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Distribution of clionid sponges in the Florida Keys National Marine Sanctuary (FKNMS), 2001-2003

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Title:
Distribution of clionid sponges in the Florida Keys National Marine Sanctuary (FKNMS), 2001-2003
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English
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Callahan, Michael K
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University of South Florida
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Tampa, Fla.
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Subjects / Keywords:
Bioerosion
Cliona delitrix
Coral reefs
Monitoring
Dissertations, Academic -- Marine Science -- Masters -- USF   ( lcsh )
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government publication (state, provincial, terriorial, dependent)   ( marcgt )
bibliography   ( marcgt )
theses   ( marcgt )
non-fiction   ( marcgt )

Notes

Summary:
ABSTRACT: In 2001, the Coral Reef Evaluation and Monitoring Program (CREMP) began monitoring the abundance and area covered by three clionid sponges (Cliona delitrix, C. lampa, and C. caribbaea). Subsequently, monitoring has been conducted annually at all 40 CREMP sites throughout the Florida Keys National Marine Sanctuary (FKNMS) and the Dry Tortugas. Between 2001 and 2002, mean clionid area decreased significantly from 7.6 cm2/m2 to 4.6 cm2/m2 (Wilcoxon; p= 0.035). Between 2002 and 2003, the decline to 4.5 cm2/m2 was not significant. Approximately 80% of all clionid colonies recorded at the CREMP stations covered less than 50 cm2. Among all recorded stony coral species, Montastraea annularis, M. cavernosa, and Siderastrea siderea were the most frequently and extensively invaded by clionid colonies. However, the vast majority of clionid colonies occurred in substrata not associated with a live coral colony.The mean percent cover for the four coral species identified to be most susceptible to clionid invasion had the greatest decline in the Dry Tortugas deep stations between 2001 and 2003. At Lower Keys patch-reef stations, mean percent cover showed a small, steady decrease, while at Upper Keys patch-reef stations, a small steady increase occurred. Fifteen water-quality parameters collected by the Water Quality Monitoring Network (WQMN) were analyzed to determine if clionid distributions correlated with water quality. When patch-reef sites were analyzed as a subset of sites, clionid area and abundance correlated strongly ( 0.65) with water-quality parameters that indicated higher nutrient flux and food resources. However, the correlation was weak when all 39 CREMP sites were considered ( 0.10). Clionid sponges are well known to be aggressive and successful bioeroders on coral reefs.
Thesis:
Thesis (M.S.)--University of South Florida, 2005.
Bibliography:
Includes bibliographical references.
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System Details:
Mode of access: World Wide Web.
Statement of Responsibility:
by Michael K. Callahan.
General Note:
Title from PDF of title page.
General Note:
Document formatted into pages; contains 88 pages.

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aleph - 001681097
oclc - 62769727
usfldc doi - E14-SFE0001017
usfldc handle - e14.1017
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ABSTRACT: In 2001, the Coral Reef Evaluation and Monitoring Program (CREMP) began monitoring the abundance and area covered by three clionid sponges (Cliona delitrix, C. lampa, and C. caribbaea). Subsequently, monitoring has been conducted annually at all 40 CREMP sites throughout the Florida Keys National Marine Sanctuary (FKNMS) and the Dry Tortugas. Between 2001 and 2002, mean clionid area decreased significantly from 7.6 cm2/m2 to 4.6 cm2/m2 (Wilcoxon; p= 0.035). Between 2002 and 2003, the decline to 4.5 cm2/m2 was not significant. Approximately 80% of all clionid colonies recorded at the CREMP stations covered less than 50 cm2. Among all recorded stony coral species, Montastraea annularis, M. cavernosa, and Siderastrea siderea were the most frequently and extensively invaded by clionid colonies. However, the vast majority of clionid colonies occurred in substrata not associated with a live coral colony.The mean percent cover for the four coral species identified to be most susceptible to clionid invasion had the greatest decline in the Dry Tortugas deep stations between 2001 and 2003. At Lower Keys patch-reef stations, mean percent cover showed a small, steady decrease, while at Upper Keys patch-reef stations, a small steady increase occurred. Fifteen water-quality parameters collected by the Water Quality Monitoring Network (WQMN) were analyzed to determine if clionid distributions correlated with water quality. When patch-reef sites were analyzed as a subset of sites, clionid area and abundance correlated strongly ( 0.65) with water-quality parameters that indicated higher nutrient flux and food resources. However, the correlation was weak when all 39 CREMP sites were considered ( 0.10). Clionid sponges are well known to be aggressive and successful bioeroders on coral reefs.
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Distribution of Clionid Sponges in the Florida Keys National Marine Sanctuary (FKNMS), 2001-2003 by Michael K. Callahan A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Department of Biological Oceanography College of Marine Science University of South Florida Major Professor: Pamela Hallock Muller, Ph.D. Carl R. Beaver, Ph.D. Walter C. Jaap, B.S. Kendra L. Daly, Ph.D. Date of Approval: March 28, 2005 Keywords: Bioerosion, Cliona delitrix Coral Reefs, Monitoring Copyright 2005, Michael K. Callahan

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AKNOWLEDGEMENTS First and foremost I would like to thank my major professor, Dr. Pamela Hallock Muller for her tireless effort and patience. I would also like to thank and acknowledge my committee members Dr. Carl Beaver, Walter Jaap, and Dr. Kendra Daly and the entire CREMP research team for their help and guidance. I have been extremely privileged to work with such dedicated professionals. A special thanks also goes to Dr. Michael Risk and Christine Ward-Paige for introducing me to the world of clionid sponges, as well as to Jenni Wheaton who gave me this opportunity. CREMP is funded by USEPA grant award #X-97468002-0 and NOAA grant award #NA160P2554. Water-quality data were pr ovided by the SERC-FIU Water Quality Monitoring Network, which is supported by SFWMD/SERC Cooperative Agreements #C-10244, and #C-13178 as well as EPA Agreement #X994621-94-0. And of course I would be nowhere or no thing without the love and incredible support of my family and friends.

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TABLE OF CONTENTS LIST OF TABLES...............................................................................................................i LIST OF FIGURES...........................................................................................................iii ABSTRACT....................................................................................................................... .v 1. INTRODUCTION..........................................................................................................1 Sponges and Bioerosion..........................................................................................2 Thesis Objectives....................................................................................................5 The Research Area..................................................................................................5 2. METHODS..................................................................................................................... 7 CREMP Monitoring Methods.................................................................................8 Identification ...............................................................................................8 Clionid Survey Methods.............................................................................. 9 Stony Coral Cover Methods...................................................................... 11 Water-Quality Methods........................................................................................13 Statistical Analyses...............................................................................................15 3. RESULTS..................................................................................................................... 17 Clionid Distribution..............................................................................................17 Clionid Species Distribution.................................................................................22 Size-class Data......................................................................................................23 Coral Species Affected.........................................................................................29 Percent Cover of the Top Four Coral Species Affected by Clionids....................32 Water-Quality Analysis........................................................................................37 4. DISCUSSION...............................................................................................................44 Variability in Clionid Distribution........................................................................44 Corals Species Affected by Clionids....................................................................49 Environmental Influences on Clionid Distributions.............................................51 Recommendations for Future Research................................................................52 5. CONCLUSION.............................................................................................................55 REFERENCES.................................................................................................................56 APPENDICES..................................................................................................................61

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i LIST OF TABLES Table 1. CREMP and WQMP site pairing list..................................................................14 Table 2. Water-quality parameters sampled by Boyer and Jones (2002). ................ ........15 Table 3. Mean clionid area (cm2/m2) standard deviation and mean clionid abundance (number of colonies/m2) standard deviation by region, 2001-2003. “N” refers to the number of CREMP stations within the region...................................................................................................19 Table 4. Mean clionid area (cm2/m2) standard deviation and mean clionid abundance (number of colonies/m2) standard deviation by habitat type, 2001-2003. “N” refers to the number of CREMP stations within the habitat type.............................................................................20 Table 5. Mean clionid area (cm2/m2) standard deviation and mean clionid abundance (number of colonies/m2) standard deviation for CREMP stations by region a nd habitat, 2001-2003. “N” refers to the number of CREMP stations within th e region and habitat.........................22 Table 6. Percentages of total clionid area and number of colonies (see Table 5) accounted for by each of the three Cliona species observed ( C. delitrix / C. lampa / C. caribbaea ). “N” refers to the number of CREMP stations...................23 Table 7. Clionid abundance by size class and region for 2001 through 2003..................27 Table 8. Clionid abundance by size class for each habitat type for 2001 through 2003.......................................................................................................................29 Table 9. Stony coral species affected by clioni ds (2002-2003).............. ................ ..........30 Table 10. Mean percent coral cover standard deviation of the four coral species most affected by clioni d invasion, by region (2000-2003). “N” refers to the number of CREMP stations..................................................................32 Table 11. Mean percent coral cover standard deviation of the top four coral species determined to be affected by clionid invasion, by habitat (20002003). “N” refers to the number of CREMP stations...........................................33

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ii Table 12. Mean percent coral cover standard deviation of the four coral species most affected by clionid invasion, by region and habitat (2000-2003). “N” refers to the number of CREMP stations.................................35 Table 13. Mean chlorophyll a values (g/l) standard deviation by region, 2000-2003.............................................................................................................37 Table 14. Mean chlorophyll a values (g/l) standard deviation by habitat type, 2000-2003....................................................................................................38 Table 15. Mean chlorophyll a values (g/l) standard deviation by region and habitat type in 2000 through 2003.................................................................40 Table 16. Summary results from the BIO-ENV routine comparing within the same year. Indicates ties in water-quality parameters.................................43 Table 17. Summary results from the BIO-ENV routine comparing clionid area and abundance matrix to the preceding year’s water-quality matrix ............ ........43

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iii LIST OF FIGURES Figure 1. Coral Reef Evaluation and Monitori ng Project (CREMP) site map...................8 Figure 2. Three common clionid sponges: Cliona delitrix ( A and B ), C. caribbaea (C), and C. lampa (D)............................................................................9 Figure 3. Station layout for the CREMP clionid survey...................................................10 Figure 4. Underwater observer creating 1-meter belt transect using meter stick perpendicular to survey tape.................................................................................11 Figure 5. PointCount for Coral Reefs image analysis software........................................12 Figure 6. Mean clionid area (cm2/ m2) for all CREMP st ations surveyed, 2001-2003. Standard error bars are shown for all three years (N =117). “N” refers to the number of CREMP stations. The mean clionid area decreased significantly between 2001 and 2002 (Wilcoxon; p = 0.035); the decrease from 2002 to 2003 was not significant (Wilcoxon; p = 0.55)...........................................................................17 Figure 7. Mean clionid abundance (colonies per m2) for all CREMP stations surveyed, 2001-2003. Standa rd error bars are shown for all three years (N=117). “N” refers to the number of CREMP stations. The mean clionid abundance decreased significantly between 2001 and 2002 (Wilcoxon; p = 0.051); the decrease from 2002 to 2003 was not significant (Wilcoxon; p = 0.53).............................................................18 Figure 8. Percentages of clionid colonies recorded in each size class (cm2), sanctuary-wide in 2003.........................................................................................24 Figure 9. Number of colonies in each size class for all stations surveyed, 2001-2003.............................................................................................................24 Figure 10. Relative percentages of clionid size cl asses for each region in 2003..............26 Figure 11. Relative percentages of clionid size classes for each habitat type in 2003................. ................ ................ ................ ................ ................ ..........28 Figure 12. Stony coral species affected by clionids (2002). Generic names as in Table 9..........................................................................................................31 Figure 13. Stony coral species affected by clionids (2003). Generic names as in Table 9..........................................................................................................31

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iv Figure 14. Mean percent coral cover of top four coral species most affected by clionid invasion, by region (2000-2003)...............................................................33 Figure 15. Mean percent coral cover of the four coral species most affected by clionid invasion, by habitat ( 2000-2003)...........................................34 Figure 16. Mean percent cover of the four coral species most affected by clionids, for patch reefs by region (2000-2003). ................... .............. ..................36 Figure 17. Mean percent cover of the four coral species most affected by clionids, for deep reefs by region (2000-2003) ................ ................ ............. ........36 Figure 18. Mean chlorophyll a values (g/l) by region, 2000-2003. Standard error bars are shown for all four years...................................................38 Figure 19. Mean chlorophyll a values (g/l) by habitat type, 2000-2003. Standard error bars are shown for all four years...................................................39 Figure 20. Mean chlorophyll a values (g/l) for patch reefs by region, 2000-2003. Standard error bars are shown for all four years...................................................40 Figure 21. Mean chlorophyll a values (g/l) for offshore deep reefs by region, 2000-2003. Standard error bars are shown for all four years..............................41 Figure 22. Mean chlorophyll a values (g/l) for the CREMP patch reef stations from 1997 to 2003...................................................................................45

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v Distribution of Clionid Sponges in the Florida Keys National Marine Sanctuary (FKNMS), 2001-2003 Michael K. Callahan ABSTRACT In 2001, the Coral Reef Evaluation and Monitoring Program (CREMP) began monitoring the abundance and area covered by three clionid sponges ( Cliona delitrix C. lampa and C. caribbaea ). Subsequently, monitoring has been conducted annually at all 40 CREMP sites throughout the Florida Keys National Marine Sanctuary (FKNMS) and the Dry Tortugas. Between 2001 and 2002, mean clionid area decreased significantly from 7.6 cm2/m2 to 4.6 cm2/m2 (Wilcoxon; p = 0.035). Between 2002 and 2003, the decline to 4.5 cm2/m2 was not significant. Approximately 80% of all clionid colonies recorded at the CREMP stations covered less than 50 cm2. Among all recorded stony coral species, Montastraea annularis M. cavernosa and Siderastrea siderea were the most frequently and extensively invaded by clionid colonies. However, the vast majority of clionid colonies occurred in substrata not associated with a live coral colony. The mean percent cover for the four coral species identified to be most susceptible to clionid invasion had the greatest decline in the Dry Tortugas deep stations between 2001 and 2003. At Lower Keys patch-reef stations, mean percent cover showed a small, steady decrease, while at Upper Keys patch-reef stations, a small steady increase occurred. Fifteen water-quality parameters

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vi collected by the Water Quality Monitoring Network (WQMN) were analyzed to determine if clionid distributions correlated with water quality. When patch-reef sites were analyzed as a subset of sites, clionid area and abundance correlated strongly ( > 0.65) with water-quality parameters that indicated higher nutrient flux and food resources. However, the correlation was weak when all 39 CREMP sites were considered ( 0.10). Clionid sponges are well known to be aggressive and successful bioeroders on coral reefs. Therefore the monitoring of clionid trends and distributions should be an integral part of any coral-reef monitoring program.

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1 1. INTRODUCTION Coral reefs are one of the most biologically diverse and productive ecosystems on Earth. Approximately one third of the world’s marine fish species can be found on coral reefs (Paulay, 1997). Coral reefs provide essential habitat for countless marine organisms, including many commercially and recreationally important species. In addition, corals reefs act as natural breakwaters for protecting shorelines from wave action and as a storehouse for future pharmaceutical discoveries. Coral reefs also have a significant positive impact on local economi es, particularly tourism and recreational industries. For example, the Florida Keys National Marine Sanctuary attracts three million tourists per year who spend 1.2 billion dollars annually (Causey, 2002). For all of Monroe County, FL, reef-related expenditures reached 490 million dollars during June 2000 to May 2001, and resulted in 9,800 jobs in Monroe County (Johns et al ., 2001). Coral reefs around the globe are in declin e due to a combination of nutrification, sedimentation, chemical pollution, overfishing, global warming, ozone depletion, and an increase in coral diseases (Hallock, 2001; Porter et al ., 2001). Recent studies suggest that 20% of the world’s coral reefs have been effectively destroyed with no prospects of recovery, and another 24% under imminent risk of collapse through human pressures (Wilkinson, 2004). During the 1970’s, coral cover throughout the Caribbean and the Florida Keys was estimated at 50-60%; whereas, today it is estimated to be below 10% (Porter et al ., 2002; Gardener et al ., 2003).

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2 Sponges and Bioerosion Conrad Neuman first defined the term “bioerosion” as the destruction and removal of substrate by the direct action of organisms (Neumann, 1966). Today, bioerosion is an important but often overlooked aspect of reef health (Holmes, 1997; Holmes et al ., 2000). Growth of a coral reef can be defined by the simple equation of reef accretion minus reef erosion. A healthy, growing reef must accrete more than it loses to erosion (Sammarco, 1996). Bioerosion weakens the coral-reef framework, making the reef more susceptible to wave and storm damage. Many different types of organisms can attack the framework of reefs, including bacteria, fungi, algae, sponges, polychaete worms, sipunculid worms, bryozoans, barnacles and bivalves (Risk and MacGeachy, 1978). Sponges (phylum Porifera) play an essential yet often overlooked role in coralreef ecosystems. In Cari bbean shallow-water benthic communities, sponges are diverse and abundant. In fact, the Porifera are among the most prominent taxa in reef ecosystems, usually exceeding corals and algae in number of species (Diaz and Rtzler, 2001). More than 640 sponge species have been recorded from the Caribbean, 420 species from Indonesia, 683 from the West Indian Ocean, and over 1,500 species from northeast Australia (Wulff, 2001). The high water-filtration rates of sponges can greatly reduce the concentration of organic matter in the water column. Although the processes are not completely understood, sponges appear to play important roles in the dynamics of nutrient and carbon cycling in the water column (Diaz and Rtzler, 2001). Despite their importance, sponges tend to be ignored or avoided in the assessment and monitoring of

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3 coral reefs because they are difficult to identify and quantify. Researchers have only recently begun to understand some of their functional roles in the marine ecosystem (Wulff, 2001). For example sponges play vital roles in calcification, cementation and bioerosion processes on coral reefs. Sponges, in particular clionid sponges, are among the most common and destructive endolithic borers on coral-reef ecosystems (Scoffin et al ., 1980; Holmes, 1997), contributing as much as 30% of the sediments in the reef environment (Hartman, 1977; Glynn, 1997). Clionid sponges successfully invade many different types of substrate including carbonate rock, coral skeleton, mollusk shells, and even man-made calcareous structures (Schnberg, 2002). In the Caribbean MacGeachy and Stearn (1976) estimated that clionids account for more than 90% of total boring in Montastraea annularis colonies. Like most other sponges, clionids feed on unicellular algae and bacteria filtered from the water column. Cli onids do not obtain nourishment from the breakdown of shells and skeletons (Goreau and Hartman, 1963). Clionid sponges chemically break down th e calcium-carbonate structure through a cellular-etching process (Rtzler and Rieger 1973). Specialized archaeocytes termed “etching cells” release a substance, most likely carbonic anhydrase, which dissolves the substrate. Then a small chip is detached th rough a noose-like constricting action (Cobb, 1969; Rtzler, 1975; Bergquist, 1978). Once free, the chip is moved through the sponge by ameboid transport to the excurrent canals. These sediment chips are expelled through the sponge’s excurrent canals or papillae, leaving the internal substrate with a pitted or scoured appearance (Hein and Risk, 1975). Cl ionids produce silt-sized sediment chips that can range from 30m to 60m, and can be identified in reef sediment (Rtzler and

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4 Rieger, 1973). As the sponge bores, new cavities are formed and existing ones are enlarged until the substrate is riddled with an interconnecting network of tunnels and cavities (Cobb, 1969). In la boratory experiments, Neumann (1966) showed that Cliona lampa was capable of removing as much as 7 kg of material from one square meter of carbonate substrate in 100 days. However, Rtzler (1975) suggested that, while initial penetration rates are high, the rate of removal declines after six months. The long-term mean boring rate does not appear to exceed 7 kg m-2 yr-1 (Rtzler, 1975). A similar value, 8 kg m-2 yr-1, was reported for C. caribbaea by Acker and Risk (1985). Nutrient availability and organic carbon supp ly appear to influence the balance between carbonate production and bioerosion ( Highsmith, 1980; Hallock and Schlager, 1986; Hallock, 1988). In two regions of Indonesia (the Java Sea and Ambon), Holmes et al (2000) documented an increase in bioerosion on polluted reefs compared to reference reefs. Rose and Risk (1985) reported an increase in C. delitrix in Montastraea annularis colonies on polluted reefs versus control reefs in Grand Cayman Island. On Reunion Island in the Indian Ocean, Cuet et al (1988) found that C. inconstans increased with higher nutrient concentrations. However, an increase of clionids on coral reefs cannot be solely attributed to increased food sources. Decreasing live coral tissue, which thereby increases the available substrate, may also play a role (McKenna, 1997). For example, after the 1983 coral-bleaching event on the Caribbean coast of Costa Rica, an increase in C. caribbaea was reported on the affected reefs (Cortez et al ., 1984). Rtzler (2002) attributed a decrease of live coral area and an increase of abundance of C. caribbaea in Belize over

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5 the past 20 years, to water warming, to catastrophic events such as hurricanes, or to a long-term trend. Clionid sponges are one of the most important framework bioeroders on coral reefs and they have the ability to out compete stressed corals. Any dramatic increases in the area or abundance of these sponges could lead to an increase in the breakdown of the reef framework and reduce the opportunity for reef recovery. Effective management of the Florida Keys National Marine Sanc tuary (FKNMS) requires a more complete understanding of clionid/coral interactions and how or how much the clionid sponges may contribute to coral-reef decline in the Florida Keys. Thesis Objectives The primary objectives of this study are to document the distribution and trends in clionid populations in the FKNMS and to identify which stony-coral species are most susceptible to infestation by clionids. Secondary objectives are to compare clionidpopulation trends with trends in water quali ty and percent coral cover. Restoration projects in South Florida, such as the Comprehensive Everglades Restoration Plan (CRERP), and increasing human development have the potential to further alter the South Florida ecosystem. This study will help serv e as a baseline for comparisons with future studies in an effort to assess changes to the Florida Keys coral-reef ecosystem. The Research Area The Florida Keys are an archipelago of subtropical limestone islands of Pleistocene origin, extending from Miami southwest to the Dry Tortugas. The Florida

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6 Reef Tract (Vaughan, 1914) is a discontinuous assemblage of reefs (hardbottom, patch reefs, and offshore bank reefs) forming an arc parallel to the Florida Keys coastline (Jaap, 1984). Water quality in the Florida Keys is directly influenced by the Florida Current, the Gulf of Mexico Loop Curr ent, inshore currents of the SW Florida Shelf, and tidal exchange with Florida Bay and Biscayne Bay, as well as by internal nutrient loading and freshwater runoff from the Keys (Boyer and Jones, 2002). Specifically, water circulation in Hawk Channel is characterized by along-channel flow that follows seasonal changes in regional wind patterns (Smith and Pitts, 2002). Despite the well documented decline in coral cover and abundance since the early 1970’s (Dustan and Halas, 1987; Porter and Meier, 1992), comprehensive long-term monitoring in the Florida Keys did not begin until 1995 with the Coral Reef Monitoring Project (CRMP) funded by the Environmental Protection Agency (Hu et al ., 2003). CRMP is part of the Florida Keys Water Quality Protection Program (WQPP), which is charged with the monitoring of seagrass habitats, coral reefs, hardbottom communities and water quality. Water quality is monitored quarterly by the Southeast Environmental Research Program (i.e., Boyer and Jones, 2002). Due to the limited scope of my study, only 2000-2003 water-quality data and coral-monitoring data will be analyzed.

