&EPA United States Environmental Protection Agency 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 decision- making. 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, Rl. EPA/600/R-13/350. This document can be downloaded from: http://water.epa.gov/scitech/swguidance/standards/criteria/aqlife/biocriteria/technical_index.cfm 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 ill ------- Appendices A. References A-l B. Workshop Participants B-l C. Workshop Agenda C-l D. Tally Sheet - Rating Condition of Coral Reef Videos (1st) D-l E. Tally Sheet - Rating Condition of Coral Reef Videos (2nd) E-l F. Notes Sheet - Rating Condition of Coral Reef Videos F-l G. Supporting Photos - Rating Condition of Coral Reef Videos G-l H. Workshop Glossary H-l I. Summary Data Results for BCG Stations 1-1 J. Formulas Used for Calculating Condition Metrics J-l iv Workshop on Biological Integ ;rity 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 Curacao (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 1-1. Comparison of the density of the major sessile invertebrates assessed in the 12 BCG stations 1-2 1-2. Comparison of density for fish carnivores vs. herbivores at BCG stations 1-3 1-3. Comparison of biomass for fish carnivores vs. herbivores at BCG stations 1-3 1-4. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 1 1-4 1-5. Percentages of stony coral species and sponge morphologies for BCG Station 2 1-6 1-6. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 3 1-8 1-7. Percentages of stony coral species and sponge morphologies for BCG Station 4 1-10 1-8. Percentages of stony coral species and sponge morphologies for BCG Station 5 1-12 1-9. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 6 1-14 1-10. Percentages of stony coral species and gorgonian morphologies for BCG Station 7 1-16 1-11. Percentages of stony coral species and gorgonian morphologies for BCG Station 8 1-18 1-12. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 9 1-20 1-13. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 10 1-22 1-14. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 11 1-24 1-15. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 12 1-26 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 1-1. Scleractinian coral summary statistics for BCG stations 1-1 1-2. Gorgonian summary statistics for BCG stations 1-1 1-3. Sponge summary statistics for BCG stations 1-2 1-4. BCG Station 1 data summary for corals and subgroups 1-4 1-5. Fish species found in BCG Station 1, with density and biomass for 100m2 transect 1-5 1-6. BCG Station 2 data summary for corals and subgroups 1-6 1-7. Fish species found in BCG Station 2, with density and biomass for 100m2 transect 1-7 1-8. BCG Station 3 data summary for corals and subgroups 1-8 1-9. Fish species found in BCG Station 3, with density and biomass for 100m2 transect 1-9 1-10. BCG Station 4 data summary for corals and subgroups 1-10 1-11. Fish species found in BCG Station 4, with density and biomass for 100m2 transect 1-11 1-12. BCG Station 5 data summary for corals and subgroups 1-12 1-13. Fish species found in BCG Station 5, with density and biomass for 100m2 transect 1-13 1-14. BCG Station 6 data summary for corals and subgroups 1-14 1-15. Fish species found in BCG Station 6, with density and biomass for 100m2 transect 1-15 1-16. BCG Station 7 data summary for corals and subgroups 1-16 1-17. Fish species found in BCG Station 7', with density and biomass for 100m2 transect 1-17 1-18. BCG Station 8 data summary for corals and subgroups 1-18 1-19. Fish species found in BCG Station 8, with density and biomass for 100m2 transect 1-19 1-20. BCG Station 9 data summary for corals and subgroups 1-20 1-21. Fish species found in BCG Station 9, with density and biomass for 100m2 transect 1-21 1-22. BCG Station 10 data summary for corals and subgroups 1-22 1-23. Fish species found in BCG Station 10, with density and biomass for 100m2 transect 1-23 1-24. BCG Station 11 data summary for corals and subgroups 1-24 1-25. Fish species found in BCG Station 11, with density and biomass for 100m2 transect 1-25 1-26. BCG Station 12 data summary for corals and subgroups 1-26 1-27. Fish species found in BCG Station 12, with density and biomass for 100m2 transect 1-27 J-l. 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 Intei ;rity 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, Rl. 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 Algae (diatoms; red, green, blue-green and brown algae) Mangroves Seagrasses (Marine Phanerogams) Sponges (Phylum Porifera) Corals, anemones, jellyfish (Phylum Cnidaria) Unsegmented worms (Phylum Nemertea) Bivalves, snails, octopus, mollusks, nudibranchs (Phylum Mollusca) Segmented worms, polychaetes (Phylum Annelida) Ostracods, crabs, shrimp (Phylum Arthropoda) Starfish, sea urchins, brittle stars (Phylum Echinodermata) Bryozoans (Phylum Ectoprocta) Fishes (Superclass Osteichthyes), sharks, rays (Class Chondrichthyes) Reptiles (turtles, snakes) Mammals # Species 492 5 7 61 171 8 1,176 129 342 165 131 677 5 18 Source Ballantine and Aponte 1997a, b; Ballantine and Aponte 2002 Cerame-Vivas 2001 Vicente 1992 Wilson 1902; Weil 2005 Vaughan 1902; Hargitt and Rogers 1902; Almy and Carrion-Torres 1963; Garcia et al. 2003; Weil 2005 Coe 1902 Dall and Simpson 1902; Grana 1993; Ortiz 1998; Garcia-Rios 2003 Treadwell 1902, 1939; Long 1975 Benedict 1902; Bigelow 1902; Moore 1902; Rathbun 1902; Menzies and Glynn 1968 Clark 1902, 1933 Osburn 1940 Dennis 2000; Dennis et al. 2004 Rivero 1978 Belleretal. 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 offish 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 Montastraea- dominated 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 (Buddetal. 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). 1-4 Workshop on Biological Integrity of Coral Reefs ------- 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 etal. 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; Croquer 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 species- complex 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 Chapter 1. Introduction 1-5 ------- 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: Eusmiliafastigiata (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 NOAANMFS. 2014: NOAA NMFS proposed seven Atlantic/Caribbean corals as endangered: Acropora cervicornis, Acropora palmata, Dendrogyra cylindrus, Orbicella annularis, Orbicellafaveolata, 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 0. annularis, 0. faveolata, 0. 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 (Buddetal. 2012). 1-6 Workshop on Biological Integrity of Coral Reefs ------- 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 (Guaynia, meaning "a place with water") on the shores of Guanica Bay. The narrow channel and calm waters of Guanica 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 Guanica sugar mill. The Central Guanica 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 Chapter 1. Introduction 1-7 ------- 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 Guanica 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 Guanica 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. 