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Distribution patterns of larger symbiont-bearing foraminifera of the Florida reef tract, usa

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Title:
Distribution patterns of larger symbiont-bearing foraminifera of the Florida reef tract, usa
Physical Description:
Book
Language:
English
Creator:
Baker, Rebekah Duncan
Publisher:
University of South Florida
Place of Publication:
Tampa, Fla
Publication Date:

Subjects

Subjects / Keywords:
Florida Keys
Bioindicators
Amphistegina
Distribution
Assemblage
Dissertations, Academic -- Marine Science -- Masters -- USF   ( lcsh )
Genre:
non-fiction   ( marcgt )

Notes

Summary:
ABSTRACT: Studies of larger symbiont-bearing foraminifers on reefs have revealed their potential as indicators of environmental stress because of their physiological analogies to corals (dependence on algal symbionts for growth and calcification) and relatively short life cycle (a few months to 2 years or more). The purpose of this study is to report distribution patterns and population densities of larger benthic foraminifers (LBF) of the Florida reef tract, specifically reporting abundance data collected from offshore (1995-2000, 2006, 2007) and patch reefs (1996, 2006, 2007). Six years of quarterly data collected from two offshore reefs, Conch (10, 18 and 30m) and Tennessee (8 and 20m), revealed that LBF assemblages primarily varied with habitat depth, in turn reflecting available light and water motion.These assemblages were dominated by Amphistegina gibbosa d'Orbigny and Laevipeneroplis proteus d'Orbigny, which tended to occur together, making up ~40-50% of the assemblages and up to 80% at the Tennessee 20m site. Both overall abundance and evenness of the LBF assemblage structure exhibited the greatest variability at shallower depths. Evenness was inversely related to densities of A. gibbosa, which were typically higher at depth keeping evenness below 0.5. Across the Keys, region (location along the reef tract), reef type (offshore shallow, deep or patch reefs) and symbiont type strongly influenced LBF assemblage dynamics. Upper Keys sites shared the highest degree of inter-region similarity among assemblages (73%), while Biscayne National Park (BNP) and lower Keys sites had the lowest similarity (~60%). This likely reflects the greater variability of habitats found in the latter areas, mainly patch reefs.Chlorophyte-bearers were typically more abundant in shallower turbid waters, with diatom-bearers more abundant at depth. Additionally, I observed a significant two-fold decrease in the proportion of chlorophyte-bearers in the middle Keys likely due to light-limitation by turbid Florida Bay outflow. Finally, data comparisons revealed an inverse relationship between LBF abundances and percent coral cover. Coral cover (2005) was staggeringly low on offshore reefs (5%), but was significantly higher on nearshore patch reefs (12%). Contrastingly, LBF species showed either no difference in abundance between reef types or a greater abundance on offshore reefs.
Thesis:
Thesis (M.S.)--University of South Florida, 2008.
Bibliography:
Includes bibliographical references.
System Details:
Mode of access: World Wide Web.
System Details:
System requirements: World Wide Web browser and PDF reader.
Statement of Responsibility:
by Rebekah Duncan Baker.
General Note:
Title from PDF of title page.
General Note:
Document formatted into pages; contains 157 pages.

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University of South Florida Library
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University of South Florida
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All applicable rights reserved by the source institution and holding location.
Resource Identifier:
aleph - 002000966
oclc - 319171566
usfldc doi - E14-SFE0002525
usfldc handle - e14.2525
System ID:
SFS0026842:00001


