). 

1998: Severe bleaching event in Puerto Rico caused by elevated SST (July–September); 99% of the 

colonies completely recovered after 9 months; 15% of the colonies bleached again in 1999 and 

recovered by January 2000 (Velazco-Dominguez et al. 2003). 

2000: Diadema seem to be making a slow return in many localities in the Caribbean, including 

La Parguera, PR (Weil et al. 2005). 

2003: YBD became chronic and colonies showed disease signs all year (Weil et al. 2009). Surveys 

of over 100 reefs along the coast and islands found that Acroporid populations continued 

to decline in some areas from persistent disease, storms and sedimentation coupled with the 

poor coastal environmental conditions (high turbidity, sub-optimal water quality, etc.) and 

algal overgrowth. 

2004: Most inshore reefs show advanced stages of degradation. Montastraea annularis speciescomplex was the dominant stony coral, but it was virtually absent on reefs with low coral 

cover. The encrusting octocoral Erythropodium caribaeorum occurred at most stations, and 

zoanthids (particularly the encrusting Palythoa species) and sponges were the dominant 

sessile benthic invertebrates in shallow waters. Macroalgae and turf algae were dominant 

instead of corals on most intermediate-depth reefs (Garcia-Sais et al. 2008). 

2005: A major bleaching event caused by elevated SST in the fall of 2005, followed in 2006 by mass 

cnidarian mortality, had a dramatic impact on Puerto Rican coral reefs. A total of 82 cnidarian 

species were impacted by the bleaching, including 52 scleractinians, 13 octocorals, four 

hydrocorals, four zoanthideans, four actiniarians, three corallimorpharians and two 

scyphozoans (Garcia-Sais et al. 2006, 2008). The most severe bleaching was observed among 

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Montastraea annularis species-complex (94%), Helioseris cucullata (94%), Colpophyllia natans 

(83%), Siderastrea siderea (65%), Millepora species (63%), Mycetophyllia species (2%), Diploria 

species2 (54%), Agaricia species (48%) and Montastraea cavernosa (46%). Three genera 

appeared to be less susceptible to bleaching: Eusmilia fastigiata (22%), Meandrina meandrites 

(26%) and all Porites species (36%). Millepora alcicornis was completely bleached at all 

stations, and most colonies (>65%) had died by December 2005. In August 2006, most corals 

had regained normal coloration, with the exception of Montastraea annularis species colonies, 

which experienced extensive partial and full colony mortality throughout the region. Total 

coral cover declined throughout the region by 40-60%. Disease epizootics followed, including a 

white plague outbreak on the east and southern coasts, and Caribbean yellow-band disease 

(YBD) that primarily affected the Montastraea annularis species-complex that occurred right 

after the peak of the 2005 bleaching event (Garcia-Sais et al. 2008). 

Intense bleaching of octocorals was first noted in late September to early October beginning 

with Erythropodium caribaeorum, followed by Muricea, Briareum and Plexaurella and later by 

Pseudoplexeaura and Pterogorgia species. Bleaching in scleractinian corals, hydrocorals and 

the zoanthid Palythoa caribaeorum, preceded bleaching of octocorals, suggesting octocorals 

may have higher tolerance to thermal stress compared to the other major cnidarian taxa. By 

late November 2005, the majority of the affected octocoral colonies had not died. The 

exceptions were the bleached colonies of Muricea, which had 90% mortality (Prada et al. 

2009). 

2006: NOAA’s National Marine Fisheries Service (NMFS) listed Acropora palmata and Acropora 

cervicornis corals as threatened throughout their known range by authority of the Endangered 

Species Act (ESA). This designation became final in May 2006 (Federal Register 2006). 

2008: The Caribbean monk seal was officially declared extinct after an exhaustive five-year search by 

NOAA NMFS. 

2014: NOAA NMFS proposed seven Atlantic/Caribbean corals as endangered: Acropora cervicornis, 

Acropora palmata, Dendrogyra cylindrus, Orbicella annularis, Orbicella faveolata, Orbicella 

franksi and Mycetophyllia ferox and two species as threatened: Agaricia lamarcki and 

Dichocoenia stokesii (Brainard et al. 2011). In their final rule (August 27, 2014), NOAA listed 

O. annularis, O. faveolata, O. franksi, D. cylindrus and M. ferox as threatened species and 

determined that D. stokesii and A. lamarcki did not warrant listing. NOAA also determined that 

the listing of Acropora cervicornis and Acropora palmata as threatened in 2006 is still 

warranted. 

2 This report does not adopt the new classifications Diploria strigosa and Diploria clivosa as the genus Pseudodiploria 

(Budd et al. 2012). 

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1.3.2 Anthropogenic Activity Timeline 

~2000-3000 B.C.: The Ortoiroid people from the Orinoco region in South America settled in Puerto 

Rico. The Saladoid and Arawak Indians populated the island between 430 BC and 1000 AD. By 

1000 AD the Taino culture was dominant (Rouse 1992). These early populations exploited 

coral reef resources, and there is strong archaeological evidence of major harvesting of fishes,

molluscs, manatees and turtles (Wilkinson 2004). 

1493: Christopher Columbus landed in Puerto Rico, beginning an intense period of colonization and 

resource extraction (mainly gold). The early explorers found the indigenous population 

cultivating, blending, rolling and smoking tobacco. Europeans had never seen tobacco. This 

discovery marked the start of an international passion for "New World" tobacco and its much 

sought after byproduct, the cigar. 

1496-1660: Tobacco was the major crop. Half the shipping tonnage between Puerto Rico and Europe 

(mainly Spain) was comprised of tobacco. 

1508: Juan Ponce de Leon founded a town (Guaynía, meaning “a place with water”) on the shores of 

Guánica Bay. The narrow channel and calm waters of Guánica Bay made it a natural refuge for 

ships sailing the Caribbean Sea. 

Early 1500s: Sugar was introduced (perhaps when Juan Ponce de Leon began colonizing the island), 

and many small landowners relied on its export as a source of income. 

1548: Hundreds of sugar mills operated by waterpower. The industry was in the hands of small 

landowners whose enterprises succeeded or failed depending on the price of sugar in the 

market or the whims of the Spanish Crown. 

1736: Coffee plants introduced to Puerto Rico, grown mostly for personal and domestic use. 

Mid-1800s: French immigrants from the Mediterranean island of Corsica settled around Yauco and 

became well known as premium coffee exporters to Europe. 

1867: (San Narciso), 1899 (San Ciricao), 1928 (San Felipe) and 1932 hurricanes virtually destroyed 

most coffee plantations and tobacco crops. Many farms never recovered. 

1873: First “Centrales” or sugar factories with equipment operated by steam were established. 

Centrifuges were used to separate the sugar crystals from the molasses. 

1898: Puerto Rico was ceded to US as a result of the Spanish American War. US markets opened 

to Puerto Rico products (tariff free). Sugar cane was the most important cash crop for the 

territory. 

1900: The US enacted the Foraker Act, which removed the previous land ownership cap of 500 acres. 

Large monoculture farming began (primarily sugar). 

1901: The South Porto Rico Sugar Company of New Jersey, USA, began construction of the Central 

Guánica sugar mill. The Central Guánica organized a company town around the sugar mill that 

included a hospital, school and housing facilities. This sugar mill was one of the largest in the 

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Caribbean and was one of the largest in the world until World War I (Ayala 1999; 

Wikipedia 2013). 

1900–1927: Puerto Rico produced around 35 million pounds of tobacco a year. Tobacco represented 

38% of the value of commercial crops in 1920 (sugar accounted for 25%). In 1910, 14% of 

farms reported the cultivation of coffee. 75% of the employed people in Puerto Rico were 

involved in the sugar industry controlled by US corporations (Miller and Lugo 2009). 

Early 1930s: The Roosevelt Administration created the Puerto Rico Emergency Relief Administration, 

which became the Puerto Rican Reconstruction Administration in 1935. Rural resettlement 

communities and demonstration farms were established, and coffee and fruit production 

was reorganized. 

1934: Jones-Costigan Act set a quota on the amount of sugar that could be exported to the 

US tariff free. 

1940s: The Puerto Rico Water Resources Authority (PRWRA) initiated the Southwestern Puerto Rico 

Project (SWPRP). The SWPRP connected five watersheds and a retention pond through 

construction of dammed reservoirs and an underground aqueduct system that diverted water 

south into the Guánica Bay/Rio Loco watershed. This increased the watershed drainage area 

from approximately 57,000 to 97,000 acres. 

1941: Land Reform Act was passed, limiting land ownership to 202 hectares (500 acres) or less. Many 

rural residents were now able to buy 10 hectare (25 acre) parcels, allowing them to grow 

crops for profit for both export and internal use. This broke up the land monopoly of the large 

sugar companies (Miller and Lugo 2009). 

Late 1940s: The US Department of Agriculture (USDA) ended sugar subsidies for Puerto Rican 

farmers. Annual production of sugar dropped soon after. Massive numbers of Puerto Ricans 

migrated to the New York area. 

1948: The Industrial Incentives Act (Operation Bootstrap) began to shift Puerto Rico from rural 

agriculture to more urbanized communities and industrial sources of income (shifts to 

manufacturing of pharmaceuticals, chemicals, machinery and electronics). 

1948: The Guánica fertilizer plant opened, with storage silos and a shipping pier. 

1952: Peak sugar production in Puerto Rico. 

1953: Puerto Rico passed Act No. 65, authorizing the Lajas Valley Irrigation System. 

1954: The Lajas Valley Irrigation (LVI) project, developed under the guidance of experts from the 

USDA led efforts to remove sugar plantations that had long characterized the region. This 

project also started small-scale agricultural farming and introduced cultivated fruits, mainly 

pineapple. The LVI project channelized 200,000 acres of land via 25 miles of a concrete-lined 

main canal, 60 miles of concrete-lined and unlined lateral canals and the corresponding 

drainage system. Two hydroelectric dams and two additional water reservoirs were built. 

Shade-grown coffee was transplanted into sun-exposed areas. 

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1955: Guánica Lagoon was drained to increase land available for agriculture. 

1970s: Government subsidies and support for sun-grown coffee were implemented. 

1981: Guánica sugar mill was closed. 

1980s: Widespread conversion to sun-grown coffee reduced biodiversity (from loss of canopy 

habitat) and increased soil erosion from steep and now poorly vegetated, unprotected slopes. 

Soil washed from hillsides into streams and was trapped in the reservoirs, reducing their water 

storage capacity (Soler-López 2001) and increasing sediment deposition in Guánica Bay. 

1999: Puerto Rico passed an agricultural reserve law in an attempt to reverse the trend of 

declining agriculture. 

2000: The final two sugar factories closed (Coloso and Roig Centrales). 

2009: The US Coral Reef Task Force (USCRTF) selected the Guánica Bay watershed as the location for 

its first multi-agency watershed initiative in an attempt to reduce watershed impacts on coral 

reefs in the coastal zone. 

1.4 Southwestern Puerto Rico 

Southwestern Puerto Rico is relatively rural, with low population density compared to northeastern 

Puerto Rico. There are, however, some population centers: Yauco (population 20,295), San Germán 

(population 12,055), Guánica (population 9,224) and Sabana Grande (population 8,961). The human 

presence has created a variety of environmental stresses in this region. 

Agricultural growth in southwestern Puerto Rico has resulted in widespread land clearing and 

modification. Nearly 90% of the area was deforested by the end of the 19th century (Warne et al. 

2005), and the largest natural freshwater body in Puerto Rico, the Guánica Lagoon, was drained in 

1955 as part of an agricultural development project (Sturm et al. 2012). These modifications have led 

to increased watershed sediment and nutrient yield, thereby increasing sediment and nutrient 

discharge to the coastal shelf (Warne et al. 2005). 

Municipal growth has increased impervious cover, generation of stormwater runoff and human 

sewage. Impervious cover increases the loading of nutrients, bacteria, sediments and contaminants 

such as polycyclic aromatic hydrocarbons (PAHs), heavy metals and other pollutants associated with 

automobiles. Stormwater accumulates debris, chemicals, dirt and other pollutants, which are 

untreated and then discharged into coastal rivers and bays. Sewage carries pathogens that can 

transmit disease to humans and other animals, contains organic matter that can cause odor and 

nuisance problems and nutrients that can cause eutrophication of receiving water bodies. Much of 

the rural population in southwestern Puerto Rico relies upon septic systems for their sewage 

treatment. Too often these are failing, inadequate or improperly maintained. There are also several 

wastewater treatment plants (WWTP) in the area, which only treat the sewage to eliminate 

pathogens and solids. Some of these WWTPs are being upgraded to advanced secondary treatment, 

which provides minimal nutrient reduction. 

Chapter 1. Introduction 1-9 
 

 

 

 

 

 

 

 

 

 

 

 

 

Communities in the coastal region of southwestern Puerto Rico rely partially on fishing and tourism 

for their livelihood. Fishing, if not conducted in a sustainable manner, can lead to overexploitation of 

marine living resources (both target species and the marine system as a whole). Boat anchors, traffic 

and groundings can adversely impact marine resources. For example, much of the seagrass in the 

shallow shelf area near La Parguera is vulnerable to damage from boat propellers. Lost fishing gear, 

such as hooks, lines, nets and lobster traps, can also be damaging to marine resources. 

Finally, elevated SSTs are correlated with mass bleaching events (Goreau et al. 1992; Glynn 1988, 

1991; Hoegh-Guldberg 1999; McClanahan et al. 2007; Meissner et al. 2012). Sea surface 

temperatures have been higher during the past three decades than at any other time since reliable 

observations began in 1880 (NOAA 2012b). Global warming is caused by human activities that emit 

heat-trapping carbon dioxide and result in increased SSTs. A summary table illustrating some of the 

major stressors and their sources is shown in Table 1-2. 

Table 1-2. Complex relationships between stressors exist in southwestern Puerto Rico. 

Source of Stressor Stressors 

Agriculture Increased sediment, nutrient, pesticide and herbicide loads 

to aquatic ecosystems 

Urban development Increased sewage (nutrients and pathogens), stormwater 

runoff (sediment, contaminants) 

Fishing Overexploitation of fish populations; by-catch; damage 

from fishing gear and boats 

Increased global CO 2 emissions 

from power generation 

and transportation 

Elevated sea surface temperature and acidification in the 

marine environment 

1.5 The Clean Water Act 

The Clean Water Act (CWA) (33 U.S.C. § 1251 et seq. 1972) is the cornerstone for surface water 

quality protection in the United States. The CWA objective is to restore and maintain the chemical, 

physical and biological integrity of the Nation’s waters. The CWA authorizes EPA to determine 

“appropriate minimum levels” of protection and to provide oversight to states (states, territories and 

commonwealths), which are required to establish water quality standards that define the goals 

(designated uses) and pollution limits (water quality criteria) for all waters within their jurisdictions. 

States are also required to monitor conditions regularly and submit biannual reports summarizing 

water quality assessments. Waterbodies that do not meet the water quality criteria are reported as 

“impaired”, triggering a series of management actions to determine the cause of impairment and to 

restore the condition of the waterbody and its resident biota. 

Biological integrity is a long-term objective of the CWA, and water quality standards and criteria can 

be defined to protect valued aquatic resources, such as coral reef ecosystems. Biological assessments 

directly measure the condition of the aquatic resource to be protected and the cumulative response 

of the biological community to all sources of stress. Biological standards (biocriteria) set biological 

quality goals. 

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The President’s Ocean Action Plan (US Commission on Ocean Policy 2004) required EPA to develop 

the tools and knowledge necessary to protect coral reefs from land-based pollution using coral reef 

biological criteria. A comprehensive guide (Bradley et al. 2010) describes the process for using the 

CWA and biological criteria to enhance coral reef protection efforts. 

1.6 Why a Coral Reef Ecosystem Conceptual Model is Needed 

Coral reef condition typically degrades as human disturbance increases. Human disturbances 

threatening coral reefs include polluted runoff from agriculture and land-use practices, over-fishing, 

ship groundings, coastal development, sewage discharge and climate change. Natural stressors such 

as tropical storms can also adversely impact coral reefs. Both natural and anthropogenic stressors 

can cause increases in coral bleaching and diseases. Reefs in the US Caribbean have declined from 

50% total coral cover to less than 10% in just 25 years (Wilkinson 2004). 

The biological communities of the coral reef reflect overall ecological integrity (i.e., chemical, 

physical and biological integrity), integrate effects of multiple stressors and provide a measure of 

aggregate impact (Barbour et al. 1999). Coastal resource managers and coral reef scientists routinely 

conduct biological assessments to evaluate the condition of coral reefs. This approach integrates the 

cumulative impacts of chemical, physical and biological stressors on aquatic life. However, while the 

stated intent of these biological assessments is to support decision-making, they more commonly 

document the decline of the coral reefs. A missing component in this approach is a scientifically 

derived process for identifying thresholds that can be coupled with management objectives and used 

to evaluate alternative decision options. A conceptual model can help to organize information and 

make sense of system components and their interactions. 

1.7 The Framework: The Biological Condition Gradient (BCG) 

Beginning in the late 1990s, EPA collaborated with aquatic scientists and managers across the United 

States to develop and implement the Biological Condition Gradient (BCG) for freshwater streams 

(Davies and Jackson 2006). The BCG is a conceptual model that describes how biological attributes 

of aquatic ecosystems (i.e., biological condition) might change along a gradient of increasing 

anthropogenic stress (e.g., physical, chemical and biological impacts). The BCG was designed to 

provide a means to map different indicators on a common scale of biological condition to facilitate 

comparisons between programs and across jurisdictional boundaries in context of the CWA. 

Since then, many states have used the BCG to support water quality management, and several states 

have used the BCG to more precisely define freshwater stream designated aquatic life uses, identify 

impairment thresholds, monitor status and trends and track progress in restoration and protection 

(EPA 2011). Additionally, stream BCGs have been developed at the regional and local government 

scale throughout the US. 

Since 2008 EPA has been collaborating with estuarine scientists and managers to adapt the stream 

BCG framework to more complex estuarine waterbodies (EPA in review). Estuarine BCG pilot work 

has focused on National Estuary Program (NEP) sites: Narragansett Bay (RI), Casco Bay (ME), Mobile 

Chapter 1. Introduction 1-11 
 

 

 

 

 

 

 

 

 

 

 

 

Bay (AL) and Tampa Bay (FL). NEPs play an important role as conveners of technical, management 

and public interests. Their ability to create connections among these constituencies makes them 

a valuable platform to work out the complexities of an estuarine BCG at different scales. 

A BCG calibrated with field data can help states more precisely define biological expectations for 

their designated aquatic life uses, interpret current condition relative to CWA objectives and goals, 

track biological community responses to management actions and communicate environmental 

outcomes to the public. The model can serve as a template for organizing field data (biological, 

chemical, physical, landscape) at an eco-regional, basin, watershed or waterbody scale. It provides 

a framework for understanding current conditions relative to natural, undisturbed conditions. 

In practice, the BCG is used to first identify the critical attributes of an aquatic community and then to 

describe how each attribute changes in response to stress. Coral reef managers can use the BCG to 

interpret biological condition along a standardized gradient, regardless of assessment method, and 

apply that information to different programs. 

The BCG model provides a framework to help water quality managers do the following: 

•	 Decide what environmental conditions are desired (goal-setting)—The BCG can provide a 

framework for organizing data and information and for setting achievable goals for 

waterbodies relative to natural conditions (e.g., condition comparable or close to undisturbed 

or minimally disturbed condition). 

•	 Interpret the environmental conditions that exist (monitoring and assessment)—Practitioners 

can get a more accurate picture of current waterbody conditions. 

•	 Plan for how to achieve the desired conditions and measure effectiveness of restoration— 

The BCG framework offers water program managers a way to help evaluate the effects of 

stressors on a waterbody, select management measures by which to alleviate those stresses 

and measure the effectiveness of management actions (EPA 2011: Case Example 3.16). 

•	 Communicate with stakeholders—When biological and stress information is presented in this 

framework, it is easier for the public to understand the status of the aquatic resources relative 

to what high-quality places exist and what might have been lost. 

1.7.1 How is the BCG Constructed? 

The BCG has been divided into six levels of biological conditions along the stressor-response curve, 

ranging from observable biological conditions found at no or very low levels of stress (level 1) to 

those found at high levels of stress (level 6) (Figure 1-1). 

The BCG was developed to serve as a scientific framework to synthesize expert knowledge with 

empirical observations and develop testable hypotheses on the response of aquatic biota to 

increasing levels of stress. 

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It is intended to support more consistent interpretations of the response of aquatic biota to stressors 

and to clearly communicate this information to the public. It is being evaluated and piloted in several 

regions and states. 

Davies and Jackson (2006) provides a description of how 10 attributes of aquatic ecosystems change 

in response to increasing levels of stressors along the gradient, from level 1 to 6. The attributes 

include several aspects of community structure, organism condition, ecosystem function, spatial and 

temporal extent and connectivity (Table 1-3). 

Figure 1-1. The Biological Condition Gradient (BCG) (modified from Davies and Jackson 2006). 

Chapter 1. Introduction 1-13 
 

 

 

 

 

 

 

 

 

 

 

 

 

Table 1-3. Biological and other ecological attributes used to characterize the freshwater streams 

Biological Condition Gradient (BCG) (Modified from Davies and Jackson 2006). 

Attribute Description 

I. Historically documented, 

sensitive, long-lived, or 

regionally endemic taxa 

Taxa known to have been supported according to historical, museum or 

archeological records, or taxa with restricted distribution (occurring only in a 

locale as opposed to a region), often due to unique life history requirements 

(e.g., Sturgeon, American Eel, Pupfish, Unionid mussel species). 

II. Highly sensitive 

(typically uncommon) 

taxa 

Taxa that are highly sensitive to pollution or anthropogenic disturbance. Tend to 

occur in low numbers, and many taxa are specialists for habitats and food type. 

These are the first to disappear with disturbance or pollution (e.g., most 

stoneflies, Brook Trout [in the east], Brook Lamprey). 

III. Intermediate sensitive 

and common taxa 

Common taxa that are ubiquitous and abundant in relatively undisturbed 

conditions but are sensitive to anthropogenic disturbance/pollution. They have 

a broader range of tolerance than Attribute II taxa and can be found at reduced 

density and richness in moderately disturbed stations (e.g., many mayflies, 

many Darter fish species). 

IV. Taxa of intermediate 

tolerance 

Ubiquitous and common taxa that can be found under almost any conditions, 

from undisturbed to highly stressed stations. They are broadly tolerant but 

often decline under extreme conditions (e.g., filter-feeding caddisflies, many 

midges, many Minnow species). 

V. Highly tolerant taxa Taxa that typically are uncommon and of low abundance in undisturbed 

conditions but that increase in abundance in disturbed stations. Opportunistic 

species able to exploit resources in disturbed stations. These are the last 

survivors (e.g., tubificid worms, Black Bullhead). 

VI. Non-native or 

intentionally 

introduced species 

Any species not native to the ecosystem (e.g., Asiatic clam, zebra mussel, Carp, 

European Brown Trout). Additionally, there are many fish native to one part of 

North America that have been introduced elsewhere. 

VII. Organism condition Anomalies of the organisms; indicators of individual health 

(e.g., deformities, lesions, tumors). 

VIII. Ecosystem function Processes performed by ecosystems, including primary and secondary 

production; respiration; nutrient cycling; decomposition; their 

proportion/dominance; and what components of the system carry the dominant 

functions, for example, shift of lakes and estuaries to phytoplankton production 

and microbial decomposition under disturbance and eutrophication. 

IX. Spatial and temporal 

extent of detrimental 

effects 

The spatial and temporal extent of cumulative adverse effects of stressors; for 

example, groundwater pumping in Kansas resulting in change of fish 

composition from fluvial dependent to sunfish. 

X. Ecosystem connectivity Access or linkage (in space/time) to materials, locations and conditions required 

for maintenance of interacting populations of aquatic life; the opposite of 

fragmentation. For example, levees restrict connections between flowing water 

and floodplain nutrient sinks (disrupt function); dams impede fish migration, 

spawning. 

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Each attribute provides some information about the biological condition of a waterbody. Combined 

into a conceptual model like the BCG, the attributes can offer a more complete understanding of 

current waterbody conditions and also provide a basis for comparison with naturally expected 

waterbody conditions. All states and tribes that have applied a BCG used the first five attributes that 

describe the composition and structure of the biotic community on the basis of the tolerance of 

species to stressors. Where available, states and tribes also included information on the presence 

or absence of native and non-native species for fish and amphibians, as well as observations 

of overall health and condition (e.g., size, weight, abnormalities, tumors and diseases). 

The last three BCG attributes (ecosystem function, spatial and temporal extent of detrimental effects 

and ecosystem connectivity) can provide valuable information when evaluating the potential for a 

waterbody to be protected or restored. Several of EPA’s NEPs, in conjunction with EPA ORD, are 

exploring application of those attributes at a whole-estuary scale (e.g., distribution and connectivity 

of critical aquatic habitats and associated biota). 