1-8 Workshop on Biological Integrity of Coral Reefs ------- 1955: Guanica Lagoon was drained to increase land available for agriculture. 1970s: Government subsidies and support for sun-grown coffee were implemented. 1981: Guanica 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-Lopez 2001) and increasing sediment deposition in Guanica 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 Guanica 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 German (population 12,055), Guanica (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 Guanica 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 Agriculture Urban development Fishing Increased global CO2 emissions from power generation and transportation Stressors Increased sediment, nutrient, pesticide and herbicide loads to aquatic ecosystems Increased sewage (nutrients and pathogens), stormwater runoff (sediment, contaminants) Overexploitation offish populations; by-catch; damage from fishing gear and boats 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. 1-10 Workshop on Biological Integrity of Coral Reefs ------- 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 (Rl), 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. 1-12 Workshop on Biological Integrity of Coral Reefs ------- 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). The Biological Condition Gradient: Biological Response to Increasing Levels of Stress Levels of Biological Condition Level 1. Natural structural, functional, and taxonomic integrity is preserved. Level 2. Structure & function similar to natural community with some additional taxa & biomass; ecosystem level functions are fully maintained. Level 3. Evident changes in structure due to loss of some rare native taxa; shifts in relative abundance; ecosystem level functions fully maintained. Level 4. Moderate changes in structure due to replacement of some sensitive ubiquitous taxa by more tolerant taxa; ecosystem functions largely maintained. Level 5. Sensitive taxa markedly diminished; conspicuously unbalanced distribution of major taxonomic groups; ecosystem function shows reduced complexity & redundancy. Level 6. Extreme changes in structure and ecosystem function; wholesale changes in taxonomic composition; extreme alterations from normal densities. Watershed, habitat, flow regime and water chemistry as naturally occurs. Chemistry, habitat, and/or flow regime severely altered from natural conditions. 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). I. 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). VIM. 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 offish 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. 1-14 Workshop on Biological Integrity of Coral Reefs ------- 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) (Yoderand Rankin 1995 a, b; Yoderand 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 1 2 3 4 5 6 7 8 9 10 11 12 Year 2010 2011 2011 2011 2011 2010 2010 2010 2010 2011 2011 2011 EPA station PR_2010_125 PR_2011_15 PR_2011_113 PR_2011_03 PR_2011_19 PR_2010_14 PR_2010_16 PR_2010_108 PR_2010_109 PR_2011_01 PR_2011_46 PR_2011_25 Latitude 17.92486 17.98198 17.95942 17.94420 17.94180 17.93875 17.93922 17.94085 17.95373 17.96380 17.93418 17.93670 Longitude -66.20363 -66.77228 -67.03902 -66.91638 -66.88060 -67.10927 -67.06197 -67.07708 -67.05012 -67.04980 -67.10108 -66.88660 Depth (ft.) 20 23 21 21 12 27 24 12 16 11 17 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. 1 2 3 4 5 6 7 8 9 10 11 12 Table 2-3 stations. between No. % Good Good 1 0 13 0 0 0 4 0 1 5 2 6 . Rankings 5 0 65 0 0 0 20 0 5 25 10 30 given Abbreviations: G No. Fair 9 0 7 2 10 6 16 15 12 14 17 12 % Fair 45 0 35 10 50 30 80 75 60 70 85 60 by experts after rated No. Poor 10 20 0 18 10 14 0 5 7 1 1 2 % Poor 50 100 0 90 50 70 0 25 35 5 5 10 Majority Rating Poor/Fair Poor Good Poor Fair/Poor Poor Fair Fair Fair Fair Fair Fair visually evaluating videos good; F rated fair; P rated Weighted Overall Score 65 20 165 28 60 44 120 80 77 121 106 122 Rank 8 12 1 11 9 10 4 6 7 3 5 2 and photographs for poor. Some ratings were intermc two classes. Station Number Expert 1 Appeldoorn P Ballantine F Bauza F Canals F Cuevas F Diaz F/G Fisher P Hutchins P McField P/F Miller F Pagan F/P Ramos F Roberson P Ruiz F Sabat P Smith P Szmant P Todd P Vicente P Yoshioka G/F 2 P P P P P P P P P- P P- P P P P P P- P P P 3 G G G F/G G F/G G F F G G/F G F/P G G F G G F G 4 P F P P P P P P P P P P P P P P P P P F 5 F F/P F P/F F F/P P P F P/F P P P/F F P/F P/F F P F F/G 6 P P P P P F/P P P P P F P F/P F P/F P/F P P F F 7 F F G F F F/G G F F F F F F G F F F G F F/G 8 F F F F F F/P F P P/F P/F F P P F F F F F F F 9 F G F P P/F F/P F P P+ F P F F/P F P P F/P F F F/P 10 F G F F F G G F F+ G/F F P F/P G F/G F F F F F/G 11 F G F F F F/P F F F F F F P/F G F F F/G F F F 12 F G F F/G F F G F P+ G F F F F F F G 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. Attributes of good stations Direction with improving condition increase increase increase increase increase increase decrease increase decrease decrease decrease increase increase increase increase increase decrease increase Attribute 3D structure stony coral abundance stony coral condition stony coral diversity stony coral population structure stony coral recruitment dominance of weedy, tolerant species coralline algae zoanthids exotic species filter feeders fish abundance balance in fish popula- tion size and structure fish biomass balance in fish trophic structure fish diversity fleshy algae gorgonian abundance Sub-attribute/measurements rugosity, cover Montastraea annularis complex, Acropora palmata, Acropora cervicornis, Diploria strigosa, large stony corals % live tissue, absence of disease high number of stony coral species large colonies Colpophyllia natans, Siderastrea siderea, Porites astreoides Palythoa species exotic fish, corals heterotrophic sponges 2-8 Workshop on Biological Integrity of Coral Reefs ------- Table 2.4 (continued) Attributes of good stations Direction with improving condition increase increase increase increase decrease increase increase increase decrease Attribute gorgonian condition gorgonian diversity other invertebrates sponge abundance sponge abundance sponge diversity substrate condition water clarity corallivores/bioeroders Sub-attribute/measurements % live tissue, absence of disease and predators (Cyphoma gibbosum) Diadema antillarum, conch, lobsters, crabs, anemones autotrophic sponges heterotrophic sponges clean, no fuzzy algae (cyanobacteria), open space recruitment 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 Curacao (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 Curacao (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 lnte§ ;rity 