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7 2. METHODS In 2001, a clionid-sponge assessment was incorporated into the CRMP sampling regime (Wheaton et al ., 2001). In additio n, nine CRMP sites thr oughout the Keys were selected in 2002 and designated as “value-a dded sites.” At these sites a populationabundance census and a coral-disease tracking survey were added to the normal CRMP sampling. Because of these additions, the program name was changed to the Coral Reef Evaluation and Monitoring Project (CREMP). Since 2001, clionid surveys have been conducted annually at all 40 CREMP sites throughout the Florida Keys. In 2003, ten CREMP monitoring sites were added along Broward, Dade, and Palm Beach counties (Fig. 1).

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8 Figure 1. Coral Reef Evaluation and Monitoring Project (CREMP) site map. CREMP Monitoring Methods Identification Clionid sponges both appear and feel lik e a thin, soft, tissue layer over a hard, calcified base. Cliona delitrix Pang 1971 (Fig. 2 A,B) is the most common clionid sponge encountered throughout the survey area. This species is characterized by a bright orange color with large, raised, excurrent openings called osculae. Cliona caribbaea Carter 1882 (Fig. 2 C) is brown to olive in color, has many small excurrent openings apparent upon close observation, and often looks and feels like a velvety scum growing

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9 over corals. Cliona lampa Laubenfels 1950 (Fig. 2 D) is less common than C. delitrix darker orange to red in color, and has slightly smaller excurrent openings. Figure 2. Three common clionid sponges: Cliona delitrix (A and B), C. caribbaea (C), and C.lampa (D). Clionid Survey Methods To facilitate incorporation of the clionid-sponge census into the CREMP sampling scheme, a method was developed based on the existing station layout. One CREMP site contains two to four stations, each composed of three transects approximately 22 m in length. Belt transects, 1 m in width, provide the maximum spatial coverage available for the clionid survey (Fig. 3).

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10 Figure 3. Station layout for the CREMP clionid survey. Starting from the offshore CREMP station marker, a fiberglass underwater survey tape is deployed to the corresponding inshore marker (approximately 22 m). A diver, holding a meter stick perpendicular to the survey tape and parallel to the bottom, swims along the survey tape (Fig. 4). For each clionid colony within the 1-meter belt transect, the location (distance in meters from the offshore marker), area (m2) and stony-coral species affected are recorded. If the clionid colony is on reef substrate other than coral, or the coral species cannot be identified, “Other” is recorded.

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11 Figure 4. Underwater observer creating 1-meter belt transect using meter stick perpendicular to survey tape. Surface area is measured with a 40 by 40 cm quadrat frame divided into 5 by 5 cm grids. The number of grids occupied by the clionid colony is recorded to the nearest half grid. Single clionid papillae are not reco rded, the area of the clionid must occupy at least one quarter of the 5 cm2 grid to be recorded. This corresponds to approximately 2.5 cm2. The quadrat is placed over the clionid colony parallel with the sea floor, creating a map or planar view. Only the clionid sponges visible from an aerial view are counted. Overhangs and holes are not surveyed. Stony Coral Cover Methods The Coral Reef Evaluation and Monitoring Project (CREMP) obtains data on the percent of stony-coral cover using underwater video transects. Three video transects are filmed at a constant distance above the substrate at each station. Two lasers mounted on the camera housing converge 40 cm from the camera lens and guide the videographer in

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12 maintaining a constant distance from the substr ate. The videographer must also maintain a uniform swimming speed of approximately 4 m per minute. Abutting video frames are selected, and converted to digital still images for image analysis (Jaap et al ., 2003). Image analysis is performed using the computer software application PointCount for Coral Reefs. This specially developed software places ten random points onto each digital image (Fig. 5). The substrate below each of these points is then identified and recorded. Once a file is completed, the spreadsheets are converted into an ASCII file and incorporated into a master Microsoft ACCESS database (Jaap et al ., 2003). Using the list of stony coral species effected by clionid sponges in the 2002 and 2003 clionid survey, a mean percent cover of the four coral species most affected by clionid invasion is determined. The mean percent cover is based on the total number of points identified for each of the seven coral species, divided by the total number of points for each station. Since the total area of a station is approximately 44 m2, each 1% coral cover represents ~0.44 m2 of coral cover. Figure 5. PointCount for Coral Reefs image analysis software.

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13 Water-Quality Methods Since 1995, quarterly sampling of at least 15 water-quality parameters (Table 1) has been conducted at more than 200 stations in the FKNMS and the Florida shelf by the Southeast Environmental Research Program at Florida International University (FIU) (Boyer and Jones, 2002). To determine if any correlation exists between water quality and clionid area or abundance, water-quality data from the Water Quality Monitoring Network (WQMN) had to be summarized in a way that could be compared with CREMP data. Using an ARCview query tool developed by Florida Fish and Wildlife Research Institute (FWRI), selected water-quality stat ions were chosen for comparison to CREMP monitoring sites. Water-quality stations were chosen based on four main criteria: 1) proximity to CREMP sites, 2) depth similarity, 3) relative distance to shore, and 4) similarity of benthic cover under the WQMN station (i.e., reef/ hardbottom/ seagrass). All CREMP sites have an associated waterquality station except for the CREMP station White Shoal in the Dry Tortugas (Table 1). Due to the close proximity of CREMP deep and shallow reef sites, both sites were paired with the same water-quality station. Waterquality parameters examined are listed in Table 2. All parameters include surface and bottom measurements except for chlorophyll a which only represents surface measurements.

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14Table 1. CREMP and WQMN site pairing list. CREMP Site Name WQMP Station Name 9P1 Turtle Patch 212Turtle Harbor 9S1 Carysfort Shallow 216Carysfort Reef 9D1 Carysfort Deep 216Carysfort Reef 9S2 Grecian Rocks 400Grecian Rocks 9P3 Porter Patch 400Grecian Rocks 9H2 El Radabob 220Radabob Key 9S3 Molasses Shallow 225Molasses Reef 9D3 Molasses Deep 225Molasses Reef 9P4 Admiral Patch 224Molasses Reef Channel 9S4 Conch Shallow 228Conch Reef 9D4 Conch Deep 264Aquarius 7S1 Alligator Shallow 401Alligator Reef 7D1 Alligator Deep 401Alligator Reef 7S2 Tennessee Shallow 243Tennessee Reef 7D2 Tennessee Deep 243Tennessee Reef 7H2 Long Key 242Long key Channel 7P1 West Turtle 248Coffins Patch Channel 7P2 Dustan Rocks 248Coffins Patch Channel 5S1 Sombrero Shallow 402Sombrero Key 5D1 Sombrero Deep 402Sombrero Key 5H1 Moser Channel 250Seven Mile Bridge 5S2 Looe Key Shallow 263Looe Key 5D2 Looe Key Deep 263Looe Key 5P4 Jaap Reef 268Saddlebunch Keys 5P1 W. Washer Woman 269W. Washerwoman 5S3 Eastern Sambo Shallow 273Eastern Sambo Offshore 5D3 Eastern Sambo Deep 273Eastern Sambo Offshore 5S4 Western Sambo Shallow 403Western Sambo 5D4 Western Sambo Deep 403Western Sambo 5P3 Cliff Green Patch 275Boca Chica Mid 5P2 Western Head 278Western Head 5S5 Rock Key Shallow 280Eastern Dry Rocks 5D5 Rock Key Deep 280Eastern Dry Rocks 2S1 Sand Key Shallow 281Middle Ground 2D1 Sand Key Deep 281Middle Ground 3H1 Content Keys 302Content Passage 2P1 Smith Shoal 318KW Northwest Channel 1D1 Bird Key 344Southwest Channel 1P1 White Shoal NANA 1D2 Black Coral Rock 347Loggerhead Offshore

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15Table 2. Water-quality parameters sampled by Boyer and Jones (2002). Water-Quality Parameters salinity (practical salinity scale) temperature ( C) dissolved oxygen (DO, mg/l) turbidity (NTU) nitrate (NO3 -, M) nitrite (NO2 -, M) ammonium (NH4 +, M) dissolved inorganic nitrogen (DIN, M) soluble reactive phosphate (SRP, M) total nitrogen (TN, M) total organic nitrogen (TON, M) total organic carbon (TOC, M) total phosphorus (TP, M) silicate (Si(OH)4, M) chlorophyll a (CHL-a, g/l) alkaline phosphatase activity (APA, M/h) Statistical Analyses The Kolmogorov-Smirnov goodness-of-fit test (Kolmogorov, 1933) revealed that neither the clionid abundance nor area data for the years 2001, 2002, and 2003 were normally distributed. Therefore non-parametric tests were selected to analyze the clionid survey data. The Wilcoxon rank-sum test for two independent samples (Wilcoxon, 1945) was used to determine if there were significant differences among the years 2001, 2002, and 2003 at the Sanctuary-wide, region, habitat, and region/habitat level. Both tests were carried out using the S-plus (2001) statistical package. Probabilities (p) are reported, and a significant level of < 0.05 is used.

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16 The BIO-ENV procedure in PRIMER 5.2 for Windows was used to analyze how well the clionid data matched with the water-quality data. The BIO-ENV procedure is a multi-variate statistical technique (Clarke and Ainsworth, 1993), which determines a correlation coefficient ( ) between a Bray-Curtis similarity matrix for clionids and a normalized Euclidean-distance similarity ma trix of water-quality parameters. The correlation coefficient is analogous to the Spearman-rank coefficient, but has no test of significance. The BIO-ENV procedure di splays the best fitting combination or combinations of water-quality variables that most accurately explain the clionid data.

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17 3. RESULTS Clionid Distribution For all stations surveyed, mean clionid area decreased from 7.6 cm2/m2 in 2001 to 4.5 cm2/m2 in 2003 (Fig. 6). Using the one-tailed Wilcoxon rank-sum test, this decrease was statistically significant ( p = 0.036). The majority of the decline was seen between 2001 and 2002 (Wilcoxon; p = 0.035). 7.6 4.6 4.50 2 4 6 8 10 12 200120022003Mean Clionid Area (cm2/m2) Figure 6. Mean clionid area (cm2/ m2) for all CREMP stations surveyed, 2001-2003. Standard error bars are shown for all three years (N =117). “N” refers to the number of CREMP stations. The mean clionid area decreased significantly between 2001 and 2002 (Wilcoxon; p = 0.035); the decrease from 2002 to 2003 was not significant (Wilcoxon; p = 0.55).

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18 Abundance of clionids closely follows their area of coverage sanctuary-wide (Fig 7). Mean number of colonies decreased from 0.08 colonies/m2 in 2001 to 0.04 colonies/m2 in 2003. Using the one-tailed Wilcoxon rank-sum test the decrease from 2001 to 2003 was determined to be statistically significant ( p = 0.05). The majority of the decrease was recorded between 2001 and 2002 (Wilcoxon; p = 0.05). 0.08 0.05 0.040 0.02 0.04 0.06 0.08 0.1 0.12 200120022003Mean Clionid Abundance (colonies/m2) Figure 7. Mean clionid abundance (colonies per m2) for all CREMP stations surveyed, 2001-2003. Standard error bars are shown for all three years (N =117). “N” refers to the number of CREMP stations. The mean clionid abundance decreased significantly between 2001 and 2002 (Wilcoxon; p = 0.051); the decrease from 2002 to 2003 was not significant (Wilcoxon; p = 0.53). Analysis of clionid abundance and surface area by region and year (Table 3) revealed several significant trends. In 2001, the highest mean clionid area (12.3 cm2/m2) and the highest number of clionid colonies (0.19 colonies/m2) were recorded at the Dry Tortugas stations. Between 2001 and 2003 those stations also had the greatest decrease

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19 in mean clionid area, which declined approximately 50%, (Wilcoxon; p = 0.077) and number of colonies, which declined approximately 70% (Wilcoxon; p = 0.016). The Lower Keys stations also experienced a loss in mean clionid area and mean abundance. Mean clionid area decreased 35%, from 8.97 cm2/m2 in 2001 to 5.8 cm2/m2 in 2003 (Wilcoxon; p = 0.086). Mean number of colonies decreased 40%, from 0.07 colonies/m2 in 2001 to 0.04 colonies/m2 in 2003 (Wilcoxon; p = 0.078). The Upper Keys stations had the lowest mean clionid area (< 2 cm2/m2) of all four regions consistently for all three years. In 2003, mean clionid area in the Dry Tortugas, the Lower Keys, and the Middle Keys regions was fairly uniform with values at nearly 6 cm2/m2. However the Dry Tortugas stations continued to have the highest number of colonies (0.06 colonies/m2). Clionid sponges in all four regions decreased in area between 2001 and 2003; however, only in the Dry Tortugas and Lower Keys were those changes statistically significant (Table 3). Table 3. Mean clionid area (cm2/m2) standard deviation and mean clionid abundance (number of colonies/m2) standard deviation by region, 2001-2003. “N” refers to the number of CREMP stations within the region. mean cm2/m2 mean number of colonies/m2 Region N 2001 2002 2003 2001 2002 2003 Upper Keys 30 1.42 2.61 1.693.53 1.012.02 0.070.13 0.06 0.14 0.040.08 Middle Keys 29 9.69 30.45 4.8814.71 5.4915.83 0.050.08 0.03 0.04 0.040.06 Lower Keys 46 8.97 17.58 5.5917.86 5.8314.32 0.070.10 0.03 0.05 0.040.06 Dry Tortugas 12 12.28 22.40 7.2614.00 5.9312.80 0.190.17 0.10 0.11 0.060.05 Analysis of clionid abundance and cover data by habitat and year (Table 4) also yielded significant trends. Hardbottom stations revealed that clionid surface area can be

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20 highly variable from year to year. In 2001, the hardbottom stations had the highest mean clionid area (11.2 cm2/m2). Patch-reef stations had the next highest mean area (9.6 cm2/m2), followed by the deep reef stations (7.8 cm2/m2). Without the Dry Tortugas deep reef stations, the mean drops to 4.7 cm2/m2. In 2002, the hardbottom stations lost all of their clionid cover and colonies. By 2003, the clionids had recovered to a mean value of 2.6 cm2/m2 and 0.04 colonies/m2. In 2002 and 2003, patch reef stations maintained the highest mean clionid area values of 8.1 cm2/m2 and 7.6 cm2/m2 respectively. Shallow reef stations had the lowest mean clionid area for 2001 and 2003, with only hardbottom stations (0.0 cm2/m2) lower in 2002. Clionid sponges in all habitat types reflected the decrease in area and number of colonies between 2001 and 2003 (Table 4). Table 4. Mean clionid area (cm2/m2) standard deviation and mean clionid abundance (number of colonies/m2) standard deviation by habitat type, 2001-2003. “N” refers to the number of CREMP stations within the habitat type. mean cm2/m2 mean number of colonies/m2 Habitat N 2001 2002 2003 2001 2002 2003 HardBottom 11 11.21 20.89 0.000.00 2.556.04 0.050.09 0.00 0.00 0.040.07 Patch 33 9.57 17.11 8.0520.74 7.5816.36 0.060.09 0.03 0.04 0.030.04 Shallow 39 4.59 26.07 1.9911.06 2.0612.18 0.020.08 0.01 0.03 0.010.02 Deep 34 7.80 14.58 5.6910.97 5.0010.31 0.160.15 0.11 0.14 0.090.08 Deep w/o Tortugas 26 4.68 6.91 4.098.60 3.808.39 0.130.16 0.10 0.10 0.090.04 Analysis of clionid area and abundance da ta by region and habitat (Table 5) reveals several important trends. Grouping the deep reefs by region, the Dry Tortugas contained the highest mean clionid area in 2001 and 2002. However, in 2003 the Middle Keys deep stations had the highest mean clionid area. Clionid area recorded at the Dry

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21 Tortugas deep stations decreased 40%, from 17.97 cm2/m2 in 2001 to 10.9 cm2/m2 in 2002 (Wilcoxon; p = 0.071). Between 2002 and 2003, the slight decline in clionid area at the Dry Tortugas stations was not significant (Wilcoxon; p = 0.54). The Middle Keys deep stations showed a significant increase in both mean clionid area and mean number of colonies between 2002 and 2003. During that time, mean clionid area increased 24%, from 8.2 cm2/m2 to 10.2 cm2/m2 (Wilcoxon; p = 0.045), and the mean number of colonies nearly doubled from 0.07 colonies/m2 to 0.13 colonies/m2 (Wilcoxon; p = 0.11). Although clionid colonies were most abundant at the Upper Keys deep stations, mean clionid area was intermediate (4 –7 cm2/m2), indicating predominantly small colonies (Table 5). The CREMP shallow stations showed strong differences among regions (Table 5). The Upper Keys and Lower Keys shallow stations had very low mean clionid area, less than 0.5 cm2/m2 between 2001 and 2003. The Middle Keys shallow stations, however, exhibited much higher mean clionid area, 16.3 cm2/m2 in 2001, which declined by more than 50% in 2002. Considering the patch reefs by region (Table 5), the Lower Keys contained the highest mean clionid area (> 17 cm2/m2) for all three years and showed no significant decrease between 2001 and 2003 (Wilcoxon; p = 0.22). The Upper Keys patch-reef stations contained the lowest mean clionid area within the patch reefs of the Florida Keys reef tract. No patch reef in the main Florida Keys reef tract showed a statistically significant change between 2001-2003. Only the Dry Tortugas patch-reef stations showed a significant decline between 2001-2003 (Wilcoxon; p = 0.093) (Table 5).