Additionally, individual attributes might uniquely respond to a specific stressor or group of 

associated stressors (biological response signatures) (Yoder and Rankin 1995 a, b; Yoder and 

Deshon 2003). That information could contribute to the causal analysis of biological impairment, 

Stressor Identification (SI) and Causal Analysis/Diagnosis Decision Information System (CADDIS) 

(http://www.epa.gov/caddis/). 

Currently, applications of the BCG that include development of a BCG-index (BCG-I) and 

incorporation of the BCG in a state’s water quality management have been used only on freshwater 

streams. More recently, ongoing pilot efforts at several NEPs are extending the BCG concept to 

assessment and management of estuaries. Efforts to develop an estuarine conceptual model have 

focused on five attributes (structure, condition, function, connectivity and non-native species 

[Cicchetti 2010]) at scales ranging from the whole estuary to the single habitat, or biotope (e.g., 

seagrass beds, salt marshes and clam flats) (Table 1-4). This multi-scale approach is intended to 

improve restoration and management efforts. At larger scales, managers can prioritize and develop 

programs to restore the historic balance of critical habitats (biotopes) relative to an undisturbed 

historic benchmark, while also targeting restoration of all living habitats, to the maximum extent 

possible. The single habitat scale is assessed using biological assessments, which enjoy an established 

history within management approaches (Cicchetti and Greening 2011; EPA 2011). 

Extending the BCG conceptual model to new waterbodies (coastal waters) and new assemblages 

(coral reef communities) is a multistep process. A successful process assembles a workgroup of 

experts on the habitats and assemblages and elicits from these experts: descriptions of the native 

aquatic assemblages under natural conditions, identifications of the predominant regional stressors 

and descriptions of degradation levels corresponding to the BCG. Descriptions should include the 

theoretical foundation and observed assemblage responses to stressors. In addition to expert 

opinion, the process makes use of empirical monitoring data. During a workshop, experts familiar 

with local conditions use the data to define the ecological attributes and set narrative statements. 

The experts determine narrative decision rules for assigning stations to a BCG level on the basis of 

Chapter 1. Introduction 1-15 
 

 

 

 

 

 

 

 

 

 

the biological information collected at the stations. Further development of quantitative decision 

rules and a quantitative BCG is more involved and requires a greater time commitment from the 

expert panel to participate in iterative calibration steps and review of more extensive monitoring 

data. 

Table 1-4. Ecological attributes used to characterize the estuarine Biological Condition Gradient 

(BCG) (EPA in review). 

Attributes Potential Metrics and Description 

Structure and 

Compositional 

Complexity 

Community or habitat structure and complexity. May also recognize loss of habitats or 

species due to human activities. 

Examples include macroinvertebrate or fish indices, phytoplankton or zooplankton 

community measures, epifaunal measures, biotope mosaics, presence/quality of 

sensitive or susceptible taxa or biotopes, wetland vegetative indices, etc. 

Condition Measures condition of the waterbody, habitat or species. Also includes measures of 

resiliency. 

Examples include harmful algal blooms, disease outbreaks (locally or system-wide), 

measure of habitat or biotope health, such as seagrass condition or wetland condition, 

fish pathology or shellfish bed condition. 

Function Measures of energy flow, trophic linkages and material cycling. They may include proxy 

or snapshot metrics that correlate to functional measures. 

Examples include photosynthesis/respiration ratios, benthic: pelagic production rates, 

chlorophyll a concentrations and macroalgal biomass. 

Connectivity Metrics of exchange or migrations of biota between adjacent waterbodies or habitats. 

Important measures within the area being studied may be strongly affected by factors 

adjacent to or larger than the immediate study area. 

Proxies may need to be used as metrics. These may include linkages, fragmentation or 

hydrological measures. 

Non-native 

Taxa 

Metrics of non-native species. May include measures of the impact of invasive species 

and non-natives. 

Examples include estimated numbers of species or individuals, biomass measures of 

natives and non-natives or replacement of native species. 

This report communicates the first results to apply the BCG conceptual model to the assessment of 

the condition of coral reefs. The first stage reported here is a proof-of-concept to introduce the 

conceptual model to coral reef experts and elicit a preliminary set of narrative decision rules for 

assigning coral reef stations to levels of the BCG. If the conceptual model passes muster among the 

experts, it will allow identification of the steps needed to develop and implement more 

comprehensive quantitative decision models. 

1-16 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

Chapter 2. Approach 

The coral reef BCG will be developed through a series of facilitated expert workshops. In the 

workshops, the experts assess the condition of coral reef sites based on biological data collected at 

the sites (species composition, abundance, health) and assign each site to a condition category 

(level) of the BCG. The experts’ reasoning for making assignments are developed into a set of 

decision rules, at first qualitative, but through iteration, increasingly quantitative. The expert-derived 

rules are translated to a quantitative decision algorithm, in this case using mathematical set theory 

(e.g., Droesen 1996). The decision algorithm allows independent assessments with results 

comparable to those of the expert panel. Furthermore, the decision rules are documented so that 

modifications can be made as information and needs change. 

The participants for the initial workshop were invited based on their scientific knowledge of the coral 

reefs and reef organisms of Puerto Rico. As a first step, participants were asked to evaluate and rank 

coral reef condition from photos, videos and data collected during EPA’s 2010 and 2011 coral reef 

assessment surveys in shallow waters (<12 m deep) of southwestern Puerto Rico. The biological 

assemblages considered were stony corals, fishes, sponges, gorgonians and benthic 

macroinvertebrates. Rugosity, a reef-scale indicator of reef complexity, was determined using a 

chain-transect method that compares the six-foot length of a chain draped along the top of corals 

and along the bottom of the reef to the length of a taut line across the same linear distance. 

Participants were asked to share videos and pictures of reefs from the present or past that they 

believed exhibited full biological integrity. 

A unique aspect of this workshop was that participants were reacting to the visual imagery of 

the reefs and evaluating different levels of coral reef condition. Participants moved from a visual, 

simple approach to more complex data-driven analysis. The workshop was designed to encourage 

brainstorming, facilitate discussion and not get mired in EPA terminology or definitions at the 

beginning of the workshop. Participants examined the visual media, rated the condition of various 

coral reefs and provided rationale for their ratings. Descriptions of good and bad characteristics 

relative to ecological condition were captured by facilitated discussions. A preliminary list was 

generated describing attributes that would characterize a coral reef with high (minimally disturbed 

or reference) or good condition. A minimally disturbed condition provides a fixed point in time and 

can help us to avoid problems associated with shifting baselines (Pauly 1995; Stoddard et al. 2006). A 

firm concept of minimally disturbed anchors ecological condition as a reference and helps us deal 

with changes (e.g., climate change), which broadly affect conditions that occur after the anchored 

point. Further, a clear picture of minimally disturbed provides a basis for effective public 

communication of changes over time and can provide a reference point for certain indices of 

ecological condition. 

The workshop was designed to last three days; however Day 3 was cancelled because of Tropical 

Storm Isaac. Certain planned activities from Day 3 were shifted into Day 2, and the remainder of 

workshop information was communicated during webinars. 

Chapter 2. Approach 2-1 
 

 

 

2.1 Video and Photo Evaluations 

On the first day, panelists were asked to view and rate the coral reef condition of 12 EPA stations on 

the south shore of Puerto Rico (Table 2-1). 

Table 2-1. Shallow inshore linear reefs used for BCG workshop stations that 

correspond to US EPA stations sampled along the southern coast of Puerto Rico. 

Station Year EPA station Latitude Longitude Depth (ft.) 

1 2010 PR_2010_125 17.92486 -66.20363 20 

2 2011 PR_2011_15 17.98198 -66.77228 23 

3 2011 PR_2011_113 17.95942 -67.03902 21 

4 2011 PR_2011_03 17.94420 -66.91638 21 

5 2011 PR_2011_19 17.94180 -66.88060 12 

6 2010 PR_2010_14 17.93875 -67.10927 27 

7 2010 PR_2010_16 17.93922 -67.06197 24 

8 2010 PR_2010_108 17.94085 -67.07708 12 

9 2010 PR_2010_109 17.95373 -67.05012 16 

10 2011 PR_2011_01 17.96380 -67.04980 11 

11 2011 PR_2011_46 17.93418 -67.10108 17 

12 2011 PR_2011_25 17.93670 -66.88660 17 

Stations were limited to shallow (<12 m), near-shore (less than 3 nautical miles from shore) linear 

reefs as designated by NOAA benthic maps (Kendall et al. 2001), see Figure 2-1. 

Figure 2-1. Map with locations of the 12 EPA stations along the 

southern coast of Puerto Rico. 

2-2 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Videos of eight stations were examined in the morning and four stations in the afternoon. Videos 

were displayed on four computers looping two stations per video in the morning and one station per 

video in the afternoon. Each station presented video footage from both panoramic and linear 

transect views, which began with 15 seconds showing the station number and the type of footage, to 

allow reviewers time to prepare for each video. A 60-second period between each station allowed 

panelists time to complete their evaluations before the next station video began. In addition to the 

video clips (ranging from 30 seconds to 3 minutes long), eight still photographs for each station 

(Appendix G) were provided in a notebook to supplement the videos and in particular, to capture 

aspects of the station not represented in the videos (e.g., fish). 

The panelists were instructed to draw upon their overall personal experience and expertise to rate 

the reef condition for each station as either good, fair or poor based on what they viewed in videos 

and photos. Workshop binders organized by station included a photo diary of key representative 

photos, two ballots to rate the stations for each session (Appendices D and E) and note sheets 

(Appendix F) to document the traits or characteristics that panelists used to support their ratings. 

The panelists were asked to consider all aspects of the reef and specifically instructed to consider the 

characteristics of the condition of corals, sponges, gorgonians, fish, algae, reef rugosity and 

topographical heterogeneity. The facilitators suggested that panelists not compare ratings with each 

other, but panelists were free to discuss and view videos as a group. The panelists were not asked to 

rate any specific number of stations as good, fair or poor, but had free rein as they circulated around 

and viewed the video loops at their own pace. The facilitators were available if panelists had 

questions. 

The panelists asked about shifting baseline conditions, and they were encouraged to draw upon their 

personal experience. Panelists also asked if each assemblage should be rated separately. Facilitators 

responded that it was all right to consider and document each assemblage, but they must finally 

select one single rating for each station. When all stations were evaluated, panelists recorded their 

individual ratings on the ballots and returned them to the facilitators. Note sheets were not 

collected—they were for each panelist to reference during subsequent discussions. 

After ballots were collected from the panelists, the facilitators tabulated all the scores by ranking the 

stations in order from best condition to worst using a weighted ranking system (Table 2-2). Each 

good vote was given a value of 10 points, each fair vote 5 points and each poor vote 1 point. 

Table 2-3 shows the ranking given by each expert after visually evaluating videos and photographs 

for 12 EPA stations. 

The panelists provided feedback on how to improve the process used to evaluate the stations. Many 

found it challenging to assess reef condition based on the video quality, which was raw footage from 

inexpensive video-enabled digital cameras. Still photos provided the best way to document fish 

populations, because many fishes were disturbed during the assessments that occurred before the 

video was taken. The fish surveyors were the first team to perform visual assessments, followed by 

Chapter 2. Approach 2-3 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table 2-2. Coral reef condition evaluated by the experts. Results were obtained from 20 coral reef 

experts after viewing videos and photos of 12 stations, with the highest score bolded. Overall rank is 

established by weighted ranking. 

Station No. % No. % No. % Majority Weighted Overall 

No. Good Good Fair Fair Poor Poor Rating Score Rank 

1 1 5 9 45 10 50 Poor/Fair 65 8 

2 0 0 0 0 20 100 Poor 20 12 

3 13 65 7 35 0 0 Good 165 1 

4 0 0 2 10 18 90 Poor 28 11 

5 0 0 10 50 10 50 Fair/Poor 60 9 

6 0 0 6 30 14 70 Poor 44 10 

7 4 20 16 80 0 0 Fair 120 4 

8 0 0 15 75 5 25 Fair 80 6 

9 1 5 12 60 7 35 Fair 77 7 

10 5 25 14 70 1 5 Fair 121 3 

11 2 10 17 85 1 5 Fair 106 5 

12 6 30 12 60 2 10 Fair 122 2 

Table 2-3. Rankings given by experts after visually evaluating videos and photographs for 12 EPA 

stations. Abbreviations: G rated good; F rated fair; P rated poor. Some ratings were intermediate 

between two classes. 

Station Number 

Expert 1 2 3 4 5 6 7 8 9 10 11 12 

Appeldoorn P P G P F P F F F F F F 

Ballantine F P G F F/P P F F G G G G 

Bauzá F P G P F P G F F F F F 

Canals F P F/G P P/F P F F P F F F/G 

Cuevas F P G P F P F F P/F F F F 

Diaz F/G P F/G P F/P F/P F/G F/P F/P G F/P F 

Fisher P P G P P P G F F G F G 

Hutchins P P F P P P F P P F F F 

McField P/F P­ F P F P F P/F P+ F+ F P+ 

Miller F P G P P/F P F P/F F G/F F G 

Pagan F/P P­ G/F P P F F F P F F F 

Ramos F P G P P P F P F P F F 

Roberson P P F/P P P/F F/P F P F/P F/P P/F F 

Ruiz F P G P F F G F F G G F 

Sabat P P G P P/F P/F F F P F/G F F 

Smith P P F P P/F P/F F F P F F F 

Szmant P P­ G P F P F F F/P F F/G G 

Todd P P G P P P G F F F F G 

Vicente P P F P F F F F F F F F 

Yoshioka G/F P G F F/G F F/G F F/P F/G F G/F 

2-4 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

the surveyors assessing other assemblages, including those photographing and video recording the 

reef. The photographers began potentially after many fishes had been scared away. The panelists 

also requested more details on the stations they were evaluating. Panelists felt they needed to know 

the location of the reef, what specific reef habitat they were viewing, the depth, the wave exposure 

and other features. They also wanted to know what stressors the station may have experienced. 

Recommendations for the future included upgrading video camera quality, standardizing the 

videography approach and providing more information to get a broader perspective of each station 

and its surrounding reef. 

A facilitated discussion followed on the attributes that the panelists had identified to justify their 

ratings. The stations rated best and worst were considered first, with each panelist’s comments 

captured on flip charts. Panelists were encouraged to edit posted pages of their comments if they 

felt their thoughts were not accurately captured. All participants were given the opportunity to 

submit comments on index cards if they wished to provide additional comments privately or 

anonymously. A summary of the characteristics considered by the panelists in rating the stations is 

provided in Section 2.2 for the best, worst and several fair stations. 

2.2 Summary of Ratings 

All of the photos given to the experts are found in Appendix G, ordered by station number. 

2.2.1 Best Station, Ranked #1 

The experts rated the condition of Station 3 as the best of the 12. It was rated good by 65% of the 

experts and fair by 35%. No expert rated it as poor. The experts were asked what characteristics or 

attributes were present that caused them to rate it as the best station. Their responses follow: 

•	 Abundance of Montastraea annularis species-complex was high, with low partial mortality of 

tissue and large colony sizes indicative of older, mature coral colonies. 

•	 Reefs showed high structural complexity, surface heterogeneity and high rugosity or presence 

of three-dimensional structures, allowing better reef development than would a flat 

topography. 

•	 Stony coral biodiversity was moderate and included Colpophyllia natans, Siderastrea siderea 

and Porites astreoides, as expected on near-shore linear reefs in southwestern Puerto Rico. 

•	 The water column showed high clarity with no visible sediment; experts also noted a lack of 

siltation or films covering the substrate. 

•	 Coralline algae were more abundant than brown algae, and Dictyota was rare or absent. 

•	 Gorgonian coverage was high, with most sea fans intact and uninjured. Diadema was present. 

Stony coral colonies had no or few boring clionid sponges. 

•	 Damselfish were seen and the presence of additional fish species contributed to a good rating. 

Chapter 2. Approach 2-5 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The experts, who rated the station as fair, expressed concern about the uncertainty in identifying fish 

species because the visual media were not adequate to consider fish size distributions or trophic 

status. A few grazing fish species were seen, but not enough to alleviate concerns of low grazing 

potential. Another expert cited the presence of coral disease. Finally, sponge abundance and 

diversity were low, with an absence of arborescent, vase and barrel morphologies, which are 

dominant in high quality habitat. 

•	 The experts were also asked what attributes were absent that caused them to not rate the 

station as excellent. Their responses follow: 

•	 The station had lower than expected diversity of stony corals, fishes and sponges, with little 

evidence of any recruitment. 

•	 Very few anemones and invertebrates were observed, again indicating low species diversity. 

•	 One expert stated that sponges, because they are efficient filter feeders, might be one of the 

assemblages most sensitive to chemicals in the water column and could act as an indicator 

species. 

2.2.2 Worst Station, Ranked #12 

All the experts agreed that Station 2 was in the worst condition, and rated it poor. This station was 

characterized by: 

•	 High sedimentation and turbidity in the water column, which appeared as large patches of 

flocculent material creating low visibility, which the experts judged to represent low water 

quality. 

•	 The reef colors were drab brown or green. 

•	 Thick goopy sediment (probably of terrigenous origin) covered most of the bottom and 

organisms living on the bottom. Exposed hard substrate was absent, with no clear surfaces for 

attachment or recruitment. 

•	 Algal cover was high, with lots of Dictyota and cyanobacteria as evidenced by a slimy
 

appearance with a “skuzzy fuzzy” texture. 

•	 Abundance of coralline algae was low. 

•	 The absence of reef relief was coupled with low rugosity and no or very few small and live 

coral colonies. 

•	 No fish or gorgonians were observed, although a few Diadema were noted. 

•	 Sponge morphologies were ropy or encrusting, indicative of poor habitat and water quality. 

•	 Heterotrophic sponges dominated, with a high abundance of filter feeders and no apparent 

autotrophic sponges. This is a characteristic typical of highly silted areas. 

2-6 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

2.2.3 Stations Rated Fair 

Station 8 ranked #6. This station was ranked as the most centric station among those with a fair 

rating. 75% of the experts rated it fair while 25% rated it poor. This station had the highest coverage 

of Acropora palmata in all stations viewed, although overall coral cover was low, with lots of coral 

rubble. A. palmata colonies varied greatly in size, condition and distribution and were present in 

about 25% of the transect area. Some very mature and large colonies were present in varying 

condition as evidenced by the amount of healthy coral tissue. Many of the A. palmata colonies 

lacked significant tissue and showed characteristics ranging from signs of tissue recovery, partial 

tissue mortality from white-band disease, lesions and white denuded tips, perhaps from fish 

predation. Some standing colonies were completely dead. The coral rubble on the bottom was 

composed of many broken and dead pieces of A. palmata skeletons, but finer sediments were 

absent. Several experts commented that the clean substrate and unconsolidated rubble showed 

significant and recent hurricane damage. Although some reef was dead, it showed signs of recovery 

and resiliency with the persistence of corals. 

The clean substrate provided suitable areas available for settlement and recruitment of corals and 

other sessile invertebrates. Some coralline algae were present but overall algal diversity was low, 

with some fleshy algae. Much of the substrate appeared as though it had been highly grazed by 

Diadema antillarum. Palythoa, often considered an emerging opportunistic species, was prevalent 

throughout the transect colonizing dead coral skeletons. Several species of fish swam in large schools 

representing a decent diversity, including evidence of herbivores. The primary sources of rugosity 

were the A. palmata colonies; most other coral colonies showed relatively low relief. Few 

invertebrates other than those already mentioned were observed, with the exception of some small 

sea fans and low relief gorgonians. 

Station 5 ranked #9. Half of the experts rated it fair and the other half rated it poor. This station 

shared many attributes with Station 8, but was judged to be in poorer condition because of higher 

sediment and turbidity, together with lower coral cover and diversity. The transect video showed 

substantial A. palmata coverage, but the colonies appeared to be in poorer condition than those 

seen in Station 8. One expert described the station as a “beat up Apal zone” (A. palmata) with large 

rubble between colonies. Thicker and larger algal turf patches and more sponges were present in 

comparison to Station 8. Parrotfish biting scars and scrapes were observed. However, it was noted 

that sedimentation, turbidity and water quality can vary with year, season and time of day, so the 

apparent condition could be extremely variable and dependent on when the video was taken. 

Station 10 ranked #3. This station was rated as good by 25% of experts, fair by 70% of experts and 

poor by 5% of experts. Many of the features seen in the previous fair descriptions were also present 

here. A novel observation was the presence of the boring sea urchin Echinometra, which bioerodes 

coral skeletons; the herbivorous urchin Diadema is usually considered an indicator of better 

condition. 

Chapter 2. Approach 2-7 
 

 

 

 

 

 

 

 

 

 

2.2.4 Station Rated Poor 

Station 6 ranked #10. This station was rated fair by 30% of experts and poor by 70% of experts. 

There was evidence of significant bioerosion on the reef surfaces, perhaps due to boring clionids and 

the encrusting sponge Chondrilla nucula. One expert asked if this was a hard bottom station (not a 

coral reef). Despite the poor condition of Station 6, all experts agreed that Station 2 was in the 

poorest condition. 

2.3 Summary of Attributes 

Attributes developed by the experts were assembled into a list. In a facilitated discussion, the 

experts reached consensus about which direction (increase or decrease) the attribute would go at a 

station with improving condition, and what types of measurements or sub-attributes would be 

important. This information is summarized in Table 2-4. 

Table 2-4. Summary of attributes and their relationships for assessing coral reef condition from 

station evaluations. 

2-8 Workshop on Biological Integrity of Coral Reefs 

Attributes of good stations 

Direction with 

improving condition Attribute Sub-attribute/measurements 

increase 3D structure rugosity, cover 

increase stony coral abundance Montastraea annularis complex, Acropora palmata, 

Acropora cervicornis, Diploria strigosa, large stony corals 

increase stony coral condition % live tissue, absence of disease 

increase stony coral diversity high number of stony coral species 

increase stony coral population 

structure large colonies 

increase stony coral recruitment 

decrease dominance of weedy, 

tolerant species 

Colpophyllia natans, Siderastrea siderea, Porites 

astreoides 

increase coralline algae 

decrease zoanthids Palythoa species 

decrease exotic species exotic fish, corals 

decrease filter feeders heterotrophic sponges 

increase fish abundance 

increase balance in fish population size and structure 

increase fish biomass 

increase balance in fish trophic 

structure 

increase fish diversity 

decrease fleshy algae 

increase gorgonian abundance 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table 2.4 (continued) Attributes of good stations 

Direction with 

improving condition Attribute Sub-attribute/measurements 

increase gorgonian condition % live tissue, absence of disease and predators (Cyphoma 

gibbosum) 

increase gorgonian diversity 

increase other invertebrates Diadema antillarum, conch, lobsters, crabs, anemones 

increase sponge abundance autotrophic sponges 

decrease sponge abundance heterotrophic sponges 

increase sponge diversity 

increase substrate condition clean, no fuzzy algae (cyanobacteria), open space 

recruitment 

increase water clarity 

decrease corallivores/bioeroders bioeroders, Coralliophila (large size), clionids 

2.4 Reference Condition for Biological Integrity 

The panel agreed that all of the stations were impaired at some level. Many of the experts had been 

working in Puerto Rico for 30–40 years, while others had recently received their PhDs. The group had 

a rather lengthy discussion about the historical condition of Puerto Rico’s coral reefs in an attempt to 

answer: What did the reefs look like before humans came along to stress them? 

The term “reference condition” is used by BCG to define biological condition in the absence of 

human disturbance (Stoddard et al. 2006). The concept of reference condition arose from the 

objective of the Clean Water Act Section 101: "to restore and maintain the chemical, physical and 

biological integrity of the nation's waters”. Biological integrity is defined as “the community of 

organisms having a species composition, diversity and functional organization comparable to those 

of natural habitats within a region” (Karr 1991). 

Unfortunately, human activities have significantly affected coral reefs. Puerto Rico’s coral reefs were 

severely degraded long before ecologists began to study them (Jackson 1997). According to Jackson 

et al. 2001, ecological extinction caused by overfishing preceded all other pervasive human

disturbance to coastal ecosystems. Overfishing reduced species populations such as marine reptiles 

(green turtle, hawksbill turtle [1700s]), mammals (manatee and extinct Caribbean monk seal 

[1800s]), conch [1980s], fishes (Nassau and goliath groupers [1950s] and reef fishes [1970s]). By the 

time scientific studies began in the 1950s, herbivores and predators were reduced to very small 

fishes and sea urchins (Jackson 1997). 

So, how can one estimate reference condition when no living human has ever seen a Puerto Rican 

reef in natural condition? One approach is the reference station approach, where scientists use reefs 

that are nearly unaffected by anthropogenic disturbance and the related stressors/exposures, or 

reefs whose present-day good condition is found in conjunction with the best available physical, 

chemical and biological habitat conditions, as surrogates for natural reefs. However, these 

Chapter 2. Approach 2-9 
 

 

 

 

 

 

approaches may fail to correctly identify the baseline population sizes, instead representing a shifted 

baseline as reference condition (Pauly 1995). 