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. Bajo las olas Beneath the Waves Puerto Rico Hector J. Ruiz Tories 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 three- dimensional 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 Very Good Excellent (approximate BCG Level 1-2) Good (approximate BCG Level 3) Attribute descriptions Physical structure: High rugosity or 3D structure; substantial reef built above bedrock; many irregular surfaces provide habitat for fish; very clear water; no sediment, floes or films 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 Physical structure: Moderate to high rugosity; moderate reef built above bedrock; some irregular cover for fish habitat; water slightly turbid; low sediment, floes or films on substrate 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 Fair (approximate BCG Level 4) Poor (approximate BCG Level 6) Attribute descriptions Physical structure: Low rugosity; limited reef built above bedrock; erosion of reef structure obvious; water turbid; more sediment accumulation, floes and films; Acropora usually gone or present as rubble for recruitment substrate 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 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 floe covering bottom; no substrate for recruits 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 Intej ;rity of Coral Reefs ------- Table 2-6. Condition levels and associated attributes Condition level Very Good- Excellent Good Ol (3 u GQ 1-2 3 Physical structure High rugosity or 3D structure; substantial reef built above bedrock; many irregular surfaces provide habitat for fish; very clear water; no sediment, floes or films Moderate to high rugosity; moderate reef built above bedrock; some irregular cover for fish habitat; water slightly turbid; low sediment, floes or film on substrate 10 re 3 High species diversity including rare; large old colonies (Montastraea) with high tissue coverage; balanced population structure (old and middle- aged colonies, recruits); Acropora thickets present 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 Gorgonians present but sub-dominant to corals Gorgonians more abundant than in Levels 1-2 i/i Ol 00 o Q. to Large autotrophic and highly sensitive sponge species abundant Autotrophic species present but highly sensitive species missing _(/> 1Z Populations have balanced species abundance, sizes and trophic inter- actions Decline of large apex predators (e.g., groupers, snappers, etc.) noticeable; small reef fish more abundant than Levels 1-2 Vertebrates Large, long-lived species present and diverse (turtles, eels, sharks) Large, long-lived species locally extirpated (e.g., turtles, eels) Other invertebrates Diadema, lobster, small crustaceans and polychaetes abundant- some large sensitive anemone species Diadema, lobster, small crustaceans and polychaetes less abundant than Levels 1-2; large sensitive anemone species missing Algae/plants Crustose coralline algae abundant; turf algae present but cropped and grazed by Diadema and herbivorous fish; low abundance fleshy algae Crustose coralline algae present but less than Levels 1-2; turf algae present and longer; more fleshy algae present Condition Low prevalence of disease or tumors; mostly live tissue on colonies Disease and tumor prevalence slightly above background level; more colonies have irregular tissue loss Chapter 2. Approach 2-17 ------- Table 2.6 (continued) o 'i3 1 « 3 1 Fair Poor Ol £ (3 U GO 4 6 0) re £ .a 5 £S £ « Low rugosity, limited reef built above bedrock; erosion of reef structure obvious; water turbid; more sediment accumula- tion, floes and films; Acropora usually gone or present as rubble for recruitment substrate Very low rugosity, no or low reef built above bedrock or poor for fish habitat; very turbid water; thick sediment film and high floes covering bottom; no substrate for recruits 10 re 3 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 un cropped turf algae Absence of colonies, those present are small, only highly tolerant species, little or no tissue i/i c _re 'E o £? o 13 Gorgonians more abundant than in Levels 1 - 3; replace sensitive coral and sponge species Small and sparse colonies, mostly small sea fans, often diseased i/i Ol 00 o Q. to Mostly heterotrophic sponges with tolerant species and clionids Heterotrophic sponges buried deep in sediment; highly tolerant sponge species f .— 1Z Absence of small reef fish (mostly Damsel fish) No large fish, few tolerant species, lack of multiple trophic levels i/i Ol +j £ & 01 e Ol > Large, long- lived species locally extirpated (e.g., turtles, eels) Usually devoid of other vertebrates 8 *j re k. .2 01 1_ 4-> * 1 oj Diadema absent; Palythoa overgrowing corals, crustaceans, polychaetes and sensitive anemones conspicuously absent Low or no reef invertebrates; high abundance of sediment dwelling organisms (e.g., polychaetes, holothurians) i/i 4-1 _ro Q. "ST re 00 < Some coralline algae; turf is un cropped 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 crust ose coralline algae High cover of fleshy algae (Dictyota); possibly covering sessile invertebrates; no turf or coralline algae; complete absence of crust ose coralline algae O J5 ^ 3 High incidence of diseased coral, sponges, gorgonians; evidence of high mortality; usually less tissue than dead portions on colonies 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 Carol 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 Gorgonion 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 Algoe 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 species- based, 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 STORE! Data Warehouse (short for STOrage and RETrieval). STORE! 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) Final Recreational fishing opportunity Recreational diving/snorkeling opportunity Recreational underwater photography opportunity Recreational surfing opportunity Opportunity to view nature and wildlife Opportunity to sunbathe and swim at the beach Opportunity to collect objects (beachcombing) Intermediate 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 Coral reef formation and maintenance; maintenance of water clarity; production of benthic and aquatic prey for consumption by recreational fish Reef breaks Biological integrity Water quality, shoreline protection, sand production Water quality Natural features (reef attributes) Fish diversity and abundance Coral diversity, abundance and health; fish diversity and abundance; water clarity Coral diversity, abundance and health; fish diversity and abundance; water clarity 3-D reef structure Biodiversity (birds, marine mammals, turtles) White coralline sands; calm waters 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 Guanica). 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. 3-6 Workshop on Biological Integrity of Coral Reefs ------- Appendix A. References Adams AJ, Dahlgren CP, Kellison GT, Kendall MS, Layman CA, LeyJA, Nagelkerken I and SerafyJE. 