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ABSTRACT: Studies of larger symbiont-bearing foraminifers on reefs have revealed their potential as indicators of environmental stress because of their physiological analogies to corals (dependence on algal symbionts for growth and calcification) and relatively short life cycle (a few months to 2 years or more). The purpose of this study is to report distribution patterns and population densities of larger benthic foraminifers (LBF) of the Florida reef tract, specifically reporting abundance data collected from offshore (1995-2000, 2006, 2007) and patch reefs (1996, 2006, 2007). Six years of quarterly data collected from two offshore reefs, Conch (10, 18 and 30m) and Tennessee (8 and 20m), revealed that LBF assemblages primarily varied with habitat depth, in turn reflecting available light and water motion.These assemblages were dominated by Amphistegina gibbosa d'Orbigny and Laevipeneroplis proteus d'Orbigny, which tended to occur together, making up ~40-50% of the assemblages and up to 80% at the Tennessee 20m site. Both overall abundance and evenness of the LBF assemblage structure exhibited the greatest variability at shallower depths. Evenness was inversely related to densities of A. gibbosa, which were typically higher at depth keeping evenness below 0.5. Across the Keys, region (location along the reef tract), reef type (offshore shallow, deep or patch reefs) and symbiont type strongly influenced LBF assemblage dynamics. Upper Keys sites shared the highest degree of inter-region similarity among assemblages (73%), while Biscayne National Park (BNP) and lower Keys sites had the lowest similarity (~60%). This likely reflects the greater variability of habitats found in the latter areas, mainly patch reefs.Chlorophyte-bearers were typically more abundant in shallower turbid waters, with diatom-bearers more abundant at depth. Additionally, I observed a significant two-fold decrease in the proportion of chlorophyte-bearers in the middle Keys likely due to light-limitation by turbid Florida Bay outflow. Finally, data comparisons revealed an inverse relationship between LBF abundances and percent coral cover. Coral cover (2005) was staggeringly low on offshore reefs (5%), but was significantly higher on nearshore patch reefs (12%). Contrastingly, LBF species showed either no difference in abundance between reef types or a greater abundance on offshore reefs.
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PAGE 1

Distribution P atte rns of Larger Symbiont B earing F oraminifer a of the Florida R eef T ract, USA by Rebekah Duncan Baker A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science College of Marine Science U niversity of South Florida Major Professor: Pam ela Hallock Muller, Ph.D. Benjamin Flower, Ph.D. Elizab eth Fisher Moses Ph.D. Date of Approval: Ju ly 2008 Keywords: Florida Keys bioindicators, Amphistegina distribution, assemblage Copyrig ht 2008, Rebekah Duncan Baker

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ACKNOWLEDG MENTS Original sample collection and processing was funded by the following grants to Pamela Hallock Muller unless otherwise noted: NOAA NURC subcontracts No. 9595, 9609, 9703.66, 9922, 2004 19B; USEPA ORD STAR G AD R825869; National Sea Grant Environmental Marine Biotechnology Award No. NA86RG0052, Am.7.1 ( PI s : Eric Lacey and C heryl M Woodley); NOAA through the Florida Hurricane Alliance (PI: Thomas Mason) ; and the U.S. Environmental Protection Agency Gulf Ecolo gy Division Grant No. X7 96465607 0. Sampling permits were issued by: Florida Department of Environmental Protection (95S 00063, 96S 016, and 00S 016); NOAA Florida Keys National Marine Sanctuary (KLNMS 07 95, (UR) 29 96, 006 97, 2000 011, 2001 008; 2003 002, 2005 002, 2007 013); and the US National Park Service ( BISC 2001 SCI 0022, 2002 SCI 0012, 2003 SCI 0019, and 2007 SCI 0023 ) Acknowledg ment does not imply endorsement of results by any of the funding or permitting agencies Tuition support was provided through a Von Rosenstiel Fellowship, for which I am much obliged. This study is based on previously collected data gathered by th e hard work of my predecessors and colleagues Heidi Crevison Souder, Elizabeth Fisher Moses, Jodi Harney, Melan ie Peters, Alexa Ramirez, Helen Talge, Strawn Toler, Dana Williams, and other members of the Reef Indicators Lab. I also utilized data on coral cover and coral decline, which was collected by members of the Coral Reef Evaluation and Monitoring Program (CR EMP), based at the Florida Fish and Wildlife Conservation Commission Research Institute in St Petersburg, Florida. I, therefore, acknowledge the diligent efforts of many in producing the data upon which my analys e s and interpretation are based I would l ike to express my deep gratitude to my advisor, Pamela Hallock Muller for her constant support and dedication to the success of my project Also, I thank my committee, Benjamin Flower and Elizabeth Fisher Moses for their guidance and assistance with stat istics, despite the unusual long distance circumstances during the drafting of this manuscript. Additionally, I thank my husband, Don Baker, who provided unending encouragement and critical technical support for my ArcGIS analysis.