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22 The CREMP hardbottom stations exhibited the greatest variability among the three regions (Table 5). In 2001, the hardbottom stations in the Lower Keys had the highest mean clionid area (34.9 cm2/m2), followed by the Middle Keys (3.1 cm2/m2). By 2002, mean clionid area decreased to zero in both the Lower Keys and Middle Keys harbottom stations. However, some regrowth had occurred by 2003. No clionids were found at any of the Upper Keys hardbottom stations (Table 5). Table 5. Mean clionid area (cm2/m2) standard deviation and mean clionid abundance (number of colonies/m2) standard deviation for CREMP stations by region and habitat, 2001-2003. “N” refers to the number of CREMP stations within the region and habitat. mean cm2/m2 mean number of colonies/m2 Region / HabitatN 2001 2002 2003 2001 2002 2003 UK Hardbottom2 0.00 0.00 0.000.00 0.000.00 0.000.00 0.00 0.00 0.000 UK Patch 9 0.29 0.88 0.210.63 0.130.38 0.020.05 0.01 0.03 0.010.03 UK Shallow 13 0.67 1.54 0.421.17 0.320.70 0.280.08 0.01 0.03 0.020.04 UK Deep 6 5.2 3.3 7.24.8 4.22.7 0.30.2 0.3 0.2 0.20.1 MK Hardbottom6 3.13 7.65 0.000.00 0.030.08 0.000.01 0.00 0.00 0.000.01 MK Patch 7 4.25 4.78 2.93.59 3.033.48 0.040.03 0.03 0.02 0.030.02 MK Shallow 10 16.34 51.55 7.2021.777.6324.070.000.01 0.02 0.04 0.010.01 MK Deep 6 11.5 11.6 8.216.9 10.216.3 0.180.11 0.07 0.05 0.130.08 LK Hardbottom3 34.85 29.58 0.000.00 9.289.43 0.180.07 0.00 0.00 0.140.07 LK Patch 13 21.5 22.5 18.730.6 17.523.0 0.110.12 0.05 0.06 0.050.06 LK Shallow 16 0.43 1.26 0.000.00 0.000.00 0.030.10 0.00 0.00 0.000 LK Deep 14 1.53 1.77 1.01.2 0.891.43 0.050.06 0.05 0.05 0.050.07 DT Patch 4 0.90 1.11 0.050.09 0.000.00 0.050.07 0.00 0.01 0.000 DT Deep 8 17.97 26.02 10.8716.238.9015.080.250.16 0.15 0.10 0.090.04 Clionid Species Distribution Cliona delitrix is the most common clionid species throughout the survey area (Table 6). Cliona lampa and C. caribbaea occur much less frequently. Cliona lampa only occurs in large areas at the Lower Ke ys hardbottom site at Content Keys, while C.

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23 caribbaea dominates the Middle Keys shallow stations, and also contributes considerably to the Middle Keys deep and Dry Tortugas deep stations, 65% and 57% respectively. Table 6. Percentages of total clionid area and number of colonies (see Table 5) accounted for by each of the three Cliona species observed ( C. delitrix / C. lampa / C. caribbaea ). “N” refers to the number of CREMP stations. Percentage of Area Number of Colonies Region / Habitat N2001 2002 2003 2001 2002 2003 Upper Keys Hardbottom 20/0/0 0/0/0 0/0/0 0/0/0 0/0/0 0/0/0 Upper Keys Patch 9100/0/0100/0/0100/0/09/0/0 6/0/0 5/0/0 Upper Keys Shallow 13100/0/0100/0/096/4/024/0/0 12/0/0 15/1/0 Upper Keys Deep 693/0/7 85/0/15100/0/096/0/4 105/0/4 66/0/0 Middle Keys Hardbottom6100/0/00/0/0 100/0/01/0/0 0/0/0 1/0/0 Middle Keys Patch 7100/0/0100/0/0100/0/016/0/0 14/0/0 14/0/0 Middle Keys Shallow 100/0/1004/0/961/0/991/0/2 13/0/3 1/0/3 Middle Keys Deep 639/19/4316/0/8335/0/6562/6/2 23/0/4 48/0/2 Lower Keys Hardbottom 31/99/0 0/0/0 0/100/02/33/0 0/0/0 0/27/0 Lower Keys Patch 1391/9/0 96/4/089/11/083/15/039/5/0 40/5/0 Lower Keys Shallow 16100/0/00/0/0 0/0/0 36/0/0 0/0/0 0/0/0 Lower Keys Deep 14100/0/087/13/0100/0/050/0/0 39/4/0 43/0/0 Dry Tortugas Patch 4100/0/0100/0/00/0/0 14/0/0 1/0/0 0/0/0 Dry Tortugas Deep 859/0/4155/0/4543/0/57127/0/676/0/3 44/0/2 Size-Class Data For all stations surveyed, approximately 80% of clionid colonies were < 50 cm2 in area (Fig 8.). All four size classes < 500 cm2 declined in abundance by roughly half from 2001 to 2003. The smallest size classes, 0 to 25 cm2 and 25 to 50 cm2, also experienced the greatest decrease in the number of colonies from 2001 to 2003. Abundances in the two larger size classes increased by 25%, from 16 to 20 between 2001 and 2003 (Fig. 9).

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24 Sanctuary-wide 2003 3% 3% 3% 11% 38% 42% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000 Figure 8. Percentages of clionid colonies recorded in each size class (cm2), sanctuary-wide in 2003. 261 211 82 20 8 8 159 127 4112 5 7 121 129 36 10 1190 50 100 150 200 250 3000 to 2525 to 5050 to 250250 to 500500 to 1,000 > 1,000cm2Number of Colonie s 2001 2002 2003 Figure 9. Number of colonies in each size class for all stations surveyed, 2001-2003. The clionid size-class data show important differences among the regions (Table 7) (Fig. 10). Clionid colonies at the Lower Keys stations exhibited the greatest size range. In the Lower Keys stations, abundance in all size classes decreased except for the 500 to 1,000 cm2 size class, which increased from 0.002 colonies per m2 in 2001 to 0.003

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25 colonies per m2 in 2003, and the >1,000 size class which remained the same from 2001 to 2003. The smallest size class, 0 to 25 cm2, declined by two-thirds, from 0.032 colonies per m2 in 2001 to 0.011 colonies per m2 in 2003. In the Middle Keys, three size classes, 25 to 50 cm2, 50 to 250 cm2, and 250 to 500 cm2, decreased in abundance by at least 50% (Table 7). Increases were recorded in the size classes 0 to 25 cm2 and 500 to 1,000 cm2. In the Upper Keys stations the abundance in size class 0 to 25 cm2 declined by 44% and the 25 to 50 cm2 by 20%, whereas, no change was recorded for the 50 to 250 cm2 size class. No colonies greater than 250 cm2 were recorded in the Upper Keys stations (Fig. 10). In the Dry Tortugas stations, abundances declined in all size classes except >1,000 cm2 size class. In the 0 to 25 cm2 size class, abundance declined more than 85% between 2001 and 2003. The 25 to 50 cm2 and 50 to 250 cm2 size classes also showed large decreases from 2001 to 2003 (Table 7).

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26 Figure 10. Relative percentages of clionid size classes for each region in 2003. Lower Keys 200338% 29% 14% 7% 8% 4% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000 Middle Keys 2003 23% 55% 12% 6% 3% 1% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000 Upper Keys 2003 50% 47% 3% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000 Dry Tortugas 2003 61% 15% 20% 2% 2% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000

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27Table 7. Clionid abundance by size class and region for 2001 through 2003. Clionid colonies per m2 by size class Upper keys 0-25 cm2 25-50 cm2 50-250 cm2250-500 cm2500-1,000 cm2 > 1,000 cm2 2001 0.039 0.026 0.002 0.000 0.000 0.000 2002 0.033 0.027 0.005 0.000 0.000 0.000 2003 0.022 0.021 0.002 0.000 0.000 0.000 Middle keys 0-25 cm2 25-50 cm2 50-250 cm2250-500 cm2500-1,000 cm2 > 1,000 cm2 2001 0.016 0.017 0.011 0.002 0.000 0.002 2002 0.016 0.009 0.003 0.000 0.001 0.002 2003 0.020 0.008 0.004 0.001 0.001 0.002 Lower keys 0-25 cm2 25-50 cm2 50-250 cm2250-500 cm2500-1,000 cm2 > 1,000 cm2 2001 0.032 0.022 0.011 0.005 0.002 0.001 2002 0.012 0.007 0.004 0.003 0.001 0.001 2003 0.011 0.014 0.005 0.003 0.003 0.001 Dry Tortugas 0-25 cm2 25-50 cm2 50-250 cm2250-500 cm2500-1,000 cm2 > 1,000 cm2 2001 0.072 0.076 0.033 0.001 0.003 0.001 2002 0.037 0.044 0.016 0.003 0.000 0.001 2003 0.009 0.035 0.011 0.000 0.001 0.001 Some distinct trends are evident when the clionid size-class data are analyzed by habitat type (Table 8, Fig. 11) over the three years. The patch-reef stations have the most even distribution among the size classes for all the habitat types. For the patch-reef stations the size classes that increased in abundance between 2001 and 2003 were the 500 to 1,000 cm2 and > 1,000 cm2. The other size classes all declined in abundance. The 0 to 25 cm2 size class declined by 80%, while the 25 to 50 cm2 size class declined by twothirds in 2003. For the hardbottom stations, abundance declined in all size classes from 2001 to 2003. As noted previously, no colonies were recorded at any of the hardbottom stations during 2002. In 2003, the highest clionid abundances were documented in the offshore-deep stations, 0.042 colonies per m2 in the 0 to 25 cm2 size class and 0.041

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28 colonies per m2 in the 25 to 50 cm2 size class. For the offshore deep stations, abundances in all size classes decreased except for the > 1,000 cm2 size class, which remained unchanged at 0.001 colonies per m2 from 2001 to 2003 in 2001. In the offshore shallow stations, no colonies larger than 250 cm2 were recorded. Small colonies (< 25 cm2) declined by more than 75% by 2003 (Table 8). Figure 11. Relative percentages of clionid size classes for each habitat type in 2003. Patch Reef Stations 2003 27% 27% 13% 14% 13% 6% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000 Deep Reef Stations 2003 47% 45% 7% 1% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000 Shallow Reef Stations 2003 65% 20% 10% 5% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000 Hardbottom Stations 2003 62% 19% 15% 4% 0 to 25 25 to 50 50 to 250 250 to 500 500 to 1,000 > 1,000

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29Table 8. Clionid abundance by size class for each habitat type for 2001 through 2003. Clionid colonies per m2 by size class Hardbottom Stations 0-25 cm225-50 cm2 50-250 cm2 250-500 cm2 500-1,000 cm2 > 1,000 cm2 2001 0.014 0.014 0.011 0.006 0.003 0.003 2002 0.000 0.000 0.000 0.000 0.000 0.000 2003 0.007 0.023 0.006 0.000 0.001 0.000 Patch Reef Stations 0-25 cm225-50 cm2 50-250 cm2 250-500 cm2 500-1,000 cm2 > 1,000 cm2 2001 0.018 0.024 0.012 0.006 0.002 0.001 2002 0.006 0.009 0.006 0.005 0.002 0.001 2003 0.004 0.008 0.008 0.004 0.004 0.002 Shallow Reef Stations 0-25 cm225-50 cm2 50-250 cm2 250-500 cm2 500-1,000 cm2 > 1,000 cm2 2001 0.021 0.002 0.001 0.000 0.000 0.000 2002 0.008 0.001 0.002 0.000 0.000 0.000 2003 0.005 0.002 0.000 0.000 0.000 0.001 Deep Reef Stations 0-25 cm225-50 cm2 50-250 cm2 250-500 cm2 500-1,000 cm2 > 1,000 cm2 2001 0.071 0.064 0.020 0.001 0.001 0.001 2002 0.055 0.047 0.010 0.001 0.000 0.001 2003 0.042 0.041 0.006 0.000 0.000 0.001 Coral Species Affected In 2002, seven different species of stony coral were directly affected by clionids (Table 9, Fig. 12). By 2003, the number increased to ten. In 2002, the highest number of clionid colonies (82) were found in Montastraea annularis colonies, with Siderastrea siderea (60) and Montastraea cavernosa (40) rounding out the top three. In 2003, the most clionid colonies were found in S. siderea (60), followed by M. annularis (41) and M. cavernosa (25). The highest clionid area, 7500 cm2, was found in M. cavernosa colonies in 2002. Siderastrea siderea, Colpophyilla natans and M. annularis had the next highest, with 2775 cm2, 1863 cm2 and 1763 cm2 respectively. In 2003, the highest clionid area (3000 cm2) was again found in M. cavernosa however it was much lower

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30 than in 2002. Siderastrea siderea, M. annularis and C. natans had the next highest, with 2438 cm2, 975 cm2 and 900 cm2 respectively. Interestingly, clionid area in C. natans decreased by half between 2002 and 2003, while the number of clionid colonies remained the same. In both years the vast majority of clionid area and colonies were located on substratum identifiable as “Other” (Table 9, Fig. 12, 13). Table 9. Stony-coral species affected by clionids (2002-2003). 2002 2003 Stony Coral Species Mean Coral Percent Cover Number of Clionid Colonies Clionid Area (cm2) Coral Percent Cover Number of Clionid Colonies Clionid Area (cm2) Colpophyllia natans 0.54% 8 1863 0.49% 8 900 Dendrogyra cylindrus 0.06% 0 0.0 0.05% 1 12.5 Diploria labyrinthiformis 0.05% 0 0.0 0.04% 3 37.5 Diploria strigosa 0.08% 4 137.5 0.12% 4 125 Montastraea annularis 3.03% 82 1763 3.13% 41 975 Montastraea cavernosa 1.47% 40 7500 1.36% 25 3000 Meandrina meandrites 0.04% 0 0.0 0.03% 1 12.5 Porites asteroides 0.66% 8 100.0 0.60% 7 112.5 Stephanocoenia michelinii 0.08% 3 150.0 0.07% 4 200.0 Siderastrea siderea 0.94% 60 2775 0.80% 60 2438 Other NA 146 21063 NA 165 27103

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31 2002 1% 23% 17% 2% 11% 43% 1% 2% C. natans D. strigosa M. annularis M. cavernosa P. asteroides S. michelinii S. siderea Other Figure 12. Stony coral species affected by clionids (2002). Generic names as in Table 9. 2003 13% 8% 19% 52% 3% 1% 1% 2% 1% C. natans D. cylindrus D. labyrinthiformis D. strigosa M. annularis M. cavernosa M. meandrites P. asteroides S. michelinii S. siderea Other Figure 13. Stony coral species affected by clionids (2003). Generic names as in Table 9.

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32 Percent Cover of the Four Coral Species Most Affected by Clionids Between the years 2000 and 2003, the four coral species identified to be most susceptible to clionid invasion declined in m ean percent cover in the Lower Keys and the Dry Tortugas (Table 10, Fig. 14). Percent cover at the Dry Tortugas stations declined from 13.0% in 2000 to 10.1% in 2003 (Wilcoxon: p = 0.15). Mean percent cover for these four corals in the Lower Keys stations decreased from 7.2% in 2000 to 6.5% in 2003 (Wilcoxon: p = 0.27). Cover by these taxa at the Middle Keys and Upper Keys stations was lower, approximately 4% and 5% respectively, and remained relatively unchanged from 2000 to 2003. Table 10. Mean percent coral cover standard deviation of the four coral species most affected by clionid invasion, by region (2000-2003). “N” refers to the number of CREMP stations. Region N 2000 2001 2002 2003 Upper Keys 30 4.9%7.9% 5.0%8.2% 4.9% 8.3% 5.0%8.8% Middle keys 29 3.7%5.3% 3.6%5.2% 4.0% 6.0% 3.7%5.3% Lower Keys 46 7.2%8.2% 7.0%8.0% 6.7% 8.6% 6.5%8.7% Dry Tortugas 12 13.0%9.1% 14.1%9.8% 10.9% 8.2% 10.1%7.6%

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33 0% 2% 4% 6% 8% 10% 12% 14% 16%2000200120022003Mean Percent Cover Upper Keys Middle Keys Lower Keys Dry Tortugas Figure 14. Mean percent coral cover of top four coral species most affected by clionid invasion, by region (2000-2003). Among the four habitat types, no statistically significant changes in the mean percent cover of the four coral species were observed between 2000 and 2003 (Fig. 15). The greatest change occurred at the deep stations, where the mean cover for the top four coral species declined from 6.6% in 2000 to 5.1% in 2003 (Table 11) (Wilcoxon; p = 0.24). Table 11. Mean percent coral cover standard deviation of the top four coral species determined to be affected by clionid invasion, by habitat (2000-2003). “N” refers to the number of CREMP stations. Mean Percent Coral Cover for the Top Four Identified Coral Species Invaded by Clionids Habitat type N 2000 2001 2002 2003 Hardbottom 11 0.4% 0.6% 0.5%0.8% 0.4%0.6% 0.4% 0.7% Patch 33 11.9% 8.2% 11.7%8.1% 11.7%9.4% 11.5% 9.5% Shallow 39 3.1% 6.6% 3.1%6.6% 3.0%6.4% 3.0% 6.8% Deep 34 6.6% 7.3% 6.8%8.0% 5.7%6.3% 5.1% 5.9%

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34 0% 2% 4% 6% 8% 10% 12% 14%2000200120022003Mean Percent Cover Hardbottom Offshore Deep Offshore Shallow Patch Reefs Figure 15. Mean percent coral cover of the four coral species most affected by clionid invasion, by habitat (2000-2003). Analyzing the mean percent cover of the four coral species most often invaded by clionids by region and habitat (Table 12) reveals several distinct patterns. Grouping the CREMP offshore shallow stations by region, the mean percent cover of the four coral species most affected by clionid invasion was three times higher in the Upper and Lower Keys stations than the Middle Keys stations. As shown in Figure 15, the patch reefs have the highest mean percent cover of the four coral species most affected by clionid invasion. Examining the patch reefs by region, the highest mean percent cover was re corded in the Lower Keys (Table 12, Fig. 16), while mean percent cover on the Dry Tortugas patch reefs was the lowest. No significant changes in mean percent cover occurred between 2000 and 2003 on the patch reefs.

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35 Dry Tortugas deep-reef stations were very different from those of the Upper, Middle and Lower Keys (Table 12, Fig. 17). The mean percent coral cover of the four coral species most affected by clionid invasi on in Dry Tortugas deep stations greatly exceeded that of the other CREMP deep reefs. A significant decrease ( p = 0.025) was observed in the Dry Tortugas deep stations between 2000 and 2003. No significant changes in mean percent coral cover were detected in the Upper, Middle and Lower Keys deep stations between 2000 and 2003. Table 12. Mean percent coral cover standard deviation of the four coral species most affected by clionid invasion, by region and habitat (2000-2003). “N” refers to the number of CREMP stations. Mean Percent Coral Cover for the Top Four Identified Coral Species Invaded by Clionids Region/Habitat N 2000 2001 2002 2003 Upper Keys Hardbottom 2 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% Upper Keys Patch 9 9.9% 10.1%10.7% 11.0%10.6% 11.3% 11.1% 12.1% Upper Keys Shallow 13 3.5% 7.1% 3.4% 6.7% 3.2% 6.6% 3.1% 6.8% Upper Keys Deep 6 2.1% 2.3% 1.7% 1.4% 1.6% 1.6% 1.4% 1.6% Middle Keys Hardbottom 6 0.7% 0.7% 0.8% 1.0% 0.6% 0.7% 0.8% 0.8% Middle Keys Patch 7 11.8% 5.2% 11.5% 5.0% 13.0% 5.8% 11.7% 5.3% Middle Keys Shallow 10 0.8% 1.1% 0.8% 1.2% 1.1% 1.7% 0.8% 1.1% Middle Keys Deep 6 2.0% 1.7% 1.8% 1.5% 1.6% 1.3% 1.9% 1.5% Lower Keys Hardbottom 3 0.0% 0.0% 0.4% 0.2% 0.2% 0.1% 0.1% 0.2% Lower Keys Patch 13 16.7% 5.3% 15.8% 5.2% 15.2% 8.9% 14.9% 8.7% Lower Keys Shallow 16 4.2% 8.0% 4.3% 8.3% 3.9% 8.1% 4.3% 8.6% Lower Keys Deep 14 3.4% 2.1% 3.3% 1.9% 3.2% 1.9% 2.6% 1.5% Dry Tortugas Patch 4 0.9% 1.1% 1.3% 1.8% 0.8% 1.1% 0.8% 1.0% Dry Tortugas Deep 8 19.1% 1.5% 20.6% 2.7% 16.0% 4.1% 14.7% 4.1%

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36 Patch Reefs 0% 2% 4% 6% 8% 10% 12% 14% 16% 18%2000200120022003Mean Percent Cover Upper Keys Middle Keys Lower Keys Dry Tortugas Figure 16. Mean percent cover of the four coral species most affected by clionids, for patch reefs by region (2000-2003). Deep Reefs 0% 4% 8% 12% 16% 20% 24% 2000200120022003Mean Percent Cover Upper Keys Middle Keys Lower Keys Dry Tortugas Figure 17. Mean percent cover of the four coral species most affected by clionids, for deep reefs by region (2000-2003).