Another approach is to apply ecological theory and empirical models to extrapolate reference 

condition. A relatively recent method is the use of historical ecology, where scientists piece together 

an understanding of what coral reef ecosystems used to be. The challenge is to use these approaches 

to adjust our expectations of what a healthy coral reef baseline looks like and use that as reference 

condition. 

2.4.1 Experts’ Examples of Reference Condition for Biological Integrity 

Workshop panelists were urged to share examples of present or past reefs that they believed to 

exhibit full biological integrity. Dr. Szmant reported that she had participated in a discussion about 

shifting baselines with other experienced coral reef scientists. This led to a report (Sale and Szmant 

2012) that summarized these scientists’ reminiscences on historical reef condition over the last 

40 years. 

Dr. Szmant also showed photographs of recent changes from 2009 to 2012 in Montastraea 

populations on a coral reef in Curaçao (Watamula) that were caused by a 2010 bleaching event 

(Figure 2-2). An estimated 50% of previously large healthy coral colonies on Watamula showed 

partial or complete mortality in less than one year. She also showed photographs of extensive 

Acropora cervicornis beds on Smith Bank (on the south coast of Roatan) near the ones on Cordelia 

Banks that Dr. McField surveyed (see below). Dr. Szmant has slides of The Buoy and other reef areas 

in Puerto Rico and the Caribbean from the 1970s that she was willing to share. 

Figure 2-2. Recent changes from 2009 to 2012 in Montastraea populations on a coral reef in
 

Curaçao (Watamula) that were caused by a 2010 bleaching event (photos: Dr. Alina Szmant).
 

2-10 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

Dr. McField brought photos from Cordelia Banks on Roatan Island, Honduras (Figures 2-3, 2-4 and 

2-5). Cordelia Banks is located near the airport and main port of Roatan, but strong onshore currents 

likely keep land-based sources of pollution away most of the time. Cordelia Banks is a good 

candidate for a reference site because it has: 

•	 52 acres of healthy reef with the highest live coral cover in the Caribbean (up to 73% 

measured in transects and averaging just over 50%). Acropora cervicornis, which is one of the 

most important reef species for structural reef growth and fish nursery habitat, dominates this 

reef. Unfortunately, this species and Acropora palmata have been reduced by about 98% over 

the last three decades throughout the Caribbean by disease and bleaching. 

•	 The presence of two important species of sharks − the nurse shark (Ginglymostoma 

cirratum) and the Caribbean reef shark (Carcharhinus perezii).
 

•	 Spawning aggregation sites for groupers and snappers. 

Figure 2-3. Two experts suggested Cordelia Banks near Roatan, Honduras, as an example of a 

reference site for excellent coral condition. This area contains 52 acres of threatened coral 

species, high fish abundance and other characteristics important in sustaining healthy reefs 

(photo: Dr. Melanie McField). 

Chapter 2. Approach 2-11 
 

 

 

 

Figure 2-4. Monitoring of massive Acropora cervicornis banks at Cordelia Banks located off a 

major airport in Roatan, Honduras (photo: Dr. Melanie McField). 

Figure 2-5. Panoramic view of Acropora cervicornis banks at Cordelia Banks, Roatan, Honduras 

(photo: Dr. Melanie McField). 

Dr. McField also brought copies of the 2012 Report Card for the Mesoamerican Reef. Dr. McField’s 

program, Healthy Reefs for Healthy People Initiative, is an international, multi-institutional effort 

that tracks the health of the Mesoamerican Reef (MAR), the human choices that shape it and the 

progress to ensure its long-term integrity. The Healthy Reefs for Healthy People Initiative seeks to 

address two overarching questions: 

2-12 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1.	 What is a healthy reef and how can we improve our tracking of reef health
 

through a shared vision and common indicators or yardsticks?
 

2.	 How can we best convey consistent, scientific information to policymakers,
 

decision-makers and the public, such that the connections between reef health and 

human health result in effective conservation action at an unprecedented scale?
 

The Healthy Reefs for Healthy People Initiative has developed a quantifiable, interpretive framework 

of measurable indicators and criteria to better understand and assess reef health in the MAR region. 

The Initiative produces report cards on the condition of the MAR resources, using a five-point 

grading system from very good to critical for key indicators: fish abundance, fleshy macroalgal index, 

Diadema abundance, herbivorous fish abundance, coral mortality, conch abundance, coral 

recruitment and coral cover. The report card also describes the main threats to the ecosystem and 

evaluates management actions. More information about the Initiative can be found at: 

http://www.healthyreefs.org 

Dr. Weil stated that the average rainfall in Puerto Rico has been increasing steadily since 2000, 

coinciding with changes in land use. Consequently, rain events have a greater impact on the decline 

in coral reef condition. He has a draft report on this topic that he could send to other attendees. Dr. 

Weil also reports that in La Parguera, Puerto Rico, the average winter SST has remained elevated 

over the last decade. He suggests that water visibility is decreasing, and sedimentation is increasing. 

Yellow-band disease, which affects the Montastraea annularis species-complex, is now chronic all 

year, whereas it used to be seasonal and limited in distribution. Bleaching events in the area are 

followed by white plague infection, which leads to increased coral mortality with little or no 

recovery, and bare coral substrate is colonized by macroalgae. 

Mr. Ruiz Torres passed around his recent book Beneath the Waves, published by the Sea Grant 

Program at the University of Puerto Rico (Figure 2-6). It contains nearly a hundred photos 

documenting the marine environment 

along the entire coast of Puerto Rico, 

including algae, fish, crustaceans, 

mollusks and corals. A description of the 

location, the depth and the characteristics 

of the organisms accompany each image. 

The text is written in English and Spanish. 

Dr. Appeldoorn commented that good 

water flow (medium to high constant 

speed) is important for high quality reefs. 

He stated that fish trophic structure is 

impaired in Puerto Rico because of the 

low number of apex predators. 

Figure 2-6. Cover for the book, Beneath the Waves, 

by Hector J. Ruiz Torres. 

Chapter 2. Approach 2-13 
 

 

 

 

 

 

 

 

 

 

Dr. Vicente said that he has over 500 one-hour videos documenting reefs around Puerto Rico and 

USVI that he is willing to share with the group. He will send an index so experts can request the 

videos of interest. 

2.4.2 Summary Discussion 

The experts remarked that gorgonians were present in the videos of the best sites but not in high 

abundance. At fair condition sites, gorgonians were most abundant, but reduced abundance was 

seen again at poor coral reef condition (bell-shaped curve). The experts agreed that there is a need 

to understand the ecology of relationships between these assemblages to predict where we find 

certain species and abundance of corals and gorgonians, and why they are distributed that way. For 

example: Are corals replaced by gorgonians when corals die on reefs in lower or poor condition? 

2.5 Attributes of a Very Good to Excellent Station 

Based on the videos and photographs, the experts identified the attributes of a very good - to 

excellent station, which would be comparable to BCG Level 2: near natural (minimally disturbed). 

A summary of the attributes is shown in Table 2-5. 

The attributes are reorganized in Table 2-6, into a format that can be more efficiently used during 

future workshops to facilitate establishing numeric criteria ranges. 

2.5.1 Three-dimensional Topographic Complexity 

The experts thought that very good - excellent stations would have high rugosity or threedimensional topographic complexity, including substantial reef built above the bedrock. High 

topographic complexity is known to be an important attribute (Friedlander and Parrish 1998; Zawada 

2011). Coral reefs with high topographic complexity have high species diversity (Talbot 1965; Risk 

1972), primary productivity (Barnes 1988) and biomass density (Luckhurst and Luckhurst 1978; 

Carpenter et al. 1981). These reefs provide refuge from predation (Steele 1999; Idjadi and Edmunds 

2006) and supplement larval settlement space (Idjadi and Edmunds 2006). Topographic complexity 

also provides hydrodynamic effects, determining water flow around, over and through the reef 

(Munk and Sargent 1954; Monismith 2007; Hearn 2008; Nunes and Pawlak 2008) and enhancing 

energy dissipation thereby, nutrient uptake and mass-transfer rates (Shashar et al. 1996; Hearn et al. 

2001). 

2-14 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

Table 2-5. Summary of descriptions of four condition categories (very good to poor) based on 

expert assessments of individual stations. The descriptions of good to poor condition are comparisons to 

a very good condition station based on panelists’ identifications of aspects missing from expectations for very 

good stations. 

Condition level Attribute descriptions 

Very Good 

Excellent 

Physical structure: High rugosity or 3D structure; substantial reef built above 

bedrock; many irregular surfaces provide habitat for fish; very clear water; no 

sediment, flocs or films 

(approximate 

BCG Level 1–2) 

Corals: High species diversity including rare; large old colonies (Montastraea) with 

high tissue coverage; balanced population structure (old and middle-sized colonies, 

recruits); Acropora thickets present 

Gorgonians: Gorgonians present but subdominant to corals 

Sponges: Large autotrophic and highly sensitive sponges abundant 

Fish: Populations have balanced species abundances, sizes and trophic interactions 

Large vertebrates: Large, long-lived species present and diverse (turtles, eels, 

sharks) 

Other invertebrates: Diadema, lobster, small crustaceans and polychaetes 

abundant; some large sensitive anemone species present 

Algae: Crustose coralline algae abundant; turf algae present but cropped and grazed 

by Diadema and herbivorous fish; low abundance of fleshy algae 

Condition: Low prevalence of disease and tumors; mostly live tissue on colonies 

Good 

(approximate 

Physical structure: Moderate to high rugosity; moderate reef built above bedrock; 

some irregular cover for fish habitat; water slightly turbid; low sediment, flocs or 

films on substrate 

BCG Level 3) Corals: Moderate coral diversity; large old colonies (Montastraea) with some tissue 

loss; varied population structure (usually old colonies, few middle aged and some 

recruits); Acropora thickets may be present; rare species absent 

Gorgonians: Gorgonians more abundant than Levels 1–2 

Sponges: Autotrophic species present but highly sensitive species missing 

Fish: Decline of large apex predators (e.g., groupers, snappers) noticeable; small 

reef fishes more abundant 

Large vertebrates: Large, long-lived species locally extirpated (turtles, eels) 

Other invertebrates: Diadema, lobster, small crustaceans and polychaetes less 

abundant than Levels 1–2; large sensitive anemone species absent 

Algae: Crustose coralline algae present but fewer than Levels 1–2; turf algae present 

and longer, more fleshy algae present than Levels 1–2 

Condition: Disease and tumor presence slightly above background level; more 

colonies have irregular tissue loss 

Chapter 2. Approach 2-15 
 

 

 

 

 

 

 

Table 2-5 (continued) 

Condition level Attribute descriptions 

Fair 

(approximate 

Physical structure: Low rugosity; limited reef built above bedrock; erosion of reef 

structure obvious; water turbid; more sediment accumulation, flocs and films; 

Acropora usually gone or present as rubble for recruitment substrate 

BCG Level 4) Corals: Reduced coral diversity; emergence of tolerant species, few or no living large 

old colonies (Montastraea); Acropora thickets gone, large remnants mostly dead 

with long uncropped turf algae 

Gorgonians: Gorgonians more abundant than Levels 1–3, replacing sensitive coral 

and sponge species 

Sponges: Mostly heterotrophic tolerant species and clionids 

Fish: Absence of small reef fishes (mostly Damselfish remain) 

Large vertebrates: Large, long-lived species locally extirpated (turtles, eels) 

Other invertebrates: Diadema absent; Palythoa overgrowing corals; crustaceans, 

polychaetes and sensitive anemones conspicuously absent 

Algae: Some coralline algae present but no crustose algae; turf is uncropped, 

covered in sediment; abundant fleshy algae (e.g., Dictyota) with high diversity 

Condition: High evidence of diseased corals, sponges, gorgonians; evidence high of 

mortality; usually less tissue than dead portions on colonies 

Poor 

(approximate 

Physical structure: Very low rugosity; no or little reef built above bedrock; no or low 

relief for fish habitat; very turbid water; thick sediment film and thick floc covering 

bottom; no substrate for recruits 

BCG Level 6) Corals: Absence of colonies, those present are small; only highly tolerant species 

with little or no live tissue 

Gorgonians: Small and sparse colonies; mostly small sea fans; often diseased 

Sponges: Heterotrophic sponges buried deep in sediment; highly tolerant species 

Fish: No large fishes; only a few tolerant species remain; lack of multiple trophic 

levels 

Large vertebrates: Usually devoid of vertebrates other than fishes 

Other invertebrates: Few or no reef invertebrates; high abundance of sediment 

dwelling organisms such as polychaetes and holothurians 

Algae: High cover of fleshy algae (Dictyota); complete absence of crustose coralline 

algae 

Condition: High incidence of disease and low or no tissue coverage on small colonies 

of corals, sponges and gorgonians, if present 

2-16 Workshop on Biological Integrity of Coral Reefs 
 

Table 2-6. Condition levels and associated attributes Condition 

levelBCG levelPhysicalstructureCoralsGorgoniansSpongesFish VertebratesOtherinvertebratesAlgae/

plants

Condition 

Very 1–2 High rugosity High species Gorgonians Large Populations Large, Diadema, Crustose Low 

Good ­ or 3D diversity present but autotrophic have balanced long-lived lobster, small coralline algae prevalence 

Excellent structure; 

substantial 

including rare; 

large old 

sub-dominant 

to corals 

and highly 

sensitive 

species 

abundance, 

species 

present 

crustaceans 

and 

abundant; turf 

algae present 

of disease 

or tumors; 

reef built colonies sponge sizes and and diverse polychaetes but cropped mostly live 

above (Montastraea) species trophic inter­ (turtles, abundant; and grazed by tissue on 

bedrock; with high abundant actions eels, some large Diadema and colonies 

many tissue sharks) sensitive herbivorous 

irregular coverage; anemone fish; low 

surfaces balanced species abundance 

provide population fleshy algae 

habitat for structure (old 

fish; very and middleclear water; aged colonies, 

no sediment, recruits); 

flocs or films Acropora 

thickets 

present 

Good 3 Moderate to 

high rugosity; 

moderate 

reef built 

above 

bedrock; 

some 

irregular 

cover for fish 

habitat; 

water slightly 

turbid; low 

sediment, 

flocs or film 

on substrate 

Moderate 

coral diversity; 

large old 

colonies 

(Montastraea) 

with some 

tissue loss; 

varied 

population 

structure 

(usually old 

colonies, few 

middle-aged 

and some 

recruitment); 

Acropora 

thickets may 

be present; 

rare species 

absent 

Gorgonians 

more 

abundant 

than in Levels 

1–2 

Autotrophic 

species 

present but 

highly 

sensitive 

species 

missing 

Decline of 

large apex 

predators (e.g., 

groupers, 

snappers, etc.) 

noticeable; 

small reef fish 

more 

abundant than 

Levels 1–2 

Large, 

long-lived 

species 

locally 

extirpated 

(e.g., 

turtles, 

eels) 

Diadema, 

lobster, small 

crustaceans 

and 

polychaetes 

less abundant 

than Levels 

1–2; large 

sensitive 

anemone 

species 

missing 

Crustose 

coralline algae 

present but less 

than Levels 1–2; 

turf algae 

present and 

longer; more 

fleshy algae 

present 

Disease and 

tumor 

prevalence 

slightly 

above 

background 

level; more 

colonies 

have 

irregular 

tissue loss 

Chapter 2. Approach 2-17 
 

 

Table 2.6 (continued) Condition level BCG level Physical structure

CoralsGorgoniansSpongesFish VertebratesOtherinvertebratesAlgae/plantsCondition 

Fair 4 Low rugosity, 

limited reef 

built above 

bedrock; 

erosion of 

reef 

structure 

obvious; 

water turbid; 

more 

sediment 

accumulation, flocs 

and films; 

Acropora 

usually gone 

or present as 

rubble for 

recruitment 

substrate 

Reduced coral 

diversity; 

emergence of 

tolerant 

species, few or 

no large old 

colonies 

(Montastraea) 

mostly dead; 

Acropora 

thickets gone; 

large remnants 

mostly dead 

with long 

uncropped turf 

algae 

Gorgonians 

more 

abundant 

than in Levels 

1 - 3; replace 

sensitive coral 

and sponge 

species 

Mostly 

heterotrophic 

sponges with 

tolerant 

species and 

clionids 

Absence of 

small reef fish 

(mostly 

Damsel fish) 

Large, longlived species 

locally 

extirpated 

(e.g., turtles, 

eels) 

Diadema 

absent; 

Palythoa 

overgrowing 

corals, 

crustaceans, 

polychaetes 

and sensitive 

anemones 

conspicuously 

absent 

Some coralline 

algae; turf is 

uncropped 

covered in 

sediment; lots of 

fleshy algae with 

high diversity 

(e.g., Dictyota); 

possibly covering 

sessile 

invertebrates; no 

turf or coralline 

algae; complete 

absence of 

crustose 

coralline algae 

High 

incidence of 

diseased 

coral, 

sponges, 

gorgonians; 

evidence of 

high 

mortality; 

usually less 

tissue than 

dead 

portions on 

colonies 

Poor 6 Very low 

rugosity, no 

or low reef 

built above 

bedrock or 

poor for fish 

habitat; very 

turbid water; 

thick 

sediment 

film and high 

flocs 

covering 

bottom; no 

substrate for 

recruits 

Absence of 

colonies, those 

present are 

small, only 

highly tolerant 

species, little 

or no tissue 

Small and 

sparse 

colonies, 

mostly small 

sea fans, 

often 

diseased 

Heterotrophic 

sponges 

buried deep in 

sediment; 

highly tolerant 

sponge 

species 

No large fish, 

few tolerant 

species, lack 

of multiple 

trophic levels 

Usually 

devoid of 

other 

vertebrates 

Low or no 

reef 

invertebrates; 

high 

abundance of 

sediment 

dwelling 

organisms 

(e.g., 

polychaetes, 

holothurians) 

High cover of 

fleshy algae 

(Dictyota); 

possibly covering 

sessile 

invertebrates; no 

turf or coralline 

algae; complete 

absence of 

crustose 

coralline algae 

High 

incidence 

disease on 

small 

colonies 

of corals, 

sponges and 

gorgonians; 

if present, 

low or no 

tissue 

coverage 

2-18 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

2.5.2 Stony Coral Attributes 

For stony corals, attendees decided that very good - excellent stations would have high species 

diversity that included large colonies of reef-building corals (i.e., Montastraea) and those colonies 

would have high tissue coverage. The Montastraea annularis species-complex (Montastraea 

annularis, Montastraea faveolata and Montastraea franksi) was historically one of the primary reef 

framework builders of the Caribbean coral reefs, characterizing the “buttress zone” or “annularis 

zone” in the classical descriptions of Caribbean reefs (Goreau 1959). These corals have declined 

dramatically throughout their range. The Montastraea annularis species-complex is susceptible to 

bleaching (Oxenford et al. 2008; Brandt 2009; Bruckner and Hill 2009; Wagner et al. 2010), disease 

(Bruckner and Hill 2009; Miller et al. 2009), sediment (Eakin et al. 1994; Carricart-Ganivet and Merino 

2001; Torres and Morelock 2002) and nutrients (Marubini and Davies 1996). 

The experts believed that the coral reef population should have a balanced size-class structure, 

including large and middle-sized colonies as well as new recruits. Ecologists consider population 

demographics to be vital statistics, particularly those statistics that can impact on present and future 

population size (Hughes 1996; Edmunds 2013; Edmunds and Elahi 2007). Typically, expanding 

populations have a large percentage of young individuals, while declining populations have a large 

percentage of older individuals and stable populations have a relatively even size distribution among 

age groups. 

The experts also concluded that Acropora palmata thickets should be present. A. palmata was 

formerly the dominant species in shallow water (3–16 ft. deep) throughout the Caribbean and on the 

Florida Reef Tract, forming extensive, densely aggregated thickets in areas of heavy surf. These coral 

colonies prefer the exposed reef crest and fore-reef environments in depths of < 20 ft., although 

isolated corals may occur to depths of 65 ft. Since 1980, populations have collapsed throughout their 

range from disease outbreaks, with losses compounded locally by hurricanes, increased predation, 

bleaching, elevated temperatures and other factors (Ruzicka et al. 2013). This species is also 

particularly susceptible to damage from sedimentation (NOAA 2013b). 

2.5.3 Gorgonian Attributes 

There was considerable discussion about the relative distribution of gorgonians and stony corals. The 

experts decided that very good - excellent stations would have gorgonians present, but the station 

should be dominated by stony corals. Gorgonians form a major benthic component of Caribbean 

reefs (Bayer 1973; Brazaeu and Lasker 1989) and can be very abundant in some sites where stony 

corals apparently are unable to proliferate. Factors controlling the distribution of shallow-water 

gorgonians include water motion and substrate relief (Kinzie 1973; Yoshioka and Yoshioka 1989a, b) 

and sediment transport (Yoshioka and Yoshioka 1989b, 2009). 

Chapter 2. Approach 2-19 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

2.5.4 Sponge Attributes 

The experts agreed that very good - excellent stations would have high abundances of large 

autotrophic and highly sensitive sponge species. Most sponges are heterotrophic organisms, 

obtaining their food from the open water column. However, 35 species of common Caribbean 

sponges possess photosynthetic endosymbionts (Vicente 1990) that supply food to their hosts 

(Wilkinson 1983; Thacker and Freeman 2012). This is similar to the relationship between 

zooxanthellae and their coral hosts. Roberts et al. (2006) found that exposure to shade and siltation 

significantly reduced the growth and reproductive status of the temperate photosynthetic reef 

sponge Cymbastela concentrica. 

2.5.5 Fish Attributes 

Workshop participants decided that populations should have balanced distributions of species 

abundances, sizes and trophic interactions. Caribbean coral reefs can contain as many as 500–700 

species of fishes (Lieske and Collins 2001). The mechanisms that lead to these concentrations of fish 

species on coral reefs have been widely debated over the last 50 years. While many reasons have 

been proposed there is no scientific consensus on a primary mechanism and it seems likely that a 

number of factors contribute. These include the rich habitat complexity and diversity inherent in 

coral reef ecosystems (Luckhurst and Luckhurst 1978; Gladfelter et al. 1980) and the variety and 

temporal availability of food resources available to coral reef fishes (Randall 1967). 

Puerto Rico reef fisheries have shown significant decline since the 1970s, and large reef fishes have 

virtually disappeared from shallow reefs around Puerto Rico (Garcia-Sais et al. 2008). Fishing may 

have direct and indirect effects on reef fish trophic structure. Removals of apex predators from the 

reef complex may result in shifts of species composition (e.g., through trophic and ecological 

cascades) and for some taxa, increased variability in population dynamics or potential effects on 

species evolution. 

2.5.6 Large Vertebrate Attributes 

Several groups of large, long-lived vertebrate species (e.g., sea turtles and manatees) are considered 

important contributors to Puerto Rican coral reef communities. Other groups (e.g., dolphins, whales, 

seabirds) spend most of their life cycle in other habitat types but are occasionally seen hunting or 

feeding in waters around coral reefs. Puerto Rico supports five species of marine turtles, two of 

which (Hawksbill and Leatherback) are critically endangered. Four sharks (Blacktip Shark, Reef Shark, 

Tiger Shark and Nurse Shark), eight eels (Brown Garden Eel, Sharptail Eel, Goldspotted Eel, Spotted 

Snake Eel, Green Moray, Golden Moray, Spotted Moray, Purplemouth Moray) and two rays (Spotted 

Eagle Ray and Southern Stingray) can also be found on Puerto Rico coral reefs. A recent study 

(Jackson et al. 2012) found that the biomass of apex predators (sharks, large snappers and groupers) 

was close to zero in Puerto Rico. The experts decided that large long-lived species should be present 

and diverse at very good - excellent stations. 

2-20 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

2.5.7 Other Invertebrate Attributes 

Queen conch, spiny lobsters and some crabs are harvested for food and have been declining 

throughout the Caribbean for decades (Santavy et al. 2012). Conchs are generally acknowledged to 

be over-exploited (Appeldoorn and Meyers 1993), and Puerto Rico has established catch limits for 

these mollusks. Sea urchins (especially Diadema antillarum) are important herbivores that were 

decimated by an epizootic throughout the western Atlantic in the 1980s (Lessios et al. 1984; Lessios 

1988, 2005). The population status for the Caribbean spiny lobster stock is unknown (NOAA 2013a). 

The experts decided that very good - excellent stations would have abundant Diadema, lobster, 

small crustaceans and polychaetes. They also felt that some large sensitive anemone species should 

be present. 

2.5.8 Algae Attributes 

Macroalgae and turf algae compete for space with coral, sponge and other sessile species. Excess 

nutrients may alter competitive interactions and favor algae over coral. Many fishes and 

invertebrates are key grazers, helping to maintain algal biomass and prevent algae from overgrowing 

coral. A number of algal species (e.g., calcareous macroalgae and crustose coralline algae) deposit 

calcium carbonate during growth and may contribute to reef structural strength. Crustose coralline 

algae may also facilitate recruitment of stony coral. Algae are primary producers and provide habitat 

and resources for marine fish and invertebrates but often not to the same degree as coral reef 

habitat (Santavy et al. 2012). The experts decided that very good - excellent stations would have 

abundant crustose coralline algae, turf algae would be present but cropped and grazed and fleshy 

algae would occur in low abundance. 