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i TABLE OF CONTENTS LIST OF TABLES ................................ ................................ ................................ .......................... iii LIST OF FIGURES ................................ ................................ ................................ ........................ vi ABSTRACT ................................ ................................ ................................ ................................ ..... x INTRODUCTION ................................ ................................ ................................ ........................... 1 Warm water larger foraminifers ................................ ................................ ......................... 1 Bleaching in Amphistegina & data set origin ................................ ................................ ..... 2 Calcification & projected climate change effects ................................ ............................... 4 Research Objectives ................................ ................................ ................................ ............ 5 Questions & Hypotheses ................................ ................................ ................................ ... 10 METHODS ................................ ................................ ................................ ................................ .... 11 Sampling ................................ ................................ ................................ ........................... 11 Limitations of the data set ................................ ................................ ................................ 12 Statistical analysis ................................ ................................ ................................ ............. 14 RESULTS ................................ ................................ ................................ ................................ ...... 16 Time series analysis ................................ ................................ ................................ .......... 16 Conch Reef ................................ ................................ ................................ .......... 16 Tennessee Reef ................................ ................................ ................................ .... 32 Keys wide analysis ................................ ................................ ................................ ........... 3 9 LBF densities & symbiont analysis ................................ ................................ ..... 39 MDS & SIMPER analysis ................................ ................................ ................... 51 BEST analysis ................................ ................................ ................................ ...... 58 Metadata analysis ................................ ................................ ................................ .............. 64 MDS & SIMPER analysis ................................ ................................ ................... 66 Evenness ................................ ................................ ................................ .............. 74 DISCUSSION ................................ ................................ ................................ ................................ 81 LBF assemblage density trends ................................ ................................ ........................ 81 Depth & temporal trends ................................ ................................ ...................... 81 Regional trends ................................ ................................ ................................ .... 85 Trend summaries by species ................................ ................................ ................ 86

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i i Diversity & habitat type ................................ ................................ ................................ .... 88 Data set comparisons ................................ ................................ ................................ ........ 90 CONCLUSIONS ................................ ................................ ................................ ........................... 96 REFERENCES ................................ ................................ ................................ ............................ 100 APPENDICES ................................ ................................ ................................ ............................. 105 A. Calculation of the Shanno n Index ( H '), H max and evenness ( E ... .. 106 B. Species density means at Conch and Tennessee reefs from 1995 C. Table D. Species density means and ANOSIM results for Keys E. Table of species density means for each sampling of Keys F. Proportions of tot al LBF assemblage by symbiont type for Keys

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iii LIST OF TABLES Table 1. Larger foraminiferal species are listed alphabetically by order with reference to species author, shell composition and sy mbiont type. 6 Table 2. Sampling sites are ordered by data set. Reef type (Patch, P, Offshore Deep, OD, and Offshore Shallow, OS) is given along with respective locations in degrees and minut es, depth sampled (m), years sampled, sample source (or new unpublished data) and notes on the site history. 7 Table 3. ANOSIM2 results for differences between sampling depths based on LBF den sities (across all years) for Conch Reef (1995 2000); Global R=0.644, starred values are significant at p<0.001. 16 Table 4. ANOSIM2 results for differences between seasons based on LBF densit ies (across all years) for Conch Reef (1995 2000); Global R=0.073, starred values are significant at p<0.05. Non significant values are represented by n.s. 16 Table 5. SIMPER results by sampl ing depth (10m, 18m and 30m) at Conch Reef (1995 2000) showing average percent similarity for each depth, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each depth. Gray shading indicates those s pecies responsible for contributing greater than 10% to the similarity between each depth. 19 Table 6. SIMPER dissimilarity results by sampling depth (10m, 18m and 30m) at Conch Reef (1995 200 0) showing average percent dissimilarity between sampling depths, average abundances (count/100 cm 2 ), and percent contribution for species contributing to dissimilarity between each depth. Gray shading indicates those species responsible for contributing greater than 10% to the dissimilarity between each depth. 20 Table 7. SIMPER results by sampling depth (8m and 20m) at Tennessee Reef (1995 2000) showing average percent similarity (dissimilar ity) within each depth, average abundances (count/100 cm 2 ), and percent contribution for taxa contributing to similarity (dissimilarity) for each depth. Gray shading indicates those species responsible for contributing greater than 10% to the similarity ( dissimilarity) between each depth. 36 Table 8. ANOSIM2 results for differences between reef types (offshore shallow, OS, offshore deep, OD and patch, P) based on LBF densities (across all regi ons) for Keys wide sites (1995, 1996, 2006, 2007); Global R=0.236. Starred values are significant at p<0.01. 39