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37 Water-Quality Analysis Water-quality results based on the pairwise comparison of CREMP site to WQMN station can be found in Appendices BD. Laws and Redalje (1979) concluded that chlorophyll a is the most sensitive indicator of nutrient enrichment in tropical marine waters, and therefore is highlighted here. Among the four regions, the highest mean chlorophyll a concentrations were recorded at the Lower Keys sites three of the four years (Table 13). In 2002, the Dry Tortugas sites had the highest chlorophyll a values (0.47 g/l), as well as the greatest variation across years, from 0.13 g/l in 2001 to 0.47 g/l in 2002. The Upper Keys sites and the Middle Keys sites show similar patterns from 2000 to 2003, with the Upper Keys sites having lower chlorophyll a concentrations for three of the four years (Table 13, Fig. 18). Table 13. Mean chlorophyll a values (g/l) standard deviation by region, 2000-2003. Mean Chlorophyll a (g/l) Region 2000 2001 2002 2003 Upper Keys 0.363 0.362 0.174 0.208 0.200 0.171 0.155 0.21 Middle Keys 0.418 0.400 0.133 0.140 0.249 0.320 0.248 0.164 Lower Keys 0.624 0.604 0.304 0.236 0.345 0.395 0.389 0.412 Dry Tortugas 0.281 0.307 0.128 0.147 0.467 0.382 0.202 0.196

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38 0.0 0.2 0.4 0.6 0.8 1.0 2000200120022003Chlorophyll a (g/L) Upper Keys Middle Keys Lower Keys Dry Tortugas Figure 18. Mean chlorophyll a values (g/l) by region, 2000-2003. Standard error bars are shown for all four years. Between 2000 and 2003 chlorophyll a grouped by habitat type shows that the hardbottom sites and the patch reefs generally have the highest mean chlorophyll a values (Table 14, Fig. 19). As noted in Method s, most offshore deep sites and corresponding shallow sites share the same WQMN site, explaining why most offshore deep and shallow regions show similar water quality values between 2000 and 2003. Table 14. Mean chlorophyll a values (g/l) standard deviation by habitat type, 2000-2003. Mean Chlorophyll a (g/l) Habitat Type 2000 2001 2002 2003 Hard bottom 0.679 0.832 0.247 0.225 0.448 0.511 0.33 0.199 Patch 0.561 0.543 0.283 0.331 0.334 0.445 0.384 0.515 Offshore Shallow 0.430 0.386 0.183 0.142 0.222 0.185 0.211 0.151 Offshore Deep 0.401 0.380 0.182 0.132 0.257 0.241 0.241 0.227

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39 0.0 0.2 0.4 0.6 0.8 1.0 2000200120022003Chlorophyll a (g/L) Hard bottom Offshore Deep Offshore Shallow Patch Figure 19. Mean chlorophyll a values (g/l) by habitat type, 2000-2003. Standard error bars are shown for all four years. Among the patch reefs, the highest mean chlorophyll a values were consistently recorded in the Lower Keys between 2000-2003 (Table 15, Fig. 20), ranging from 0.70 g/l in 2000 to 0.42 g/l in 2001. The Upper Keys patch reefs had the lowest mean chlorophyll a values three of the four years. The same trend was seen for the offshore deep and shallow sites, with the Lower Keys exhibiting higher mean chlorophyll a values than the corresponding sites in the Upper or Middle Keys.

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40Table 15. Mean chlorophyll a values (g/l) standard deviation by region and habitat type in 2000 through 2003. Mean Chlorophyll a (g/l) Region and Habitat 2000 2001 2002 2003 Upper Keys Hardbottom 0.362 0.4310.171 0.2630.193 0.132 0.198 0.096 Upper Keys Patch 0.407 0.3700.190 0.2970.196 0.152 0.122 0.066 Upper Keys Shallow 0.364 0.3670.159 0.1730.209 0.186 0.119 0.089 Upper Keys Deep 0.318 0.3710.178 0.1420.196 0.197 0.223 0.381 Middle Keys Hardbottom 0.446 0.3970.202 0.1890.457 0.681 0.318 0.238 Middle Keys Patch 0.444 0.3850.092 0.1400.255 0.072 0.265 0.232 Middle Keys Shallow 0.399 0.4310.123 0.1210.177 0.104 0.219 0.098 Middle Keys Deep 0.399 0.4310.123 0.1210.177 0.104 0.219 0.098 Lower Keys Hardbottom 1.31 1.29 0.412 0.2240.684 0.218 0.486 0.027 Lower Keys Patch 0.700 0.6560.415 0.3580.449 0.602 0.589 0.655 Lower Keys Shallow 0.501 0.3810.238 0.1100.259 0.220 0.28 0.179 Lower Keys Deep 0.501 0.3810.238 0.1100.259 0.220 0.28 0.179 Dry Tortugas Deep 0.281 0.3070.128 0.1470.467 0.382 0.202 0.196 0.0 0.2 0.4 0.6 0.8 1.0 2000200120022003Chlorophyll a (g/L) Upper Keys Patch Middle Keys Patch Lower Keys Patch Figure 20. Mean chlorophyll a values (g/l) for patch reefs by region, 2000-2003. Standard error bars are shown for all four years.

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41 0.0 0.2 0.4 0.6 0.8 1.0 2000200120022003Chlorophyll a (g/L) Upper Keys Deep Middle Keys Deep Lower Keys Deep Figure 21. Mean chlorophyll a values (g/l) for offshore deep reefs by region, 2000-2003. Standard error bars are shown for all four years. When all 39 sites were analyzed using the BIO-ENV routine, low correlations were observed ( < 0.12). However, when the sites are analyzed by habitat type, correlations increased (Table 16, 17). Th e results from the BIOENV routine generally show good stratification across habitat ty pes. The CREMP mid-channel patch reefs consistently exhibit a strong correlation ( 0.7) with the water-qua lity parameters, while the offshore deep reefs typically displayed a weak correlation ( 0.4). The CREMP hardbottom sites and offshore shallow sites show much greater variability. The hardbottom sites correlated very strongly in 2001 and 2003 ( = 0.97), but not in 2002 ( = 0.0). A large number of ties occurred in the water quality parameter correlations in 2001 and 2003. Only one hardbottom site (Content Keys) contains substantial amounts of clionids, and with high concentrations in the different water quality parameters, there is no way to differentiate among the different parameters. The offshore shallow reefs

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42 exhibited a wide range in correlations, from = 0.19 in 2002 to = 0.77 in 2003 (Table 16). Similar results were found by comparing the clionid area and abundance matrix to the preceding year’s water-quality matrix (Table 17). All sites grouped together exhibited weak correlations ( < 0.12), and the hardbottom and offshore shallow sites showed high variability. A notable exception is the patch reefs, where the correlation was much stronger when comparing the 2003 clionid area and abundance matrix with the 2002 water-quality matrix. The water-quality parameters selected by the BIO-ENV routine were highly variable (Table 16, 17). Each year’s comparison resulted in a different set of waterquality parameters. Even w ithin the patch reefs, whose correlations were the most consistent, no single water-quality parameter was repeatedly selected in all three years.

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43Table 16. Summary results from the BIO-ENV routine comparing within the same year. Indicates ties in water-quality parameters. Matrices Tested Sites Correlation Coefficient Water Quality Parameters Clionid 2001 vs. WQ 2001 All Sites = 0.123 Chl-a Clionid 2001 vs. WQ 2001 Deep Reefs = 0.508 Chl-a, Turbs, SRPs Clionid 2001 vs. WQ 2001 Shallow reefs = 0.349 DOb, Si(OH4)s Clionid 2001 vs. WQ 2001 Patch Reefs = 0.777 Turbb, APAb, DOb, Si(OH4)s, Si(OH)4b Clionid 2001 vs. WQ 2001 Hardbottom sites = 0.971 Clionid 2002 vs. WQ 2002 All Sites = 0.102 NH4b, Turbs, TONs Clionid 2002 vs. WQ 2002 Deep Reefs = 0.315 TNs, NO3s, TOCs, Si(OH4)s, DOb Clionid 2002 vs. WQ 2002 Shallow reefs = 0.186 Salb Clionid 2002 vs. WQ 2002 Patch Reefs = 0.722 NOxs, NO3s, DINb, APAb Clionid 2002 vs. WQ 2002 Hardbottom sites = 0.000 NA Clionid 2003 vs. WQ 2003 All Sites = 0.099 Chl-a, SRPs, Temps, Salb Clionid 2003 vs. WQ 2003 Deep Reefs = 0.470 Turbs, TONs, TOCs, SI(OH4)s, Sals Clionid 2003 vs. WQ 2003 Shallow reefs = 0.772 Chl-a, NH4s, NO3s, DINs Clionid 2003 vs. WQ 2003 Patch Reefs = 0.603 SI(OH4)b, Temps Clionid 2003 vs. WQ 2003 Hardbottom sites = 0.971 Table 17. Summary results from the BIO-ENV routine comparing clionid area and abundance matrix to the preceding year’s water-quality matrix. Matrices Tested Sites Correlation CoefficientWater Quality Parameters Clionid 2002 vs. WQ 2001 All Sites = 0.120Chl-a, Turbb, TOCb, APAb Clionid 2002 vs. WQ 2001 Deep Reefs = 0.425Chl-a, SRPs, APAb, TOCs, Sals, DOs Clionid 2002 vs. WQ 2001 Shallow reefs = 0.438Chl-a, SI(OH4)s Clionid 2002 vs. WQ 2001 Patch Reefs = 0.743Tempb, SI(OH4)b Clionid 2002 vs. WQ 2001 Hardbottom sites = 0.000NA Clionid 2003 vs. WQ 2002 All Sites = 0.081NO3s Clionid 2003 vs. WQ 2002 Deep Reefs = 0.415TNs, TOCs, Si(OH4)s, Si(OH4)b Clionid 2003 vs. WQ 2002 Shallow reefs = 0.231NH4b Clionid 2003 vs. WQ 2002 Patch Reefs = 0.936NH4b, TPs, TONs, TOCb, DOs Clionid 2003 vs. WQ 2002 Hardbottom sites = 0.794Temps, DINs, APAs

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44 4. DISCUSSION Variability in Clionid Distribution In general, the clionid area and abundance data for the Florida Keys National Marine Sanctuary (FKNMS) exhibit high variability, i.e., large areas absent of any clionids and small areas where clionids are clustered. One explanation may be low clionid larval dispersal ability, as described by Mariani et al (2000) for Cliona viridis A low larval dispersal mechanism for C. delitrix C. lampa and C. caribbaea would concentrate newly settled larvae around the parent colonies. When clionids are already established in an area and environmental conditions change, a low larval dispersion mechanism clusters the new clionid colonies, resulting in a boom of clionid growth in a limited area. Either increasing food resources or an increase in available substrate could trigger clionid overgrowth. High variability makes mu lti-year studies with broad geographic ranges and a large number of samples the most useful method to monitor clionid sponges. For all CREMP stations surveyed, clionid area and abundance decreased significantly between 2001 and 2002. This decr ease is in contrast to the overall increase documented by Ward-Paige (2003), who analyzed archived CREMP video from 1996 to 2001 to estimate C. delitrix and C. lampa area. This contrast can be explained by reviewing the mean chlorophyll a concentrations from 1997 to 2003 (Fig. 22). Between 1997 amd 2000, chlorophyll a concentrations increased. However between 2000 and 2001 there was a sharp decrease, which may have lead to the decrease seen in the clionid

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45 data between 2001 and 2002. There are no other recent clionid studies in the Florida Keys for comparison. However, on a stu dy reef in Belize, Rtzler (2002) also documented an increase in C. caribbaea abundance over the past 20 years. The majority of the decrease in clionid area and abundance occurred between the years 2001 and 2002. Only continued monitoring will determine if th is decrease is simply an anomaly. 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 1997199819992000200120022003Chlorophyll a (g/L) LK patch MK patch UK patch Figure 22. Mean chlorophyll a values (ug/L) for the CREMP patch reef stations from 1997 to 2003. Using CREMP archived video of a small selected number of sites, Ward-Paige (2003) found the highest clionid cover in the Lower Keys. In contrast, in 2001, I found the highest mean clionid area in the Dry Tortugas. By 2003, the Lower Keys, Middle Keys and Dry Tortugas all had similar values of clionid area. Area and abundance of clionid colonies at the Upper Keys stations remained low during all three years. One

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46 difference between studies is the different numb er of samples. Using the archived video, Ward-Paige (2003) examined fewer data. In the Florida Keys National Marine Sanctuary, clionid sponges were most common on CREMP patch reefs. Stony coral cover is also highest on the CREMP patch reef stations. This gives the clionid sponges ample opportunity to find suitable corals for invasion. Areas covered by clionids were highest on patch reefs in the Lower Keys. Very few clionids were found at the Upper Keys patch reef stations between 2001 and 2003, despite sufficient coral cover (> 10% mean cover). Moreover roughly half the clionids recorded were not located on a live coral colony. Thus, coral cover may not be an important factor in clionid abundance or colony area. Clionid area and abundance data exhibit high variability among the regions and between years at the CREMP hardbottom sites. Clionid trends at the CREMP hardbottom sites are dominated by results from two sites, Content Keys and Long Key. The two other hardbottom sites, El Radabob (Upper Keys) and Moser Channel (Middle Keys), are dominated by octocorals and algae, and have no significant stony coral cover. Content Keys is a very rugose site in Florida Bay north of Big Pine Key. Content Keys is the only CREMP site where C. lampa is present and not C. delitrix or C. caribbaea Numerous, large C. lampa colonies were recorded in the Content Keys in the 2001 survey, yet no colonies were seen at that site during the 2002 survey. Hu et al (2003) suggested that this dramatic die off was the result of the water-quality event generally known as “Blackwater” (SWFDOG 2002). By the 2003 survey, C. lampa was starting to reestablish and in 2004, C. lampa colonies had continued to expand in area and abundance (pers. obs). Some clionids also ha ve the ability to create asexual reproductive

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47 bodies similar to freshwater sponge gemmules. These gemmules remain attached to the substrate after the sponge has disintegrated and enable the sponge to recolonize when conditions become favorable (Hopkins, 1956; Bergquist, 1978). These asexual reproductive bodies may have given C. lampa the ability to quickly recolonize in Content Keys. Long Key is a more typical FKNMS hardbottom site. Located oceanside of the Long Key viaduct, this site has low to moderate coral cover and is influenced by water flow from Florida Bay. Just as in Content Keys, Long Key lost all of its clionid area between 2001 and 2002. However, unlike in Content Keys, C. delitrix was the dominant clionid species at Long Key. The Long Key site was not included in the Hu et al (2003) study, so the influence of the “Blackwater” event is unknown. As a habitat group, the offshore shallow stations typically have low clionid area. However, analyzing the offshore shallow stations by region, this conclusion is only valid for the Upper and Lower Keys shallow stations. In the Middle Keys, shallow reefs contain significant amounts of clionid area. Th e bulk of the clionid area is present in the form of a few, massive C. caribbaea colonies. It would be logical to assume that Florida Bay influence may account for the higher clionid area in the Middle Keys offshore shallow stations. However elevated concentrations of chlorophyll a were not documented. Intermittent influence from Florida Bay makes the water-quality in the Middle Keys highly variable. Quarterly wa ter-quality sampling is apparently not sufficiently sensitive to document pulses or sporadic water-quality events that are likely a major influence on the reefs in the Middle Keys.

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48 Offshore deep stations contain moderate clionid areas and high mean abundance. Offshore deep stations are dominated by small (< 50 cm2) clionid colonies. Among the deep stations, the highest clionid areas occurred at the Dry Tortugas and Middle Keys stations. Interestingly, colony abundances we re highest at the Upper Keys deep stations for all three years. Clionid distribution trends in the offshore deep stations did not follow trends in chlorophyll a in surface waters. Chlorophyll a concentrations reported for the Upper, Middle, and Lower Keys deep reefs are very similar, and did not reflect the differences seen in the clionid area and abundance data. Reduced light intensities at the offshore deep stations might limit growth of the clionid sponges with symbiotic zooxanthellae, C. caribbaea and C. varians (Hill, 1996). However, reduced light intensities should not affect the azooxanthellate clionid sponges, C. delitrix and C. lampa Reasons for regional differences in clionid abundances and size distributions at deep stations are not known. The adult life cycle of a clionid sponge can be classified into three life stages: the alpha stage, the beta stage and the gamma stage (Vosmaer, 1933). During the alpha stage only the small papillae of the sponge are visible on the surface of the coral. The beta stage is an intermediate stage where the sponge tissue begins to link up with the papillae and the sponge begins to expand across the coral surface. Finally, in the gamma stage, the sponge completely overgrows the coral colony (Bergquist, 1978). In the Florida Keys National Marine Sanctuary most clionid colonies are small (< 50 cm2) alpha or beta stage clionids. Only in the mid-channel patch reef s is there a consistent pattern of larger gamma-stage clionid colonies. Thirty-three percent of clionid colonies on the patch reef stations were > 250 cm2. In contrast, only 1% of clionid colonies on the deep reef

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49 stations were > 250 cm2. Therefore the size-class data supports the claim that clionids influence patch reefs more than offshore reefs. Whether more mature size distribution on the patch reefs can be solely attributed to consistently higher food resources, as indicated by water-quality parameters, is unclear. Corals Species Affected by Clionids Only 10 out of 45 stony-coral species identified by CREMP were documented to be affected by clionid invasion. Three species, M. meandrites D. labyrinthiformis and D. cylindru s were affected by clionids in 2003, but not in 2002. An increasing trend in stony-coral species affected by clionids is alarming, however with only two years of data it is impossible to interpret the significance. Nearly half of all clionid area was seen on substrate where the stony coral species could not be identified. Sponge and coral interactions are species specific (McKenna, 1997; Wilkinson, 1978). Rtzler (2002) observed several sto ny corals successfully defend against spongetissue invasion when the corals were healthy. For example, Montastraea cavernosa deters colonization of the boring sponge C. lampa through the use of mesenterial filaments and extracoelentric dige stion of sponge tissue (Sullivan et al ., 1983; McKenna, 1997). However, when the corals are stressed or damaged, sponge tissue invasion is more likely to succeed (Aerts, 2000; Rtzler, 2002). Sponges have been known to use secondary metabolites (allelochemicals) to compete for space and defend themselves (Sullivan et al ., 1983; McKenna, 1997). Bioactive chemical compounds, which cause acute cell lysis and appear to inhibit the grow th of coral polyps, have been discovered in

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50 some bioeroding sponge species (Schnberg and Wilkinson, 2001). However, these types of toxic chemicals have not been reported in clionids (Rtlzer, 2002). Among the stony corals, clionid area was highest in M. cavernosa S. siderastrea, M. annularis, and C. natans These four stony coral species are also some of the most important reef builders (Jaap, 1984). These four stony coral species make up 74% of the mean percent cover documented at CREMP stations. Ginsburg et al (2001) found M. annularis had the most amount of dead surfaces in the Florida Keys patch reefs, and clusters of Montastrea had more dead surfaces in the Lower Keys than in any other region. That study unfortunately does not indicate what caused the dead surfaces. However, Ginsburg et al (2001) speculate the increased amount of dead tissue in the Middle and Lower Keys is the resu lt of unfavorable water quality. Percent cover of the four coral species mo st affected by clionid sponges declined in the Dry Tortugas deep stations (Bird Key and Black Coral Rock) between 2001 and 2002. In particular, M. annularis and C. natans sharply declined in response to an unidentified coral disease (Jaap et al ., 2002; Kidney and Hackett, 2003). It will be interesting to see if clionids take advantage of this newly available substrate. In the patch-reef stations, percent cover by the four stony coral species most affected by clionid invasion was stable over the survey period. Interestingly, the patch reefs have large clionid colonies and high mean clionid area, possibly indicating a balance between reef accretion and reef erosion in the patch reefs. An interesting interregional pattern may be developing among patch reefs, specifically the small increase in the percent coral cover in the Upper Keys patch-reef stations and small decrease at the Lower Keys patch-reef stations.