2.5.9 Condition 

Bleaching, disease or predation can affect health and condition of stony corals, gorgonians and 

sponges. An indicator of stony coral/gorgonian health is the amount of live tissue on the organism 

or colony. However, coral reef fish rarely appear to suffer from tumors or lesions (Panek 2005). 

The experts decided that there should be a very low prevalence of disease on very good - excellent 

stations, with mostly live tissue on coral colonies and gorgonians, and low prevalence of tumors on 

coral reef fish. 

Chapter 2. Approach 2-21 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Discussion and Next Steps 

3.1 Discussion 

EPA convened a group of experts to attempt, for the first time, to develop a coral reef BCG. There 

was a consensus among the experts that this was an important contribution, because “We have been 

documenting the demise of coral reefs, instead of taking action to change the direction of their 

existence”. 

A preliminary BCG based on stony corals, fishes, gorgonians, sponges, vertebrates and other 

invertebrates has been assembled for shallow-water linear reefs of southwestern Puerto Rico. The 

experts were able to identify four distinct levels of condition: very good – excellent, good, fair and 

poor. Additional discussion is needed to develop reference condition for biological integrity (e.g., 

natural level). 

Attribute development during the first workshop relied primarily on viewing videos and photos from 

individual coral reef monitoring sites. This approach resulted in attributes that were largely speciesbased, with a single notable addition (e.g., organism condition). 

EPA anticipates that ecosystem connectivity is also an appropriate attribute to include in a coral reef 

BCG, since connectivity among coral reefs, mangroves, sea grass beds and lagoons provides a 

complex and dynamic mosaic that is well documented as a critical ecosystem attribute (Christensen 

et al. 2003; Cerveny 2006; Mumby et al. 2004, 2008; Aguilar-Perera and Appeldoorn 2007; McField 

and Kramer 2007; Meynecke et al. 2008; Sale et al. 2008; Pittman et al. 2011). 

EPA would like to suggest that considering the attributes at multiple scales, similar to the approach 

being developed for estuarine ecosystems, may also be informative for coral reef ecosystems. The 

estuarine BCG framework considers structure, function, condition, connectivity and non-native 

species in waterbodies at multiple scales, using measures such as seagrass health, benthic faunal 

indices and habitat mosaics (Cicchetti and Pryor 2010; EPA in review). This holistic and integrated 

approach is intended to improve the understanding and management of the cumulative impacts of 

multiple stressors in complex waterbodies and should work well for coral reefs. 

3.2 Next Steps 

3.2.1 Second Workshop 

EPA is planning to hold a second workshop in early 2014. At the second workshop EPA hopes to focus 

more on: 1) different scales and attributes associated with the entire reef ecosystem, 2) tolerance of 

coral reef species to various anthropogenic stressors and 3) the process for moving towards a 

quantitative BCG, including development of a data portal to organize and share all of the available 

data from Puerto Rican coral reef ecosystems. EPA would also like to continue the discussion of 

reference condition and try to reach consensus on attributes for the reference condition level. 

Chapter 3. Discussion and Next Steps 3-1 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

3.2.2 Species Tolerance Database 

In preparation for the first workshop, Ms. Bradley and Dr. Santavy began developing spreadsheets of 

coral reef taxa for each assemblage (e.g., stony corals, octocorals, sponges, other invertebrates, 

fishes, reptiles, mammals, mangroves, seagrasses and algae) and their characteristics as related to 

the ten attributes of the BCG, including tolerance levels to various stressors, vulnerabilities, habitat, 

etc. Thresholds, when known, were documented. 

Species lists for the database rows were derived from Miller and Lugo (2009). Some columns are 

consistent across assemblages (e.g., scientific name, common name, common/rare, tolerance to 

pollution, tolerance to temperature change, tolerance to wave energy and susceptibility to disease). 

Other columns are unique to specific assemblages (e.g., for stony corals: maximum colony size, 

tolerance to acidity, collection or trade; while for fish: juvenile habitat, adult habitat, food 

preference, solitary/aggregating). Ms. Bradley and Dr. Santavy began to populate the spreadsheets 

with data, beginning with information from the Humann and DeLoach field guides (Humann and 

DeLoach 2002a, b; 2003) and Sefton and Webster (1986). 

During the first workshop, Ms. Bradley gave a short presentation to introduce the spreadsheets. 

The group then moved into a brief facilitated discussion. Workshop participants seemed to respond 

very positively to the concept and were interested in collaboratively working to complete the 

spreadsheets. The group will discuss how to go about completing the spreadsheets during the 

second workshop. 

3.2.3 Assembling the Monitoring Data 

To complete the BCG, the group will utilize pre-existing data collected by others in laboratory and 

field studies. In Phase 1, EPA is working with EPA and NOAA data for Puerto Rico and USVI (stony 

corals, fish and benthic invertebrates). The initial biological data set will include fish measurements 

from several studies conducted by NOAA and EPA. Both groups used the same survey methods for 

fish, so standardization will easily occur as existing datasets are compiled. The second data set 

will include stony coral measurements from the same studies by NOAA and EPA. In this case, the 

methods are very different and will require discussion with the EPA coral reefs BCG team to extract 

the most meaningful and comparable data for standardized reporting. The third data set will include 

benthic invertebrates from the same studies by NOAA and EPA. The two survey methods are quite 

similar, although NOAA counts lobsters, conch and Diadema, while EPA also counts crabs and 

additional urchin species. 

For all datasets, EPA will normalize taxonomic naming protocols to the Integrated Taxonomic 

Information System (ITIS). The standardized data set will contain data in the original format, a 

crosswalk with translations for converting data and the final standardized format. The data set 

will also include a field for the organization that generated the data (data owner). 

EPA is planning on completing Phase 1 (as described above) prior to the second workshop and plans 

to use these data during the workshop. 

3-2 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Phase 2 activities will include direct submission into the STORET Data Warehouse (short for STOrage 

and RETrieval). STORET is a repository for water quality, biological and physical data and is used by 

state and territorial environmental agencies for their water quality data under the CWA. Phase 2 will 

also include incorporation of additional data and fields, when additional datasets from the coral reef 

BCG partners are provided (Puerto Rico Department of Natural and Environmental Resources, Puerto 

Rico Environmental Quality Board, USVI Department of Planning and Environmental Resources, 

University of Puerto Rico, University of the Virgin Islands, US Geological Survey and National Park 

Service). The EPA Office of Water has agreed to make the necessary modifications to STORET to 

include these data. Additionally, metadata for the database in STORET (with URL) will be developed 

for inclusion in NOAA’s Coral Reef Information System (CORIS). 

3.2.4 Calibrating the BCG 

The group will begin calibrating the BCG by using found (or existing) data to confirm the ecological 

attributes developed during this first workshop. The experts have determined narrative decision 

rules for assigning stations to a BCG level on the basis of the photographs and videos collected at 

multiple stations. Documentation of expert opinion in assigning stations to BCG levels is critical to 

the process. Next, a decision model will be developed that incorporates those rules and will be 

tested with independent data sets. The decision model using the tested decision rules will provide 

a transparent, formal and verifiable method for documenting and validating expert knowledge. 

A quantitative data analysis program can be developed using those rules. 

BCG level descriptions in the conceptual model are qualitative (e.g., high diversity, reduced diversity; 

Table 2-5) to allow for consistent assignments of stations to levels. It is necessary to formalize and 

quantify the expert knowledge by codifying level descriptions into a set of quantitative rules (e.g., 

Droesen 1996). If formalized and quantified, any person (with data) can follow the rules to obtain the 

same level assignments as the group of experts. This makes the actual decision criteria transparent 

to stakeholders and potentially applicable to similar types of coral reefs in other areas. 

Rules are logic statements that experts use to make their decisions, for example: “If taxon richness is 

high, then biological condition is high.” Rules on attributes can be combined, for example: “If the 

number of highly sensitive coral taxa (Attribute II) is high, and the number of tolerant colonies 

(Attribute V) is low, then the assignment is to Level 2.” The categories high, moderate, low, etc., are 

ordinal categories: we know that moderate is greater than low; but the boundaries of the categories 

are fuzzy and somewhat subjective. In iterations of the process, the expert panel is asked to put 

quantitative boundaries on the categories they have defined. The objective is to derive combined 

rules, for example, “If there are more than 10 highly sensitive coral taxa, and the percentage of 

colonies of tolerant taxa is less than 15%, then assignment is Level 2.” The quantitative rules 

preserve the collective professional judgment of the expert group and set the stage for the 

development of quantitative models that reliably assign stations to levels without having to 

reconvene the same expert group. In essence, the rules and the models capture the panel’s 

collective decision criteria. 

Chapter 3. Discussion and Next Steps 3-3 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The decision rule for a single level of the BCG does not usually rest on a single attribute (e.g., highly 

sensitive taxa) and generally includes other attributes (intermediate sensitive taxa, tolerant taxa, 

indicator species); such rules are termed Multiple Attribute Decision Rules. After verification with 

independent data, the quantified rules allow users to consistently assess stations according to the 

same rules used by the expert panel and allow a computer algorithm, or other persons, to obtain the 

same level assignments as the original panel. Documentation of the rules and algorithm allow new 

panels to review and modify the decision rules as necessary. 

3.2.5 Economic Valuation of Coastal Ecosystem Services 

Despite their open-access nature and many contributions to the public good, coral reefs have often 

been undervalued in decision-making (Brander et al. 2009). The natural features of a coral reef 

(including physical structure, water quality, biological organisms and ecological functions) provide 

many natural benefits to human societies, collectively known as ecosystem goods and services. The 

economic values of some services (e.g., commercial fishing) are established in markets, while other 

services provide nonmarket value for local, state/regional and national/international segments of the 

population (Principe et al. 2012). Most ecosystem service studies have focused on market benefits, 

which are relatively easy to incorporate in trade-off analyses, but coral reefs also provide numerous 

nonmarket ecosystem services (e.g., existence value and cultural value) that can be estimated using 

a variety of methods. 

Estimates of the global value of coral reefs range from US $30 billion per year (Cesar et al. 2003) to 

US $377 billion per year (Costanza et al. 1997). However, global estimates are coarse and rarely 

relevant to local management decisions. Decision contexts differ with reef type and habitat, political 

climate, stakeholder interests, decision authorities and responsibilities, knowledge, management 

capacity and expertise. Every decision contains an element of valuation, but values are not always at 

the forefront of finding optimal decisions (Keeney 1996). Consequences resulting from a decision are 

often described in terms of value (Hastie 2001). Yet, the values of stakeholders often go ignored 

before management strategies are implemented. Public and stakeholder values, cares, and priorities 

should be considered throughout in the focus and design of assessments and management planning 

and should not be an afterthought in the process. 

The BCG effort focuses on how attributes of the coral reef ecosystem change in response to 

increasing anthropogenic stress. The attributes of the coral reef ecosystem represent the “glue” 

(Pearce and Moran 1994; Turner et al. 2000) of the properly functioning ecosystem, supporting the 

growth of reef-building corals for ecosystem services (e.g., shoreline protection, the presence of 

unique and diverse species to attract tourists, the creation of potentially useful natural products and 

the maintenance of habitat and nurseries for harvestable fish stocks). The development of concise, 

rigorous definitions and levels of condition along the human disturbance gradient will provide the 

fundamental understanding of the factors that affect delivery of ecosystem services. 

3-4 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

EPA and NOAA, in partnership with the University of Puerto Rico and the Puerto Rico Sea Grant, are 

conducting a study to provide the economic valuation of tourism and recreation associated with 

Puerto Rico’s coral reefs to help improve our understanding of the real costs of decisions and 

management options. Reef-related tourism activities include snorkeling, diving, fishing, viewing 

wildlife, boating, beach use and surfing. The project will consist of a modified form of the method 

NOAA used in the Florida Keys National Marine Sanctuary (Leeworthy and Wiley 1996, 1997, 2003; 

Leeworthy and Bowker 1997; Leeworthy and Vanasse 1999; Park et al. 2002; Bhat 2003; Shivlany et 

al. 2008), in Southeast Florida (Johns et al. 2001) and in Hawaii (Bishop et al. 2011). 

The study is estimating the use and associated market (spending and associated impacts on total 

output/sales, income and employment) and non-market economic value (consumer’s surplus or the 

net value received by those doing recreation activities on the reef over and above what they pay to 

undertake the activities) and how those values change with changes in reef attributes. Linking the 

relationships of how reef attribute values change with changes in the physical/natural levels of those 

attributes can be used to measure the economic benefits of the changes and thus provide additional 

performance measures of management actions to protect and restore coral reef ecosystems. 

Table 3-1 shows coral reef ecosystem services and examples of coral reef attributes that are 

associated with them. 

Table 3-1. Coral reef ecosystem services and reef attributes (adapted from Principe et al. 2012). 

Ecosystem service(s) Natural features 

Final (reef attributes) Intermediate 

Recreational fishing 

opportunity 

Recreational diving/snorkeling 

opportunity 

Production of benthic and aquatic prey 

for consumption by recreational fish 

Coral reef formation and maintenance; 

maintenance of water clarity; production 

of benthic and aquatic prey for 

consumption by recreational fish 

Fish diversity and abundance 

Coral diversity, abundance and 

health; fish diversity and 

abundance; water clarity 

Recreational underwater 

photography opportunity 

Coral reef formation and maintenance; 

maintenance of water clarity; production 

of benthic and aquatic prey for 

consumption by recreational fish 

Coral diversity, abundance and 

health; fish diversity and 

abundance; water clarity 

Recreational surfing 

opportunity 

Reef breaks 3-D reef structure 

Opportunity to view nature 

and wildlife 

Biological integrity Biodiversity (birds, marine 

mammals, turtles) 

Opportunity to sunbathe and 

swim at the beach 

Water quality, shoreline protection, sand 

production 

White coralline sands; calm 

waters 

Opportunity to collect objects 

(beachcombing) 

Water quality Wide sandy beaches, 

biodiversity, occasional storms 

Chapter 3. Discussion and Next Steps 3-5 
 

 

 

 

 

 

 

 

 

 

 

Definitions 

• Final ecosystem service – Output of ecological functions or processes that directly contributes to 

social welfare or has the potential to do so in the future (sensu Boyd and Banzhaff 2007). 

• Intermediate ecosystem service – Output of ecological functions or processes that indirectly
 

contributes to social welfare or has the potential to do so in the future.
 

• Natural features – The biological, chemical and physical attributes of an ecosystem or
 

environment.
 

Estimates of use and value will be made for five regions in Puerto Rico to provide information on the 

economic value of reefs in various levels of condition, including present condition. Use and economic 

information can be used in evaluating the economic benefits of investments in protection and 

restoration of the coral reef ecosystems. Results can be used by both private businesses and 

government agencies responsible for managing coral reefs in marketing, education and outreach 

efforts, including Puerto Rico’s coral reef management activities in the four coral reef priority areas 

(Culebra, the Northeast Reserve, Cabo Rojo and Guánica). 

3.3 Final Thoughts 

The first workshop was a new experience for all involved. While EPA has worked with states and 

territories to develop BCGs for streams and estuaries, no one has ever attempted to develop a BCG 

for coral reefs. The experts met the challenge head-on and great progress was made. EPA anticipates 

that this is just the first of several expert workshops. EPA will host conference calls and webinars as 

appropriate. EPA has asked that the experts from the first workshop commit to working with us 

throughout the process. Experts who were not able to attend the first workshop will also be invited 

to participate in future workshops and webinars. 

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Appendix A. References 

Adams AJ, Dahlgren CP, Kellison GT, Kendall MS, Layman CA, Ley JA, Nagelkerken I and Serafy JE. 

2006. Nursery function of tropical back-reef systems. Marine Ecology Progress Series 318: 

287–301. 

Aguilar-Perera A and Appeldoorn RS. 2007. Variation in juvenile fish density along the mangroveseagrass-coral reef continuum in SW Puerto Rico. Marine Ecology Progress Series 348:139–148. 

Almy CC and Carrion-Torres CC. 1963. Shallow-water stony corals of Puerto Rico. Caribbean Journal 

of Science 2/3:133–162. 

Alvarez-Filip L, Kulvy N, Gill JA, Isabelle M and Watkinson AR. 2009. Flattening of Caribbean coral 

reefs: region wide declines in architectural complexity. Proceedings of the Royal Society B, 

276:3019–3025. 

Andrews JC and Pickard GL. 1990. The physical oceanography of coral-reef systems. In: Ecosystems of 

the World, Volume 25, Coral Reefs. Z. Dubinsky. (Ed.). New York. pp. 11–48. 

Appeldoorn RS and Meyers S. 1993. Part Z. Puerto Rico and Hispaniola. In: Marine fishery resources 

of the Antilles. FAO Fisheries Technical Paper No. 326 Rome, FAO. pp. 99–158. 

Ayala CJ. 1999. American sugar kingdom: the plantation economy of the Spanish Caribbean. 

UNC Press. ISBN 978-0-8078-4788-6. 

Bak RPM, Carpay MJE and de Ruyter van Steveninck. (Eds). 1983. Density of the sea urchin Diadema 

antillarum before and after mass mortalities on the coral reefs of Curaçao. Marine Ecology 

Progress Series 17:105–108. 

Ballantine DL and Aponte NE. 1997a. A revised checklist of the benthic marine algae known to 

Puerto Rico. Caribbean Journal of Science 33:150–179. 

Ballantine DL and Aponte NE. 1997b. Notes on the benthic marine algae of Puerto Rico VI. Additions 

to the flora. Botanica Marina 40:39–44. 

Ballantine DL and Aponte NE. 2002. A Checklist of the Benthic Marine Algae Known to Puerto Rico, 

Second Revision. Revised 2002, URL: http://128.32.109.44/fest PRCL/checklist.html. 

Ballantine D, Appeldoorn R, Yoshioka P, Weil E, Armstrong R, Garcia J, Otero E, Pagan F, Sherman C, 

Hernandez-Delgado E, Bruckner A and Lilyestrom C. 2008. Biology and Ecology of Puerto Rican 

Coral Reefs. In: Riegl BM, Dodge RE. (Eds). Coral Reefs of the USA. Springer, pp. 375–406. 

Barber RT, Hilting AK and Hayes ML. 2001. The changing health of coral reefs. Human and Ecological 

Risk Assessment 7:1255–1270. 

Barbour MT, Gerritsen J, Snyder BD and Stribling JB. 1999. Rapid Bioassessment Protocols for Use in 

Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates and Fish, Second Edition. 

US Environmental Protection Agency, Office of Water, Washington, DC. EPA 841-B-99-002. 

Appendix A. References A-1 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Barnes DJ. 1988. Seasonality in community productivity and calcification at Davies Reef, central Great 

Barrier Reef. Proceedings of the Sixth International Coral Reef Symposium. 6: 521-527. 

Bayer FM. 1973. Colonial organization in octocorals. In: Animal Colonies: Development and Function 

Through Time. Boardman RS, Cheetham AH and Oliver Jr. (Eds.). WA. Wiley and Sons, Inc. 

pp. 69–93. 

Beets J and Friedland A. 1998. Evaluation of a conservation strategy: a spawning aggregation closure 

for red hind, Epinephelus guttatus, in the U.S. Virgin Islands. Environmental Biology of Fishes 

55:91–98. 

Beller W, Casellas MA, Cerame-Vivas MJ, Duffy L, El Koury J, Gelabert PA, Gonzales Liboy JA, 

Hernandez-Avila M, Maldonado N, Matos CA, Mignucci-Giannonni A, Pantoja-Garcia E, Rigau J, 

Shelley D, Tacher-Roffe M and N. Zerbi N. 1999. Puerto Rico and the Sea: An action program for 

marine affairs. Report to the governor, PR. Department of Natural Resources, San Juan, PR. 

Benedict JE. 1902. Anomuran collection of Porto Rico. Bulletin of the United States Fish Commission 

20:129–148. 

Bhat MG. 2003. Application of non-market valuation to the Florida Keys marine reserve 

management. Journal of Environmental Management 67:315–325. 

Bigelow RP. 1902. The Stomatopoda of Porto Rico. Bulletin of the United States Fish Commission 

20:149–160. 

Bishop RS, Chapman DJ, Kanninen BJ, Krosnick JA, Leeworthy B and Neade NF. 2011. Total Economic 

Value for Protecting and Restoring Hawaiian Coral Reef Ecosystems Final Report. Silver Spring, 

MD: NOAA Office of National Marine Sanctuaries, Office of Response and Restoration, and Coral 

Reef Conservation Program. NOAA Technical Memorandum CRCP 16, 405 pp. 

Bradley P, Fisher WS, Bell H, Davis WS, Chan V, LoBue C and Wiltse W. 2008. Development and 

implementation of coral reef biocriteria in US jurisdictions. Environmental Monitoring and 

Assessment 150:43–51. 

Bradley P, Fore L, Fisher W and Davis W. 2010. Coral Reef Biological Criteria: Using the Clean Water 

Act to Protect a National Treasure. Narragansett (RI): U.S. Environmental Protection Agency, 

Office of Research and Development, EPA/600/R-10/054, July 2010. 

Brainard RE, Birkeland C, Eakin CM, McElhany P, Miller MW, Patterson M and Piniak GA. 2011. Status 

review report of 82 candidate coral species petitioned under the U.S. Endangered Species Act. US 

Department of Commerce. NOAA Technical Memorandum. NOAA-TM-NMFS-PIFSC-27, 530 p. + 1 

Appendix. 

Brander LM, Rehdanz K, Tol RSJ and van Beukering PJH. 2009. The economic impact of ocean 

acidification on coral reefs. ESRI Working Paper No. 282. 

Brandt ME. 2009. The effect of species and colony size on the bleaching response of reef-building 

corals in the Florida Keys during the 2005 mass bleaching event. Coral Reefs 28: 911–924. 

Brazeau DA and Lasker HR. 1989. The reproductive cycle and spawning in a Caribbean gorgonian. 

Biological Bulletin 176:1–7. 

A-2 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

Brown BE and Howard LS. 1985. Assessing the effects of “stress” on reef coral. Advances in Marine 

Biology 22:1–63. 

Bruckner AW and Bruckner RJ. 1997. Outbreak of coral disease in Puerto Rico. Coral Reefs 16:260. 

Bruckner AW and Bruckner RJ. 2006. Consequences of yellow band disease (YBD) on Montastraea 

annularis (species complex) populations on remote reefs off Mona Island, Puerto Rico. Diseases 

of Aquatic Organisms 69:67–73. 

Bruckner AW and Hill RL. 2009. Ten years of change to coral communities off Mona and Desecheo 

Islands, Puerto Rico, from disease and bleaching. Diseases of Aquatic Organisms 87:19–31. 

Budd AF, Fukami H, Smith ND and Knowlton N. 2012. Taxonomic classification of the reef coral family 

Mussidae (Cnidaria: Anthozoa: Scleractinia). Zoological Journal of the Linnean Society 

166:465–529. 

Burke L and Maidens J. 2004. Reefs at risk in the Caribbean. World Resources Institute, 

Washington, DC. 81 pp. 

Carpenter KE, Miclat RI, Albaladejo VD and Corpuz VT. 1981. The influence of substrate structure 

on the abundance and diversity of Philippine reef fishes. Proceedings of the Fourth International 

Coral Reef Symposium 2:497–502. 

Carricart-Ganivet JP and Merino M. 2001. Growth responses of the reef-building coral Montastraea 

annularis along a gradient of continental influence in the southern Gulf of Mexico. Bulletin of 

Marine Science 68:133–146. 

Cerame-Vivas MJ. (Ed.). 2001. Ecologıa de Puerto Rico. Publications Puertorriqueñas, xviii. 207 pp. 

Cerveny K. 2006. Distribution patterns of reef fishes in southwest Puerto Rico, relative to structural 

habitat, cross-shelf location, and ontogenetic stage. Department of Marine Sciences, University of 

Puerto Rico, Mayagüez, Puerto Rico. Masters Thesis. 172 pp. 

Cesar H, Burke L and Pet-Soede L. 2003. Economics of worldwide coral reef degradation. World 

Wildlife Foundation. Veenman Drukkers, Ede. Netherlands. pp. 24. 

Christensen JD, Jeffrey CFG, Caldow C, Monaco ME, Kendall MS and Appeldoorn RS. 2003. CrossShelf Habitat Utilization Patterns of reef fishes in southwestern Puerto Rico. Gulf and Caribbean 

Research 14:9–27. 

Cicchetti G and Greening H. 2011. Estuarine biotope mosaics and habitat management goals: An 

application in Tampa Bay, FL, USA. Estuaries and Coasts 34:1278–1292. 

Cicchetti G. 2010. Summary of a Technical Workshop held October 28 and 29, 2009: Developing a 

Biological Condition Gradient for Narragansett Bay. US Environmental Protection Agency, 

Narragansett, RI. Internal Report. 