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iv Table 9. ANOSIM2 results for differences between regions (upper, middle and low er Keys) based on LBF densities (across all reef types) for Keys wide sites (1995, 1996, 2006, 2007); Global R=0.132. Starred values are significant at p<0.05. Non significant values are represented by n.s. 40 Table 10. Summary of analysis of similarity (ANOSIM) tests for Keys wide summer data by region (upper, middle and lower Keys, across all years) and reef type (offshore deep, OD, offshore shallow, OS, and patch, P, reefs, across all year s) and by year (1995, 1996, 2006 and 2007, across all sites). Tests that supported the null hypothesis, indicating that no differences were found between groups, are denoted by n.s. (not significant). Starred differences are significant at p<0.05 and dou ble starred differences are significant at p<0.01. 43 Table 11. Summary of untransformed LBF density means SE across all years for Keys wide summer only data. 44 Table 12. Mean proportion of total assemblage by symbiont type with standard error for Keys wide sites. Overall means are given as well as for each region and reef type in 1995 : lower (N=4) and middle (N=4) Keys, offsho re deep, OD (N=4) and offshore shallow, OS (N=4); 1996 : lower (N=4), middle (N=6) and upper Keys (N=4), offshore deep, OD (N=7) and offshore shallow, OS (N=7) reefs; and 2006 and 2007 : lower (N=13), middle (N=9) and upper Keys (N=15), offshore deep, OD (N= 11); offshore shallow, OS (N=11); and patch, P (N=15) reefs. 46 Table 13. SIMPER results by reef type for all Keys wide sites including patch, offshore deep and offshore shallow reefs showing average percent similarity within each reef type, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each reef type. Gray shading indicates those species responsible for contributing greater than 10% to the similarity within each reef type. 52 Table 14. SIMPER results by reef type for all Keys wide sites including patch (P), offshore deep (OD) and offshore shallow (OS) reefs showing avera ge percent dissimilarity for each sampling reef type, average abundances (count/100 cm 2 ), and percent contribution for species contributing to dissimilarity between each reef type. Gray shading indicates those species responsible for contributing greater than 10% to the dissimilarity between each reef type. 53 Table 15. SIMPER results by region for Keys wide sites within the upper, middle and lower Keys showing average percent similarity withi n each sampling region, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each region. Gray shading indicates those species responsible for contributing greater than 10% to the similarity within eac h region. 56 Table 16. SIMPER results by region for Keys wide sites within the upper, middle and lower Keys showing average percent dissimilarity for each sampling region, average abundances ( count/100 cm 2 ), and percent contribution for species contributing to dissimilarity between each region. Gray shading indicates those

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v species responsible for contributing greater than 10% to the dissimilarity between each region. 57 Table 17. BEST results from 2006 LBF species density data from corresponding Keys wide and CREMP sites. The top ten correlation values are listed for each test. The highest correlations are significant at p<0.01 ( starred). 60 Table 18. ANOSIM2 results for differences between regions (Biscayne National Park (BNP) and upper, middle and lower Keys) based on LBF densities (across all reef types) for metada ta analysis; Global R=0.358. Starred values are significant at p<0.05 and double starred values are significant at p<0.001. 65 Table 19. ANOSIM2 results for differences between reef types (of fshore shallow, OS, offshore deep, OD and patch, P) based on LBF densities (across all regions) for metadata analysis; Global R=0.227. Bolded values are significant at p<0.001, while starred values are significant at p<0.05. 65 Table 20. SIMPER results by region for metadata analysis including Biscayne National Park (BNP) and upper, middle and lower Keys showing average percent similarity for each sampling region, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each region. Gray shading indicates those species responsible for contributing greater than 10% to the similarity between each region. 68 Table 21. SIMPER results by region for metadata analysis including Biscayne National Park (BNP) and upper, middle and lower Keys showing average percent dissimilarity for each sampling region, average abundances (count/100 cm 2 ), an d percent contribution for species contributing to dissimilarity between each region. Gray shading indicates those species responsible for contributing greater than 10% to the dissimilarity between each region. Note: Table continues on following page. 69 Table 22. SIMPER results by reef type for metadata analysis including patch, offshore deep and offshore shallow reefs showing average percent similarity for each reef type, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each reef type. Gray shading indicates those species responsible for contributing greater than 10% to the similarity between each reef type. 72 Table 23. SIMPER results by reef type for metadata analysis including patch (P), offshore deep (OD) and offshore shallow (OS) reefs showing average percent dissimilarity for each reef type, average abundances (coun t/100 cm 2 ), and percent contribution for species contributing to dissimilarity between each reef type. Gray shading indicates those species responsible for contributing greater than 10% to the dissimilarity between each reef type. 73