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51 Environmental Influences on Clionid Distributions Reporting WQMN data, Boyer and Jones (2002) found that seawater in the Upper Keys generally contained lower nutrient concentrations than the Middle or Lower Keys. Those findings are reflected in the chlorophyll a concentrations in Table 12 and Figure 18, which are based upon a subset of WQMN stations paired with CREMP sites. However, in Table 12 and Figure 18, elevated nutrient concentrations in the Lower Keys stand out above the data for the Upper and Middle Keys. Examination of the data for patch reefs in Figure 20 reveal an even greater divergence of data for the Lower Keys from that of the Upper and Middle Keys. Similarly, Lapointe et al (2004) documented overall higher chlorophyll a concentrations in the Lower Keys, as well as seasonal highs during the summer wet season According to the nutrient gradient presented by Mutti and Hallock (2003), the majority of chlorophyll a concentrations documented throughout my study are classified in the mesotrophic range (0.2 g/L to 0.5 g/L). Mesotrophic conditions represent intermediate nutrient flux sufficient to favor algae and sponge domination of the benthos (M utti and Hallock, 2003). The results from the BIO-ENV routine indicate that the correlations between clionid area and water quality parameters are strongest for the patch reefs. Little emphasis should be placed on the individual water quality parameters selected by the BIO-ENV routine, since each year’s comparison results in a different set of parameters. The variability may be an artifact of only co llecting water quality on a quarterly schedule. Quarterly sampling is most likely not sensitive enough for the BIO-ENV routine to begin discriminate among individual parameters. Quarterly sampling, however, appears to be

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52 sufficient to demonstrate an overall correlation between clionid distribution and nutrient resources within the patch reef sites. It is unclear what other factors, such as grazing and sedimentation, influence clionid distribution. Bioeroding sponges such as clionids are partly sheltered from grazers by having substantial amounts of their tissue within the hard substrate. However, as Schnberg and Wilkinson (2001) observed, recently settled larva-derived sponge colonies would seem to be at a high risk of being entirely removed by grazing. Living within the hard substrate may also allow clionids to survive certain environmental stresses that would otherwise kill stony corals, octocorals and macroalage. The 2002 “Blackwater” event and the subsequent rapid regrowth of C. lampa at Content Keys maybe one such example. Recommendations for Future Research Continued monitoring of clionid sponges is essential to understand the complex coral-reef ecosystem in the Florida Keys. Annual clionid surveys, however, are insufficient to determine the causes of the extreme variability in clionids. An increased sampling effort, including quarterly clionid sampling and a larger number of samples, would greatly improve the ability to explain th is variability. A specific goal of future research should be directed to understanding the distribution of clionids on the offshore deep and shallow reefs. For example, what is limiting the clionid colony growth on offshore deep reefs and what is causing the variability observed between regions? In addition, future monitoring shoul d include the sponge species, Cliona varians Cliona

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53 varians is a common sponge on shallow reefs and has the potential for quickly overgrowing other organisms. The results of this study highlight the limitations of water-quality sampling on a quarterly schedule. Increasing the frequency of water-quality sampling and the addition of WQMN stations directly over CREMP s ites would greatly increase the ability to identify correlations between the WQMN and CREMP databases. Controlled laboratory experiments manipulating water-quality pa rameters while measuring clionid tissue growth is long overdue and critical to the next phase of understanding clionids and how they interact with the coral-reef ecosystem. Overall, clionid sponges are most commonly found on patch reefs in the Florida reef tract. Within the patch reefs, Lower Keys sites have higher clionid cover, decreasing mean percent cover of C. natans, S. siderastrea, M. annularis, and M. cavernosa as well as higher chlorophyll a concentrations. In contrast to the Lower Keys patch-reefs, the Upper Keys patch-reef sites have low clionid cover, increasing mean percent cover of C. natans S. siderastrea, M. annularis, and M. cavernosa and lower chlorophyll a concentrations. The results of this study suggest that clionid sponges may be impacting the growth and recovery of the major reef-b uilding corals in the Florida Keys National Marine Sanctuary patch reefs, and that at ti mes these impacts follow the same patterns as water quality. Therefore, these findings support previous reports that the impact of boring sponges is elevated in areas enriched with nutrients. However, the results from the BIO-ENV routine suggest that these correlations are limited to the patch reefs. Trends in clionid distributions do not correlate with patterns in water quality for the offshore deep or shallow reefs. Continued monitoring with an increased sampling effort

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54 to understand variability in habitats between regions and laboratory experimentation on tissue growth is necessary to determ ine the extent of these impacts.

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55 5. CONCLUSIONS 1. In the CREMP monitoring stations, mean clionid area and mean clionid abundance significantly declined between 2001and 2002; no significant change occurred between 2002 and 2003. 2. The Lower Keys patch reef stations had the highest mean clionid area, while the Upper Keys patch reef stations had the lowest mean clionid area. 3. Approximately 80% of all clionid colonies observed at the CREMP stations were less than 50 cm2 in area. 4. Abundance of clionid colonies less than 50 cm2 in area declined by roughly half from 2001 to 2003. 5. In the Upper Keys stations no clionid colonies larger than 250 cm2 were measured. 6. Small colonies (< 50 cm2) dominated the offshore deep stations, while the patch reef stations exhibited a more even distribution among the size classes. 7. The stony corals most affected by clionid invasion were Montastraea cavernosa Siderastrea siderea M. annularis and Colopophyllia natans. However, the vast majority of clionid area was located on substratum identifiable as “other”. 8. The four coral species most susceptible to clionid invasion declined in mean percent cover by 22% in the Dry Tortugas deep stations between 2001 and 2003. Mean percent cover at the Lower Keys patch-reef stations also declined, while at the Upper Keys and Middle Keys patch-reef stations mean percent cover was stable. 9. Waters over the Lower Keys patch reef sites consistently contain higher chlorophyll a concentrations than waters over the Upper Keys or Middle Keys patch reefs. 10. The BIO-ENV routine consistently iden tified strong correlations between the clionid similarity matrix and the water-quality matrix within patch reefs; however, the water quality parameters responsible for the correlation differed among years.

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56 REFERENCES Acker KL, Risk MJ (1985) Substrate destruction and sediment production by the boring sponge Cliona caribbaea on Grand Cayman Island. Sediment Petrol 55: 705-711 Aerts LAM (2000) Dynamics behind standoff interactions in three reef sponge species and the coral Montastraea cavernosa Mar Ecol 21: 191-204 Bergquist PR (1978) Sponges. University of California Press Berkeley and Los Angeles Boyer J, Jones R (2002) A View from the Brid ge: External and Internal Forces Affecting the Ambient Water Quality of the Florida Keys National Marine Sanctuary (FKNMS). In: Porter J, Porter K (Eds) The Everglades, Florida Bay, and coral reefs of the Florida Keys. An Ecosystem Sourcebook. CRC Press, Boca Raton. pp 609-628 Causey BD (2002) The Role of the Florida Keys National Marine Sanctuary in the South Florida Ecosystem Restoration Initiative. In: Porter J, Porter K (Eds) The Everglades, Florida Bay, and coral reefs of the Florida Keys. An Ecosystem Sourcebook. CRC Press, Boca Raton. pp 883-894 Clarke KR, Ainsworth M (1993) A method of linking multivariate community structure to environment variables. Mar Ecol Prog Ser 92: 205-219 Cobb WR (1969) Penetration of Calcium Car bonate Substrates by the Boring Sponges, Cliona Am Zool 9: 783-790 Cortez J, Murillo M.M, Guzman H.M, Acuna J (1984) Perida de zooxantelas y muerte de corales y otros organismos arrecifales en el Caribe y Pacifico de Costa Rica. Rev Biol Trop 32: 227-231 Cuet P, Naim O, Faure G, Conan J-Y (1988) Nutrient-rich groundwater impact on benthic communities of La Saline fringing reef (Reunion Island, Indian Ocean): preliminary results. Proc 6th Int Coral Reef Symp 2: 207-212 Diaz MC, Rtzler K (2001) Sponges: An essent ial component of Caribbean coral reefs. Bull Mar Sci 69: 535-546 Dustan P, Halas JC (1987) Changes in the reef coral community of Carysfort Reef, Key Largo, Florida: 1974 to 1982. Coral Reefs 16: 91-106

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57 Gardener TA, Cote IM, Gill JA, Grant A, Watkinson AR (2003) Long-term region-wide declines in Caribbean corals. Science 301: 958-960 Ginsburg RN, Gischler E, Kiene WE (2001) Partial mortality of massive reef-building corals: An index of patch reef condition, Florida reef tract. Bull Mar Sci 69:1149-1173 Glynn PW (1997) Bioerosion and coral-reef growth: A dynamic balance, in life and death of coral reefs. Birkeland C, Ed Chapman and Hall. pp 68-95 Goreau TF, Hartman WD (1963) Boring sponges as controlling factors in the formation and maintenance of coral reefs. Amer Assoc for the Adv of Sci Spec Publ 75: 25-54 Hallock P (1988) The role of nutrient availability in bioerosion: consequences to carbonate buildups. Palaeogeogr Palaeoclim Palaeoecol 63: 275-291 Hallock P (2001) Cora l Reefs in the 21st Century: Is the past the key to the future? In: Greenstein BJ, Carney CK (Eds) Proc. 10th Sym on the geology of the Bahamas and other carbonate regions. Gerace Research Center San Salvador, Baha mas. pp viii-xxiv Hallock P, Schlager W (1986) Nutrient excess and the demise of coral reefs and carbonate platforms. Palaios 1: 389-398 Hartman WD (1977) Sponges as reef builders and shapers. Stud Geol 4:127-134 Hein FJ, Risk MJ (1975) Bioerosion of coral heads: inner patch reefs, Florida reef tract. Bull Mar Sci 25: 133-138 Highsmith RC (1980) Geographic patterns of coral bioerosion: a productivity hypothesis. J Exp Mar Biol Ecol 46: 177-196 Hill MS (1996) Symbiotic zooxanthellae enhance boring and growth rates of the tropical sponge Anthosigmella varians forma varians Mar Biol 125: 649-654 Holmes KE (1997) Eutrophication and its effect on bioeroding sponge communities. Proc 8th Int Coral Reef Sym 2: 1411-1416 Holmes KE, Edinger EN, Hariyadi, Limmon GV, Risk MJ (2000) Bioerosion of live massive corals and branching coral rubble on Indonesian coral reefs. Mar Pollut Bull 40:606-617 Hopkins SH (1956) Notes on the boring sponge in gulf coast estuaries and their relation to salinity. B Mar Sci of the Gulf and Caribbean 6: 44-58

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58 Hu C, Hackett KH, Callahan MK, Andrfout S, Wheaton J, Porter J, Muller-Karger FE (2003) The 2002 ocean color anomaly in the Florida Bight: A cause of local coral reef decline? Geo Res Lett 30:1151-1154 Jaap WC (1984) The ecology of the south Florida coral reefs: A community profile. U.S. Department of the Interior Minerals Management Service MMS 84-0038. pp 120 Jaap WC, Wheaton JL, Hackett KE, Callahan MK, Kupfner S, Kidney J, Lybolt M. Long-term (1989-present) monitoring of selected coral reef sites at Dry Tortugas National Park. (2002) Florida Fish and Wildlife Conservation Commission FMRI. pp 43 Jaap WC, Porter JW, Wheaton J, Beaver CR, Callahan MK, Kidney J, Hackett KE, Lybolt M, Kupfner S, Torres CT, Sutherland K (2003) EPA/NOAA coral reef evaluation and monitoring project executive summary 2002. Florida Marine Research Institute. pp 28 Johns GM, Leeworthy VR, Bell FW, Bonn MA (2001) Socioeconomic study of reefs in southeast Florida final report Hwd:40289R028.doc Kidney J, Hackett K (2003) Demise of the brain coral Colpophyllia natans at Bird Key Reef, Dry Tortugas National Park, Florida. Joint Conference on the Science and Restoration of the Greater Everglades and Florida Bay Ecosystem. Kolomogorov AN (1933) Sulla determinazione empirica di una legge di distribuziane. Giornale dell’ Istituto Italiano degli attuari 4: 83-91 Lapointe BE, Barile PJ, Matzie WR (2004) Anthropogenic nutrient enrichment of seagrass and coral reef communities in the Lower Keys: discrimination of local versus regional nitrogen sources. J Exp Mar Biol Ecol 308:23-58 Laws EA, Redalje DG (1979) Effect of sewage enrichment on the phytoplankton population of a subtropical estuary. Pac Sci 33: 129-144 MacGeachy JK, Stearn CW (1976) Boring by macro-organisms in the coral Montastraea annularis on Barbados reefs. Int Revue ges Hydrobiol 61:715-745 Mariani S, Uriz MJ, Turon X (2000) Larval bloom of the oviparous sponge Cliona viridis : coupling of larval abundance and adult distribution. Mar Biol 137: 783-790 McKenna SA (1997) Interactions between the boring sponge, Cliona lampa and two hermatypic corals from Bermuda. Proc 8th Int Coral Reef Sym 2:1369-1374 Mutti M, Hallock P (2003) Carbonate systems along nutrient and temperature gradients: some sedimentological and geochemical constraints. Int J Earth Sci. 92:4 65-475

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59 Neumann AC (1966) Observations on coastal erosion in Bermuda and measurements of the boring rate of the sponge, Cliona lampa Limnol Oceanogr 11: 92-108 Paulay G (1997) Diversity and distribution of reef organisms. In: Life and death of coral reefs, Birkeland C (Ed) Chapman and Hall. pp 298-353 Porter JW, Meier OW (1992) Quantification of loss and change in Floridian reef coral populations. Amer Zool 32: 625-640 Porter JW, Jaap WC, Patterson KL, Kosmynin V, Meier OW, Patterson ME, Parsons M (2001) Patterns of spread of coral disease in the Florida Keys. Hydrobiologia 460: 1-24 Porter JW, Kosmynin V, Patterson KL, Porter KG, Jaap WC, Wheaton J, Hackett KE, Lybolt M, Tsokos CP, Yanev G, Marcinek D, Dotten J, Eaken D, Patterson M, Meier OW, Brill M, Dustan P (2002) Detection of coral reef change by the Florida Keys coral reef monitoring project. In: The Everglades, Florida Bay, and coral reefs of the Florida Keys: An Ecosystem Sourcebook Porter J, Porter K (Eds) CRC Press, Boca Raton. pp 749-769 Risk MJ, MacGeachy JK (1978) Aspects of bioerosion of modern Caribbean reefs. Rev Biol Trop 26: 85-105 Rose CS, Risk MJ (1985) Increase in Cliona delitrix infestation of Montastrea cavernosa heads on an organically polluted portion of the Grand Cayman fringing reef. P.S.Z.N.I. Mar Ecol 6: 345-363 Rtzler K (1975) The role of burrowing sponges in bioerosion. Oecologia 19: 203-216 Rtzler K (2002) Impact of crustose clionid sponges on Caribbean reef corals. Acta Geol Hisp 37: 61-72 Rtzler K, Rieger G (1973) Sponge burrowing: fine structure of Cliona lampa penetrating calcareous substrata. Mar Biol 21: 144-162 Sammarco PW (1996) Comments on coral reef regeneration, bioerosion, biogeography, and chemical ecology: future directions. J Exp Mar Bio Ecol 200: 135-168 Schnberg CHL (2002) Substrate effe cts on the bioeroding Demosponge Cliona orientalis 1. Bioerosion rates. Mar Ecol 23: 313-326 Schnberg CHL, Wilkinson CR (2001) Induced colonization of corals by a clionid bioeroding sponge. Coral Reefs 20: 69-76

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60 Scoffin TP, Stearn CW, Boucher D, Frydl P, Hawkins CM, Hunter IG, MacGeachy JK (1980) Calcium carbonate budget of a fringing reef on the west coast of Barbados. Bull Mar Sci 30: 475-508 Smith NP, Pitts PA (2002) Regional-scale and long-term transport patterns in the Florida Keys. In: The Everglades, Florida Bay, and coral reefs of the Florida Keys: An Ecosystem Sourcebook Porter J, Porter K (Eds) CRC Press Boca Raton. pp 343-360 South-West Florida Dark-Water Observations Group (SWFDOG) (2002) Satellite images track “black water” event off Florid a coast. EOS Trans AGU 83:281-285 Sullivan B, Faulkner J, Webb L (1983) Siphonodictidine a metabolite of the burrowing sponge Siphonodictyon sp. that inhibits coral growth. Science 221:1175-1176 Vaughan TW (1914) Investigations of the geology and geologic processes of the reef tracts and adjacent areas in the Bahamas and Florida. Carnegie Inst. Wash. Year Book 12. pp 183 Vosmaer GCJ (1933) The sponges of the bay of Naples: Porifera incalcaria. The Haque, Martinus Nijhoff pp 828 Ward-Paige CA (2003) Bioerosion surveys on the Florida reef tract suggest widespread land-based stress on reefs. MS Th esis McMaster University, Ontario Wheaton J, Jaap WC, Porter JW, Kosmynin V, Hackett KE, Lybolt M, Callahan MK, Kidney J, Kupfner S, Tsokos CP, Yanev G (2001) EPA/FKNMS Coral Reef Monitoring Project Executive Summary 2001 FKNMS Symposium: An Ecosystem Report Card Washington D.C., December 2001. Florida Marine Research Institute IHR2001-004. pp 19 Wilcoxon F (1945) Individual comparisons by ranking methods. Biometrika 1: 80-83 Wilkinson CR (1978) Microbial populations in sponges 1. Ecology, physiology and microbial populations of coral reef sponges. Mar Biol 49:161-167 Wilkinson CR (2004) Status of coral reefs of the world: 2004. Global Coral Reef Monitoring Network and Australian Institute of Marine Science, Townsville, Australia 2004 Wulff J (2001) Assessing and monitoring coral reef sponges: Why and how? Bull Mar Sci 69: 831-846

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61 APPENDICES

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62 Appendix A. Clionid area (cm2/m2) by station for 2001-2003. Site Name Site Code StationRegion Habitat Type 2001 2002 2003 Bird Key 1D1 1 Dry TortugasDeep 10.231.70 2.08 Bird Key 1D1 2 Dry TortugasDeep 1.89 1.14 2.46 Bird Key 1D1 3 Dry TortugasDeep 11.936.44 4.17 Bird Key 1D1 4 Dry TortugasDeep 8.90 2.08 1.70 Black Coral Rock 1D2 1 Dry TortugasDeep 12.695.68 3.98 Black Coral Rock 1D2 2 Dry TortugasDeep 9.85 20.64 9.66 Black Coral Rock 1D2 3 Dry TortugasDeep 81.8247.73 45.64 Black Coral Rock 1D2 4 Dry TortugasDeep 6.44 1.52 1.52 White Shoal 1P1 1 Dry TortugasPatch 1.33 0.19 0.00 White Shoal 1P1 2 Dry TortugasPatch 0.00 0.00 0.00 White Shoal 1P1 3 Dry TortugasPatch 0.00 0.00 0.00 White Shoal 1P1 4 Dry TortugasPatch 2.27 0.00 0.00 Sand Key 2D1 1 Lower KeysDeep 0.00 0.00 0.38 Sand Key 2D1 2 Lower KeysDeep 0.00 0.38 0.00 Sand Key 2D1 4 Lower KeysDeep 0.00 0.38 0.38 Looe Key 5D2 1 Lower KeysDeep 3.79 0.57 3.79 Looe Key 5D2 2 Lower KeysDeep 5.30 1.14 0.19 Looe Key 5D2 3 Lower KeysDeep 0.76 0.00 4.17 Eastern Sambo 5D3 2 Lower KeysDeep 2.27 3.22 1.14 Eastern Sambo 5D3 3 Lower KeysDeep 3.41 2.84 0.00 Eastern Sambo 5D3 4 Lower KeysDeep 0.76 1.33 0.00 Western Sambo 5D4 1 Lower KeysDeep 0.00 0.00 0.00 Western Sambo 5D4 2 Lower KeysDeep 0.00 0.00 0.00 Western Sambo 5D4 3 Lower KeysDeep 0.00 0.00 0.00 Rock Key 5D5 3 Lower KeysDeep 2.65 1.14 0.38 Rock Key 5D5 4 Lower KeysDeep 2.46 3.03 2.08 Content Keys 3H1 1 Lower KeysHardbottom67.420.00 19.70 Content Keys 3H1 3 Lower KeysHardbottom9.66 0.00 1.33 Content Keys 3H1 4 Lower KeysHardbottom27.460.00 6.82 Smith Shoal 2P1 2 Lower KeysPatch 21.970.00 0.00 Smith Shoal 2P1 3 Lower KeysPatch 13.640.00 0.00 Smith Shoal 2P1 4 Lower KeysPatch 1.70 0.00 0.00 W. Washer Woman 5P1 1 Lower KeysPatch 21.9715.91 11.74 W. Washer Woman 5P1 3 Lower KeysPatch 10.0410.42 1.70 Western Head 5P2 2 Lower KeysPatch 10.0416.10 26.14 Western Head 5P2 3 Lower KeysPatch 68.94111.36 63.64 Western Head 5P2 4 Lower KeysPatch 35.9826.14 54.92 Cliff Green 5P3 3 Lower KeysPatch 39.5836.74 36.93 Cliff Green 5P3 4 Lower KeysPatch 56.0626.52 32.61