Cicchetti G and Pryor M. 2010. Summary of the Estuarine BCG Workgroup November 2008 

Workshop, and a Proposed Organizing Framework for Bioassessment of Estuaries. US 

Environmental Protection Agency, Narragansett, RI. Internal Report. pp. 25. 

Clark HL. 1902. The Echinoderms of Porto Rico. Bulletin of the United States Fish Commission 

20:231–263. 

Appendix A. References A-3 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Clark HL. 1933. Handbook of the littoral Echinoderms of Puerto Rico and other West Indian Islands. 

New York Academy of Science 16:1–147. 

Clark RD, Pittman S, Caldow C, Christensen J, Roque B, Appeldoorn RS and Monaco ME. 2009. 

Nocturnal fish movement and trophic flow across habitat boundaries in a coral reef ecosystem 

(SW Puerto Rico). Caribbean Journal of Science 45:282–303. 

Coe WR. 1902. The Nemerteans of Porto Rico. Bulletin of the United States Fish Commission 

20:223–229. 

Costanza R, d'Arge R, de Groot R, Farber S, Grasso M, Hannon B, Naeem S, Limburg K, Paruelo J, 

O'Neill RV, Raskin R, Sutton P and van den Belt M. 1997. The value of the world's ecosystem 

services and natural capital. Nature 387:253–260. 

Cróquer A and Weil E. 2009. Changes in Caribbean coral disease prevalence after the 2005 bleaching 

event. Diseases of Aquatic Organisms 87:33–43. 

Dahlgren CP, Kellison T, Adams AJ, Gillanders BM, Kendall MS, Ley JA, Nagelkerken I and Serafy JE. 

2006. Marine nurseries and effective juvenile habitats: concepts and applications. Marine Ecology 

Progress Series 312:291–295. 

Dall WH and Simpson CT. 1902. The Mollusca of Porto Rico. Bulletin of the United States Fish 

Commission 20:353–524. 

Davies SP and Jackson SK. 2006. The Biological Condition Gradient: a descriptive model for 

interpreting change in aquatic ecosystems. Ecological Applications 16:1251–1266. 

Debrot A. 2000. A review of records of the extinct W. Indian monk seal. Marine Mammal Science 

16:834–837. 

Dennis G. 2000. Annotated checklist of shallow-water marine fishes from the Puerto Rico Plateau

including Puerto Rico, Culebra, Vieques, St. Thomas, St. John, Tortola, Virgin Gorda and Anegada. 

http://www.fcsc.usgs.gov/Marine_Studies/Marine_Puerto_Rico_Plateau/marine_puerto_rico_pla 

teau.html. 

Dennis GD, Hensley DL, Colin PL and Kimmel GG. 2004. New records of marine fishes from the 

Puerto Rico Plateau. Caribbean Journal of Science 40:70–87. 

Droesen WJ. 1996. Formalisation of ecohydrological expert knowledge applying fuzzy techniques. 

Ecological Modeling 85:75–81. 

Eakin CM. Feingold JS and Glynn PW. 1994. Oil refinery impacts on coral reef communities in Aruba, 

N.A. In: Ginsburg RN. Proceedings of the Colloquium on Global Aspects of Coral Reefs: Health, 

Hazards and History. Rosenstiel School of Marine and Atmospheric Science, University of Miami. 

1994. pp. 139–145. 

Edmunds PJ. 2013. Decadal-scale changes in the community structure of coral reefs of St. John, US 

Virgin Islands. Marine Ecology Progress Series 489:107–123. 

Edmunds PJ and Elahi E. 2007. The demographics of a 15-year decline in cover of the Caribbean reef 

coral Montastraea annularis. Ecological Monographics 77: 3–18. 

Federal Register. Rules and Regulations. 71:26852–26861. 

A-4 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Fisher WS. 2007. Stony Coral Rapid Bioassessment Protocol. US Environmental Protection Agency, 

Office of Research and Development, Washington, D.C. EPA/600/R-06/167, 60 pp. 

Friedlander AM and Parrish JD. 1998. Habitat characteristics affecting fish assemblages on a 

Hawaiian coral reef. Journal of Experimental Marine Biology and Ecology 224:1–30. 

Garcıa JR, Morelock J, Castro R, Goenaga C and Hernandez-Delgado EA. 2003. Puerto Rican reefs: 

research synthesis, present threats and management perspectives. In: Latin American Coral Reef. 

J. Cortés (Ed.). pp. 111–130. Amsterdam: Elsevier Science B.V. 

Garcıa-Rios CI (Ed.). 2003. Los Chitones de Puerto Rico. Editorial Isla Negra. 

García-Sais J, Appeldoorn R, Battista T, Bauer L, Bruckner A, Caldow C, Carrubba L, Corredor J, Diaz E, 

Lilyestrom C, García-Moliner G, Hernández-Delgado E, Menza C, Morell J, Pait A, Sabater J, Weil E, 

Williams E and Williams S. 2008. The State of Coral Reef Ecosystems of Puerto Rico. In: The state 

of coral reef ecosystems of the United States and Pacific Freely Associated States: 2008. Waddell JE 

and Clarke AM. (Eds). NOAA Technical Memorandum NOS NCCOS 73. 569 pp. 

García-Sais JR, Castro R, Sabater-Clavell J, Esteves R and Carlo M. 2006. Monitoring of coral reef 

communities from natural reserves in Puerto Rico, 2006: Isla Desecheo, Rincon, Mayagüez Bay, 

Guánica, Ponce and Isla Caja de Muerto. Final Report submitted to the Department of Natural and 

Environmental Resources of Puerto Rico. San Juan, PR. 151 pp. 

Gladfelter WB, Ogden JC and Gladfelter EH. 1980. Similarity and diversity among coral reef fish 

communities: a comparison between Tropical Western Atlantic (Virgin Islands) and Tropical 

Central Pacific (Marshall Islands) patch reefs. Ecology 61:1156–1168. 

Gladfelter WB. 1982. White-Band Disease in Acropora palmata: implications for the structure and 

growth of shallow reefs. Bulletin of Marine Science 32:639–643. 

Glynn PW. 1988. El-Nino Southern Oscillation 1982–1983. Near shore population, community, and 

ecosystem responses. Annual Review of Ecology and Systematics 19:309–345. 

Glynn PW. 1991. Coral-reef bleaching in the 1980s and possible connections with global warming. 

Trends in Ecology and Evolution 6:175–179. 

Goenaga C, Vicente VP and Armstrong RA. 1989. Bleaching Induced Mortalities in Reef Corals from La 

Parguera, Puerto Rico: A Precursor of Change in the Community Structure of Coral Reefs? 

Caribbean Journal of Science 25:59–65. 

Goreau TF. 1959. The ecology of Jamaican coral reefs. I. Species composition and zonation. Ecology 

40:67–90. 

Goreau TJ, Hayes RH, Clark JW, Basta DJ and Robertson CN. 1992. Elevated Sea Surface Temperatures 

Correlate with Caribbean Coral Reef Bleaching. In: A Global Warming Forum: Scientific, Economic, 

and Legal Overview. Geyer RA. (Ed.). CRC Press, Boca Raton, Florida USA, Chapter 9, pp. 225–255. 

Grana FA. 1993. Catalogo de la nomenclatura de los Moluscos de Puerto Rico e Islas Vırgenes. 

Technical report, Deptmento Recursos Naturales, Puerto Rico. 

Grimsditch GD and Salm RV. 2006. Coral Reef Resilience and Resistance to Bleaching. IUCN, Gland, 

Switzerland. 52pp. 

Appendix A. References A-5 
 

 

 

 

 

 

 

 

 

 

 

 

 

Gundlach DJ. 1887. Apuntes para la Fauna Puerto-Riqueña (VI). Crustaceos. Anales de la Sociedad 

Española de Historia Natural 16: 115–133. 

Gundlach J. 1883. Apuntes para la Fauna Puerto-Riqueña (V). Moluscos. Anales de la Sociedad 

Española de Historia Natural 12:441–484. 

Hargitt CW and Rogers CG. 1902. The Alcyonaria of Puerto Rico. Bulletin of the United States Fish 

Commission 20:265–287. 

Harvell CD, Altizer S, Cattadori IM, Harrington L and Weil E. 2009. Climate change and wildlife 

diseases: When does the host matter the most? Ecology 90:912–920. 

Hastie R. 2001. Problems for judgment and decision-making. Annual Review of Psychology 

52:653–683. 

Hatcher BG, Imberger J and Smith SV. 1987. Scaling analysis of coral reef systems: An approach to 

problems of scale. Coral Reefs 5:171–181. 

Hauck F. 1888. Meeresalgen von Puerto-Rico. Botanische Jahrbücher für Systematik. 

Pflanzengeschichte und Pflanzengeographie 9:457–470. 

Healthy Reefs for Healthy People Initiative. 2012. Report Card for the Mesoamerican Reef 2012. 

25 pp. 

Hearn CJ, Atkinson MJ and Falter JL. 2001. A physical derivation of nutrient uptakes in coral reefs: 

Effects of roughness and waves. Coral Reefs 20:347–356. 

Hearn CJ. 2008. The Dynamics of Coastal Models. Cambridge University Press, 488 pp. 

Hoegh-Guldberg O. 1999. Climate change, coral bleaching and the future of the world’s coral reefs. 

Marine and Freshwater Research 50:839–866. 

Hubbard DK. 1997. Reefs as dynamic systems. In: Life and Death of Coral Reefs. Birkeland C. (Ed.). 

Chapman and Hall Publishing, New York. pp. 43–67. 

Hughes, TP. 1996. Demographic approaches to community dynamics: a coral reef example. Ecology 

77:2256–2260. 

Humann P and DeLoach N. 2002. Reef Coral Identification. New World Publications, Inc., Jacksonville, 

FL. 287 pp. 

Humann P and DeLoach N. 2002. Reef Fish Identification: Florida, Caribbean, Bahamas. New World 

Publications, Inc. 481 pp. 

Humann P and DeLoach N. 2003. Reef Creature Identification: Florida, Caribbean, Bahamas. 

New World Publications, Inc. 420 pp. 

Idjadi JA and Edmunds PJ. 2006. Scleractinian corals as facilitators for other invertebrates on a 

Caribbean reef. Marine Ecology Progress Series 319:117–127. 

Jackson J, Cramer K, Donovan M, Friedlander A, Hooten A and Lam V. 2012. Tropical Americas Coral 

Reef Resilience Workshop. 29 April–5 May 2012, Tupper Center, Smithsonian Tropical Research 

Center, Panama City, Republic of Panama. 

A-6 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

Jackson JBC, Kirby MX, Berger WH, Bjorndal KA, Botsford LW, Bourque BJ, Bradbury RH, Cooke R, 

Erlandson J, Estes JA, Hughes TP, Kidwell S, Lange CB, Lenihan HS, Pandolfi JM, Peterson CH, 

Steneck RS, Tegner MJ and Warner RR. 2001. Historical overfishing and the recent collapse of 

coastal ecosystems. Science 293:629–637. 

Jackson JBC. 1997. Reefs since Columbus. Coral Reefs 16:S23–S32. 

Johns GM, Leeworthy VR, Bell FW and Bonn MA. 2001. Socioeconomic study of reefs in southeast 

Florida. Report (Hazen and Sawyer) to Broward County, Palm Beach County, Miami-Dade County 

(Florida). Florida Fish and Wildlife Commission and the National Oceanic and Atmospheric 

Administration, 255 pp. 

Karr JR. 1991. Biological Integrity: A Long-Neglected Aspect of Water Quality Resource Management. 

Ecological Applications 1: 66-84. 

Karr JR and Chu EW. 1999. Restoring life in running waters: Better biological monitoring. Island Press, 

Washington, DC, 206 pp. 

Keeney RL. 1996. Value-focused thinking: Identifying decision opportunities and creating 

alternatives. European Journal of Operational Research 92:537–549. 

Kendall MS, Monaco ME, Buja KR, Christensen JD, Kruer CR, Finkbeiner M and Warner RA. 2001. 

Methods used to map the benthic habitats of Puerto Rico. NOAA Technical Memorandum NOS 

NCCOS CCMA 152. 

Kinzie RA III. 1973. The zonation of West Indian gorgonians. Bulletin of Marine Science 23:93–155. 

Leeworthy VR and Bowker JM. 1997. Nonmarket economic user values of the Florida Keys/Key West. 

NOAA, Silver Spring, MD. 

Leeworthy VR and Vanasse P. 1999. Economic contribution of recreating visitors to the Florida 

Keys/Key West: updates for years 1996–97 and 1997–98. NOAA, Silver Spring, MD. 

Leeworthy VR and Wiley PC. 1996. Importance and satisfaction ratings by recreating visitors to the 

Florida Keys/Key West. NOAA, Silver Spring, MD. 

Leeworthy VR and Wiley PC. 1997. A socioeconomic analysis of the recreation activities of Monroe 

County residents in the Florida Keys/Key West. NOAA, Silver Spring, MD. 

Leeworthy VR and Wiley PC. 2003. Profiles and economic contribution: General visitors to Monroe 

County, Florida 2001–2001. NOAA, Silver Spring, MD. 

Lessios H. 2005. Diadema antillarum populations in Panama twenty years following mass mortality. 

Coral Reefs 24:125–127. 

Lessios HA, Robertson DR and Cubit JD. 1984. Spread of Diadema mass mortality through the 

Caribbean. Science 226:335–337. 

Lessios HA. 1988. Mass mortality of Diadema antillarum in the Caribbean: What have we learned? 

Annual Review of Ecology and Systematics 19:371–393. 

Lieske E and Myers R. 2001.Coral Reef Fishes: Indo-Pacific & Caribbean. Princeton University Press, 

Princeton, NJ, USA. 

Appendix A. References A-7 
 

 

 

 

 

 

 

 

 

Long C. 1975. The Polychaeta from La Parguera, Puerto Rico. University of Puerto Rico, Department 

of Marine Sciences. 

Luckhurst BE and Luckhurst K. 1978. Analysis of the influence of substrate variables on coral reef fish 

communities. Marine Biology 49:317–323. 

Marubini F and Davies PS. 1996. Nitrate increases zooxanthellae population density and reduces 

skeletogenesis in coral. Marine Biology 127:319–328. 

McClanahan TR, Ateweberhan M, Muhando CA, Maina J and Mohammed MS. 2007. Effects of 

climate and seawater temperature variation on coral bleaching and mortality. Ecological 

Monographs 77:503–525. 

McClanahan TR, Weil E, Cortés J, Baird A and Ateweberhan M. 2009. Consequences of coral 

bleaching for sessile organisms. In M. van Oppen and J. Lough (Eds.) Coral Bleaching: Patterns, 

Processes, Causes and Consequences. Ecological Studies. pp: 121–138. Springer-Verlag. 

McField M and Kramer PR. 2007. Healthy Reefs for Healthy People: A Guide to Indicators of Reef 

Health and Social Well-being in the Mesoamerican Reef Region. 208 pp. 

Meissner KJ, Lippmann T and Gupta AS. 2012. Large-scale stress factors affecting coral reefs: Open 

ocean sea surface temperature and surface seawater aragonite saturation over the next 400 

years. Coral Reefs 31: 309–319. 

Menzies RJ and Glynn PW. 1968. The common marine Isopod crustaceans of Puerto Rico. In: Studies 

of the Fauna of Curaçao and other Caribbean Islands 23:133. 

Meynecke JO, Lee SY and Duke NC. 2008. Linking spatial metrics and fish catch reveals the 

importance of coastal wetland connectivity to inshore fisheries in Queensland, Australia. 

Biological Conservation 141:981–996. 

Miller GL and Lugo AE. 2009. Guide to the ecological systems of Puerto Rico. General Technical 

Report. IITF-GTR-35. San Juan, PR: US Department of Agriculture, Forest Service, International 

Institute of Tropical Forestry. 437 pp. 

Miller J, Muller E, Rogers C, Waara R, Atkinson A, Whelan KRT, Patterson M and Witcher B. 2009. 

Coral disease following massive bleaching in 2005 causes 60% decline in coral cover on reefs in the 

US Virgin Islands. Coral Reefs 28:925–937. 

Monismith SG. 2007. Hydrodynamics of coral reefs. Annual Reviews of Fluid Mechanics 39:37–55. 

Moore HF. 1902. Porto Rican Isopoda. Bulletin of the United States Fish Commission 20:161–176. 

Morelock J, Ramirez W, Bruckner A and Carlo M. 2001. Status of coral reefs, southwest Puerto Rico. 

Caribbean Journal of Science, Online Special Publication 4:57. URL: 

www.uprm.edu/biology/cjs/reefstatus.htm. 

Mumby PJ, Broad K, Brumbaugh DR, Dahlgren CP, Harborne AR, Hastings A, Holmes KE, Kappel CV, 

Micheli F and Sanchirico JN. 2008. Coral reef habitats as surrogates of species, ecological 

functions, and ecosystem services. Conservation Biology 22:941–951. 

A-8 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

Mumby PJ, Edwards AJ, Arias-Gonzalez JE, Lindeman KC, Blackwell PG, Gall A, Gorczynska MI, 

Harborne AR, Pescod CL, Renken H, Wabnitz CC and Llewellyn G. 2004. Mangroves enhance the 

biomass of coral reef fish communities in the Caribbean. Nature 427:533–536. 

Munk W and Sargeant M. 1954. Adjustment of Bikini Atoll to ocean waves. US Geological Survey 

Professional Paper 260. pp. 275–280. 

Nagelkerken I, Van der Velde G, Gorissen MW, Meijer GJ, van't Hof T and den Hartog C. 2000. 

Importance of mangroves, seagrass beds and the shallow coral reef as a nursery for important 

coral reef fishes, using a visual census technique. Estuarine, Coastal and Shelf Science 51:31–44. 

National Oceanic and Atmospheric Administration (NOAA). 2012a. Marine Invertebrates and Plants. 

URL:www.nmfs.noaa.gov/pr/species/invertebrates/ 

National Oceanic and Atmospheric Administration (NOAA). 2012b. Laboratory for Satellite Altimetry: 

Sea level rise. URL:ibis.grdl.noaa.gov/SAT/SeaLevelRise/LSA_SLR_timeseries_global.php. 

National Oceanic and Atmospheric Administration (NOAA). 2013a. Fish watch, Caribbean Spiny 

Lobster. URL: 

www.fishwatch.gov/seafood_profiles/species/lobster/species_pages/caribbean_spiny_lobster. 

htm. 

National Oceanic and Atmospheric Administration (NOAA). 2013b. Elkhorn Coral (Acropora palmata). 

NOAA Fisheries, Office of Protected Resources. URL: 

www.nmfs.noaa.gov/pr/species/invertebrates/elkhorncoral.htm 

Nunes V and Pawlak G. 2008. Observations of bed roughness of a coral reef. Journal of Coastal 

Research 24:39–50. 

Odum E. 1997. Ecology: A bridge between science and society. Sinauer Associates, Inc., Sunderland, 

MA. 330 pp. 

Ogden JC. 1997. Ecosystem interactions in the tropical coastal seascape. In: Life and death of coral 

reefs. Birkeland C. (Ed.). Chapman and Hall Publishing. New York. pp. 288–297. 

Ortiz E. 1998. Los Moluscos recientes de Puerto Rico. Ph.D. thesis, Department of Marine Sciences, 

University of Puerto Rico, Mayagüez. 

Osborne PL. 2000. Tropical Ecosystem and Ecological Concepts. Cambridge: Cambridge University 

Press. 464 pp. 

Osburn RC. 1940. Bryozoa of Porto Rico with a resume of the West Indian Bryozoan fauna. New York 

Academy of Science 16:321–486. 

Oxenford H, Roach R, Brathwaite A, Nurse L, Goodridge R, Hinds F, Baldwin K and Finney C. 2008. 

Quantitative observations of a major coral bleaching event in Barbados, southeastern Caribbean. 

Climatic Change 87:435–449. 

Panek FM. 2005. Epizootics and disease of coral reef fish in the tropical western Atlantic and Gulf 

of Mexico. Reviews in Fisheries Science 13:1–21. 

Park T, Bowker JM and Leeworthy VR. 2002. Valuing snorkeling visits to the Florida Keys with stated 

and revealed preference models. Journal of Environmental Management 65:301–312. 

Appendix A. References A-9 
 

 

 

 

 

 

 

 

 

 

 

 

 

Pauly D. 1995. Anecdotes and the shifting base-line syndrome of fisheries. Trends in Ecology and 

Evolution 10:430. 

Pearce DW and Moran D. 1994. The Economic Value of Biodiversity. In association with the 

Biodiversity Programme, The World Conservation Union. London: Earthscan Publications, 172 pp. 

Pittman SJ, Renchen GF, Clark R, Caldow C, Olsen D and Hill RL. 2011. Applications of estuarine and 

coastal applications in marine spatial planning. Treatise on Estuarine and Coastal Science 1: 

163–205. 

Pittman SJ, Caldow C, Hile SD and Monaco ME. 2007a. Using seascape types to explain the spatial 

patterns of fish in the mangroves of SW Puerto Rico. Marine Ecology Progress Series 348:273–284. 

Pittman SJ, Christensen JD, Caldow C, Menza C and Monaco ME. 2007b. Predictive mapping of fish 

species richness across shallow-water seascapes in the Caribbean. Ecological Modeling 204:9–21. 

Pittman SJ, Hile SD, Jeffrey CFG, Caldow C, Kendall MS, Monaco ME, and Hillis-Starr Z. 2008. Fish 

assemblages and benthic habitats of Buck Island Reef National Monument (St. Croix, U.S. Virgin 

Islands) and the surrounding seascape: A characterization of spatial and temporal patterns. NOAA 

Technical Memorandum NOS NCCOS 71. Silver Spring, MD. 96 pp. 

Pittman SJ, Hile SD, Jeffrey CFG, Clark R, Woody K, Herlach BD, Caldow C, Monaco ME and 

Appeldoorn R. 2010. Coral Reef Ecosystems of Reserva Natural La Parguera (Puerto Rico): 

Spatial and Temporal Patterns in Fish and Benthic Communities (2001–2007). NOAA Technical 

Memorandum NOS NCCOS 107, Silver Spring, MD. 202 pp. 

Poey F. 1881. Peces. In: Gundlach DJ. Apuntes para la fauna Puerto-Riqueña (III). Anales de la 

Sociedad Española de Historia Natural 10:317–350. 

Prada C, Weil E and Yoshioka P. 2009. Octocoral bleaching under unusual thermal stress. Coral Reefs 

29:41–45. 

Principe P, Bradley P, Yee S, Fisher W, Johnson E, Allen P and Campbell D. 2012. Quantifying Coral 

Reef Ecosystem Services. US Environmental Protection Agency, Office of Research and 

Development, Research Triangle Park, NC. EPA/600/R-11/206. 

Randall JE. 1967. Food habitats of reef fishes of the West Indies. Studies of Tropical Oceanography 

5:665–847. 

Rathbun NJ. 1902. Brachyura and Macrura of Porto Rico. Bulletin of the United States Fish 

Commission 20:1–127. 

Richmond RH. 1993. Coral reefs: Present problems and future concerns resulting from anthropogenic 

disturbance. American Zoologist 33:524–536. 

Risk MJ. 1972. Fish diversity on a coral reef in the Virgin Islands. Atoll Research Bulletin 153:1–6. 

Rivero JA. (Ed). 1978. Los anfibios y reptiles de Puerto Rico. Editorial Universitaria, Universidad de 

Puerto Rico. 

Roberts DE, Davis AR and Cummins SP. 2006. Experimental manipulation of shade, silt, nutrients and 

salinity on the temperate reef sponge Cymbastela concentrica. Marine Ecology Progress Series 

307:143–154. 

A-10 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Rouse I. 1992. The Tainos: Rise and Decline of the People Who Greeted Columbus. Yale University 

Press. 232 pp. 

Ruiz Torres H. 2012. Beneath the Waves. University of Puerto Rico, Sea Grant. 131 pp. 

Ruzicka RR, Colella MA, Porter JW, Morrison JM, Kidney JA, Brinkhuis V, Lunz KS, Macaulay KA, 

Bartlett LA, Meyers MK and Colee J. 2013. Temporal changes in benthic assemblages on Florida 

Keys reefs 11 years after the 1997/1998 El Niño. Marine Ecology Progress Series 489:125–141. 

Sale PF and Szmant AM. (Eds). 2012. Reef Reminiscences: Ratcheting back the shifted baselines 

concerning what reefs used to be. United Nations University Institute for Water, Environment 

and Health, Hamilton, ON, Canada, 35 pp. 

Sale PF, Jacob P and Kritzer JP. 2008. Connectivity: What it is, how it is measured, and why it is 

important for management of reef fishes. In: Grober-Dunsmore R and Keller BD. (Eds). 