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 mangrove- seagrass-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 Ruytervan Steveninck. (Eds). 1983. Density of the sea urchin Diadema antillarum before and after mass mortalities on the coral reefs of Curacao. 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 DLand 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-l ------- 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. Seller W, Casellas MA, Cerame-Vivas MJ, Duffy L, El KouryJ, Gelabert PA, Gonzales LiboyJA, 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, KrosnickJA, 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 (Rl): 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 Bio logy 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 Rl, Albaladejo VD and Corpuz VT. 1981. 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Population characteristics of the black sea urchin Diadema antillarum (Philippi) in La Parguera, Puerto Rico, 17 years after the mass mortality event. Revista de Biologia Tropical 53:219-231. Weil E, Croquer 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 Guanica. URL: http://en.wikipedia.org/wiki/CentraLGu%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 RioPiedras, 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 Munoz 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 Mayaguez, 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, Mayaguez 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 Mayaguez, PR 00681-9013 Francisco.pagan@upr.edu Mr. Hector Ruiz Torres University of Puerto Rico Department of Marine Sciences Mayaguez, PR 00681-9013 787-691-7410 hectorruizt@me.com Appendix B. Workshop Participants B-l ------- Mr. Jeff Miller Virgin Islands National Park 1300 Cruz Bay Creek St. John, VI 00830 340-693-8950 x227 William J Miller@nps.gov Dr. Jeroen Gerritsen (Facilitator) Aquatic Ecologist Tetra Tech, Center for Ecological Sciences 400 Red Brook Blvd., Suite 200 Owings Mills, MD 21117 410-356-8993 jeroen.gerritsen@tetratech.com Dr. Jorge Bauza San Juan Bay Estuary Program P.O. Box 9509 San Juan, PR 00908-9509 787-638-9979 jbauza@estuario.org Dr. Loretta Roberson University of Puerto Rico College of Natural Sciences Ponce de Leon Ave. RioPiedras, PR 00931-3300 787-764-0000 xl-2713 Loretta.Roberson@gmail.com Dr. Melanie McField Smithsonian Institution Director, Healthy Reefs for Healthy People 1755 Coney Dr. Belize City, Belize, Central America 501-223-4898 mcfield@healthyreefs.org Mr. Miguel Canals PRDNER Guanica State Forest P.O. Box 1185 Guanica, PR 00653 787-821-5706 menqui@hotmail.com Ms. Patricia Bradley (Organizer) US EPA, AED 33 East Quay Road Key West, FL 33040 305-809-4690 bradley.patricia@epa.gov Dr. Paul Yoshioka University of Puerto Rico Department of Marine Sciences Mayaguez, PR 00681-9000 Paul.yoshioka@upr.edu Dr. Richard Appeldoorn University of Puerto Rico Department of Marine Sciences Mayaguez, PR 00681-9013 787-899-2048x251 Richard.appeldoorn@upr.edu Mr. Roberto Viqueira Protectores de Cuencas Guanica Coordinator Box 673 Yauco, PR 00698 787-457-8803 rviqueira@hotmail.com Dr. Tyler Smith University of the Virgin Islands #2 John Brewer's Bay St. Thomas, VI 00802-9990 340-693-1394 tsmith@uvi.edu Dr. Vance Vicente Vicente and Associates, Inc. Garden Hills Pz 1353 19 Guaynabo, PR 00966 787-781-6503 vance@prtc.net Dr. William Fisher US EPA, GED ISabine 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-l ------- 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. 1 2 3 4 5 6 7 8 Rating (Good, Fair, Poor) Rationale (indicate 3 most important characteristics considered in ranking) Appendix D. Tally Sheet (1 st) D-l ------- ------- Appendix E. Tally Sheet - Rating Condition of Coral Reef Videos (2nd) Name: Ballot Station No. 9 10 11 12 Rating (Good, Fair, Poor) Rationale (indicate 3 most important characteristics considered in ranking) Appendix E. Tally Sheet - (2nd) E-l ------- ------- 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-l ------- ------- 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-l ------- Station 1 G-2 Workshop on Biological Integrity of Coral Reefs ------- Station 2 Appendix G. Supporting Photos G-3 ------- Station 3 G-4 Workshop on Biological Integrity of Coral Reefs ------- Station 4 Appendix G. Supporting Photos G-5 ------- Station 5 G-6 Workshop on Biological Integrity of Coral Reefs ------- Station 6 Appendix G. Supporting Photos G-7 ------- Station 7 G-8 Workshop on Biological Integrity of Coral Reefs ------- Station 8 Appendix G. Supporting Photos G-9 ------- Station 9 G-10 Workshop on Biological Integrity of Coral Reefs ------- Station 10 Appendix G. Supporting Photos G-ll ------- Station 11 G-12 Workshop on Biological Integrity of Coral Reefs ------- Station 12 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 non- indigenous, 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-l ------- 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 1-1. 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. 6 z E O (5 "^ GQ (5? 1 2 3 4 5 6 7 8 9 10 11 12 e CO tin rx o uj Z 125 15 113 3 19 14 16 108 109 1 46 25 *Rugosity is the bottom Species Richness 13 3 10 6 7 10 11 7 8 11 9 8 % Total Abundance 11.61 2.68 8.93 5.36 6.25 8.93 9.82 6.25 8.04 9.82 8.04 7.14 linear ratio of 6m No. Colonies 51 4 79 21 31 54 73 71 87 70 44 95 divided Shannon Diversity Index (H1) 2.040 1.040 1.657 1.234 1.261 1.793 1.971 1.512 1.410 1.784 1.827 1.469 Dy the taut 01 Q 3.40 0.16 3.16 0.84 1.24 3.6 4.87 4.73 5.80 2.8 1.16 3.8 CO flj ^r* (N £ E O ^ Q 1 CO •«— • 6,560 185 9,518 2,706 18,228 5,359 14,210 19,637 20,080 11,026 11,635 9,199 CO QJ 1"E O ^ Q S 1,533 106 2,843 565 3,673 1,530 5,089 4,549 5,917 3,698 2,598 3,498 o 60 U. 2.18 1.12 1.52 1.52 1.54 1.71 1.83 1.48 1.88 1.48 1.12 1.25 linear distance of a 6m chain draped o 60 UJ 3 to ce. 0.107 0.019 0.107 0.087 0.108 0.106 0.119 0.116 0.134 0.052 0.039 0.086 ja 60 — CO B 11 (O ._ P CC > 2. poor/fair poor (worst) good (best) poor fair/poor poor fair fair fair fair fair fair 60 '& CO ce. "co 3 8 12 1 11 9 10 4 6 7 3 5 2 over the tops of corals and along the Rugosity is a reef-scale indicator of reef contour or surface heterogeneity. See Appendix J for formulas. Table 1-2. Gorgonian summary statistics for BCG stations (Puerto Rico surveys in 2010 and 2011). Ave. 3D SA is average 3-dimensional surface area cm2/m2or per individual. Maximum number of morphologies that can be BCG Station Station No. No. 1 2 3 4 5 6 7 8 9 10 11 12 125 15 113 3 19 14 16 108 109 1 46 25 present at one station is nine. Morpho. Richness3 4 0 7 0 0 6 8 2 4 2 7 8 No. Individuals 21 0 24 0 0 27 37 6 7 10 52 86 Density Ave. 3D #/m2 SAb/m2 4.2 0 4.8 0 0 5.4 7.4 1.2 1.4 2 10.4 17.2 5,154 0 30,346 0 0 38,352 33,342 86 11,229 17,649 26,954 58,558 Ave. 3D SAc/ind 1,227 0 6,322 0 0 7,102 4,506 71 8,021 8,825 2,592 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 = I Gorgonian surface area in transect area/total transect area c: Ave. 3D SA/ind= I 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 1-1 ------- Table 1-3. 