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63 Appendix A (Cont.). Clionid area (cm2/m2) by station for 2001-2003. Site Name Site Code StationRegion Habitat Type 2001 2002 2003 Jaap Reef 5P4 1 Lower KeysPatch 0.00 0.00 0.00 Jaap Reef 5P4 2 Lower KeysPatch 0.00 0.00 0.00 Jaap Reef 5P4 4 Lower KeysPatch 0.00 0.00 0.00 Sand Key 2S1 2 Lower KeysShallow 0.00 0.00 0.00 Sand Key 2S1 3 Lower KeysShallow 0.00 0.00 0.00 Sand Key 2S1 4 Lower KeysShallow 0.00 0.00 0.00 Looe Key 5S2 2 Lower KeysShallow 0.00 0.00 0.00 Looe Key 5S2 3 Lower KeysShallow 0.00 0.00 0.00 Looe Key 5S2 4 Lower KeysShallow 0.00 0.00 0.00 Eastern Sambo 5S3 2 Lower KeysShallow 0.00 0.00 0.00 Eastern Sambo 5S3 3 Lower KeysShallow 0.00 0.00 0.00 Eastern Sambo 5S3 4 Lower KeysShallow 0.00 0.00 0.00 Western Sambo 5S4 1 Lower KeysShallow 0.00 0.00 0.00 Western Sambo 5S4 2 Lower KeysShallow 0.00 0.00 0.00 Western Sambo 5S4 4 Lower KeysShallow 0.00 0.00 0.00 Rock Key 5S5 1 Lower KeysShallow 2.08 0.00 0.00 Rock Key 5S5 2 Lower KeysShallow 4.73 0.00 0.00 Rock Key 5S5 3 Lower KeysShallow 0.00 0.00 0.00 Rock Key 5S5 4 Lower KeysShallow 0.00 0.00 0.00 Sombrero 5D1 3 Middle KeysDeep 12.880.57 3.60 Sombrero 5D1 4 Middle KeysDeep 5.87 2.84 1.52 Alligator 7D1 3 Middle KeysDeep 2.65 0.57 3.60 Tennessee 7D2 2 Middle KeysDeep 6.44 0.57 6.25 Tennessee 7D2 3 Middle KeysDeep 6.82 2.08 3.03 Moser Channel 5H1 2 Middle KeysHardbottom0.00 0.00 0.00 Moser Channel 5H1 4 Middle KeysHardbottom0.00 0.00 0.00 Long Key 7H2 1 Middle KeysHardbottom0.00 0.00 0.00 Long Key 7H2 2 Middle KeysHardbottom18.750.00 0.19 Long Key 7H2 3 Middle KeysHardbottom0.00 0.00 0.00 Long Key 7H2 4 Middle KeysHardbottom0.00 0.00 0.00 W. Turtle Shoal 7P1 1 Middle KeysPatch 0.00 0.38 0.19 W. Turtle Shoal 7P1 2 Middle KeysPatch 2.27 1.89 3.79 W. Turtle Shoal 7P1 3 Middle KeysPatch 1.89 0.76 2.08 W. Turtle Shoal 7P1 4 Middle KeysPatch 14.3910.42 9.85 Dustan Rocks 7P2 2 Middle KeysPatch 5.49 0.00 0.00 Dustan Rocks 7P2 3 Middle KeysPatch 2.08 3.22 4.55 Dustan Rocks 7P2 4 Middle KeysPatch 3.60 3.60 0.76 Sombrero 5S1 1 Middle KeysShallow 0.00 1.52 0.00 Sombrero 5S1 2 Middle KeysShallow 0.00 0.19 0.00

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64 Appendix A (Cont.). Clionid area (cm2/m2) by station for 2001-2003. Site Name Site Code StationRegion Habitat Type 2001 2002 2003 Sombrero 5S1 3 Middle KeysShallow 0.00 0.38 0.00 Sombrero 5S1 4 Middle KeysShallow 0.00 0.00 0.00 Alligator 7S1 1 Middle Key sShallow 0.00 0.76 0.00 Alligator 7S1 2 Middle Key sShallow 0.00 0.00 0.00 Alligator 7S1 3 Middle Key sShallow 0.00 0.00 0.00 Tennessee 7S2 2 Middle KeysShallow 0.38 0.00 0.00 Tennessee 7S2 3 Middle KeysShallow 163.0769.13 76.14 Tennessee 7S2 4 Middle KeysShallow 0.00 0.00 0.19 Carysfort 9D1 1 Upper KeysDeep 6.25 12.31 8.33 Carysfort 9D1 2 Upper KeysDeep 10.8011.74 5.49 Molasses 9D3 1 Upper KeysDeep 5.11 3.79 1.70 Molasses 9D3 2 Upper KeysDeep 3.41 4.73 5.49 Conch 9D4 3 Upper KeysDeep 0.95 0.76 1.89 Conch 9D4 4 Upper KeysDeep 4.73 9.85 2.08 El Radabob 9H2 2 Upper KeysHardbottom0.00 0.00 0.00 El Radabob 9H2 4 Upper KeysHardbottom0.00 0.00 0.00 Turtle Patch 9P1 1 Upper KeysPatch 0.00 0.00 0.00 Turtle Patch 9P1 2 Upper KeysPatch 2.65 1.89 1.14 Porter Patch 9P3 1 Upper KeysPatch 0.00 0.00 0.00 Porter Patch 9P3 2 Upper KeysPatch 0.00 0.00 0.00 Porter Patch 9P3 3 Upper KeysPatch 0.00 0.00 0.00 Admiral 9P4 2 Upper KeysPatch 0.00 0.00 0.00 Admiral 9P4 3 Upper KeysPatch 0.00 0.00 0.00 Admiral 9P4 4 Upper KeysPatch 0.00 0.00 0.00 Carysfort 9S1 1 Upper KeysShallow 0.00 0.00 0.00 Carysfort 9S1 2 Upper KeysShallow 0.00 0.00 0.00 Carysfort 9S1 3 Upper KeysShallow 0.00 0.00 0.00 Grecian Rocks 9S2 1 Upper KeysShallow 0.00 1.14 0.00 Grecian Rocks 9S2 2 Upper KeysShallow 0.00 0.00 0.00 Grecian Rocks 9S2 3 Upper KeysShallow 3.41 4.17 1.89 Grecian Rocks 9S2 4 Upper KeysShallow 0.00 0.00 0.19 Molasses 9S3 1 Upper KeysShallow 0.00 0.00 0.00 Molasses 9S3 2 Upper KeysShallow 0.00 0.00 0.00 Molasses 9S3 3 Upper KeysShallow 4.73 0.00 1.89 Conch 9S4 1 Upper KeysShallow 0.19 0.00 0.00 Conch 9S4 3 Upper KeysShallow 0.19 0.00 0.00 Conch 9S4 4 Upper KeysShallow 0.19 0.19 0.19

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65 Appendix B. Clionid abundance (colonies/m2) by station for 2001-2003. Site Name Site Code StationRegion Habitat Type 2001 2002 2003 Bird Key 1D1 1 Dry TortugasDeep 0.273 0.061 0.061 Bird Key 1D1 2 Dry TortugasDeep 0.046 0.046 0.076 Bird Key 1D1 3 Dry TortugasDeep 0.333 0.182 0.121 Bird Key 1D1 4 Dry TortugasDeep 0.167 0.076 0.061 Black Coral Rock 1D2 1 Dry TortugasDeep 0.227 0.152 0.061 Black Coral Rock 1D2 2 Dry TortugasDeep 0.121 0.333 0.136 Black Coral Rock 1D2 3 Dry TortugasDeep 0.591 0.227 0.136 Black Coral Rock 1D2 4 Dry TortugasDeep 0.258 0.121 0.046 White Shoal 1P1 1 Dry TortugasPatch 0.076 0.015 0.000 White Shoal 1P1 2 Dry TortugasPatch 0.000 0.000 0.000 White Shoal 1P1 3 Dry TortugasPatch 0.000 0.000 0.000 White Shoal 1P1 4 Dry TortugasPatch 0.136 0.000 0.000 Sand Key 2D1 1 Lower KeysDeep 0.000 0.000 0.030 Sand Key 2D1 2 Lower KeysDeep 0.000 0.030 0.000 Sand Key 2D1 4 Lower KeysDeep 0.000 0.030 0.030 Looe Key 5D2 1 Lower KeysDeep 0.076 0.030 0.136 Looe Key 5D2 2 Lower KeysDeep 0.061 0.046 0.015 Looe Key 5D2 3 Lower KeysDeep 0.015 0.000 0.227 Eastern Sambo 5D3 2 Lower KeysDeep 0.182 0.152 0.076 Eastern Sambo 5D3 3 Lower KeysDeep 0.167 0.106 0.000 Eastern Sambo 5D3 4 Lower KeysDeep 0.046 0.076 0.000 Western Sambo 5D4 1 Lower KeysDeep 0.000 0.015 0.000 Western Sambo 5D4 2 Lower KeysDeep 0.000 0.000 0.000 Western Sambo 5D4 4 Lower KeysDeep 0.000 0.000 0.000 Rock Key 5D5 3 Lower KeysDeep 0.106 0.046 0.015 Rock Key 5D5 4 Lower KeysDeep 0.106 0.121 0.121 Content Keys 3H1 1 Lower KeysHard bottom0.227 0.000 0.182 Content Keys 3H1 3 Lower KeysHard bottom0.091 0.000 0.061 Content Keys 3H1 4 Lower KeysHard bottom0.212 0.000 0.167 Smith Shoal 2P1 2 Lower KeysPatch 0.303 0.000 0.000 Smith Shoal 2P1 3 Lower KeysPatch 0.349 0.000 0.000 Smith Shoal 2P1 4 Lower KeysPatch 0.076 0.000 0.000 W. Washer Woman 5P1 1 Lower KeysPatch 0.167 0.167 0.091 W. Washer Woman 5P1 3 Lower KeysPatch 0.030 0.030 0.030 Western Head 5P2 2 Lower KeysPatch 0.030 0.091 0.136 Western Head 5P2 3 Lower KeysPatch 0.152 0.106 0.106 Western Head 5P2 4 Lower KeysPatch 0.227 0.091 0.121 Cliff Green 5P3 3 Lower KeysPatch 0.076 0.091 0.076 Cliff Green 5P3 4 Lower KeysPatch 0.076 0.091 0.121

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66 Appendix B (Cont.). Clionid abundance (colonies/m2) by station for 2001-2003. Site Name Site Code StationRegion Habitat Type 2001 2002 2003 Jaap Reef 5P4 1 Lower KeysPatch 0.000 0.000 0.000 Jaap Reef 5P4 2 Lower KeysPatch 0.000 0.000 0.000 Jaap Reef 5P4 4 Lower KeysPatch 0.000 0.000 0.000 Sand Key 2S1 2 Lower KeysShallow 0.000 0.000 0.000 Sand Key 2S1 3 Lower KeysShallow 0.000 0.000 0.000 Sand Key 2S1 4 Lower KeysShallow 0.000 0.000 0.000 Looe Key 5S2 2 Lower KeysShallow 0.000 0.000 0.000 Looe Key 5S2 3 Lower KeysShallow 0.000 0.000 0.000 Looe Key 5S2 4 Lower KeysShallow 0.000 0.000 0.000 Eastern Sambo 5S3 2 Lower KeysShallow 0.000 0.000 0.000 Eastern Sambo 5S3 3 Lower KeysShallow 0.000 0.000 0.000 Eastern Sambo 5S3 4 Lower KeysShallow 0.000 0.000 0.000 Western Sambo 5S4 1 Lower KeysShallow 0.000 0.000 0.000 Western Sambo 5S4 2 Lower KeysShallow 0.000 0.000 0.000 Western Sambo 5S4 4 Lower KeysShallow 0.000 0.000 0.000 Rock Key 5S5 1 Lower KeysShallow 0.167 0.000 0.000 Rock Key 5S5 2 Lower KeysShallow 0.379 0.000 0.000 Rock Key 5S5 3 Lower KeysShallow 0.000 0.000 0.000 Rock Key 5S5 4 Lower KeysShallow 0.000 0.000 0.000 Sombrero 5D1 3 Middle KeysDeep 0.197 0.046 0.197 Sombrero 5D1 4 Middle KeysDeep 0.136 0.106 0.061 Alligator 7D1 3 Middle Key sDeep 0.030 0.015 0.015 Alligator 7D1 4 Middle Key sDeep 0.091 0.061 0.091 Tennessee 7D2 2 Middle KeysDeep 0.273 0.030 0.182 Tennessee 7D2 3 Middle KeysDeep 0.333 0.152 0.212 Moser Channel 5H1 2 Middle KeysHard bottom0.000 0.000 0.000 Moser Channel 5H1 4 Middle KeysHard bottom0.000 0.000 0.000 Long Key 7H2 1 Middle KeysHard bottom0.000 0.000 0.000 Long Key 7H2 2 Middle KeysHard bottom0.015 0.000 0.015 Long Key 7H2 3 Middle KeysHard bottom0.000 0.000 0.000 Long Key 7H2 4 Middle KeysHard bottom0.000 0.000 0.000 W. Turtle Shoal 7P1 1 Middle KeysPatch 0.000 0.030 0.015 W. Turtle Shoal 7P1 2 Middle KeysPatch 0.015 0.015 0.030 W. Turtle Shoal 7P1 3 Middle KeysPatch 0.030 0.015 0.030 W. Turtle Shoal 7P1 4 Middle KeysPatch 0.076 0.061 0.030 Dustan Rocks 7P2 2 Middle KeysPatch 0.061 0.000 0.000 Dustan Rocks 7P2 3 Middle KeysPatch 0.030 0.061 0.076 Dustan Rocks 7P2 4 Middle KeysPatch 0.046 0.030 0.030 Sombrero 5S1 1 Middle KeysShallow 0.000 0.121 0.000 Sombrero 5S1 2 Middle KeysShallow 0.000 0.015 0.000 Sombrero 5S1 3 Middle KeysShallow 0.000 0.030 0.000 Sombrero 5S1 4 Middle KeysShallow 0.000 0.000 0.000

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67 Appendix B (Cont.). Clionid abundance (colonies/m2) by station for 2001-2003. Site Name Site Code StationRegion Habitat Type 2001 2002 2003 Alligator 7S1 1 Middle KeysShallow 0.000 0.030 0.000 Alligator 7S1 2 Middle KeysShallow 0.000 0.000 0.000 Alligator 7S1 3 Middle KeysShallow 0.000 0.000 0.000 Tennessee 7S2 2 Middle KeysShallow 0.015 0.000 0.000 Tennessee 7S2 3 Middle KeysShallow 0.030 0.046 0.046 Tennessee 7S2 4 Middle KeysShallow 0.000 0.000 0.015 Carysfort 9D1 1 Upper KeysDeep 0.303 0.515 0.333 Carysfort 9D1 2 Upper KeysDeep 0.576 0.591 0.212 Molasses 9D3 1 Upper KeysDeep 0.242 0.182 0.091 Molasses 9D3 2 Upper KeysDeep 0.091 0.182 0.152 Conch 9D4 3 Upper KeysDeep 0.076 0.030 0.136 Conch 9D4 4 Upper KeysDeep 0.227 0.152 0.076 El Radabob 9H2 2 Upper KeysHard bottom0.000 0.000 0.000 El Radabob 9H2 4 Upper KeysHard bottom0.000 0.000 0.000 Turtle Patch 9P1 1 Upper KeysPatch 0.000 0.000 0.000 Turtle Patch 9P1 2 Upper KeysPatch 0.136 0.091 0.076 Porter Patch 9P3 1 Upper KeysPatch 0.000 0.000 0.000 Porter Patch 9P3 2 Upper KeysPatch 0.000 0.000 0.000 Porter Patch 9P3 3 Upper KeysPatch 0.000 0.000 0.000 Admiral 9P4 1 Upper KeysPatch 0.000 0.000 0.000 Admiral 9P4 2 Upper KeysPatch 0.000 0.000 0.000 Admiral 9P4 3 Upper KeysPatch 0.000 0.000 0.000 Admiral 9P4 4 Upper KeysPatch 0.000 0.000 0.000 Carysfort 9S1 1 Upper KeysShallow 0.000 0.000 0.000 Carysfort 9S1 2 Upper KeysShallow 0.000 0.000 0.000 Carysfort 9S1 3 Upper KeysShallow 0.000 0.000 0.030 Grecian Rocks 9S2 1 Upper KeysShallow 0.000 0.091 0.000 Grecian Rocks 9S2 2 Upper KeysShallow 0.000 0.000 0.000 Grecian Rocks 9S2 3 Upper KeysShallow 0.030 0.076 0.061 Grecian Rocks 9S2 4 Upper KeysShallow 0.000 0.000 0.015 Molasses 9S3 1 Upper KeysShallow 0.000 0.000 0.000 Molasses 9S3 2 Upper KeysShallow 0.000 0.000 0.000 Molasses 9S3 3 Upper KeysShallow 0.288 0.000 0.121 Conch 9S4 1 Upper KeysShallow 0.015 0.000 0.000 Conch 9S4 3 Upper KeysShallow 0.015 0.000 0.000 Conch 9S4 4 Upper KeysShallow 0.015 0.015 0.015

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68 Appendix C. Mean percent cover of the four stony coral species most affected by clionids, 2000-2003. Site Name Site Code StationRegion Habitat Type 2000 2001 2002 2003 Bird Key 1D1 1 Dry TortugasDeep 19.1%20.7% 12.0% 11.2% Bird Key 1D1 2 Dry TortugasDeep 18.5%17.6% 11.4% 11.2% Bird Key 1D1 3 Dry TortugasDeep 18.9%16.4% 11.8% 10.4% Bird Key 1D1 4 Dry TortugasDeep 17.7%21.6% 14.9% 13.2% Black Coral Rock 1D2 1 Dry TortugasDeep 20.4%21.4% 18.9% 16.0% Black Coral Rock 1D2 2 Dry TortugasDeep 21.3%23.1% 18.0% 21.6% Black Coral Rock 1D2 3 Dry TortugasDeep 16.9%19.3% 18.5% 14.9% Black Coral Rock 1D2 4 Dry TortugasDeep 20.0%24.4% 22.6% 19.6% White Shoal 1P1 1 Dry TortugasPatch 2.5% 4.0% 2.4% 2.3% White Shoal 1P1 2 Dry TortugasPatch 0.3% 0.6% 0.4% 0.4% White Shoal 1P1 3 Dry TortugasPatch 0.1% 0.2% 0.5% 0.6% White Shoal 1P1 4 Dry TortugasPatch 0.6% 0.5% 0.0% 0.2% Sand Key 2D1 1 Lower KeysDeep 3.0% 2.1% 2.0% 2.0% Sand Key 2D1 2 Lower KeysDeep 1.8% 1.6% 1.5% 1.5% Sand Key 2D1 4 Lower KeysDeep 0.7% 0.8% 0.9% 0.6% Smith Shoal 2P1 2 Lower KeysPatch 11.1%10.7% 2.4% 1.9% Smith Shoal 2P1 3 Lower KeysPatch 9.5% 7.4% 0.5% 0.3% Smith Shoal 2P1 4 Lower KeysPatch 14.7%12.5% 2.2% 1.9% Sand Key 2S1 2 Lower KeysShallow 5.0% 5.4% 4.2% 3.8% Sand Key 2S1 3 Lower KeysShallow 2.4% 2.2% 2.3% 2.2% Sand Key 2S1 4 Lower KeysShallow 4.5% 2.6% 3.8% 2.1% Content Keys 3H1 1 Lower KeysHard bottom0.1% 0.1% 0.0% 0.0% Content Keys 3H1 3 Lower KeysHard bottom0.0% 0.6% 0.2% 0.0% Content Keys 3H1 4 Lower KeysHard bottom0.1% 0.4% 0.3% 0.3% Looe Key 5D2 1 Lower KeysDeep 7.8% 7.4% 6.7% 4.8% Looe Key 5D2 2 Lower KeysDeep 1.7% 5.2% 2.5% 2.9% Looe Key 5D2 3 Lower KeysDeep 3.3% 2.1% 2.6% 1.7% Eastern Sambo 5D3 2 Lower KeysDeep 6.8% 6.3% 7.1% 5.2% Eastern Sambo 5D3 3 Lower KeysDeep 5.1% 3.8% 4.3% 4.9% Eastern Sambo 5D3 4 Lower KeysDeep 5.2% 4.4% 4.2% 3.1% Western Sambo 5D4 1 Lower KeysDeep 3.6% 3.1% 3.2% 3.2% Western Sambo 5D4 2 Lower KeysDeep 2.0% 2.4% 1.9% 1.8% Western Sambo 5D4 4 Lower KeysDeep 2.4% 2.1% 1.5% 1.6% Rock Key 5D5 3 Lower KeysDeep 1.7% 1.6% 3.1% 1.3% Rock Key 5D5 4 Lower KeysDeep 2.6% 2.8% 3.7% 2.1% W. Washer Woman 5P1 1 Lower KeysPatch 18.2%17.6% 22.4% 15.7% W. Washer Woman 5P1 3 Lower KeysPatch 27.1%24.3% 30.7% 23.9% Western Head 5P2 2 Lower KeysPatch 17.9%15.6% 17.3% 17.1% Western Head 5P2 3 Lower KeysPatch 26.3%25.7% 23.4% 26.1% Western Head 5P2 4 Lower KeysPatch 20.1%21.3% 20.7% 21.2% Cliff Green 5P3 3 Lower KeysPatch 15.1%14.0% 15.4% 13.8% Cliff Green 5P3 4 Lower KeysPatch 12.4%11.9% 13.8% 11.8%