Caribbean connectivity: Implications for marine protected area management. Proceedings of a 

Special Symposium, 9–11 November 2006, 59th Annual Meeting of the Gulf and Caribbean 

Fisheries Institute, Belize City, Belize. Marine Sanctuaries Conservation Series ONMS-08-07. Silver 

Spring (MD): US Department of Commerce, National Oceanic and Atmospheric Administration, 

Office of National Marine Sanctuaries, pp. 16–30. 

Santavy DL, Fisher WS, Campbell JG and Quarles RL. 2012. Field Manual for Coral Reef Assessments. 

US Environmental Protection Agency, Office of Research and Development, Gulf Ecology Division, 

Gulf Breeze, FL. EPA/600/R-12/029. 92 pp. 

Santavy DL, Courtney LA, Fisher WS, Quarles RL and Jordan SJ. 2013. Estimating surface area of 

sponges and gorgonians as indicators of habitat availability on Caribbean coral reefs. 

Hydrobiologia 707:1–16. 

Sebens KP. 1994. Biodiversity of coral reefs: What we are losing and why? American Zoologist 

34:115–133. 

Sefton N and Webster SV. 1986. Caribbean Reef invertebrates. Sea Challengers. Monterey, CA. 

112 pp. 

Shashar N, Kinane S, Jokiel PL and Patterson MR. 1996. Hydromechanical boundary layers over a 

coral reef. Journal of Experimental Marine Biology and Ecology 199:17–28. 

Shivlany M, Leeworthy VR, Murray TJ, Suman DO and Tonioh F. 2008. Knowledge, attitudes and 

perceptions of management strategies and regulations of the Florida Keys National Marine 

Sanctuary by commercial fishers, dive operators, and environmental group members: A baseline 

characterization and 10-year comparison. National Oceanic and Atmospheric Administration, 

Silver Spring, MD. 

Soler-López LR. 2001. Sedimentation Survey Results of the Principal Water Supply Reservoirs of 

Puerto Rico. In: Sylva WF (Ed.). Proceedings of the Sixth Caribbean Islands Water Resources 

Congress, Mayagüez, Puerto Rico, February 22 and 23, 2001. 

Stahl A. 1883. Fauna de Puerto Rico, Clasificación sistemática de lo animales que corresponden á esta 

fauna, y catálogo del gabinete zoológica del Dr. A. Stahl en Bayamon. San Juan, PR. 249 pp. 

Appendix A. References A-11 
 

 

 

 

 

 

 

 

 

 

 

 

 

Steele MA. 1999. Effects of shelter and predators on reef fishes. Journal of Experimental Marine 

Biology and Ecology 233:65–79. 

Stoddard JL, Larsen DP, Hawkins CP, Johnson RK and Norris RH. 2006. Setting expectations for the 

ecological condition of streams: The concept of reference condition. Ecological Applications 

16:1267–1276. 

Sturm P, Viqueira R, Ferguson R and Moore T. 2012. Addressing land based sources of pollution in 

Guánica, Puerto Rico. In: D. Yellowlees and TP Huges, Proceedings of the 12th International Coral 

Reef Symposium, 9-13 July 2012 Cairns, Australia. URL:http://www.icrs2012.com/Proceedings.htm 

Talbot FH. 1965. A description of the coral structure of Tutia reefs (Tanganyika territory, East Africa) 

and its fish fauna. Proceedings of the Zoological Society of London 145:431–470. 

Thacker RW and Freeman CJ. 2012. Chapter two - Sponge-Microbe Symbioses: Recent Advances and 

New Directions. In: Advances in Marine Biology. Becerro MA, Uriz MJ, Maldonado M and Turon X. 

(Eds.), Academic Press 62:57–111. 

The Nature Conservancy (TNC). 2006. Are Florida’s reefs resilient? A guide to the Florida reef 

resilience program. Summerland Key, Florida. 

Torres JL and Morelock J. 2002. Effect of terrigenous sediment influx on coral cover and linear 

extension rates of three Caribbean massive coral species. Caribbean Journal of Science 

38:222–229. 

Treadwell AL. 1902. Polychaetous annelids of Puerto Rico. Bulletin of the United States Fish 

Commission 20:181–210. 

Treadwell AL. 1939. Polychaetous annelids of Puerto Rico and Vicinity. In: Scientific Survey of 

Porto Rico and the Virgin Islands 16:313. New York Academy of Sciences. 

Turner RK, Brouwer R, Georgiou S and Bateman IJ. 2000. Ecosystem functions and services: An 

integrated framework and case study for environmental valuation. Norwich (UK): University of 

East Anglia, The Centre for Social and Economic Research on the Global Environment (CSERGE), 

CSERGE Working Paper GEC 2000-21, 32 pp. 

US Commission on Ocean Policy. 2004. US Ocean Action Plan. 41 pp. 

US Environmental Protection Agency (EPA). 2005. Use of Biological Information to Better Define 

Designated Aquatic Life Uses in State and Tribal Water Quality Standards: Tiered Aquatic Life Uses. 

EPA-822-R-05-001. 

US Environmental Protection Agency (EPA). 2011. A Primer on Using Biological Assessments to 

Support Water Quality Management. EPA 810-R-11-001. Washington, DC. 

US Environmental Protection Agency (EPA). In review. A BCG Framework for Bioassessment of 

Estuaries and Coasts. 

Vaughan TW. 1902. The Stony Corals of Porto Rico. Bulletin of the United States Fish Commission 

20:289-320. 

Velazco-Domínguez AT, Weil E and Bruckner A. 2003. Climate Change and Coral Bleaching in Puerto 

Rico: Efforts and Challenges. Presentation given in Oahu, Hawaii. 

A-12 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

Vicente VP. 1990. Response of sponges with autotrophic endosymbionts during the coral-bleaching 

episode in Puerto Rico. Coral Reefs 8:199–202. 

Vicente VP. 1992. A summary of ecological information on the seagrass beds of Puerto Rico. In: 

Coastal Plant Communities of Latin America, Seliger E. (Ed.). Academic Press, New York, pp. 

123–133. 

Vicente VP and Goenaga C. 1984. Mass mortalities of the sea urchin Diadema antillarum (Philippi) 

in Puerto Rico. CEER- M-195:1–30. 

Wagner DE, Kramer P and Woesik RV. 2010. Species composition, habitat, and water quality 

influence coral bleaching in southern Florida. Marine Ecology Progress Series 408:65–78. 

Walker BK, Jordan LKB and Spieler RE. 2009. Relationship of reef fish assemblages and topographic 

complexity on southeastern Florida coral reef habitats. Journal of Coastal Research 53:39–48. 

Warne AG, Webb RMT and Larsen MC. 2005. Water, sediment, and nutrient discharge characteristics 

of rivers in Puerto Rico and their potential influence on coral reefs. USGS Science Investigative 

Report 2005–5206. 

Warner GF, Smith SR, Jordan-Dahlgren E, Linton DM, Woodley JD, Alcolado P, Bonaire K, Bone D, 

Buchan KC, Bush P, Cortés J, Croquer A, De Meyer K, Fernandez RG, Fonseca A, Garcia JR, GarciaParrado P, Garzón-Ferreira J, Gayle P, Gerace DT, Geraldes FX, Gunther J, Guppy R, Juman R, 

Koltes KH, Knobbe E, Klein E, Laydoo R, Losada F, Menendez G, Mow-Robinson JM, Ostrander G, 

Oxenford HA, Parker C, Pors LPJJ, Perez D, Ramirez AR, Rodriguez R, Ruiz-Rentaria F, Ryan J, 

Tschirky JJ and Weil E. 2002. Status and temporal trends at CARICOMP coral reef sites. 

Proceedings of the 9th International Coral Reef Symposium, Bali, Indonesia. pp. 325–330. 

Warren-Rhodes K, Sadovy Y and Cesar HSJ. 2003. Marine ecosystem appropriation in the IndoPacific: A case study of the live reef fish food trade. Ambio 32:481–488. 

Weil E, Hernandez-Delgado EA, Bruckner AW, Ortiz AL, Nemeth M and Ruiz H. (2003). Distribution 

and status of Acroporid coral (Scleractinia) populations in Puerto Rico. Proceedings of the 

Caribbean Workshop: Potential Application of the US Endangered Species Act (ESA) as a 

Conservation Strategy. NOAA-NMFS and NCORE-RSMAS. University of Miami. pp. 71–92. 

Weil E. 2005. Current Status of the Marine Biodiversity of Puerto Rico. In: Miloslavich P and Klein E. 

(Eds). Caribbean Marine Biodiversity: The known and unknown, pp. 85–109. DEStech Publications 

Inc., Lancaster, PA, USA. 

Weil E, Torres JL and Ashton M. 2005. Population characteristics of the black sea urchin Diadema 

antillarum (Philippi) in La Parguera, Puerto Rico, 17 years after the mass mortality event. Revista 

de Biología Tropical 53:219–231. 

Weil E, Cróquer A and Urreiztieta I. 2009. Temporal variability and consequences of coral diseases 

and bleaching in La Parguera, Puerto Rico from 2003-2007. Caribbean Journal of Science 

45:221–246. 

Weil E and Rogers CS. 2011. Coral reef disease in the Atlantic-Caribbean. In Z. Dubinski and N. 

Stambler. (Eds.). Coral Reefs: An Ecosystem in Transition. Chapter 27. pp. 465–492. 

Springer-Verlag. 

Appendix A. References A-13 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Wells JW. 1957. Scleractinia. In: Treatise on invertebrate paleontology. Part F. Coelentrata. Moore 

RC. (Ed.). Geological Society of America, Boulder, Colorado. pp. 328–444. 

Wikipedia. 2013. Central Guánica. URL: http://en.wikipedia.org/wiki/Central_Gu%C3%A1nica. 

Wilkinson C (Ed.). 2004. Status of coral reefs of the world: 2004. Vol.1. Townsville, Queensland, 

Australia: Australian Institute of Marine Science. 316pp. 

Wilkinson CR. 1983. Net primary productivity in coral reef sponges. Science 219:410–412. 

Wilkinson CR. 1996. Global change and coral reefs: Impacts on reefs, economies and human cultures. 

Global Change Biology 2:547–558. 

Williams EH Jr. and Bunkley-Williams L. 1989. Bleaching of Caribbean coral reef symbionts in 

1987–1988. Proceedings of the 6th International Coral Reef Symposium 3:313–318. 

Williams EH Jr. and Bunkley-Williams L. 1990. The world-wide coral reef bleaching cycle and related 

sources of coral mortality. Atoll Research Bulletin 335:1–71. 

Williams EH Jr., Goenega C and Vicente V. 1987. Mass bleaching on Atlantic coral reefs. Science 

237:877–878. 

Wilson HV. 1902. The sponges collected in Porto Rico in 1899 by the US Fish Commission 1900. 

Bulletin of the United States Fish Commission 20:375–411. 

Yoder CO and DeShon JE. 2003. Using biological response signatures within a framework of multiple 

indicators to assess and diagnose causes and sources of impairments to aquatic assemblages in 

selected Ohio rivers and streams. In: Biological Response Signatures: Indicator Patterns Using 

Aquatic Communities. Simon TP. (Ed.). CRC Press, Boca Raton, FL. pp. 23–81. 

Yoder CO and Rankin ET. 1995a. Biological criteria program development and implementation in 

Ohio. In: Biological assessment and criteria: Tools for water resource planning and decision 

making. Davis WS and Simon TP. (Eds.). Lewis Publishers, Boca Raton, FL. pp. 109–144. 

Yoder CO and Rankin ET. 1995b. Biological response signatures and the area of degradation value: 

New tools for interpreting multimetric data. In: Biological Assessment and Criteria: Tools for 

Water Resource Planning and Decision Making. Davis WS and Simon TP. (Eds.). Lewis Publishers, 

Boca Raton, FL. pp. 236–286. 

Yoshioka PM. 2009. Sediment transport and the distribution of shallow water gorgonians. Caribbean 

Journal of Science 45:254–259. 

Yoshioka PM and Yoshioka BB. 1989a. A multispecies, multiscale analysis of spatial pattern and its 

application to a shallow-water gorgonian community. Marine Ecological Progress Series 

54:257–264. 

Yoshioka PM and Yoshioka BB. 1989b. Effects of wave energy, topographic relief and sediment 

transport on the distribution of shallow-water gorgonians of Puerto Rico. Coral Reefs 8:145–152. 

Zawada DG. 2011. Reef Topographic Complexity. In: Encyclopedia of Modern Coral Reefs: Structure, 

Form and Process. Hopley D. (Ed.). pp. 902–906. 

A-14 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Appendix B. Workshop Participants 

Mr. Aaron Hutchins
 

The Nature Conservancy
 

3052 Estate Little Princess
 

Christiansted, St. Croix, VI 00820 

340-718-5575
 

ahutchins@tnc.org
 

Dr. Alberto Sabat
 

University of Puerto Rico, Dept. of Biology
 

P.O. Box 23360
 

Rio Piedras, PR 00931-3360
 

787-764-0000 x2113
 

amsabat@gmail.com
 

Dr. Alina Szmant
 

University of North Carolina, Wilmington
 

Center for Marine Science
 

5600 Marvin K. Moss Lane
 

Wilmington, NC 28409
 

910-962-2362
 

szmanta@uncw.edu
 

Ms. Antares Ramos Alvarez
 

NOAA Office of Ocean and
 

Coastal Resource Mgmt.
 

654 Muñoz Avenue, Suite 604
 

San Juan, PR 00918
 

787-766-5206 ext. 224 

Antares.ramos@noaa.gov
 

Ms. Brandi Todd
 

US EPA, Region 6
 

1445 Ross Ave.
 

Dallas, TX 75202
 

214-665-2233
 

todd.brandi@epa.gov
 

Dr. David Ballantine
 

University of Puerto Rico
 

Department of Marine Sciences
 

P.O. Box 9000
 

Mayagüez, PR 00681-9013
 

david.ballantine@upr.edu
 

Dr. David Cuevas 

US EPA, Region 2 

Caribbean Environ. Prot. Div. 

City View Plaza II - Suite 7000 

#48 RD. 165km 1.2 

Guaynabo, PR 00968-8069 

787-977-5856 

cuevas.david@epa.gov 

Dr. Deborah Santavy (Organizer) 

US EPA, GED 

1 Sabine Island Dr. 

Gulf Breeze, FL 32561 

850-934-9358 

santavy.debbie@epa.gov 

Mr. Ernesto Diaz 

PR Department of Natural and Environment 

Resources (DNER) 

Coastal Zone Management Director 

P.O. Box 366147 

San Juan, PR 00936 

787-999-2200 x2729 

ediaz@drna.gobierno.pr 

Dr. Ernesto Weil 

University of Puerto Rico, 

Mayagüez Campus 

P.O. Box 908 

Lajas, PR 00667-0908 

787-899-2048 x241, x272 

eweil@caribe.net 

Dr. Francisco Pagan 

Caribbean Coral Reef Institute 

University of Puerto Rico 

Mayagüez, PR 00681-9013 

Francisco.pagan@upr.edu 

Mr. Hector Ruiz Torres 

University of Puerto Rico 

Department of Marine Sciences 

Mayagüez, PR 00681-9013 

787-691-7410 

hectorruizt@me.com 

Appendix B. Workshop Participants B-1 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Mr. Jeff Miller Ms. Patricia Bradley (Organizer) 

Virgin Islands National Park US EPA, AED 

1300 Cruz Bay Creek 33 East Quay Road 

St. John, VI 00830 Key West, FL 33040 

340-693-8950 x227 305-809-4690 

William_J_Miller@nps.gov bradley.patricia@epa.gov 

Dr. Jeroen Gerritsen (Facilitator) Dr. Paul Yoshioka 

Aquatic Ecologist University of Puerto Rico 

Tetra Tech, Center for Ecological Sciences Department of Marine Sciences 

400 Red Brook Blvd., Suite 200 Mayagüez, PR 00681-9000 

Owings Mills, MD 21117 Paul.yoshioka@upr.edu 

410-356-8993 

jeroen.gerritsen@tetratech.com Dr. Richard Appeldoorn 

University of Puerto Rico 

Dr. Jorge Bauzá Department of Marine Sciences 

San Juan Bay Estuary Program Mayagüez, PR 00681-9013 

P.O. Box 9509 787-899-2048 x251 

San Juan, PR 00908-9509 Richard.appeldoorn@upr.edu 

787-638-9979 

jbauza@estuario.org Mr. Roberto Viqueira 

Protectores de Cuencas 

Dr. Loretta Roberson Guánica Coordinator 

University of Puerto Rico Box 673 

College of Natural Sciences Yauco, PR 00698 

Ponce de Leon Ave. 787-457-8803 

Rio Piedras, PR 00931-3300 rviqueira@hotmail.com 

787-764-0000 x1-2713 

Loretta.Roberson@gmail.com Dr. Tyler Smith 

University of the Virgin Islands 

Dr. Melanie McField #2 John Brewer’s Bay 

Smithsonian Institution St. Thomas, VI 00802-9990 

Director, Healthy Reefs for Healthy People 340-693-1394 

1755 Coney Dr. tsmith@uvi.edu 

Belize City, Belize, Central America 

501-223-4898 Dr. Vance Vicente 

mcfield@healthyreefs.org Vicente and Associates, Inc. 

Garden Hills Pz 1353 19 

Mr. Miguel Canals Guaynabo, PR 00966 

PR DNER 787-781-6503 

Guánica State Forest vance@prtc.net 

P.O. Box 1185 

Guánica, PR 00653 Dr. William Fisher 

787-821-5706 US EPA, GED 

menqui@hotmail.com 1 Sabine Island Dr. 

Gulf Breeze, FL 32561 

850-934-9394 

Fisher.william@epa.gov 

B-2 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

Appendix C. Workshop Agenda 

(Workshop was compressed to two days due to Tropical Storm Isaac; times shown below are approximate) 

Goal: To develop a conceptual, narrative model that describes how biological attributes of coral 

reefs change along a gradient of increasing anthropogenic stress. 

DAY 1 – Setting the Stage: A Visual Evaluation of Stations 

9:00	 Registration 

9:30	 Purpose of the Workshop 

9:45	 Introductions 

Purpose: Who is attending; organization they represent; what scientific expertise? 

Desired Outcomes: Relaxed atmosphere, prepare to work as a team. 

10:00	 Coral Reef Video Evaluations 

Purpose: Participants individually review coral reef videos, located throughout the 3 rooms in the
 

conference center.
 

Desired Outcomes: Every participant will have evaluated 8 videos.
 

12:00 Lunch 

1:00	 Complete Coral Reef Video Evaluations 

Purpose: Complete final 4 stations. 

Desired Outcomes: Participants have rated EPA stations and documented their rationale. 

2:00	 Break 

2:15	 Freshwater Stream and Estuarine Attributes 

Presenter: Jeroen Gerritsen (Brief introduction to the attributes developed for freshwater streams
 

and estuaries).
 

Purpose: Introduce the stream and estuarine attributes.
 

Desired Outcomes: Understand where others have been and where we hope to go. Further explore 

the attribute concept. 

2:45	 Presentation of Ratings and Discussion of Rationale 

Presenter: Debbie Santavy (ranked stations) 

Purpose: Try to reach consensus on station assignments stating the rationale for the decision. 

Desired Outcomes: Share rating of stations; document criteria considered during selection and 

capture on flip charts. 

Appendix C. Workshop Agenda C-1 
 

 

 

 

 

 

 

 

 

 

 

 

4:30	 Thresholds 

Presenter: Jeroen Gerritsen (management uses of BCG and how to move forward). 

Purpose: Establish preliminary thresholds for different levels of conceptual model. 

Desired Outcomes: What relative abundance of sessile invertebrates for each level: hard corals, 

sponges and gorgonians? What else defines each level? Fish, rugosity, other invertebrates? Any 

inclusion of water quality factors: both qualitative and quantitative. 

5:15 Adjourn 

DAY 2 – Biological Integrity 

9:00	 Biological Integrity Discussion 

Presenters: Debbie Santavy (results from coral reef video evaluations and attributes discussion); 

Experts (share their videos and photos that exhibit full biological integrity of a coral reef); Pat Bradley 

(reference condition); Pat Bradley (list of coral reef taxa). 

Purpose: Discuss biological integrity and reference condition. 

10:30	 Break 

10:45 Reference Condition Discussion 

Desired Outcomes: Preliminary consensus on what the reference station should be. Begin to 

assemble the attributes. 

12:30	 Lunch 

1:30	 Using Data to Rank Stations 

Presenter: Debbie Santavy (overview of EPA data). 

Purpose: Focus thinking about the attributes in breakout groups. 

Desired Outcomes: Begin thinking about levels of condition and lists of associated attributes. 

3:00	 Break 

3:15	 Attributes as Condition Changes 

Purpose: Begin to consider different levels of condition along a human disturbance gradient, using 

visual and data-derived attributes. 

Desired Outcomes: Begin to compile lists of both visual and data-derived attributes that are not 

station specific, but more overarching characteristics. Perhaps develop levels of attributes from data 

metrics to begin populating BCG framework. 

5:00	 Thank you and next steps 

5:30	 Adjourn 

C-2 Workshop on Biological Integrity of Coral Reefs 
 

Appendix D.
 

Tally Sheet – Rating Condition of Coral Reef Videos (1st)
 

Name: _____________________ 

Ballot 

Station 

No. 

Rating 

(Good, Fair, Poor) 

Rationale (indicate 3 most important 

characteristics considered in ranking) 

1 

2 

3 

4 

5 

6 

7 

8 

Appendix D. Tally Sheet (1st) D-1 

 

 

 

Appendix E.
 

Tally Sheet – Rating Condition of Coral Reef Videos (2nd)
 

Name: _____________________ 

Ballot 

Station 

No. 

Rating 

(Good, Fair, Poor) 

Rationale (indicate 3 most important 

characteristics considered in ranking) 

9 

10 

11 

12 

Appendix E. Tally Sheet - (2nd) E-1 

 

 

 

 

 

Appendix F. 

Notes Sheet – Rating Condition of Coral Reef Videos
 

Notes Sheet - Station 1 Rating: Good - - - Fair- - -Poor 

(Circle your condition rating) 

Use this sheet to capture salient points about this station while viewing the video. You also have a 

photo handout of key photos to assist you. The salient points should provide your rationale for 

rating condition as good, fair or poor. 

Appendix F. Notes Sheet F-1 

 

 

Appendix G.
 

Supporting Photos – Rating Condition of Coral Reef Videos
 

The following pages show supporting photos for each station (1 page per station). The experts used 

these as supplemental material to evaluate the videos. 

Appendix G. Supporting Photos G-1 
G-2 Workshop on Biological Integrity of Coral Reefs 
Appendix G. Supporting Photos G-3 
G-4 Workshop on Biological Integrity of Coral Reefs 
Appendix G. Supporting Photos G-5 
G-6 Workshop on Biological Integrity of Coral Reefs 
Appendix G. Supporting Photos G-7 
G-8 Workshop on Biological Integrity of Coral Reefs 
Appendix G. Supporting Photos G-9 
G-10 Workshop on Biological Integrity of Coral Reefs 
Appendix G. Supporting Photos G-11 
G-12 Workshop on Biological Integrity of Coral Reefs 
Appendix G. Supporting Photos G-13 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Appendix H. Workshop Glossary 

Attribute: Any measurable component of a biological system (Karr and Chu 1999).
 

Best attainable condition: A condition that is equivalent to the ecological condition of
 

(hypothetical) least disturbed stations where the best possible management practices are in use.
 

This condition can be determined using techniques such as historical reconstruction, best ecological
 

judgment and modeling, restoration experiments, or inference from data distributions.
 

Biological integrity: The ability of an aquatic ecosystem to support and maintain a balanced,
 

adaptive community of organisms having a species composition, diversity, and functional
 

organization comparable to that of natural habitats within a region.
 

Human disturbance: Human activity that alters the natural state and can occur at or across many
 

spatial and temporal scales.
 

Ecosystem-level functions: Processes performed by ecosystems, including, among other things,
 

primary and secondary production, respiration, nutrient cycling, and decomposition (EPA 2005).
 

Historical condition: The ecological condition at some previous point in history. Conditions
 

reflective of the historic time period may no longer exist in actual ecosystems in an area.
 

Least disturbed condition: The best available existing conditions with regard to physical, chemical,
 

and biological characteristics or attributes of a waterbody within a class or region. These waters
 

have the least amount of human disturbance in comparison to others within the waterbody class,
 

region or basin. Least disturbed conditions can be readily found but may depart significantly from 

natural, undisturbed conditions or minimally disturbed conditions. Least disturbed condition may
 

change significantly over time as human disturbances change (EPA 2005).
 

Minimally disturbed condition: The physical, chemical and biological conditions of a waterbody
 

with very limited or minimal human disturbance in comparison to others within the waterbody class
 

or region. Minimally disturbed conditions can change over time in response to natural processes 

(EPA 2005).
 

Non-native species: Any species that is not naturally found in that ecosystem. Species introduced or
 

spread from one region of the US to another outside their normal range are non-native or nonindigenous, as are species introduced from other continents (EPA 2005).
 