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 No. 1 2 3 4 5 6 7 8 9 10 11 12 Station No. 125 15 113 3 19 14 16 108 109 1 46 25 Morpho. Richness3 3 3 1 2 1 2 0 0 3 5 3 5 No. Individuals 22 20 5 7 5 8 0 0 7 33 21 28 Density #/m2 4.4 4 1 1.4 1 1.6 0 0 1.4 6.6 4.2 5.6 Ave. 3D SAb/m2 1,615 1,146 48 173 208 410 0 0 1,389 10,776 53,824 6,213 Ave. 3D SAc/ind 367 286 48 124 208 256 0 0 992 1,633 12,815 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 = I Sponge surface area in transect area/total transect area. c: Ave. 3D SA/ind= I Sponge surface area in transect area/total # Sponges in transect. See Appendix J, Table J-2 for formulas. I (0 20 15 10 Density of sessile invertebrates no./m2 n Coral DGorgonian • Sponge rfh rm 1234567 Station no. 10 11 12 Figure 1-1. Comparison of the density of the major sessile invertebrates assessed in the 12 BCG stations. 1-2 Workshop on Biolo; l\ca\ Integrity of Coral Reefs ------- 350 -i 300 - 250 - 200 - CM E =**: 150 - 100 - 50 - n - -J in carnivores • herbivores 1.13 11.34 ffi 0 - 51 n 5.45 0.75 — — 0.54 i r 2.63 n 0.60 _ 0.22 . — 1.07 r — 03 1 0.27 ^D 1234567 Station no. 10 11 12 Figure 1-2. 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 D) 25000 -i 20000 - 15000 - in carnivores • herbivores 0.24 5.45 0000 - 5000 - n - 0.17 3.01 ^ rll 1.07 1 0. 0.67 • rid 15 0. 16 — 9 .23 n 1. 49 0.50 12345678 Station no. 10 11 12 Figure 1-3. 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 1-3 ------- BCG Station 1 (Field Station 125_2010) Coral Species Richness: 13 Photo rank and rating: 8, Poor/Fair Table 1-4. BCG Station 1 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters All Massive Acroporid Siderastrea Forties Species Species Species siderea astreoides Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 3.40 2,146 7,297 1,929 6,560 1,533 0.53 2,462 1,313 2,284 1,218 228 0.13 20,077 2,677 16,446 2,193 198 0.13 417 56 417 56 54 0.73 435 319 435 319 16 Cora! Species Ssid 4% Gorgonian Morphs SWbr 57% Mlam 2% Mcom 2% Mcav 14% Sponge Morphs mound 91% Figure I -4. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 1. 1-4 Workshop on Biological Integrity of Coral Reefs ------- Table 1-5. Fish species found in BCG Station 1, with density and biomass for 100 m2 transect. Fish Species Ab udefduf saxa tills Acanthurus coeruleus Anisotremus surinamensis Anisotremus virginicus Caranx ruber Gramma loreto Haemulon flavolineatum Halichoeres poeyi Holacanthus bermudensis Lut janus ana Us Lutjanus a pod us Microspathodon chrysurus Ocyurus chrysurus Ophioblennius macclurei Pempheris schomburgkii Scarus iseri Sparisoma aurofrenatum Sparisoma viride Stegastes adustus Thalassoma bifasciatum Common Name Sergeant Major Blue Tang Black Margate Porkfish Bar Jack Fairy Basslet French Grunt Blackear Wrasse Blue Angelfish Mutton Snapper Schoolmaster Yellowtail Damselfish Yellowtail Snapper Redlip Blenny Glassy Sweeper Striped Parrotfish Redband Parrotfish Stoplight Parrotfish Dusky Damselfish Bluehead Abundance/ 100m2 2 5 1 1 1 3 1 1 1 1 1 5 8 3 1 2 1 3 49 55 Total Biomass (g/100 m2) 90 167 1,274 9 17 1 40 5 11 637 215 174 242 12 33 15 40 3 510 198 Appendix I. Summary Data Results for BCG Stations 1-5 ------- BCG Station 2 (Field Station 15_2011) Coral Species Richness: 3 Photo rank and rating: 12, Poor (Worst) Table 1-6. BCG Station 2 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters Colony density (#/m2) Ave. 3D colony skeletal area Ave. 3D colony skeletal area Ave. 3D coral tissue area (cm Ave. 3D coral tissue area (cm Ave. 2D coral tissue area (cm (cm2)/colony (cm2)/m2 2)/colony 2)/m2 2)/m2 All Species 0.16 1,248 200 1,157 185 106 Massive Species 0 0 0 0 0 0 Acroporid Species 0 0 0 0 0 0 Siderastrea siderea 0.08 980 78 822 66 37 Porites astreoides 0 0 0 0 0 0 Coral Species Sponge Morphs Ssid Sbou 25% br. ropey 25% mound 10% Figure 1-5. Percentages of stony coral species and sponge morphologies for BCG Station 2. No gorgonians were present at BCG Station 2. 1-6 Workshop on Biolof |ical Integrity of Coral Reefs ------- Table 1-7. Fish species found in BCG Station 2, with density and biomass for 100 m2 transect. Fish Species Common Name Abundance/ 100m2 Total Biomass (g/100 m2) Acanthurus bahianus Anisotremus virginicus Canthigaster rostrata Ocean Surgeonfish Porkfish Sharpnose Puffer 10 5 1 457 220 0 Cephalopholis fulva Chaetodon capistratus Elacatinus saucrum Coney Foureye Butterflyfish Leopard Goby 2 7 6 68 105 298 Haemulon flavolineatum Haemulon macrostomum Halichoeres poeyi French Grunt Spanish Grunt Blackear Wrasse 10 1 1 404 40 26 Lachnolaimus maximus Mulloidichthys martinicus Ocyurus chrysurus Hogfish Yellow Goatfish Yellowtail Snapper 1 2 7 10 81 212 Scarus iseri Stegastes adustus Stegastes diencaeus Striped Parrotfish Dusky Damselfish Longfin Damselfish 1 8 4 33 496 127 Stegastes partitas Stegastes variabilis Bicolor Damselfish Cocoa Damselfish 4 5 2 49 Appendix I. Summary Data Results for BCG Stations 1-7 ------- BCG Station 3 (Field Station 113_2011) Coral Species Richness: 10 Photo rank and rating: 1, Good (Best) Table 1-8. BCG Station 3 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters All Massive Acroporid Siderastrea Forties Species Species Species siderea astreoides Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 3.16 4,537 14,337 3,012 9,518 2,843 0.92 13,445 12,369 8,646 7,954 2,212 0 0 0 0 0 0 0.48 949 456 626 300 135 1.36 704 957 609 829 326 Coral Species Aaga Ssid 15% Ahum 1% Dlab 1% Male 3% Mann 5% Gorgonian Morphs SRunbr 9% SRbush 13% Past 43% fan 3D ' 13% plume 13% SRbr 44% Sponge Morphs mound 100% Figure 1-6. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 3. 1-8 Workshop on Biological Integrity of Coral Reefs ------- Table 1-9. Fish species found in BCG Station 3, with density and biomass for 100 m2 transect. Fish Species Acanthurus bahianus Acanthurus coeruleus Canthigaster rostrata Caranx ruber Chaetodon capistratus Coryphopterus glaucofraenum Haemulon macrostomum Halichoeres bivittatus Hypoplectrus chlorurus Lutjanus apodus Microspathodon chrysurus Scarus iseri Serranus ti grin us Sparisoma aurofrenatum Sparisoma viride Stegastes adustus Stegastes partitas Stegastes planifrons Thalassoma bifasciatum Common Name Ocean Surgeonfish Blue Tang Sharpnose Puffer Bar Jack Foureye Butterflyfish Bridled Goby Spanish Grunt Slippery Dick Yellowtail Hamlet Schoolmaster Yellowtail Damselfish Striped Parrotfish Harlequin Bass Redband Parrotfish Stoplight Parrotfish Dusky Damselfish Bicolor Damselfish Threespot Damselfish Bluehead Abundance/ 100m2 1 9 2 2 1 15 1 5 3 2 2 51 1 5 6 30 4 2 21 Total Biomass (g/100 m2) 46 638 14 34 15 10 242 574 43 431 324 5,749 7 482 979 360 32 13 106 Appendix I. Summary Data Results for BCG Stations 1-9 ------- BCG Station 4 (Field Station 3_2011) Coral Species Richness: 6 Photo rank and rating: 11, Poor Table 1-10. BCG Station 4 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 All Species 0.84 4,251 3,571 3,221 2,706 565 Massive Species 0.12 17,387 2,086 10,681 1,282 315 Acroporid Species 0 0 0 0 0 0 Siderastrea siderea 0 0 0 0 0 0 Porites astreoides 0.04 157 6 141 6 4 Coral Species Ppor 5% Sponge Morphs Aaga Past Mfav 14% Ahum 5% mound 25% Mcom 62% Figure 1-7. Percentages of stony coral species and sponge morphologies for BCG Station 4. No gorgonians were present at BCG Station 4. 