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69 Appendix C. (Cont.) Mean percent cover of the four stony coral species most affected by clionids, 2000-2003. Site Name Site Code StationRegion Habitat Type 2000 2001 2002 2003 Jaap Reef 5P4 1 Lower KeysPatch 14.1%14.5% 16.6% 21.0% Jaap Reef 5P4 2 Lower KeysPatch 15.8%15.4% 17.7% 21.3% Jaap Reef 5P4 4 Lower KeysPatch 14.2%15.0% 14.3% 18.3% Looe Key 5S2 2 Lower KeysShallow 5.1% 6.5% 7.1% 5.3% Looe Key 5S2 3 Lower KeysShallow 8.7% 8.8% 5.8% 7.0% Looe Key 5S2 4 Lower KeysShallow 32.8%34.0% 33.1% 35.8% Eastern Sambo 5S3 2 Lower KeysShallow 0.1% 0.5% 0.7% 0.2% Eastern Sambo 5S3 3 Lower KeysShallow 0.2% 0.2% 0.0% 0.1% Eastern Sambo 5S3 4 Lower KeysShallow 1.2% 1.8% 0.3% 2.5% Western Sambo 5S4 1 Lower KeysShallow 0.4% 0.2% 0.1% 0.5% Western Sambo 5S4 2 Lower KeysShallow 3.4% 3.0% 2.8% 2.1% Western Sambo 5S4 4 Lower KeysShallow 1.0% 1.0% 1.3% 2.1% Rock Key 5S5 1 Lower KeysShallow 0.9% 1.0% 0.8% 0.8% Rock Key 5S5 2 Lower KeysShallow 0.5% 0.5% 0.7% 0.5% Rock Key 5S5 3 Lower KeysShallow 0.5% 0.4% 0.1% 0.3% Rock Key 5S5 4 Lower KeysShallow 0.5% 0.2% 0.1% 3.0% Sombrero 5D1 3 Middle KeysDeep 1.4% 1.8% 1.8% 2.2% Sombrero 5D1 4 Middle KeysDeep 1.8% 2.0% 1.5% 2.1% Moser Channel 5H1 2 Middle KeysHard bottom0.2% 0.4% 0.1% 0.2% Moser Channel 5H1 4 Middle KeysHard bottom0.3% 0.1% 0.5% 0.1% Sombrero 5S1 1 Middle KeysShallow 3.7% 3.7% 5.2% 3.1% Sombrero 5S1 2 Middle KeysShallow 0.8% 0.6% 0.6% 1.9% Sombrero 5S1 3 Middle KeysShallow 1.8% 1.8% 3.0% 1.5% Sombrero 5S1 4 Middle KeysShallow 0.0% 0.0% 0.4% 0.0% Alligator 7D1 3 Middle KeysDeep 0.2% 0.0% 0.1% 0.2% Alligator 7D1 4 Middle KeysDeep 0.4% 0.5% 0.3% 0.0% Tennessee 7D2 2 Middle KeysDeep 4.0% 4.4% 3.4% 3.8% Tennessee 7D2 3 Middle KeysDeep 4.2% 2.2% 2.6% 2.9% Long Key 7H2 1 Middle KeysHard bottom1.8% 2.7% 1.9% 1.9% Long Key 7H2 2 Middle KeysHard bottom1.4% 0.7% 0.9% 1.5% Long Key 7H2 3 Middle KeysHard bottom0.2% 0.4% 0.1% 0.6% Long Key 7H2 4 Middle KeysHard bottom0.1% 0.4% 0.2% 0.3% W. Turtle Shoal 7P1 1 Middle KeysPatch 7.6% 8.4% 7.7% 8.4% W. Turtle Shoal 7P1 2 Middle KeysPatch 7.0% 7.1% 8.7% 7.4% W. Turtle Shoal 7P1 3 Middle KeysPatch 8.5% 8.7% 10.2% 9.4% W. Turtle Shoal 7P1 4 Middle KeysPatch 18.4%20.3% 22.3% 17.9% Dustan Rocks 7P2 2 Middle KeysPatch 9.4% 9.7% 11.9% 8.7% Dustan Rocks 7P2 3 Middle KeysPatch 11.8%9.2% 10.3% 9.7% Dustan Rocks 7P2 4 Middle KeysPatch 19.6%16.7% 20.2% 20.7%

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70 Appendix C. (Cont.) Mean percent cover of the four stony coral species most affected by clionids, 2000-2003. Site Name Site Code StationRegion Habitat Type 2000 2001 2002 2003 Alligator 7S1 1 Middle KeysShallow 0.2% 0.1% 0.1% 0.1% Alligator 7S1 2 Middle KeysShallow 0.1% 0.2% 0.0% 0.1% Alligator 7S1 3 Middle KeysShallow 0.2% 0.0% 0.1% 0.0% Tennessee 7S2 2 Middle KeysShallow 0.5% 0.4% 0.6% 0.3% Tennessee 7S2 3 Middle KeysShallow 0.6% 0.6% 0.4% 0.6% Tennessee 7S2 4 Middle KeysShallow 0.4% 0.6% 0.6% 0.2% Carysfort 9D1 1 Upper KeysDeep 4.2% 3.0% 2.7% 2.8% Carysfort 9D1 2 Upper KeysDeep 5.7% 3.6% 4.2% 4.1% Molasses 9D3 1 Upper KeysDeep 0.1% 0.2% 0.4% 0.4% Molasses 9D3 2 Upper KeysDeep 0.4% 0.2% 0.1% 0.1% Conch 9D4 3 Upper KeysDeep 1.5% 1.9% 1.4% 1.0% Conch 9D4 4 Upper KeysDeep 0.4% 1.2% 0.6% 0.2% El radabob 9H2 2 Upper KeysHard bottom0.0% 0.0% 0.0% 0.0% El radabob 9H2 4 Upper KeysHard bottom0.0% 0.0% 0.0% 0.0% Turtle Patch 9P1 1 Upper KeysPatch 4.1% 4.8% 4.1% 3.9% Turtle Patch 9P1 2 Upper KeysPatch 1.7% 1.7% 2.1% 0.9% Porter Patch 9P3 1 Upper KeysPatch 1.7% 1.9% 1.4% 1.6% Porter Patch 9P3 2 Upper KeysPatch 4.4% 3.7% 3.3% 2.7% Porter Patch 9P3 3 Upper KeysPatch 0.5% 1.0% 0.7% 0.6% Admiral 9P4 1 Upper KeysPatch 24.2%26.2% 22.7% 27.6% Admiral 9P4 2 Upper KeysPatch 25.2%29.4% 31.6% 30.5% Admiral 9P4 3 Upper KeysPatch 19.4%16.6% 19.9% 21.3% Admiral 9P4 4 Upper KeysPatch 7.9% 10.7% 9.9% 11.0% Carysfort 9S1 1 Upper KeysShallow 0.2% 0.3% 0.0% 0.1% Carysfort 9S1 2 Upper KeysShallow 0.2% 0.5% 0.2% 0.1% Carysfort 9S1 3 Upper KeysShallow 1.4% 1.8% 2.5% 0.7% Grecian Rocks 9S2 1 Upper KeysShallow 26.0%24.9% 24.6% 25.2% Grecian Rocks 9S2 2 Upper KeysShallow 4.4% 3.4% 2.3% 2.1% Grecian Rocks 9S2 3 Upper KeysShallow 6.9% 6.6% 5.5% 5.7% Grecian Rocks 9S2 4 Upper KeysShallow 1.9% 1.4% 2.0% 1.5% Molasses 9S3 1 Upper KeysShallow 1.0% 1.0% 0.7% 0.8% Molasses 9S3 2 Upper KeysShallow 0.2% 0.3% 0.2% 0.3% Molasses 9S3 3 Upper KeysShallow 1.9% 3.0% 2.7% 3.1% Conch 9S4 1 Upper KeysShallow 0.5% 0.3% 0.3% 0.5% Conch 9S4 3 Upper KeysShallow 0.6% 0.6% 0.4% 0.2% Conch 9S4 4 Upper KeysShallow 0.0% 0.0% 0.1% 0.0%

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71 Appendix D. Results for the water quality analysis by region, 2000-2003. Chlorophyll-a (g/l) NOxs (M) SRPb (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 0.281 0.128 0.4670.202Dry Tortugas0.5000.0630.101 0.079 Dry Tortugas0.0380.0090.0240.045 Lower keys 0.624 0.304 0.3450.389Lower keys 0.4990.1370.114 0.187 Lower keys 0.0460.0190.0290.043 Middle keys 0.418 0.133 0.2490.248Middle keys0.4180.0860.127 0.253 Middle keys0.0320.0300.0190.067 Upper keys 0.363 0.174 0.2000.155Upper keys 0.5520.1400.177 0.216 Upper keys 0.0420.0160.0210.040 NH4s (M) TNs (M) TPs (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 0.321 0.203 0.2320.236Dry Tortugas6.8187.59316.675 14.687 Dry Tortugas0.2450.2290.2850.192 Lower keys 0.333 0.252 0.1970.270Lower keys 10.0428.82220.887 15.530 Lower keys 0.3080.2360.2420.180 Middle keys 0.235 0.191 0.2300.372Middle keys9.9119.18914.362 18.930 Middle keys0.2340.1570.2460.132 Upper keys 0.207 0.225 0.2390.286Upper keys 7.8809.97213.770 16.760 Upper keys 0.2520.2070.2270.228 NH4b (M) TNb (M) TPb (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 0.230 0.179 0.2180.301Dry Tortugas6.0735.73014.802 14.661 Dry Tortugas0.2330.2500.2830.157 Lower keys 0.391 0.242 0.1670.267Lower keys 8.7137.97518.856 15.154 Lower keys 0.2580.1820.2040.155 Middle keys 0.219 0.142 0.1760.410Middle keys7.3348.15814.606 17.637 Middle keys0.1960.1400.2200.134 Upper keys 0.275 0.169 0.1490.265Upper keys 6.2327.1429.464 16.678 Upper keys 0.1880.1410.1430.226 Turbb (NTU) NOxb (M) SRPs (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 0.363 0.511 0.8910.551Dry Tortugas0.3400.0830.101 0.154 Dry Tortugas0.0440.0160.0220.042 Lower keys 1.007 0.931 0.9890.816Lower keys 0.4640.1400.111 0.209 Lower keys 0.0400.0270.0390.042 Middle keys 0.328 0.442 0.2850.590Middle keys0.3430.0680.093 0.269 Middle keys0.0500.0300.0220.052 Upper keys 0.383 0.300 0.2810.419Upper keys 0.4140.1240.116 0.213 Upper keys 0.0530.0260.0300.040 Si(OH)4b (M) APAs (M) APAb (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 0.087 0.196 0.5530.273Dry Tortugas0.0480.0460.053 0.038 Dry Tortugas0.0440.0690.0290.051 Lower keys 0.994 0.738 1.1500.858Lower keys 0.0800.0840.055 0.058 Lower keys 0.0810.0880.0490.053 Middle keys 0.740 0.276 0.3580.989Middle keys0.0520.0620.058 0.066 Middle keys0.0470.0650.0520.067 Upper keys 0.052 0.585 0.2150.268Upper keys 0.0630.0610.045 0.069 Upper keys 0.0620.0650.0550.059

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72 Appendix D. Results for the water quality analysis by region, 2000-2003. Turbs (NTU) NO3b (M) NO3s (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 0.335 0.419 0.8990.419Dry Tortugas0.309 0.0390.067 0.110 Dry Tortugas0.4590.0060.0700.048 Lower keys 1.246 0.864 1.0400.838Lower keys 0.491 0.0970.094 0.164 Lower keys 0.4550.0870.0780.151 Middle keys 0.469 0.681 0.4600.548Middle keys0.350 0.0370.075 0.223 Middle keys 0.3850.0430.0980.207 Upper keys 0.462 0.421 0.4130.399Upper keys 0.467 0.1190.128 0.167 Upper keys 0.5220.0940.1470.172 DINs (M) DINb (M) TONs (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 0.920 0.266 0.3330.310Dry Tortugas0.605 0.2620.319 0.455 Dry Tortugas5.9977.32816.34214.377 Lower keys 0.994 0.389 0.3110.450Lower keys 1.205 0.4370.329 0.474 Lower keys 9.2128.43320.57615.080 Middle keys 0.754 0.277 0.3560.626Middle keys0.728 0.2330.298 0.679 Middle keys 9.2588.91214.37918.305 Upper keys 0.935 0.365 0.4150.502Upper keys 1.143 0.4030.365 0.477 Upper keys 7.1239.60713.35416.258 TONb (M) TOCs (M) TOCb (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 6.342 5.469 14.48414.206Dry Tortugas157.2 151.1120.3 103.9 Dry Tortugas159.4150.9115.2105.1 Lower keys 9.212 9.007 21.76214.680Lower keys 173.2 176.6146.9 134.1 Lower keys 168.1172.0136.1118.9 Middle keys 7.987 8.831 15.93017.005Middle keys161.7 175.6149.2 145.1 Middle keys 147.2168.5135.8142.4 Upper keys 7.317 9.418 12.64816.201Upper keys 145.0 163.8138.5 129.9 Upper keys 146.2161.6138.5119.3 DOs (mg/l) DOb (mg/l) Si(OH)4s (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 5.802 5.331 5.5325.540Dry Tortugas5.921 5.4385.958 6.045 Dry Tortugas0.1080.1470.9800.236 Lower keys 5.644 5.586 5.8845.490Lower keys 5.712 5.5905.713 5.934 Lower keys 1.0710.6741.0361.046 Middle keys 5.694 5.688 5.8695.790Middle keys5.886 5.6125.884 5.732 Middle keys 1.3720.6510.7481.246 Upper keys 5.455 5.631 6.1375.074Upper keys 5.671 6.0215.807 5.375 Upper keys 0.0630.3630.2620.282 Temps Tempb Sals 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 Dry Tortugas 26.3 25.7 26.6 26.1 Dry Tortugas25.5 25.5 26.5 26.0 Dry Tortugas36.2 36.4 36.1 36.1 Lower keys 26.9 26.4 27.3 27.6 Lower keys 26.9 26.3 27.0 27.0 Lower keys 36.3 36.5 36.2 36.0 Middle keys 27.2 26.7 27.5 27.5 Middle keys27.2 26.6 27.5 27.4 Middle keys 36.4 36.2 36.3 35.9 Upper keys 26.8 25.8 27.1 26.8 Upper keys 26.8 25.7 27.1 26.7 Upper keys 36.2 36.1 36.3 35.9

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73 Appendix E. Results for the water quality analysis by habitat, 2000-2003. Chlorophyll-a (g/l) NOxs (M) SRPb (M) 2000 200120022003 2000 2001 2002 2003 2000200120022003 Hard bottom 0.679 0.2470.4480.330Hard bottom 0.5040.118 0.1270.375Hard bottom 0.0620.0330.0350.059 Offshore deep 0.401 0.1820.2570.241Offshore deep 0.4780.100 0.1330.159Offshore deep 0.0440.0240.0280.048 Offshore shallow 0.430 0.1830.2220.211Offshore shallow0.4640.113 0.1390.176Offshore shallow 0.0510.0260.0290.048 Patch 0.561 0.2830.3340.384Patch 0.5430.158 0.1330.237Patch 0.0420.0210.0270.048 NH4s (M) TNs (M) TPs (M) 2000 200120022003 2000 2001 2002 2003 2000200120022003 Hard bottom 0.270 0.222 0.205 0.413 Hard bottom 11.5638.949 14.82218.545Hard bottom 0.3170.2230.3000.187 Offshore deep 0.270 0.206 0.220 0.254 Offshore deep 8.4719.080 16.09215.762Offshore deep 0.2590.2010.2400.191 Offshore shallow 0.257 0.214 0.216 0.272 Offshore shallow8.9069.535 16.83316.004Offshore shallow 0.2630.2060.2260.182 Patch 0.293 0.270 0.225 0.345 Patch 9.6488.967 19.58518.038Patch 0.2740.2110.2360.168 NH4b (M) TNb (M) TPb (M) 2000 200120022003 2000 2001 2002 2003 2000200120022003 Hard bottom 0.349 0.1950.2130.398Hard bottom 10.3328.767 16.08820.067Hard bottom 0.2500.2070.2700.138 Offshore deep 0.325 0.2070.2090.280Offshore deep 8.7708.675 16.58715.174Offshore deep 0.2580.1980.2350.156 Offshore shallow 0.381 0.2130.1990.279Offshore shallow9.1189.512 17.69315.557Offshore shallow 0.2610.1920.2170.178 Patch 0.381 0.2860.1870.366Patch 8.9529.727 19.45117.340Patch 0.2840.1820.2320.174 Turbb (NTU) NOxb (M) SRPs (M) 2000 200120022003 2000 2001 2002 2003 2000200120022003 Hard bottom 1.126 1.1610.5071.057Hard bottom 0.6370.092 0.1420.317Hard bottom 0.0620.0330.0350.059 Offshore deep 0.540 0.6410.6580.556Offshore deep 0.4330.131 0.1280.211Offshore deep 0.0440.0240.0280.048 Offshore shallow 0.589 0.6260.6070.544Offshore shallow0.4620.142 0.1330.213Offshore shallow 0.0510.0260.0290.048 Patch 1.439 0.8300.9910.810Patch 0.5220.141 0.1200.231Patch 0.0420.0210.0270.048 Si(OH)4b (M) APAs (M) APAb (M) 2000 200120022003 2000 2001 2002 2003 2000200120022003 Hard bottom 2.745 0.5910.4672.059Hard bottom 0.0800.084 0.1020.076Hard bottom 0.0910.0960.0800.094 Offshore deep 0.435 0.5320.5500.467Offshore deep 0.0560.062 0.0450.052Offshore deep 0.0550.0680.0440.047 Offshore shallow 0.460 0.3650.5090.469Offshore shallow0.0580.064 0.0430.055Offshore shallow 0.0580.0670.0450.047 Patch 0.649 0.7651.1081.090Patch 0.0830.080 0.0550.079Patch 0.0850.0900.0590.083

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74 Appendix E. Results for the water quality analysis by habitat, 2000-2003. Turbs (NTU) NO3b (M) NO3s (M) 2000 2001 2002 2003 20002001 20022003 2000200120022003 Hard bottom 1.268 1.582 1.0621.105Hard bottom 0.5900.040 0.1150.251Hard bottom 0.4660.0710.0960.315 Offshore deep 0.458 0.483 0.5940.447Offshore deep 0.3940.083 0.0940.168Offshore deep 0.4410.0560.1020.126 Offshore shallow 0.498 0.480 0.5500.453Offshore shallow 0.4220.092 0.1000.171Offshore shallow 0.4270.0700.1070.141 Patch 1.336 0.775 0.9020.845Patch 0.4820.080 0.0850.183Patch 0.5050.1020.0990.187 DINs (M) DINb (M) TONs (M) 2000 2001 2002 2003 20002001 20022003 2000200120022003 Hard bottom 0.911 0.340 0.3320.788Hard bottom 1.2080.287 0.3560.715Hard bottom 10.798.6114.5117.76 Offshore deep 0.888 0.306 0.3530.409Offshore deep 0.9110.339 0.3370.490Offshore deep 7.728.7715.7415.35 Offshore shallow 0.858 0.327 0.3560.443Offshore shallow 1.0300.354 0.3320.491Offshore shallow 8.199.2116.4815.56 Patch 1.011 0.427 0.3580.581Patch 1.1290.427 0.3070.597Patch 8.818.5419.2317.46 TONb (M) TOCs (M) TOCb (M) 2000 2001 2002 2003 20002001 20022003 2000200120022003 Hard bottom 9.347 8.481 15.73319.353Hard bottom 209.9201.2197.4195.0Hard bottom 185.4185.5145.3182.2 Offshore deep 8.118 8.336 16.45614.681Offshore deep 151.9163.6133.8121.8Offshore deep 152.1162.5130.5115.7 Offshore shallow 8.345 9.157 17.61215.062Offshore shallow 151.6163.4135.3122.3Offshore shallow 151.7162.1132.5115.8 Patch 8.060 9.285 19.14516.823Patch 165.4179.4145.2139.7Patch 162.5176.9143.8133.4 DOs (mg/l) DOb (mg/l) Si(OH)4s (M) 2000 2001 2002 2003 20002001 20022003 2000200120022003 Hard bottom 5.8856.0045.7815.611Hard bottom 5.8286.1165.7285.562Hard bottom 3.4321.2601.4931.970 Offshore deep 5.5985.5425.8675.404Offshore deep 5.6785.6275.7805.735Offshore deep 0.4250.3450.3810.498 Offshore shallow 5.5445.5995.8945.365Offshore shallow 5.7515.6825.7245.677Offshore shallow 0.4400.4120.2610.515 Patch 5.5965.5696.1275.551Patch 5.8245.6995.9325.842Patch 0.6630.7201.4841.224 Temps Tempb Sals 2000 2001 2002 2003 20002001 20022003 2000200120022003 Hard bottom 26.626.027.327.2Hard bottom 26.525.827.227.1Hard bottom 36.536.236.635.9 Offshore deep 26.926.327.227.2Offshore deep 26.826.227.026.8Offshore deep 36.236.336.136.0 Offshore shallow 27.026.427.227.3Offshore shallow 27.026.327.027.0Offshore shallow 36.236.336.235.9 Patch 27.026.227.427.3Patch 27.026.127.427.1Patch 36.336.336.336.0