Reference condition: The condition that approximates natural, unimpacted conditions (biological,
 

chemical, physical, etc.) for a waterbody. Reference condition (biological integrity) is best 

determined by collecting measurements at a number of stations in a similar waterbody class or 

region under undisturbed or minimally disturbed conditions (by human activity), if they exist. Since
 

undisturbed or minimally disturbed conditions may be difficult or impossible to find, least disturbed 

conditions combined with historical information, models or other methods, may be used to
 

approximate reference condition as long as the departure from natural or ideal is understood.
 

Reference condition is used as a benchmark to determine how much other water bodies depart 

from this condition due to human disturbance (EPA 2005).
 

Appendix H. Workshop Glossary H-1 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Reference station: A station selected for comparison with stations being assessed. The type of 

stations selected and the type of comparative measures used will vary with the purpose of the
 

comparisons. For the purposes of assessing the ecological condition of stations, a reference station 

is a specific locality on a waterbody that is undisturbed or minimally disturbed and is representative
 

of the expected ecological integrity of other localities on the same waterbody or nearby
 

waterbodies (EPA 2005).
 

Sensitive-rare taxa: Taxa that naturally occur in low numbers relative to total population density
 

but may make up large relative proportion of richness. May be ubiquitous in occurrence or may be
 

restricted to certain microhabitats, but because of low density recorded occurrence is dependent on
 

sample effort. Often stenothermic (having a narrow range of thermal tolerance) or cold-water
 

obligates, commonly k-strategists (populations maintained at a fairly constant level, slower 

development, longer life-span), may have specialized food resource needs or feeding strategies.
 

Generally intolerant to significant alteration of the physical or chemical environment; are often the
 

first taxa observed to be lost from a community (EPA 2005).
 

Sensitive or regionally endemic taxa: Taxa with restricted, geographically isolated distribution
 

patterns (occurring only in a locale as opposed to a region), often due to unique life history
 

requirements. May be long lived, late maturing, low fecundity, limited mobility or require
 

mutualistic relationships with other species. May be listed as threatened, endangered or of special
 

concern species. Predictability of occurrence often low, therefore, requires documented
 

observation. Recorded occurrence may be highly dependent on sample methods, station selection 

and level of effort (EPA 2005).
 

Sensitive taxa: Taxa that are intolerant to a given anthropogenic stress, often the first species
 

affected by the specific stressor to which they are “sensitive" and the last to recover following
 

restoration (EPA 2005).
 

Taxa: A grouping of organisms given a formal taxonomic name such as species, genus, family, etc.
 

(EPA 2005).
 

Taxa of intermediate tolerance: Taxa that comprise a substantial portion of natural communities,
 

which may increase in number in waters which have moderately increased organic resources and
 

reduced competition, but they are intolerant of excessive pollution loads or habitat alteration.
 

These may be r-strategists (early colonizers with rapid turn-over times; boom/bust population
 

characteristics), eurythermal (having a broad thermal tolerance range), or have generalist or
 

facultative feeding strategies enabling them to utilize more diversified food types. They are readily
 

collected with conventional sample methods (EPA 2005).
 

Tolerant taxa: Taxa that comprise a low proportion of natural communities. Tolerant taxa often are
 

tolerant of a broader range of environmental conditions and are thus resistant to a variety of
 

pollution or habitat-induced stress. They may increase in number (sometimes greatly) in the
 

absence of competition. They are commonly r-strategists (early colonizers with rapid turn-over
 

times; boom/bust population characteristics), able to colonize when stress conditions occur.
 

Last survivors (EPA 2005).
 

H -2 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Appendix I. Summary Data Results for BCG Stations 

Table I-1. Scleractinian coral summary statistics for BCG stations (Puerto Rico surveys in 2010 

and 2011). Ave. 3D SA is average 3-dimensional surface area cm2

/m2. SE=standard error of mean. 

BCGStation No.EPA Station No.SpeciesRichness% TotalAbundanceNo.ColoniesShannon Diversity Index(H')Colony Density(#/m2 

)

3D Coral Area(cm 2 /m 2 

)

2D Coral Area(cm 2 /m 2 

)

Rugosity*SE RugosityRating byVisualMediaVisual Rating 

1 125 13 11.61 51 2.040 3.40 6,560 1,533 2.18 0.107 poor/fair 8 

2 15 3 2.68 4 1.040 0.16 185 106 1.12 0.019 poor (worst) 12 

3 113 10 8.93 79 1.657 3.16 9,518 2,843 1.52 0.107 good (best) 1 

4 3 6 5.36 21 1.234 0.84 2,706 565 1.52 0.087 poor 11 

5 19 7 6.25 31 1.261 1.24 18,228 3,673 1.54 0.108 fair/poor 9 

6 14 10 8.93 54 1.793 3.6 5,359 1,530 1.71 0.106 poor 10 

7 16 11 9.82 73 1.971 4.87 14,210 5,089 1.83 0.119 fair 4 

8 108 7 6.25 71 1.512 4.73 19,637 4,549 1.48 0.116 fair 6 

9 109 8 8.04 87 1.410 5.80 20,080 5,917 1.88 0.134 fair 7 

10 1 11 9.82 70 1.784 2.8 11,026 3,698 1.48 0.052 fair 3 

11 46 9 8.04 44 1.827 1.16 11,635 2,598 1.12 0.039 fair 5 

12 25 8 7.14 95 1.469 3.8 9,199 3,498 1.25 0.086 fair 2 

*Rugosity is the linear ratio of 6m divided by the taut linear distance of a 6m chain draped over the tops of corals and along the 

bottom. Rugosity is a reef-scale indicator of reef contour or surface heterogeneity. See Appendix J for formulas. 

Table I-2. Gorgonian summary statistics for BCG stations (Puerto Rico surveys in 2010 and 2011). 

Ave. 3D SA is average 3-dimensional surface area cm2

/m2 or per individual. Maximum number of 

morphologies that can be present at one station is nine. 

BCG Station Morpho. No. Density Ave. 3D Ave. 3D 

Station No. No. Richnessa Individuals #/m2 SAb/m2 SAc/ind 

1 125 4 21 4.2 5,154 1,227 

2 15 0 0 0 0 0 

3 113 7 24 4.8 30,346 6,322 

4 3 0 0 0 0 0 

5 19 0 0 0 0 0 

6 14 6 27 5.4 38,352 7,102 

7 16 8 37 7.4 33,342 4,506 

8 108 2 6 1.2 86 71 

9 109 4 7 1.4 11,229 8,021 

10 1 2 10 2 17,649 8,825 

11 46 7 52 10.4 26,954 2,592 

12 25 8 86 17.2 58,558 3,405 

a: Morphological shapes and regression equations for 3D surface estimation of an individual by morphology in 

Santavy et al., 2012, pp. 36-38. 

b: Ave. 3D SA/m2 = Σ Gorgonian surface area in transect area/total transect area 

c: Ave. 3D SA/ind= Σ Gorgonian surface area in transect area/total # Gorgonians in transect. See Appendix J, Table J-2 for formulas 

Appendix I. Summary Data Results for BCG Stations I-1 
 

 

 

 

 

 

 

Table I-3. Sponge summary statistics for BCG stations (Puerto Rico surveys in 2010 

and 2011). Ave. 3D SA is average 3-dimensional surface area cm2/m2 or per individual. 

Maximum number of morphologies present at one station is eight. 

BCG Station Morpho. No. Density Ave. 3D Ave. 3D 

Station No. No. Richnessa Individuals #/m2 SAb/m2 SAc

/ind 

1 125 3 22 4.4 1,615 367 

2 15 3 20 4 1,146 286 

3 113 1 5 1 48 48 

4 3 2 7 1.4 173 124 

5 19 1 5 1 208 208 

6 14 2 8 1.6 410 256 

7 16 0 0 0 0 0 

8 108 0 0 0 0 0 

9 109 3 7 1.4 1,389 992 

10 1 5 33 6.6 10,776 1,633 

11 46 3 21 4.2 53,824 12,815 

12 25 5 28 5.6 6,213 1,110 

a: Morphological shapes and regression equations for 3D surface estimation of an individual by morphology in 

Santavy et al., 2012, pp. 36-38. 

b: Ave. 3D SA/m2 = Σ Sponge surface area in transect area/total transect area. 

c: Ave. 3D SA/ind= Σ Sponge surface area in transect area/total # Sponges in transect. See Appendix J, Table J-2 for formulas. 

Density of sessile invertebrates no./m2 

20 

Individuals/m2

15 

10 

5 

0 

Coral 

Gorgonian 

Sponge 

1 2 3 4 5 6 7 8 9 10 11 12 

Station no. 

Figure I-1. Comparison of the density of the major sessile invertebrates assessed in the 12 BCG 

stations. 

I-2 Workshop on Biological Integrity of Coral Reefs 
 

 

 

#/m2 

Density of carnivores vs. herbivores 350 

carnivores 2.63 300 herbivores 

250 

0.60 

200 0.22 

6.13 150 5.45 

0.51 

100 1.13 

0.54 1.07 0.75 

1.34 50 0.27 

0 

1 2 3 4 5 6 7 8 9 10 11 12 

Station no. 

Figure I-2. Comparison of density for fish carnivores vs. herbivores at BCG stations. Number above 

bar pairs is the ratio of carnivore/herbivore density. 

Biomass of carnivores vs. herbivores 

25000
 

carnivores 0.24
 

20000 herbivores 

g/m2

15000 

5.45 

10000 0.17 0.16 

9.23 

1.07 

1.49 

5000 0.45 

0.67 3.01 

1.26 0.50 

0 

1 2 3 4 5 6 7 8 9 10 11 12 

Station no. 

Figure I-3. Comparison of biomass for fish carnivores vs. herbivores at BCG stations. Number 

above bar pairs is the ratio of carnivore/herbivore biomass. 

Appendix I. Summary Data Results for BCG Stations I-3 
 

BCG Station 1
 

(Field Station 125_2010)
 

Coral Species Richness: 13
 

Photo rank and rating: 8, Poor/Fair
 

Table I-4. BCG Station 1 data summary for corals and subgroups. See Appendix J for formulas used 

and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 3.40 0.53 0.13 0.13 0.73 

Ave. 3D colony skeletal area (cm2)/colony 2,146 2,462 20,077 417 435 

2 Ave. 3D colony skeletal area (cm2

)/m 7,297 1,313 2,677 56 319 

Ave. 3D coral tissue area (cm2)/colony 1,929 2,284 16,446 417 435 

Ave. 3D 2 coral tissue area (cm2)/m 6,560 1,218 2,193 56 319 

Ave. 2D 2 coral tissue area (cm2)/m 1,533 228 198 54 16 

Figure I -4. Percentages of stony coral species, gorgonian morphologies and sponge morphologies 

for BCG Station 1. 

I-4 Workshop on Biological Integrity of Coral Reefs 
 

 

 

Table I-5. Fish species found in BCG Station 1, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Abudefduf saxatilis Sergeant Major 2 90 

Acanthurus coeruleus Blue Tang 5 167 

Anisotremus surinamensis Black Margate 1 1,274 

Anisotremus virginicus Porkfish 1 9 

Caranx ruber Bar Jack 1 17 

Gramma loreto Fairy Basslet 3 1 

Haemulon flavolineatum French Grunt 1 40 

Halichoeres poeyi Blackear Wrasse 1 5 

Holacanthus bermudensis Blue Angelfish 1 11 

Lutjanus analis Mutton Snapper 1 637 

Lutjanus apodus Schoolmaster 1 215 

Microspathodon chrysurus Yellowtail Damselfish 5 174 

Ocyurus chrysurus Yellowtail Snapper 8 242 

Ophioblennius macclurei Redlip Blenny 3 12 

Pempheris schomburgkii Glassy Sweeper 1 33 

Scarus iseri Striped Parrotfish 2 15 

Sparisoma aurofrenatum Redband Parrotfish 1 40 

Sparisoma viride Stoplight Parrotfish 3 3 

Stegastes adustus Dusky Damselfish 49 510 

Thalassoma bifasciatum Bluehead 55 198 

Appendix I. Summary Data Results for BCG Stations I-5 
BCG Station 2
 

(Field Station 15_2011)
 

Coral Species Richness: 3
 

Photo rank and rating: 12, Poor (Worst)
 

Table I-6. BCG Station 2 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 0.16 0 0 0.08 0 

Ave. 3D colony skeletal area (cm2)/colony 1,248 0 0 980 0 

2 Ave. 3D colony skeletal area (cm2

)/m 200 0 0 78 0 

Ave. 3D coral tissue area (cm2)/colony 1,157 0 0 822 0 

Ave. 3D 2 coral tissue area (cm2)/m 185 0 0 66 0 

Ave. 2D 2 coral tissue area (cm2)/m 106 0 0 37 0 

Figure I-5. Percentages of stony coral species and sponge morphologies for BCG Station 2. 

No gorgonians were present at BCG Station 2. 

I-6 Workshop on Biological Integrity of Coral Reefs 
 

 

 

Table I-7. Fish species found in BCG Station 2, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Acanthurus bahianus Ocean Surgeonfish 10 457 

Anisotremus virginicus Porkfish 5 220 

Canthigaster rostrata Sharpnose Puffer 1 0 

Cephalopholis fulva Coney 2 68 

Chaetodon capistratus Foureye Butterflyfish 7 105 

Elacatinus saucrum Leopard Goby 6 298 

Haemulon flavolineatum French Grunt 10 404 

Haemulon macrostomum Spanish Grunt 1 40 

Halichoeres poeyi Blackear Wrasse 1 26 

Lachnolaimus maximus Hogfish 1 10 

Mulloidichthys martinicus Yellow Goatfish 2 81 

Ocyurus chrysurus Yellowtail Snapper 7 212 

Scarus iseri Striped Parrotfish 1 33 

Stegastes adustus Dusky Damselfish 8 496 

Stegastes diencaeus Longfin Damselfish 4 127 

Stegastes partitus Bicolor Damselfish 4 2 

Stegastes variabilis Cocoa Damselfish 5 49 

Appendix I. Summary Data Results for BCG Stations I-7 
 

BCG Station 3
 

(Field Station 113_2011)
 

Coral Species Richness: 10 

Photo rank and rating: 1, Good (Best) 

Table I-8. BCG Station 3 data summary for corals and subgroups. See Appendix J for formulas used 

and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 3.16 0.92 0 0.48 1.36 

Ave. 3D colony skeletal area (cm2)/colony 4,537 13,445 0 949 704 

2 Ave. 3D colony skeletal area (cm2

)/m 14,337 12,369 0 456 957 

Ave. 3D coral tissue area (cm2)/colony 3,012 8,646 0 626 609 

Ave. 3D 2 coral tissue area (cm2)/m 9,518 7,954 0 300 829 

Ave. 2D 2 coral tissue area (cm2)/m 2,843 2,212 0 135 326 

Figure I-6. Percentages of stony coral species, gorgonian morphologies and sponge morphologies 

for BCG Station 3. 

I-8 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

Table I-9. Fish species found in BCG Station 3, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Acanthurus bahianus Ocean Surgeonfish 1 46 

Acanthurus coeruleus Blue Tang 9 638 

Canthigaster rostrata Sharpnose Puffer 2 14 

Caranx ruber Bar Jack 2 34 

Chaetodon capistratus Foureye Butterflyfish 1 15 

Coryphopterus glaucofraenum Bridled Goby 15 10 

Haemulon macrostomum Spanish Grunt 1 242 

Halichoeres bivittatus Slippery Dick 5 574 

Hypoplectrus chlorurus Yellowtail Hamlet 3 43 

Lutjanus apodus Schoolmaster 2 431 

Microspathodon chrysurus Yellowtail Damselfish 2 324 

Scarus iseri Striped Parrotfish 51 5,749 

Serranus tigrinus Harlequin Bass 1 7 

Sparisoma aurofrenatum Redband Parrotfish 5 482 

Sparisoma viride Stoplight Parrotfish 6 979 

Stegastes adustus Dusky Damselfish 30 360 

Stegastes partitus Bicolor Damselfish 4 32 

Stegastes planifrons Threespot Damselfish 2 13 

Thalassoma bifasciatum Bluehead 21 106 

Appendix I. Summary Data Results for BCG Stations I-9 
BCG Station 4 

(Field Station 3_2011)
 

Coral Species Richness: 6
 

Photo rank and rating: 11, Poor
 

Table I-10. BCG Station 4 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 0.84 0.12 0 0 0.04 

Ave. 3D colony skeletal area (cm2)/colony 4,251 17,387 0 0 157 

2 Ave. 3D colony skeletal area (cm2

)/m 3,571 2,086 0 0 6 

Ave. 3D coral tissue area (cm2)/colony 3,221 10,681 0 0 141 

Ave. 3D 2 coral tissue area (cm2)/m 2,706 1,282 0 0 6 

Ave. 2D 2 coral tissue area (cm2)/m 565 315 0 0 4 

Figure I-7. Percentages of stony coral species and sponge morphologies for BCG Station 4. 

No gorgonians were present at BCG Station 4. 

I-10 Workshop on Biological Integrity of Coral Reefs 
 

 

Table I-11. Fish species found in BCG Station 4, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2

) 

Acanthurus bahianus Ocean Surgeonfish 1 129 

Acanthurus chirurgus Doctorfish 6 629 

Acanthurus coeruleus Blue Tang 5 1,081 

Aulostomus maculatus Trumpetfish 1 256 

Canthigaster rostrata Sharpnose Puffer 1 7 

Chaetodon capistratus Foureye Butterflyfish 1 15 

Decapterus macarellus Mackerel Scad 2 395 

Gymnothorax sp. Moray Eel sp. 1 3 

Haemulon carbonarium Caesar Grunt 5 1,024 

Haemulon chrysargyreum Smallmouth Grunt 5 475 

Haemulon flavolineatum French Grunt 5 609 

Haemulon parra Sailors Choice 1 404 

Halichoeres radiatus Puddingwife 1 168 

Lutjanus apodus Schoolmaster 9 2,193 

Malacanthus plumieri Sand Tilefish 13 318 

Microspathodon chrysurus Yellowtail Damselfish 8 1,296 

Odontoscion dentex Reef Croaker 1 21 

Rypticus saponaceus Greater Soapfish 1 82 

Scarus iseri Striped Parrotfish 10 1,119 

Sparisoma aurofrenatum Redband Parrotfish 3 580 

Sparisoma rubripinne Yellowtail Parrotfish 1 401 

Sparisoma viride Stoplight Parrotfish 1 314 

Stegastes adustus Dusky Damselfish 33 384 

Synodus intermedius Sand Diver 1 339 

Thalassoma bifasciatum Bluehead 3 31 

Appendix I. Summary Data Results for BCG Stations I-11 
 

 

 

 

BCG Station 5
 

(Field Station 19_2011)
 

Coral Species Richness: 7
 

Photo rank and rating: 9, Fair/Poor
 

Table I-12. BCG Station 5 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 1.24 0.2 0.8 0.08 0 

Ave. 3D colony skeletal area (cm2)/colony 23,116 5,030 34,248 520 0 

2 Ave. 3D colony skeletal area (cm2

)/m 28,664 1,006 27,399 42 0 

Ave. 3D coral tissue area (cm2)/colony 14,700 2,950 21,764 520 0 

2 Ave. 3D coral tissue area (cm2

)/m 18,228 590 17,411 42 0 

2 Ave. 2D coral tissue area (cm2

)/m 3,673 71 3,526 16 0 

Figure I-8. Percentages of stony coral species and sponge morphologies for BCG Station 5. 

No gorgonians were present at BCG Station 5. 

I-12 Workshop on Biological Integrity of Coral Reefs 
 

 

Table I-13. Fish species found in BCG Station 5, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Acanthurus bahianus Ocean Surgeonfish 1 46 

Acanthurus coeruleus Blue Tang 2 72 

Anisotremus virginicus Porkfish 1 128 

Aulostomus maculatus Trumpetfish 3 439 

Bodianus rufus Spanish Hogfish 1 32 

Caranx ruber Bar Jack 1 17 

Decapterus macarellus Mackerel Scad 2 275 

Haemulon carbonarium Caesar Grunt 1 41 

Haemulon chrysargyreum Smallmouth Grunt 6 570 

Haemulon flavolineatum French Grunt 63 6,989 

Haemulon macrostomum Spanish Grunt 1 242 

Heteropriacanthus cruentatus Glasseye Snapper 1 214 

Holocentrus adscensionis Squirrelfish 1 237 

Lutjanus apodus Schoolmaster 2 203 

Malacanthus plumieri Sand Tilefish 13 300 

Microspathodon chrysurus Yellowtail Damselfish 3 486 

Mulloidichthys martinicus Yellow Goatfish 7 283 

Myripristis jacobus Blackbar Soldierfish 1 107 

Pempheris schomburgkii Glassy Sweeper 5 164 

Scarus iseri Striped Parrotfish 3 458 

Sparisoma aurofrenatum Redband Parrotfish 2 151 

Sparisoma viride Stoplight Parrotfish 3 521 

Stegastes adustus Dusky Damselfish 14 168 

Stegastes partitus Bicolor Damselfish 1 1 

Thalassoma bifasciatum Bluehead 16 134 

Appendix I. Summary Data Results for BCG Stations I-13 
 

 

 

BCG Station 6 

(Field Station 14_2010)
 

Coral Species Richness: 10
 

Photo rank and rating: 10, Poor
 

Table I-14. BCG Station 6 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 3.6 1.2 0 0.33 1.4 

Ave. 3D colony skeletal area (cm2)/colony 5,431 14,255 0 1,400 466 

2 Ave. 3D colony skeletal area (cm2

)/m 19,552 17,106 0 467 653 

Ave. 3D coral tissue area (cm2)/colony 1,489 3,298 0 1,193 443 

2 Ave. 3D coral tissue area (cm2

)/m 5,359 3,958 0 398 621 

2 Ave. 2D coral tissue area (cm2

)/m 1,530 892 0 141 330 

Figure I-9. Percentages of stony coral species, gorgonian morphologies and sponge morphologies 

for BCG Station 6. 

I-14 Workshop on Biological Integrity of Coral Reefs 
 

 

Table I-15. Fish species found in BCG Station 6, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Acanthurus bahianus Ocean Surgeonfish 1 129 

Acanthurus chirurgus Doctorfish 1 121 

Chaetodon capistratus Foureye Butterflyfish 4 60 

Elacatinus genie Cleaning Goby 1 0 

Epinephelus adscensionis Rock Hind 1 174 

Halichoeres garnoti Yellowhead Wrasse 2 195 

Hypoplectrus chlorurus Yellowtail Hamlet 1 19 

Hypoplectrus puella Barred Hamlet 1 19 

Lutjanus apodus Schoolmaster 1 649 

Mulloidichthys martinicus Yellow Goatfish 2 472 

Ocyurus chrysurus Yellowtail Snapper 1 177 

Scarus iseri Striped Parrotfish 36 632 

Sparisoma aurofrenatum Redband Parrotfish 5 466 

Sparisoma viride Stoplight Parrotfish 11 1,606 

Stegastes diencaeus Longfin Damselfish 3 36 

Stegastes leucostictus Beaugregory 4 31 

Stegastes partitus Bicolor Damselfish 7 24 

Stegastes planifrons Threespot Damselfish 12 229 

Thalassoma bifasciatum Bluehead 12 55 

Appendix I. Summary Data Results for BCG Stations I-15 
 

BCG Station 7
 

(Field Station 16_2010)
 

Coral Species Richness: 11
 

Photo rank and rating: 4, Fair
 

Table I-16. BCG Station 7 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 4.87 1.13 0 0.53 1.53 

Ave. 3D colony skeletal area (cm2)/colony 3,529 10,160 0 895 567 

2 Ave. 3D colony skeletal area (cm2

)/m 17,173 11,515 0 477 870 

Ave. 3D coral tissue area (cm2)/colony 2,920 9,057 0 790 469 

Ave. 3D 2 coral tissue area (cm2)/m 14,210 10,264 0 421 720 

Ave. 2D 2 coral tissue area (cm2)/m 5,089 3,537 0 167 303 

Figure I-10. Percentages of stony coral species and gorgonian morphologies for BCG Station 7. 

No sponges were present at BCG Station 7. 