1-10 Workshop on Biolof |ical Integrity of Coral Reefs ------- Table 1-11. Fish species found in BCG Station 4, with density and biomass for 100 m2 transect. Fish Species Acanthurus bahianus Acanthurus chirurgus Acanthurus coeruleus Aulostomus maculatus Canthigaster rostrata Chaetodon capistratus Decapterus macarellus Gymnothorax sp. Haemulon carbonarium Haemulon chrysargyreum Haemulon flavolineatum Haemulon parr a Halichoeres radio tus Lutjanus apod us Malacanthus plumieri Microspathodon chrysurus Odontoscion dentex Rypticus saponaceus Scarus iseri Sparisoma aurofrenatum Sparisoma rubripinne Sparisoma viride Stegastes adustus Synodus intermedius Thalassoma bifasciatum Common Name Ocean Surgeonfish Doctorfish Blue Tang Trumpetfish Sharpnose Puffer Foureye Butterflyfish Mackerel Scad Moray Eel sp. Caesar Grunt Smallmouth Grunt French Grunt Sailors Choice Puddingwife Schoolmaster Sand Tilefish Yellowtail Damselfish Reef Croaker Greater Soapfish Striped Parrotfish Redband Parrotfish Yellowtail Parrotfish Stoplight Parrotfish Dusky Damselfish Sand Diver Bluehead Abundance/ 100m2 1 6 5 1 1 1 2 1 5 5 5 1 1 9 13 8 1 1 10 3 1 1 33 1 3 Total Biomass (g/100 m2) 129 629 1,081 256 7 15 395 3 1,024 475 609 404 168 2,193 318 1,296 21 82 1,119 580 401 314 384 339 31 Appendix I. Summary Data Results for BCG Stations Ml ------- BCG Station 5 (Field Station 19_2011) Coral Species Richness: 7 Photo rank and rating: 9, Fair/Poor Table 1-12. BCG Station 5 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters All Massive Acroporid Siderastrea Forties Species Species Species siderea astreoides Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 1.24 23,116 28,664 14,700 18,228 3,673 0.2 5,030 1,006 2,950 590 71 0.8 34,248 27,399 21,764 17,411 3,526 0.08 520 42 520 42 16 0 0 0 0 0 0 Coral Species Sponge Morphs Mfav 10% Mcom 3% Dstr 3% Deli 7% mound 100% Figure 1-8. Percentages of stony coral species and sponge morphologies for BCG Station 5. No gorgonians were present at BCG Station 5. 1-12 Workshop on Biolof |ical Integrity of Coral Reefs ------- Table 1-13. Fish species found in BCG Station 5, with density and biomass for 100 m2 transect. Fish Species Acanthurus bahianus Acanthurus coeruleus Anisotremus virginicus Aulostomus maculatus Bodianus rufus Caranx ruber Decapterus macarellus Haemulon carbonarium Haemulon chrysargyreum Haemulon flavolineatum Haemulon macrostomum Heteropriacanthus cruentatus Holocentrus adscensionis Lutjanus apod us Malacanthus plumieri Microspathodon chrysurus Mulloidichthys martinicus Myripristis jacobus Pempheris schomburgkii Scarus iseri Sparisoma aurofrenatum Sparisoma viride Stegastes adustus Stegastes partitus Thalassoma bifasciatum Common Name Ocean Surgeonfish Blue Tang Porkfish Trumpetfish Spanish Hogfish Bar Jack Mackerel Scad Caesar Grunt Smallmouth Grunt French Grunt Spanish Grunt Glasseye Snapper Squirrelfish Schoolmaster Sand Tilefish Yellowtail Damselfish Yellow Goatfish Blackbar Soldierfish Glassy Sweeper Striped Parrotfish Redband Parrotfish Stoplight Parrotfish Dusky Damselfish Bicolor Damselfish Bluehead Abundance/ 100m2 1 2 1 3 1 1 2 1 6 63 1 1 1 2 13 3 7 1 5 3 2 3 14 1 16 Total Biomass (g/100 m2) 46 72 128 439 32 17 275 41 570 6,989 242 214 237 203 300 486 283 107 164 458 151 521 168 1 134 Appendix I. Summary Data Results for BCG Stations 1-13 ------- BCG Station 6 (Field Station 14_2010) Coral Species Richness: 10 Photo rank and rating: 10, Poor Table 1-14. BCG Station 6 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area Ave. 3D coral tissue area Ave. 2D coral tissue area (cm2)/colony (cm2)/m2 (cm2)/m2 All Species 3.6 5,431 19,552 1,489 5,359 1,530 Massive Species 1.2 14,255 17,106 3,298 3,958 892 Acroporid Species 0 0 0 0 0 0 Siderastrea siderea 0.33 1,400 467 1,193 398 141 Porites astreoides 1.4 466 653 443 621 330 Coral Species Aaga Unk 2% Ahum Ssid 2%-) [ f 2% Ma|c ' !• j Ppor 6% Gorgonian Morphs SWbush 8% fan 3D 4% fan 11% Mcav 13% SRbr 15% Mfav 20% Mmea 2% plume 54% Sponge Morphs mound 67% br. ropey 33% Figure 1-9. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 6. 1-14 Workshop on Biological Integrity of Coral Reefs ------- Table 1-15. Fish species found in BCG Station 6, with density and biomass for 100 m2 transect. Fish Species Acanthurus bahianus Acanthurus chirurgus Chaetodon capistratus Elacatinus genie Epinephelus adscensionis Halichoeres garnoti Hypoplectrus chlorurus Hypoplectrus puella Lutjanus a pod us Mulloidichthys martinicus Ocyurus chrysurus Scarus iseri Sparisoma aurofrenatum Sparisoma viride Stegastes diencaeus Stegastes leucostictus Stegastes partitas Stegastes planifrons Thalassoma bifasciatum Common Name Ocean Surgeonfish Doctorfish Foureye Butterflyfish Cleaning Goby Rock Hind Yellowhead Wrasse Yellowtail Hamlet Barred Hamlet Schoolmaster Yellow Goatfish Yellowtail Snapper Striped Parrotfish Redband Parrotfish Stoplight Parrotfish Longfin Damselfish Beaugregory Bicolor Damselfish Threespot Damselfish Bluehead Abundance/ 100m2 1 1 4 1 1 2 1 1 1 2 1 36 5 11 3 4 7 12 12 Total Biomass (g/100 m2) 129 121 60 0 174 195 19 19 649 472 177 632 466 1,606 36 31 24 229 55 Appendix I. Summary Data Results for BCG Stations 1-15 ------- BCG Station 7 (Field Station 16_2010) Coral Species Richness: 11 Photo rank and rating: 4, Fair Table 1-16. BCG Station 7 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 All Species 4.87 3,529 17,173 2,920 14,210 5,089 Massive Species 1.13 10,160 11,515 9,057 10,264 3,537 Acroporid Species 0 0 0 0 0 0 Siderastrea siderea 0.53 895 477 790 421 167 Porites astreoides 1.53 567 870 469 720 303 Coral Species Gorgonian Morphs Ssid 11% Aaga Deli 1% DcyM% Dsto 1% Mcav 6% Mfav 16% SWbush 14% SWbr 13% SRunbr 3% SRbush 3% SRbr 24% fan 3D 3% plume 13% Figure 1-10. Percentages of stony coral species and gorgonian morphologies for BCG Station 7. No sponges were present at BCG Station 7. 