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75 Appendix F. Results for the water quality analysis by region and habitat, 2000-2003. Chlorophyll-a (g/l) NOxs (M) SRPb (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 0.281 0.128 0.4670.202 DT Deep 0.500 0.063 0.101 0.079 DT Deep 0.038 0.009 0.024 0.045 LK Hardbottom 1.306 0.412 0.6840.486LK Hardbottom0.492 0.038 0.058 0.217 LK Hardbottom0.000 0.000 0.000 0.000 LK Deep 0.501 0.238 0.2590.280LK Deep 0.450 0.125 0.109 0.145 LK Deep 0.059 0.022 0.036 0.045 LK Shallow 0.501 0.238 0.2590.280LK Shallow 0.450 0.125 0.109 0.145 LK Shallow 0.059 0.022 0.036 0.045 LK Patch 0.700 0.415 0.4490.589 LK Patch 0.598 0.180 0.136 0.260 LK Patch 0.038 0.023 0.031 0.038 MK Hardbottom 0.446 0.202 0.4570.318MK Hardbottom0.498 0.172 0.159 0.545 MK Hardbottom0.040 0.038 0.019 0.079 MK Deep 0.399 0.123 0.1770.219MK Deep 0.433 0.062 0.124 0.161 MK Deep 0.036 0.039 0.021 0.062 MK Shallow 0.399 0.123 0.1770.219MK Shallow 0.433 0.062 0.124 0.161 MK Shallow 0.036 0.039 0.021 0.062 MK Patch 0.444 0.092 0.2550.265 MK Patch 0.294 0.071 0.103 0.239 MK Patch 0.030 0.017 0.023 0.076 UK Hardbottom 0.362 0.171 0.1930.198UK Hardbottom0.533 0.090 0.131 0.193 UK Hardbottom0.084 0.029 0.051 0.039 UK Deep 0.318 0.178 0.1960.223UK Deep 0.557 0.122 0.205 0.232 UK Deep 0.027 0.023 0.024 0.042 UK Shallow 0.364 0.159 0.2090.119UK Shallow 0.504 0.137 0.190 0.223 UK Shallow 0.053 0.020 0.026 0.040 UK Patch 0.407 0.190 0.1960.122 UK Patch 0.618 0.178 0.148 0.197 UK Patch 0.060 0.021 0.025 0.040 NH4s (M) TNs (M) TPs (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 0.321 0.203 0.2320.236 DT Deep 6.818 7.593 16.67514.687 DT Deep 0.245 0.229 0.285 0.192 LK Hardbottom 0.233 0.188 0.1710.297LK Hardbottom11.89010.656 21.12112.367LK Hardbottom0.465 0.270 0.417 0.205 LK Deep 0.333 0.239 0.1780.210LK Deep 9.412 8.255 17.39214.705LK Deep 0.284 0.213 0.221 0.181 LK Shallow 0.333 0.239 0.1780.210LK Shallow 9.412 8.255 17.39214.705LK Shallow 0.284 0.213 0.221 0.181 LK Patch 0.357 0.293 0.2380.385 LK Patch 10.8419.590 27.83017.812 LK Patch 0.314 0.274 0.247 0.174 MK Hardbottom 0.305 0.169 0.1980.484MK Hardbottom12.9718.639 11.22520.921MK Hardbottom0.259 0.160 0.211 0.190 MK Deep 0.216 0.193 0.2490.326MK Deep 9.330 9.856 17.93017.628MK Deep 0.239 0.176 0.256 0.114 MK Shallow 0.216 0.193 0.2490.326MK Shallow 9.330 9.856 17.93017.628MK Shallow 0.239 0.176 0.256 0.114 MK Patch 0.222 0.207 0.2030.398 MK Patch 8.593 7.738 8.199 20.846 MK Patch 0.195 0.099 0.253 0.129 UK Hardbottom 0.247 0.363 0.2540.388UK Hardbottom8.339 7.864 14.81819.971UK Hardbottom0.250 0.301 0.361 0.163 UK Deep 0.188 0.166 0.2520.268UK Deep 7.145 10.670 11.69916.376UK Deep 0.246 0.186 0.226 0.284 UK Shallow 0.193 0.199 0.2400.308UK Shallow 7.954 10.894 15.31216.409UK Shallow 0.254 0.221 0.211 0.234 UK Patch 0.232 0.274 0.2190.242 UK Patch 8.364 8.747 13.43516.541 UK Patch 0.259 0.179 0.207 0.184

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76 Appendix F. Results for the water quality analysis by region and habitat, 2000-2003. NH4b (M) TNb (M) TPb (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 0.230 0.179 0.2180.301 DT Deep 6.941 5.730 14.80214.661 DT Deep 0.233 0.250 0.283 0.157 LK Hardbottom 0.000 0.000 0.0000.000LK Hardbottom0.000 0.000 0.000 0.000 LK Hardbottom0.000 0.000 0.000 0.000 LK Deep 0.481 0.251 0.1930.246LK Deep 10.1828.909 19.31914.461LK Deep 0.281 0.200 0.228 0.148 LK Shallow 0.481 0.251 0.1930.246LK Shallow 10.1828.909 19.31914.461LK Shallow 0.281 0.200 0.228 0.148 LK Patch 0.385 0.341 0.2100.318 LK Patch 9.943 11.005 27.12516.886 LK Patch 0.348 0.227 0.244 0.173 MK Hardbottom 0.467 0.159 0.1770.443MK Hardbottom12.4478.939 18.44922.303MK Hardbottom0.259 0.169 0.231 0.128 MK Deep 0.218 0.163 0.2070.354MK Deep 7.836 9.869 18.32816.383MK Deep 0.239 0.175 0.233 0.136 MK Shallow 0.218 0.163 0.2070.354MK Shallow 7.836 9.869 18.32816.383MK Shallow 0.239 0.175 0.233 0.136 MK Patch 0.209 0.140 0.1720.560 MK Patch 8.896 6.714 8.821 19.123 MK Patch 0.193 0.092 0.289 0.132 UK Hardbottom 0.230 0.232 0.2500.353UK Hardbottom8.217 8.596 13.72817.831UK Hardbottom0.239 0.245 0.310 0.148 UK Deep 0.189 0.192 0.2410.233UK Deep 8.196 9.244 8.931 15.805UK Deep 0.255 0.175 0.206 0.206 UK Shallow 0.380 0.198 0.2000.257UK Shallow 8.567 10.159 14.34816.722UK Shallow 0.250 0.196 0.182 0.270 UK Patch 0.527 0.322 0.1560.267 UK Patch 7.025 10.502 14.73416.912 UK Patch 0.250 0.183 0.153 0.219 Turbb (NTU) NOxb (M) SRPs (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 0.359 0.509 0.8900.551DT Deep 0.340 0.083 0.101 0.154 DT Deep 0.044 0.016 0.022 0.042 LK Hardbottom 0.000 0.000 0.0000.000LK Hardbottom0.000 0.000 0.000 0.000 LK Hardbottom0.069 0.048 0.044 0.033 LK Deep 0.877 1.004 0.9270.713LK Deep 0.514 0.165 0.133 0.211 LK Deep 0.038 0.026 0.039 0.048 LK Shallow 0.877 1.004 0.9270.713LK Shallow 0.514 0.165 0.133 0.211 LK Shallow 0.038 0.026 0.039 0.048 LK Patch 2.515 1.204 1.6351.073LK Patch 0.601 0.146 0.128 0.204 LK Patch 0.037 0.025 0.037 0.033 MK Hardbottom 1.315 1.618 0.4641.376MK Hardbottom0.515 0.064 0.105 0.444 MK Hardbottom0.060 0.030 0.022 0.051 MK Deep 0.256 0.345 0.3130.474MK Deep 0.383 0.081 0.115 0.242 MK Deep 0.047 0.030 0.023 0.053 MK Shallow 0.256 0.345 0.3130.474MK Shallow 0.383 0.081 0.115 0.242 MK Shallow 0.047 0.030 0.023 0.053 MK Patch 0.206 0.350 0.2510.546MK Patch 0.307 0.064 0.066 0.266 MK Patch 0.047 0.027 0.018 0.052 UK Hardbottom 0.938 0.704 0.5500.738UK Hardbottom0.758 0.119 0.180 0.191 UK Hardbottom0.057 0.030 0.046 0.048 UK Deep 0.331 0.306 0.2700.256UK Deep 0.403 0.170 0.164 0.221 UK Deep 0.048 0.024 0.028 0.041 UK Shallow 0.452 0.278 0.3680.312UK Shallow 0.456 0.163 0.152 0.189 UK Shallow 0.053 0.027 0.028 0.039 UK Patch 0.519 0.563 0.4430.548UK Patch 0.573 0.209 0.157 0.251 UK Patch 0.057 0.026 0.028 0.036

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77 Appendix F. Results for the water quality analysis by region and habitat, 2000-2003. Si(OH)4b (M) APAs (M) APAb (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 0.087 0.196 0.5530.273 DT Deep 0.048 0.046 0.053 0.038 DT Deep 0.044 0.069 0.029 0.051 LK Hardbottom 0.000 0.000 0.0000.000LK Hardbottom0.076 0.091 0.163 0.078 LK Hardbottom0.000 0.000 0.000 0.000 LK Deep 0.942 0.555 0.8490.634LK Deep 0.069 0.079 0.045 0.046 LK Deep 0.070 0.080 0.046 0.042 LK Shallow 0.942 0.555 0.8490.634LK Shallow 0.069 0.079 0.045 0.046 LK Shallow 0.070 0.080 0.046 0.042 LK Patch 1.121 1.171 1.8651.420 LK Patch 0.102 0.093 0.055 0.079 LK Patch 0.110 0.106 0.055 0.081 MK Hardbottom 5.466 0.521 0.7143.373MK Hardbottom0.069 0.079 0.080 0.069 MK Hardbottom0.075 0.094 0.074 0.099 MK Deep 0.119 0.200 0.2660.547MK Deep 0.047 0.056 0.049 0.060 MK Deep 0.044 0.057 0.046 0.056 MK Shallow 0.119 0.200 0.2660.547MK Shallow 0.047 0.056 0.049 0.060 MK Shallow 0.044 0.057 0.046 0.056 MK Patch 0.242 0.381 0.4581.123 MK Patch 0.050 0.065 0.060 0.084 MK Patch 0.044 0.073 0.058 0.084 UK Hardbottom 0.025 0.661 0.2200.746UK Hardbottom0.109 0.089 0.084 0.088 UK Hardbottom0.108 0.098 0.086 0.088 UK Deep 0.038 1.309 0.2200.126UK Deep 0.050 0.052 0.038 0.063 UK Deep 0.043 0.054 0.047 0.040 UK Shallow 0.033 0.228 0.1880.117UK Shallow 0.053 0.054 0.037 0.063 UK Shallow 0.050 0.055 0.043 0.046 UK Patch 0.111 0.383 0.2430.398 UK Patch 0.073 0.069 0.051 0.076 UK Patch 0.078 0.074 0.066 0.085 Turbs (NTU) NO3b (M) NO3s (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 0.335 0.419 0.8990.419DT Deep 0.309 0.039 0.067 0.110 DT Deep 0.459 0.006 0.070 0.048 LK Hardbottom 1.861 1.469 1.6461.333LK Hardbottom0.000 0.000 0.000 0.000 LK Hardbottom0.446 0.011 0.035 0.189 LK Deep 0.734 0.707 0.8370.596LK Deep 0.466 0.105 0.096 0.170 LK Deep 0.408 0.079 0.074 0.117 LK Shallow 0.734 0.707 0.8370.596LK Shallow 0.466 0.105 0.096 0.170 LK Shallow 0.408 0.079 0.074 0.117 LK Patch 2.118 1.058 1.3271.222LK Patch 0.553 0.077 0.089 0.150 LK Patch 0.550 0.118 0.093 0.208 MK Hardbottom 1.144 2.065 0.9711.051MK Hardbottom0.443 0.009 0.069 0.369 MK Hardbottom0.450 0.126 0.120 0.471 MK Deep 0.305 0.338 0.3370.403MK Deep 0.355 0.046 0.088 0.199 MK Deep 0.403 0.023 0.097 0.127 MK Shallow 0.305 0.338 0.3370.403MK Shallow 0.355 0.046 0.088 0.199 MK Shallow 0.403 0.023 0.097 0.127 MK Patch 0.284 0.324 0.3200.480MK Patch 0.286 0.026 0.037 0.222 MK Patch 0.265 0.023 0.078 0.182 UK Hardbottom 0.774 0.728 0.6590.985UK Hardbottom0.738 0.072 0.160 0.134 UK Hardbottom0.523 0.021 0.109 0.131 UK Deep 0.235 0.296 0.2440.260UK Deep 0.360 0.127 0.127 0.176 UK Deep 0.524 0.083 0.173 0.191 UK Shallow 0.348 0.302 0.3520.312UK Shallow 0.417 0.117 0.118 0.143 UK Shallow 0.469 0.095 0.156 0.180 UK Patch 0.735 0.602 0.5800.459UK Patch 0.531 0.138 0.127 0.209 UK Patch 0.591 0.127 0.121 0.157

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78 Appendix F. Results for the water quality analysis by region and habitat, 2000-2003. DINs (M) DINb (M) TONs (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 0.920 0.266 0.3330.310 DT Deep 0.605 0.262 0.319 0.455 DT Deep 5.997 7.328 16.34214.377 LK Hardbottom 0.846 0.225 0.2290.513LK Hardbottom0.000 0.000 0.000 0.000 LK Hardbottom11.16510.43120.89211.854 LK Deep 0.927 0.364 0.2870.347LK Deep 1.197 0.417 0.326 0.455 LK Deep 8.630 7.891 17.10514.358 LK Shallow 0.927 0.364 0.2870.347LK Shallow 1.197 0.417 0.326 0.455 LK Shallow 8.630 7.891 17.10514.358 LK Patch 1.166 0.472 0.3740.644 LK Patch 1.224 0.487 0.338 0.522 LK Patch 9.886 9.118 27.45617.169 MK Hardbottom 0.913 0.341 0.3571.029MK Hardbottom1.158 0.223 0.282 0.886 MK Hardbottom12.1688.298 10.89719.892 MK Deep 0.750 0.255 0.3720.487MK Deep 0.686 0.244 0.320 0.596 MK Deep 8.682 9.601 17.55717.141 MK Shallow 0.750 0.255 0.3720.487MK Shallow 0.686 0.244 0.320 0.596 MK Shallow 8.682 9.601 17.55717.141 MK Patch 0.605 0.278 0.3060.638 MK Patch 0.641 0.204 0.238 0.826 MK Patch 8.077 7.461 7.893 20.209 UK Hardbottom 0.993 0.452 0.3840.581UK Hardbottom1.259 0.352 0.430 0.544 UK Hardbottom7.559 7.411 14.43419.390 UK Deep 0.940 0.288 0.4570.501UK Deep 0.821 0.363 0.405 0.451 UK Deep 6.401 10.38111.24215.875 UK Shallow 0.852 0.336 0.4290.530UK Shallow 1.094 0.361 0.352 0.445 UK Shallow 7.258 10.55914.88315.880 UK Patch 1.022 0.452 0.3670.439 UK Patch 1.426 0.531 0.313 0.517 UK Patch 7.520 8.296 13.06816.103 TONb (M) TOCs (M) TOCb (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 6.342 5.469 14.48414.206DT Deep 157.2 151.1 120.3 103.9 DT Deep 159.4 150.9 115.2 105.1 LK Hardbottom 0.000 0.000 0.0000.000LK Hardbottom235.2 237.5 293.4 220.0 LK Hardbottom0.0 0.0 0.0 0.0 LK Deep 9.314 8.492 19.64614.006LK Deep 160.6 161.2 130.9 122.0 LK Deep 162.1 164.2 132.5 114.4 LK Shallow 9.314 8.492 19.64614.006LK Shallow 160.6 161.2 130.9 122.0 LK Shallow 162.1 164.2 132.5 114.4 LK Patch 8.958 10.47826.78716.365LK Patch 182.9 195.3 149.6 140.0 LK Patch 183.0 191.4 144.7 129.0 MK Hardbottom 11.464 8.716 18.16721.418MK Hardbottom215.6 194.6 175.4 201.1 MK Hardbottom201.0 194.7 140.1 224.4 MK Deep 7.212 9.625 18.00615.763MK Deep 147.5 177.4 144.4 122.8 MK Deep 138.6 171.4 135.3 122.6 MK Shallow 7.212 9.625 18.00615.763MK Shallow 147.5 177.4 144.4 122.8 MK Shallow 138.6 171.4 135.3 122.6 MK Patch 8.381 6.510 8.58418.616MK Patch 150.4 151.2 137.4 155.8 MK Patch 144.0 147.0 135.2 155.8 UK Hardbottom 7.229 8.245 13.29917.288UK Hardbottom166.7 178.1 145.3 157.8 UK Hardbottom169.9 176.3 150.4 139.9 UK Deep 7.927 8.881 8.52615.354UK Deep 138.5 162.1 137.3 132.3 UK Deep 140.6 156.7 133.7 119.8 UK Shallow 7.814 9.798 13.99616.281UK Shallow 143.5 155.8 134.1 122.2 UK Shallow 146.8 149.3 129.6 111.7 UK Patch 5.945 9.971 14.42216.394UK Patch 146.2171.6 143.2128.3UK Patch 139.9 177.8 150.6 119.8

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79 Appendix F. Results for the water quality analysis by region and habitat, 2000-2003. DOs (mg/l) DOb (mg/l) Si(OH)4s (M) 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 5.802 5.331 5.5325.540DT Deep 5.921 5.438 5.958 6.045 DT Deep 0.108 0.147 0.980 0.236 LK Hardbottom 6.300 6.933 6.1756.038LK Hardbottom5.980 7.003 5.635 5.823 LK Hardbottom2.399 0.452 1.095 1.237 LK Deep 5.581 5.515 5.8545.412LK Deep 5.585 5.523 5.649 5.915 LK Deep 0.837 0.530 0.344 0.730 LK Shallow 5.581 5.515 5.8545.412LK Shallow 5.585 5.523 5.649 5.915 LK Shallow 0.837 0.530 0.344 0.730 LK Patch 5.607 5.460 5.8825.528LK Patch 5.897 5.442 5.851 5.991 LK Patch 1.206 1.008 2.410 1.640 MK Hardbottom 5.903 5.483 5.3645.597MK Hardbottom5.851 5.650 5.765 5.625 MK Hardbottom5.763 1.953 2.318 2.989 MK Deep 5.633 5.786 5.7775.752MK Deep 5.901 5.589 5.811 5.671 MK Deep 0.285 0.312 0.224 0.588 MK Shallow 5.633 5.786 5.7775.752MK Shallow 5.901 5.589 5.811 5.671 MK Shallow 0.285 0.312 0.224 0.588 MK Patch 5.665 5.575 6.6516.100MK Patch 5.877 5.648 6.220 6.020 MK Patch 0.239 0.366 0.750 1.478 UK Hardbottom 5.330 5.988 6.2215.213UK Hardbottom5.593 6.045 5.745 5.175 UK Hardbottom0.059 0.684 0.242 0.667 UK Deep 5.453 5.485 6.2024.951UK Deep 5.468 5.965 5.839 5.309 UK Deep 0.091 0.202 0.202 0.194 UK Shallow 5.431 5.563 6.0315.018UK Shallow 5.846 5.952 5.748 5.400 UK Shallow 0.060 0.341 0.185 0.193 UK Patch 5.533 5.748 6.1855.226UK Patch 5.665 6.160 5.874 5.475 UK Patch 0.041 0.455 0.431 0.362 Temps Tempb Sals 2000 2001 2002 2003 2000 2001 2002 2003 2000 2001 2002 2003 DT Deep 26.3 25.7 26.6 26.1 DT Deep 25.5 25.5 26.5 26.0 DT Deep 36.236.436.136.1 LK Hardbottom 25.7 25.9 26.0 26.2 LK Hardbottom25.4 25.5 25.9 25.9 LK Hardbottom36.636.736.536.0 LK Deep 27.0 26.5 27.3 27.6 LK Deep 26.9 26.4 26.8 27.0 LK Deep 36.236.436.035.9 LK Shallow 27.0 26.5 27.3 27.6 LK Shallow 26.9 26.4 26.8 27.0 LK Shallow 36.236.436.035.9 LK Patch 27.2 26.4 27.6 27.7 LK Patch 27.2 26.4 27.5 27.4 LK Patch 36.436.636.336.1 MK Hardbottom 27.1 26.7 27.8 27.8 MK Hardbottom27.0 26.5 27.8 27.7 MK Hardbottom36.536.436.635.8 MK Deep 27.2 26.6 27.4 27.5 MK Deep 27.3 26.5 27.4 27.3 MK Deep 36.336.236.335.9 MK Shallow 27.2 26.6 27.4 27.5 MK Shallow 27.3 26.5 27.4 27.3 MK Shallow 36.336.236.335.9 MK Patch 27.1 27.0 27.3 27.3 MK Patch 27.0 26.9 27.4 27.2 MK Patch 36.336.036.235.8 UK Hardbottom 26.8 24.9 27.5 26.9 UK Hardbottom26.7 24.9 27.5 26.9 UK Hardbottom36.435.536.735.9 UK Deep 26.9 26.2 27.1 26.8 UK Deep 26.8 26.2 27.1 26.6 UK Deep 36.236.236.235.9 UK Shallow 26.9 26.0 27.1 26.8 UK Shallow 26.9 25.9 27.1 26.7 UK Shallow 36.236.336.235.9 UK Patch 26.7 25.4 27.2 26.6 UK Patch 26.7 25.2 27.1 26.6 UK Patch 36.236.036.335.9