I-16 Workshop on Biological Integrity of Coral Reefs 
 

 

Table I-17. Fish species found in BCG Station 7, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Acanthurus coeruleus Blue Tang 9 414 

Chaetodon striatus Banded Butterflyfish 2 124 

Chromis multilineata Brown Chromis 16 126 

Haemulon aurolineatum Tomtate 3 21 

Haemulon flavolineatum French Grunt 2 81 

Holocentrus adscensionis Squirrelfish 2 474 

Lutjanus apodus Schoolmaster 1 215 

Microspathodon chrysurus Yellowtail Damselfish 13 1,133 

Ocyurus chrysurus Yellowtail Snapper 10 303 

Pomacanthus paru French Angelfish 1 342 

Scarus iseri Striped Parrotfish 16 1,515 

Sparisoma aurofrenatum Redband Parrotfish 17 475 

Stegastes diencaeus Longfin Damselfish 8 294 

Stegastes leucostictus Beaugregory 2 89 

Stegastes partitus Bicolor Damselfish 3 31 

Thalassoma bifasciatum Bluehead 36 110 

Appendix I. Summary Data Results for BCG Stations I-17 
 

 

 

 

BCG Station 8
 

(Field Station 108_2010)
 

Coral Species Richness: 7 

Photo rank and rating: 6, Fair
 

Table I-18. BCG Station 8 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

Coral Parameters 

All 

Species 

Massive 

Species 

Acroporid 

Species 

Siderastrea 

siderea 

Porites 

astreoides 

Colony density (#/m2) 4.73 0.20 1.47 0.13 1.93 

Ave. 3D colony skeletal area (cm2)/colony 4,938 1,473 14,658 157 258 

2 Ave. 3D colony skeletal area (cm2

)/m 23,372 295 21,499 21 499 

Ave. 3D coral tissue area (cm2)/colony 4,149 949 12,274 157 239 

2 Ave. 3D coral tissue area (cm2

)/m 19,637 190 18,002 21 462 

2 Ave. 2D coral tissue area (cm2

)/m 4,549 52 3,964 10 273 

Figure I-11. Percentages of stony coral species and gorgonian morphologies for BCG Station 8. 

No sponges were present at BCG Station 8. 

I-18 Workshop on Biological Integrity of Coral Reefs 
 

 

 

Table I-19. Fish species found in BCG Station 8, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Abudefduf saxatilis Sergeant Major 3 99 

Acanthurus bahianus Ocean Surgeonfish 3 386 

Acanthurus coeruleus Blue Tang 31 1,479 

Aulostomus maculatus Trumpetfish 1 130 

Haemulon flavolineatum French Grunt 1 111 

Halichoeres bivittatus Slippery Dick 4 182 

Halichoeres maculipinna Clown Wrasse 6 24 

Halichoeres radiatus Puddingwife 1 0 

Lutjanus apodus Schoolmaster 4 341 

Microspathodon chrysurus Yellowtail Damselfish 28 961 

Ophioblennius macclurei Redlip Blenny 1 4 

Pomacanthus paru French Angelfish 1 156 

Scarus iseri Striped Parrotfish 69 4,592 

Sparisoma aurofrenatum Redband Parrotfish 4 332 

Sparisoma viride Stoplight Parrotfish 2 326 

Stegastes diencaeus Longfin Damselfish 54 603 

Stegastes partitus Bicolor Damselfish 6 3 

Thalassoma bifasciatum Bluehead 98 331 

Appendix I. Summary Data Results for BCG Stations I-19 
 

BCG Station 9
 

(Field Station 109_2010)
 

Coral Species Richness: 9
 

Photo rank and rating: 7, Fair
 

Table I-20. BCG Station 9 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 5.80 3.47 0 0.53 0.67 

Ave. 3D colony skeletal area (cm2)/colony 9,091 8,102 0 806 781 

2 Ave. 3D colony skeletal area (cm2

)/m 52,731 28,088 0 430 521 

Ave. 3D coral tissue area (cm2)/colony 3,462 4,040 0 734 739 

Ave. 3D 2 coral tissue area (cm2)/m 20,080 14,006 0 391 493 

Ave. 2D 2 coral tissue area (cm2)/m 5,917 4,015 0 213 298 

Figure I-12. Percentages of stony coral species, gorgonian morphologies and sponge 

morphologies for BCG Station 9. 

I-20 Workshop on Biological Integrity of Coral Reefs 
 

 

Table I-21. Fish species found in BCG Station 9, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Abudefduf saxatilis Sergeant Major 4 263 

Acanthurus bahianus Ocean Surgeonfish 1 129 

Acanthurus chirurgus Doctorfish 10 1,206 

Acanthurus coeruleus Blue Tang 76 11,429 

Anisotremus virginicus Porkfish 3 851 

Aulostomus maculatus Trumpetfish 1 442 

Cephalopholis cruentata Graysby 1 178 

Chaetodon striatus Banded Butterflyfish 2 25 

Coryphopterus glaucofraenum Bridled Goby 10 7 

Haemulon carbonarium Caesar Grunt 3 915 

Haemulon plumierii White Grunt 1 539 

Halichoeres bivittatus Slippery Dick 2 342 

Holocentrus adscensionis Squirrelfish 1 433 

Hypoplectrus chlorurus Yellowtail Hamlet 3 12 

Lutjanus apodus Schoolmaster 2 431 

Microspathodon chrysurus Yellowtail Damselfish 7 402 

Mulloidichthys martinicus Yellow Goatfish 1 236 

Scarus iseri Striped Parrotfish 19 98 

Sparisoma aurofrenatum Redband Parrotfish 4 1,008 

Sparisoma viride Stoplight Parrotfish 16 5,024 

Stegastes diencaeus Longfin Damselfish 30 348 

Stegastes leucostictus Beaugregory 2 20 

Stegastes partitus Bicolor Damselfish 18 79 

Stegastes planifrons Threespot Damselfish 2 24 

Thalassoma bifasciatum Bluehead 4 14 

Appendix I. Summary Data Results for BCG Stations I-21 
 

 

BCG Station 10
 

(Field Station 2011_1)
 

Coral Species Richness: 11
 

Photo rank and rating: 3, Fair
 

Table I-22. BCG Station 10 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 2.8 1.88 0.04 0.08 0.4 

Ave. 3D colony skeletal area (cm2

)/colony 7,205 10,095 9,503 3,662 794 

2 Ave. 3D colony skeletal area (cm2

)/m 20,174 18,979 380 293 317 

Ave. 3D coral tissue area (cm2

)/colony 3,938 5,549 0 1,405 640 

Ave. 3D 2 coral tissue area (cm2

)/m 11,026 10,432 0 112 256 

Ave. 2D 2 coral tissue area (cm2

)/m 3,698 3,496 0 50 94 

Figure I-13. Percentages of stony coral species, gorgonian morphologies and sponge morphologies 

for BCG Station 10. 

I-22 Workshop on Biological Integrity of Coral Reefs 
 

 

Table I-23. Fish species found in BCG Station 10, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Chaetodon capistratus Foureye Butterflyfish 2 30 

Decapterus macarellus Mackerel Scad 4 250 

Haemulon flavolineatum French Grunt 22 2,441 

Hypoplectrus chlorurus Yellowtail Hamlet 2 24 

Malacanthus plumieri Sand Tilefish 1 24 

Malacoctenus triangulatus Saddled Blenny 4 1 

Odontoscion dentex Reef Croaker 14 804 

Pomacanthus paru French Angelfish 2 2,161 

Scarus iseri Striped Parrotfish 6 45 

Sparisoma viride Stoplight Parrotfish 15 789 

Stegastes partitus Bicolor Damselfish 3 2 

Stegastes planifrons Threespot Damselfish 96 1,982 

Appendix I. Summary Data Results for BCG Stations I-23 
 

BCG Station 11
 

(Field Station 46_2011)
 

Coral Species Richness: 9 

Photo rank and rating: 5, Fair
 

Table I-24. BCG Station 11 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 1.76 0.16 0.60 0.20 0.60 

Ave. 3D colony skeletal area (cm2)/colony 8,236 639 21,258 1,210 422 

2 Ave. 3D colony skeletal area (cm2

)/m 14,495 102 12,755 242 253 

Ave. 3D coral tissue area (cm2)/colony 6,610 495 16,902 491 363 

Ave. 3D 2 coral tissue area (cm2)/m 11,635 79 10,141 98 218 

Ave. 2D 2 coral tissue area (cm2)/m 2,598 41 2,187 44 96 

Figure I-14. Percentages of stony coral species, gorgonian morphologies and sponge morphologies 

for BCG Station 11. 

I-24 Workshop on Biological Integrity of Coral Reefs 
 

 

Table I-25. Fish species found in BCG Station 11, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Acanthurus bahianus Ocean Surgeonfish 21 959 

Acanthurus coeruleus Blue Tang 7 831 

Aulostomus maculatus Trumpetfish 1 15 

Caranx ruber Bar Jack 20 134 

Cephalopholis cruentata Graysby 1 82 

Chaetodon capistratus Foureye Butterflyfish 10 150 

Chaetodon striatus Banded Butterflyfish 4 247 

Haemulon carbonarium Caesar Grunt 15 1,543 

Haemulon chrysargyreum Smallmouth Grunt 30 1,011 

Haemulon flavolineatum French Grunt 15 606 

Halichoeres garnoti Yellowhead Wrasse 1 82 

Halichoeres maculipinna Clown Wrasse 1 5 

Halichoeres radiatus Puddingwife 4 68 

Holocentrus rufus Longspine Squirrelfish 2 190 

Lutjanus apodus Schoolmaster 5 185 

Malacanthus plumieri Sand Tilefish 15 367 

Microspathodon chrysurus Yellowtail Damselfish 14 1,204 

Myripristis jacobus Blackbar Soldierfish 1 107 

Scarus iseri Striped Parrotfish 46 386 

Sparisoma aurofrenatum Redband Parrotfish 2 119 

Stegastes adustus Dusky Damselfish 11 132 

Stegastes leucostictus Beaugregory 1 1 

Stegastes partitus Bicolor Damselfish 10 45 

Thalassoma bifasciatum Bluehead 170 698 

Appendix I. Summary Data Results for BCG Stations I-25 
 

 

BCG Station 12
 

(Field Station 25_2011)
 

Coral Species Richness: 8
 

Photo rank and rating: 2, Fair
 

Table I-26. BCG Station 12 data summary for corals and subgroups. See Appendix J for formulas 

used and species abbreviations. 

All Massive Acroporid Siderastrea Porites 

Coral Parameters Species Species Species siderea astreoides 

Colony density (#/m2) 3.8 1.56 0 0.36 1.72 

Ave. 3D colony skeletal area (cm2)/colony 3,525 7,563 0 592 740 

2 Ave. 3D colony skeletal area (cm2

)/m 13,396 11,799 0 213 1,273 

Ave. 3D coral tissue area (cm2)/colony 2,421 5,037 0 460 619 

Ave. 3D 2 coral tissue area (cm2)/m 9,199 7,857 0 166 1,065 

Ave. 2D 2 coral tissue area (cm2)/m 3,498 2,928 0 61 472 

Figure I-15. Percentages of stony coral species, gorgonian morphologies and sponge 

morphologies for BCG Station 12. 

I-26 Workshop on Biological Integrity of Coral Reefs 
 

 

Table I-27. Fish species found in BCG Station 12, with density and biomass for 100 m2 transect. 

Abundance/ Total Biomass 

Fish Species Common Name 100 m2 (g/100 m2) 

Acanthurus bahianus Ocean Surgeonfish 2 91 

Acanthurus chirurgus Doctorfish 1 44 

Haemulon flavolineatum French Grunt 3 262 

Labrisomus nuchipinnis Hairy Blenny 1 33 

Lutjanus apodus Schoolmaster 1 101 

Myripristis jacobus Blackbar Soldierfish 1 107 

Scarus iseri Striped Parrotfish 8 85 

Sparisoma aurofrenatum Redband Parrotfish 6 247 

Sparisoma viride Stoplight Parrotfish 4 534 

Stegastes adustus Dusky Damselfish 1 12 

Appendix I. Summary Data Results for BCG Stations I-27 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Appendix J. Formulas Used for Calculating Condition Metrics 

1. Stony Corals 

Coral metrics 

Colony surface area
 

Coral abundance
 

Percent live tissue
 

Live colony three-dimensional surface area
 

Live colony two-dimensional surface area
 

Colony condition measurements 

Every scleractinian coral within a 25 m2 transect area (25 m x 1 m) and greater than 10 cm was 

identified to species. The maximum height and diameter of each colony was measured in cms, and 

the percent of living coral tissue on the skeleton of the colony was estimated in 10% increments. 

The percent tissue (living coral) was estimated for the entire colony in three dimensions, not only 

from an aerial planar view. The observations and measurements made for each coral colony 

included: scleractinian taxon, height (cm), maximum diameter (cm) and percent living colony tissue. 

Formulas 

Colony surface area (CSA) was the total three-dimensional colony surface area (cm2) including both 

living and dead portions of a single coral colony. 

CSA = πr2 M 

r = [colony height (cm) + (colony diameter (cm)/2)] /2 

M = morphological conversion factor (values of 1, 2, 3, or 4 depending on coral 

species morphology), see Table J-1 

Coral abundance (n) was total number of colonies in the entire transect area 

% Live tissue (LT) was estimation of percent live tissue on a single coral colony over the entire 

surface area. It was estimated for every coral colony in transect. 

Live colony 3D surface area (LCSA_3D) was a calculated value for the total three-dimensional colony 

surface area (cm2) of only living tissue on a single coral colony. 

LCSA_3D = CSA ∗ (LT/100) 

Live colony 2D surface area (LCSA_2D) was a calculated value for the total planar colony surface 

area (cm2

) of living tissue on a single coral colony as though it were viewed from above. This 

calculation assumes equal distribution of living tissue on a colony, which was initially recorded for 

three dimensions rather than two. It approximates percent coral cover used as the standard in 

many historical assessments. 

LCSA_2D = π [colony diameter (cm)/2]

2 ∗ (LT/100) 

Appendix J. Formulas Used for Calculating Condition Metrics J-1 
 

 

 

Coral metrics calculated for each BCG station 

Ave. 3D colony skeletal area (cm2)/colony = Σ CSA/n 

Ave. 3D colony skeletal area (cm2)/m2 = Σ CSA/area of transect

Ave. 3D coral tissue (live) area (cm2)/colony = Σ LCSA_3D/n 

Ave. 3D coral tissue (live) area (cm2

)/m2 = Σ LCSA_3D/area of transect 

Ave. 2D coral tissue (live) area (cm2)/m2 = Σ LCSA_2D/area of transect

Table J-1. Stony corals included in Western Atlantic and Caribbean assessments (as provided by 

Humann and DeLoach 2002) with the three-letter identification code and the morphological 

conversion factor for calculating 3D surface area (Santavy et al. 2012). 

Genus and Species ID Code Conversion Factor 

Acropora cervicornis Acer 4 

Acropora palmata Apal 4 

Acropora prolifera Apro 4 

Agaricia agaricites Aaga 1 

Agaricia fragilis Afra 1 

Agaricia humilis Ahum 1 

Agaricia lamarcki Alam 1 

Agaricia tenuifolia Aten 3 

Cladocora arbuscula Carb 2 

Colpophyllia natans Cnat 2 

Dendrogyra cylindrus Dcyl 3 

Dichocoenia stokesii Dsto 2 

Diploria clivosa1 Dcli 2 

Diploria labyrinthiformis Dlab 2 

Diploria strigosa1 Dstr 2 

Eusmilia fastigiata Efas 3 

Favia fragum Ffra 2 

Leptoseris cucullata Lcuc 1 

Isophyllastrea rigida Irig 2 

Isophyllia sinuosa Isin 2 

Madracis decactis Mdec 3 

Madracis formosa Mfor 3 

Madracis mirabilis Mmir 3 

Madracis pharensis Mpha 1 

Manicina areolata Mare 2 

Meandrina meandrites Mmea 2 

Millepora complanata Mcom 3 

Montastraea annularis2 Mann 3 

Montastraea cavernosa Mcav 2 

Montastraea faveolata2 Mfav 2 

J-2 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

Table J-1. (continued) 

Genus and Species ID Code Conversion Factor 

Mussa angulosa Mang 2 

Mycetophyllia aliciae Mali 1 

Mycetophyllia danaana Mdan 1 

Mycetophyllia ferox Mfer 1 

Mycetophyllia lamarckiana Mlam 1 

Oculina varicosa Ovar 3 

Porites astreoides Past 2 

Porites colonensis Pcol 1 

Porites divaricata Pdiv 3 

Porites furcata Pfur 3 

Porites porites Ppor 3 

Siderastrea siderea Ssid 2 

Solenastrea bournoni Sbou 2 

Solenastrea hyades Shya 3 

Stephanocoenia intersepta Sint 2 

1: This report does not adopt the new classifications for Diploria strigosa and Diploria clivosa as the 

original genus Pseudodiploria (Budd et al. 2012). 

2: This report does not adopt the new classification for the Montastraea annularis species-complex 

(Montastraea annularis, Montastraea faveolata and Montastraea franksi) which has been reclassified 

as the original genus Orbicella (Budd et al. 2012). 

2. Rugosity 

Rugosity measurement and metric 

Rugosity was the linear ratio of a 6 m chain length compared to the taunt linear distance in 

centimeters of a draped chain. Rugosity is a reef-scale indicator of reef contour. It was determined 

using a chain-transect method that compares the length of a chain draped along the top of corals 

and along the bottom of the reef to the length of a taut line across the same linear distance using a 

separate tape measure, laid parallel but not on top of the transect tape. The linked chain was placed 

such that it follows the relief of hard bottom substrate. The chain was placed on top of any hard 

substrate encountered, but not on top of gorgonians or sponges since only hard bottom rugosity 

was being measured. 

Formula 

Rugosity was the ratio of the overall length of chain draped over the reef contour divided by the 

straight horizontal distance between the beginning and the end of the chain. Therefore, if 6 m of 

chain is laid out over a 4 m horizontal distance, the rugosity is 6/4 = 1.5 for that segment. Rugosity 

will always be > 1. Higher values relate to increased rugosity or reef relief. The average rugosity was 

calculated per transect. 

Appendix J. Formulas Used for Calculating Condition Metrics J-3 
 

 

 

 

 

 

 

 

 

 

 

3. Fish 

Fish metrics 

Abundance at lowest taxonomic level possible
 

Length in cms
 

Biomass of fish in g/100 m2
 

Fish measurements 

Fish contained within a 100 m2 transect area, 25 m length x 4 m width (height was water depth) 

were recorded to the lowest taxonomic level possible. All fish greater than 3 cm in size were 

included in the assessment. Each fish was scored as 5 cm size class increments up to 35 cm for fork 

length using visual estimation. If a fish was longer than 35 cm, an estimate of the actual fork length 

was made. The fork length was measured from the fish snout (with mouth closed) to the fork at the 

base of the tail or caudal fin. Observations and measurements made for each fish included taxon 

and size class. 

Formulas 

Abundance (n) was total number of fish in the entire transect area 

Density was the number of fish of a single taxon per 100 m2 

Biomass (W) was the weight recorded as g/100 m2 of a single fish 

W = αLβ

L = fork length as midpoint between 5 cm increment class (e.g., 10–15 cm class using 

12.5 as length in calculation). L > 35 cm uses actual length. 

α and β are species specific coefficients obtained from FishBase (www.fishbase.org)

for calculating fish biomass (see Appendix A in Santavy et al. 2013). Biomass 

for species with no published length-weight relationships can be calculated 

using terms for the closest congener based on morphology. 

Fish metrics calculated for each BCG station 

Total biomass for each taxon per 100 m2 = ∑i=1

n W 

J-4 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

 

 

 

 

෎

෎

4. Gorgonians 

Gorgonian metrics 

Density was the number of individuals/m2 

Average three-dimensional surface area gorgonian/m2 

Average three-dimensional surface area gorgonian/individual 

Gorgonian measurements 

Every gorgonian ≥ 10 cm (in any dimension) that falls within the quadrat was classified as one of ten 

gorgonian morphologies (Table J-2). If the base of the gorgonian was in the quadrat, it was 

considered in the transect area. Colony height (greatest distance from substrate) and maximum 

diameter (parallel to the substrate) were measured in cms. The observations and measurements 

made for each individual were gorgonian colony shape, height and maximum diameter. Although 

gorgonians are prominent reef inhabitants, they are often excluded from monitoring programs. This 

is partially because they are not widely recognized for their important functional contributions to 

reef environments, and partially because taxonomic distinctions can be difficult. In this approach, 

classification was based on morphology, categorized by predetermined shapes, which can be easier 

to apply than taxonomy and still can influence their ecosystem functions. 

Formulas and BCG station metrics 

Abundance (n) was total number of gorgonians in the entire transect area 

Average three-dimensional surface area of each gorgonian morph/m2 

= 

n

(regression equation for SA in Table J − 2) 

area of transect 

i=1

Average three-dimensional surface area of each gorgonian morph/colony = 

n

(regression equation for SA in Table J − 2) 

n

i=1

Appendix J. Formulas Used for Calculating Condition Metrics J-5 
 

 

 

 

 

 

 

Table J-2. Gorgonian morphological shapes, abbreviations, simulated model, in situ example 

and regression models to estimate three-dimensional surface area (Santavy et al. 2013). 

Gorgonian 

Morphology Species Example 

Simulated 

Model in situ Example Surface Area Estimations 

Sea Fans Planar (fan pl) SA=0.68h2+0.66d2–3.61 

(Gorgonia 

ventalina, 

Leptogorgia) 

Three-dimensional SA=0.0113h3+106d–1190 

(3D fan) 

(Gorgonia 

flabellum)
 

Sea Rods 

branch and 

branchlet diameter 

≥ 15–≤30 mm 

Unbranched (SR ub) 

digitate form 

(Briareum) 

Branched (SR br) 

(Plexaura) 

Bushy (SR bush) 

(Eunicea fusca) 

Planar (SR pl) 

(Eunicea 

tourneforti) 

SA=0.341d3+11.2h–127 

SA=1.46d2+399 

SA=0.0288h3+ 939 

SA=76.4d–806 

Sea Whips Branched (SW br) SA=–0.479h3+3.37h2– 

(Pterogorgia) 51.3h+354 branch and 

branchlet diameter 

≥5–≤15 mm 

Bushy (SW bush) SA=0.0672d3+1610 

(Pterogorgia 

guadalupensi)
 

Sea Plumes (Plume) SA=4.77h2

–2990 

(Muriceopsis smallest branch 

flavida, and branchlet 

Pseudopterogorgia) diameter usually 

≤5 mm 

Encrusting (Briareum, SA=dw 

Gorgonians Erythopodium) 

Minimum height (h) and diameter (d) of colony size required for use in the equations. h is the 

maximum colony height measured in cm, d is the maximum colony diameter measured in cm. 

J-6 Workshop on Biological Integrity of Coral Reefs 
 

 

 

 

 

 

 

 

 

෍

෍

5. Sponges 

Sponge metrics 

Density was the number of individuals/m2 

Average three-dimensional surface area of sponges/m2 

Average three-dimensional surface area of sponges/individual 

Sponge measurements 

Every sponge ≥ 10 cm (in any dimension) falling within the quadrat was classified as one of ten 

sponge morphologies (Table J-3). If the base of sponge was in the quadrat, it was considered in the 

transect area. Colony height (greatest distance from substrate) and maximum diameter (parallel to 

the substrate) were recorded in cms. The observations and measurements made for each sponge 

were colony shape, height and maximum diameter. Although sponges are one of the most 

prominent sessile invertebrates on coral reefs, they are often overlooked in monitoring programs. 

This may be in part because sponge taxonomic classification is confounded by high diversity and 

morphological plasticity. In this approach, classification was based on morphology rather than 

taxonomy and can influence their ecosystem functions. 

Formulas and BCG station metrics 

Abundance (n) was total number of sponges in the entire transect area 

Average three-dimensional surface area of each sponge morph/m2 

= 

n (regression equation for SA in Table J−3) 

area of transect i=1

Average three-dimensional surface area of each sponge morph per individual = 

n (regression equation for SA in Table J−3) 

n i=1

Appendix J. Formulas Used for Calculating Condition Metrics J-7 
 

 

 

Table J-3. Sponge morphological shapes, abbreviations, simulated model, in situ example and 

regression models to estimate surface area (Santavy et al. 2013). 

Sponge 

Morphology Species Example 

Simulated 

Model 

in situ 

Example Surface Area Estimations 

Barrel Xestospongia SA=4.31d2 + 0.827h2 +108 

muta, 

Verongula 

reiswigi 

Vase Callyspongia SA=3.71h2–161 

plicifera, 

Callyspongia 

vaginalis 

Globe Iricinia strobilina, SA=1.88h2 +0.0573d3+83.3 

Spheciospongia 

vesparium 

Tube Aplysina archeri, SA=0.493d3+109 

Aplysina fistularis 

Mound Oligoceras SA=30.0h+18.7d–193 

hemorrhages, 

Iricinia felix 

Rod Aplysina SA=7.69h+1.83d3–33.5 

cauliformis, 

Niphates erecta 

Bushy Aplysina fulva SA=0.462h2+0.834d2+19.3 

Branched Iotrochota SA=18.8d+7.97h–132 

Ropey birotulata 

Encrusting Amphimedon SA=dw 

compressa, 

Chrondrilla 

caribensis 

Minimum height (h) and diameter (d) of colony size required for use in the equations. h is the 

maximum colony height measured in cm, d is the maximum colony diameter measured in cm. 

J-8 Workshop on Biological Integrity of Coral Reefs 
 

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Environmental Protection 

Agency 

Office of Research and Development 

National Health and Environmental

 Effects Research Laboratory 

Atlantic Ecology Division 

Narragansett, RI 02882 

Official Business 

Penalty for Private use 

$300 

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