1-16 Workshop on Biolof |ical Integrity of Coral Reefs ------- Table 1-17. Fish species found in BCG Station 7, with density and biomass for 100 m2 transect. Fish Species Common Name Abundance/ 100m2 Total Biomass (g/100 m2) Acanthurus coeruleus Chaetodon striatus Chromis multilineata Blue Tang Banded Butterflyfish Brown Chromis 9 2 16 414 124 126 Haemulon aurolineatum Haemulon flavolineatum Holocentrus adscensionis Tomtate French Grunt Squirrelfish 3 2 2 21 81 474 Lutjanus apod us Microspathodon chrysurus Ocyurus chrysurus Schoolmaster Yellowtail Damselfish Yellowtail Snapper 1 13 10 215 1,133 303 Pomacanthus paru Scarus iseri Sparisoma aurofrenatum French Angelfish Striped Parrotfish Redband Parrotfish 1 16 17 342 1,515 475 Stegastes diencaeus Stegastes leucostictus Stegastes partitus Thalassoma bifasciatum Longfin Damselfish Beaugregory Bicolor Damselfish Bluehead 8 2 3 36 294 89 31 110 Appendix I. Summary Data Results for BCG Stations 1-17 ------- BCG Station 8 (Field Station 108_2010) Coral Species Richness: 7 Photo rank and rating: 6, Fair Table 1-18. BCG Station 8 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area Ave. 3D coral tissue area Ave. 2D coral tissue area (cm2)/colony (cm2)/m2 (cm2)/m2 All Species 4.73 4,938 23,372 4,149 19,637 4,549 Massive Species 0.20 1,473 295 949 190 52 Acroporid Species 1.47 14,658 21,499 12,274 18,002 3,964 Siderastrea siderea 0.13 157 21 157 21 10 Porites astreoides 1.93 258 499 239 462 273 Coral Species Gorgonian Morphs Ssid SWbr 50% Deli 10% Mfav 4% Dstr 4% Figure 1-11. Percentages of stony coral species and gorgonian morphologies for BCG Station 8. No sponges were present at BCG Station 8. 1-18 Workshop on Bioloj ;ical Integrity of Coral Reefs ------- Table 1-19. Fish species found in BCG Station 8, with density and biomass for 100 m2 transect. Fish Species Abudefdufsaxatilis Acanthurus bahianus Acanthurus coeruleus Aulostomus maculatus Haemulon flavolineatum Halichoeres bivittatus Halichoeres maculipinna Halichoeres radio tus Lutjanus apod us Microspathodon chrysurus Ophioblennius macclurei Pomacanthus paru Scarus iseri Sparisoma aurofrenatum Sparisoma viride Stegastes diencaeus Stegastes partitas Thalassoma bifasciatum Common Name Sergeant Major Ocean Surgeonfish Blue Tang Trumpetfish French Grunt Slippery Dick Clown Wrasse Puddingwife Schoolmaster Yellowtail Damselfish Redlip Blenny French Angelfish Striped Parrotfish Redband Parrotfish Stoplight Parrotfish Longfin Damselfish Bicolor Damselfish Bluehead Abundance/ 100m2 3 3 31 1 1 4 6 1 4 28 1 1 69 4 2 54 6 98 Total Biomass (g/100 m2) 99 386 1,479 130 111 182 24 0 341 961 4 156 4,592 332 326 603 3 331 Appendix I. Summary Data Results for BCG Stations 1-19 ------- BCG Station 9 (Field Station 109_2010) Coral Species Richness: 9 Photo rank and rating: 7, Fair Table 1-20. BCG Station 9 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters All Massive Acroporid Siderastrea Forties Species Species Species siderea astreoides Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 5.80 9,091 52,731 3,462 20,080 5,917 3.47 8,102 28,088 4,040 14,006 4,015 0 0 0 0 0 0 0.53 806 430 734 391 213 0.67 781 521 739 493 298 Coral Species Ssid 9% Ppor Gorgonian Morphs SWbush 20% Mfav 60% SWbr 20% Sponge Morphs mound 65% Figure 1-12. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 9. 1-20 Workshop on Biolof |ical Integrity of Coral Reefs ------- Table 1-21. Fish species found in BCG Station 9, with density and biomass for 100 m2 transect. Fish Species Ab udefduf saxatilis Acanthurus bahianus Acanthurus chirurgus Acanthurus coeruleus Anisotremus virginicus Aulostomus maculatus Cephalopholis cruentata Chaetodon striatus Coryphopterus glaucofraenum Haemulon carbonarium Haemulon plumierii Halichoeres bivittatus Holocentrus adscensionis Hypoplectrus chlorurus Lutjanus apod us Microspathodon chrysurus Mulloidichthys martinicus Scarus iseri Sparisoma aurofrenatum Sparisoma viride Stegastes diencaeus Stegastes leucostictus Stegastes partitus Stegastes planifrons Thalassoma bifasciatum Common Name Sergeant Major Ocean Surgeonfish Doctorfish Blue Tang Porkfish Trumpetfish Graysby Banded Butterflyfish Bridled Goby Caesar Grunt White Grunt Slippery Dick Squirrelfish Yellowtail Hamlet Schoolmaster Yellowtail Damselfish Yellow Goatfish Striped Parrotfish Redband Parrotfish Stoplight Parrotfish Longfin Damselfish Beaugregory Bicolor Damselfish Threespot Damselfish Bluehead Abundance/ 100m2 4 1 10 76 3 1 1 2 10 3 1 2 1 3 2 7 1 19 4 16 30 2 18 2 4 Total Biomass (g/100 m2) 263 129 1,206 11,429 851 442 178 25 7 915 539 342 433 12 431 402 236 98 1,008 5,024 348 20 79 24 14 Appendix I. Summary Data Results for BCG Stations 1-21 ------- BCG Station 10 (Field Station 2011_1) Coral Species Richness: 11 Photo rank and rating: 3, Fair Table 1-22. BCG Station 10 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters All Massive Acroporid Siderastrea Porites Species Species Species siderea astreoides Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 2.8 7,205 20,174 3,938 11,026 3,698 1.88 10,095 18,979 5,549 10,432 3,496 0.04 9,503 380 0 0 0 0.08 3,662 293 1,405 112 50 0.4 794 317 640 256 94 Coral Species Aaga Ssid 2% Gorgonian Morphs Mfra 3% Mfav 14% Mann 43% SWbr 13% plume 87% Sponge Morphs br. ropey 34% mound 18% Figure 1-13. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 10. 1-22 Workshop on Biological Integrity of Coral Reefs ------- Table 1-23. Fish species found in BCG Station 10, with density and biomass for 100 m2 transect. Fish Species Common Name Abundance/ 100m2 Total Biomass (g/100 m2) Chaetodon capistratus Decapterus macarellus Haemulon flavolineatum Hypoplectrus chlorurus Malacanthus plumieri Malacoctenus triangulatus Odontoscion dentex Pomacanthus paru Scarus iseri Sparisoma viride Stegastes partitas Stegastes planifrons Foureye Butterflyfish Mackerel Scad French Grunt Yellowtail Hamlet Sand Tilefish Saddled Blenny Reef Croaker French Angelfish Striped Parrotfish Stoplight Parrotfish Bicolor Damselfish Threespot Damselfish 2 4 22 2 1 4 14 2 6 15 3 96 30 250 2,441 24 24 1 804 2,161 45 789 2 1,982 Appendix I. Summary Data Results for BCG Stations 1-23 ------- BCG Station 11 (Field Station 46_2011) Coral Species Richness: 9 Photo rank and rating: 5, Fair Table 1-24. BCG Station 11 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters All Massive Acroporid Siderastrea Forties Species Species Species siderea astreoides Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 1.76 8,236 14,495 6,610 11,635 2,598 0.16 639 102 495 79 41 0.60 21,258 12,755 16,902 10,141 2,187 0.20 1,210 242 491 98 44 0.60 422 253 363 218 96 Coral Species Gorgonian Morphs Acer 21% SRunbr 2% fan 3D 2% fan SRbush 2% Ahum 2% Apal 14% Dstr 2% Male Mfav 5o/ 9% Sponge Morphs plume 2% SRbr 81% mound 65% Figure 1-14. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 11. 1-24 Workshop on Biological Integrity of Coral Reefs ------- Table 1-25. Fish species found in BCG Station 11, with density and biomass for 100 m2 transect. Fish Species Acanthurus bahianus Acanthurus coeruleus Aulostomus maculatus Caranx ruber Cephalopholis cruentata Chaetodon capistratus Chaetodon striatus Haemulon carbonarium Haemulon chrysargyreum Haemulon flavolineatum Halichoeres garnoti Halichoeres maculipinna Halichoeres radiatus Holocentrus rufus Lutjanus apodus Malacanthus plumieri Microspathodon chrysurus Myripristis jacobus Scarus iseri Sparisoma aurofrenatum Stegastes adustus Stegastes leucostictus Stegastes partitus Thalassoma bifasciatum Common Name Ocean Surgeonfish Blue Tang Trumpetfish Bar Jack Graysby Foureye Butterflyfish Banded Butterflyfish Caesar Grunt Smallmouth Grunt French Grunt Yellowhead Wrasse Clown Wrasse Puddingwife Longspine Squirrelfish Schoolmaster Sand Tilefish Yellowtail Damselfish Blackbar Soldierfish Striped Parrotfish Redband Parrotfish Dusky Damselfish Beaugregory Bicolor Damselfish Bluehead Abundance/ 100m2 21 7 1 20 1 10 4 15 30 15 1 1 4 2 5 15 14 1 46 2 11 1 10 170 Total Biomass (g/100 m2) 959 831 15 134 82 150 247 1,543 1,011 606 82 5 68 190 185 367 1,204 107 386 119 132 1 45 698 Appendix I. Summary Data Results for BCG Stations 1-25 ------- BCG Station 12 (Field Station 25_2011) Coral Species Richness: 8 Photo rank and rating: 2, Fair Table 1-26. BCG Station 12 data summary for corals and subgroups. See Appendix J for formulas used and species abbreviations. Coral Parameters All Massive Acroporid Siderastrea Forties Species Species Species siderea astreoides Colony density (#/m2) Ave. 3D colony skeletal area (cm2)/colony Ave. 3D colony skeletal area (cm2)/m2 Ave. 3D coral tissue area (cm2)/colony Ave. 3D coral tissue area (cm2)/m2 Ave. 2D coral tissue area (cm2)/m2 3.8 3,525 13,396 2,421 9,199 3,498 1.56 7,563 11,799 5,037 7,857 2,928 0 0 0 0 0 0 0.36 592 213 460 166 61 1.72 740 1,273 619 1,065 472 Coral Species Aaga Gorgonian Morphs Mcav 22% SWbush 7% SWbr 17% plume 14% SRunbr 7% SRbush 8% SRbr 34% Sponge Morphs vase 4% br. ropey 50% mound 11% Figure 1-15. Percentages of stony coral species, gorgonian morphologies and sponge morphologies for BCG Station 12. 1-26 Workshop on Biolof |ical Integrity of Coral Reefs ------- Table 1-27. Fish species found in BCG Station 12, with density and biomass for 100 m2 transect. Fish Species Common Name Abundance/ 100m2 Total Biomass (g/100 m2) Acanthurus bahianus Acanthurus chirurgus Haemulon flavolineatum Ocean Surgeonfish Doctorfish French Grunt 2 1 3 91 44 262 Labrisomus nuchipinnis Lutjanus a pod us Myripristis jacobus Hairy Blenny Schoolmaster Blackbar Soldierfish 33 101 107 Scarus iseri Sparisoma aurofrenatum Sparisoma viride Stegastes adustus Striped Parrotfish Redband Parrotfish Stoplight Parrotfish Dusky Damselfish 8 6 4 1 85 247 534 12 Appendix I. Summary Data Results for BCG Stations 1-27 ------- ------- 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 = nr2 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-l 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 = TT [colony diameter (cm)/2]2 * (LT/100) Appendix J. Formulas Used for Calculating Condition Metrics J-l ------- Coral metrics calculated for each BCG station Ave. 3D colony skeletal area (cm2)/colony = I CSA/n Ave. 3D colony skeletal area (cm2)/m2 = I CSA/area of transect Ave. 3D coral tissue (live) area (cm2)/colony = I LCSA_3D/n Ave. 3D coral tissue (live) area (cm2)/m2 = I LCSA_3D/area of transect Ave. 2D coral tissue (live) area (cm2)/m2 = I LCSA_2D/area of transect Table J-l. 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 Acropora cervicornis Acropora palmata Acropora prolifera Agaricia agaricites Agaricia fragilis Agaricia hum His Agaricia lamarcki Agaricia tenuifolia Cladocora arbuscula Colpophyllia natans Dendrogyra cylindrus Dichocoenia stokesii Diploria clivosa1 Diploria labyrinthiformis Diploria strigosa1 Eusmilia fastigiata Favia fragum Leptoseris cucullata Isophyllastrea rigida Isophyllia sinuosa Madracis decactis Madracis formosa Madracis mirabilis Madracis pharensis Manicina areolata Meandrina meandrites Millepora complanata Montastraea annularis2 Montastraea cavernosa Montastraea faveolata2 ID Code Acer Apal Apro Aaga Afra Ahum Alam Aten Carb Cnat Dcyl Dsto Deli Dlab Dstr Efas Ffra Lcuc Irig Isin Mdec Mfor Mmir Mpha Mare Mmea Mcom Mann Mcav Mfav Conversion Factor 4 4 4 1 1 1 1 3 2 2 3 2 2 2 2 3 2 1 2 2 3 3 3 1 2 2 3 3 2 2 J-2 Workshop on Biological Integrity of Coral Reefs ------- Table J-l. (continued) Genus and Species Mussa angulosa Mycetophyllia aliciae Mycetophyllia danaana Mycetophyllia ferox Mycetophyllia lamarckiana Oculina varicosa Porites astreoides Porites colonensis Porites divaricata Porites furcata Porites porites Siderastrea siderea Solenastrea bournoni Solenastrea hyades Stephanocoenia intersepta ID Code Mang Mali Mdan Mfer Mlam Ovar Past Pcol Pdiv Pfur Ppor Ssid Sbou Shya Sint Conversion Factor 2 1 1 1 1 3 2 1 3 3 3 2 2 3 2 1: This report does not adopt the new classifications for Diploria sthgosa 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 offish 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 offish 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 = aLp 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. a and 3 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 W J-4 Workshop on Biological Integrity of Coral Reefs ------- 4. Gorgonians Gorgonion 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 go rgonian > 10 cm (in any dimension) that falls within the quadrat was classified as one often 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 I (regression equation for SA in Table J-2) area of transect Average three-dimensional surface area of each gorgonian morph/colony = n I (regression equation for SA in Table J — 2) n 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 pi) (Gorgonia ventalina, Leptogorgia) Three-dimensional (3D fan) (Gorgonia flabellum) \_ SA=0.68hi+0.66d-3.61 SA=0.0113h3+106d-1190 Sea Rods Unbranched (SR ub) branch and digitate form branchlet diameter (B"°reum) > 15-<30 mm Branched (SR br) (Plexaura) Bushy (SR bush) (Eunicea fusca) Planar (SR pi) (Eunicea tourneforti) Sea Whips branch and branchlet diameter >5-<15 mm Branched (SW br) (Pterogorgia) Bushy (SW bush) (Pterogorgia guadalupensi) SA=0.341d3+11.2h-127 SA=1.46d2+399 SA=0.0288h3+ 939 SA=76.4d-806 SA=-0.479h3+3.37h2- 51.3h+354 SA=0.0672d3+1610 Sea Plumes smallest branch and branchlet diameter usually <5 mm (Plume) (Muriceopsis flavida, Pseudopterogorgia) SA=4.77h-2990 Encrusting Gorgonians (Briareum, Erythopodium) ft SA=dw 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 often 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 = (regression equation for SA in Table J-3) ,-=1 area of transect Average three-dimensional surface area of each sponge morph per individual = Z (regression equation for SA in Table J-3) n 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 Vase Xestospongia muta, Verongula reiswigi Callyspongia plicifera, Callyspongia vaginalis SA=4.31d2+0.827h2+108 SA=3.71h-161 Globe Tube Iricinia strobilina, Spheciospongia vesparium Aplysina archeri, Aplysina fistula ris SA=1.88h2 +0.0573d3+83.3 SA=0.493cT+109 * -..A-. Mound Rod Bushy Branched Ropey Encrusting Oligoceras hemorrhages, Iricinia felix Aplysina cauliformis, Niphates erecta Aplysina fulva lotrochota birotulata Amphimedon compressa, Chrondrilla caribensis SA=30.0h+18.7d-193 SA=7.69h+1.83d-33.5 SA=0.462hi+0.834dN-19.3 SA=18.8d+7.97h-132 SA=dw 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 ------- &EPA United States Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division Narragansett, Rl 02882 Official Business Penalty for Private use $300 EPA/600/R-13/350 | December 2014 www.epa.gov/ord ------- |