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vi LIST OF FIGURES Figure 1. Florida Keys sampling sites listed by reef type: patch (P, triangles), offshore shallow (OS, squares) and offshore deep (OD, circles) and set within the con text of benthic habitat type (from Florida Fish and Wildlife Conservation Commission National Ocean Service, 1998): bare substrate, seagrass, hardbottom with seagrass, hardbottom, platform margin reef and patch reef using ArcMap (v. 9.2). Some sites appea r to overlap due to the map scale. Note: the original document contains color that is necessary for understanding the data presented here. The original thesis is on file with the USF library in Tampa, Florida. 13 Figure 2. Bray Curtis dendrogram of LBF assemblage across all depths sampled (10m, 18m and 30m) at Conch Reef (1995 2000). 17 Figure 3. MDS plot for Conch Reef (1995 18 Figure 4. Amphistegina gibbosa density me ans (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch Reef 2000. 22 Figure 5. Laevipeneroplis proteus density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch f (TN): 8m 2000. Note: scales are different. 24 Figure 6. Archaias angulatus density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites N=2) with standard error bars at Conch Reef 2000. Note: scales are different. 25 Figure 7. Cyclorbiculina compressa density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch 2000. Note: scales are different. 26 Figure 8. Asterigerina carinata density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conc h Reef 2000. 27

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vii Figure 9. Heterostegina antillarium density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch 2000. 28 Figure 10. Broeckina orbitolitoides density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch sites from 1995 2000. Note: scales are different. 29 Figure 11. Mean evenness ( E ) of LBF assemblage with standard error bars (N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) at Conch Reef (CR): 10m sites from 1995 2000. 30 Figure 12. Evenness ( E ) plotted against A. gibbosa densities with linea r regression for combined 10m, 18m and 30m depths at Conch Reef (R 2 = 0.36). 31 Figure 13. Evenness ( E ) plotted against A. gibbosa densities with individual linear regressions for 10m, 18m and 30m depths at Conch Reef with R 2 = 0.44, 0.39 and 0.18, respectively. 32 Figure 14. Bray Curtis dendrogram of LBF assemblage across all depths sampled (8m and 20m) at Tennessee Reef (1995 2000). 33 Figure 15. MDS plot for Tennessee Reef (1995 34 2000. 2D Stress: 0.12. 35 Figure 17. Combined linear regression for both shallow (8m) and deep (20m) sites at Tennessee Reef (R 2 = 0.06). 38 Figure 18. Linear and logarithmic regression for Tennessee Reef at shallow (8m) and deep (20m) sites (R 2 = 0.52 and 0.55, respectively). 39 Figure 19. Bray Curtis dendrogram of LBF assemblage across all years sampled at all Keys wide sites. 41 Figure 20. Mean proportion of total assemblage for each symbiont type with standard error bars for summer only assemblage data (across all years) plotted by region: lower (N=34), middle (N=28) and upper (N=34) Keys. Means SE are listed below the figure for each symbiont: Dinoflagellate (solid white) and Rhodophyte (solid gray), Chlorop hyte (crossbar pattern), Diatom (diagonal stripes). Significant differences between regions within each symbiont type are indicated by different group letters. Non significant results within a symbiont type are denoted by n.s. 47

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viii Figure 21. Mean proportion of total assemblage for each symbiont type with standard error bars for summer only assemblage data (across all years) plotted by reef type: offshore deep (OD, N=33), offshore shallow (OS, N=33) and patch (P, N=30). Means SE are listed below the figure for each symbiont: Dinoflagellate (solid white) and Rhodophyte (solid gray), Chlorophyte (crossbar pattern), Diatom (diagonal stripes). Significant differences between reef types within ea ch symbiont type are indicated by different group letters. Non significant results within a symbiont type are denoted by n.s. 48 Figure 22. Proportion of total assemblage for each symbiont ty pe (Dinoflagellate, solid white, Rhodophyte, solid gray, Chlorophyte, crossbar pattern, and Diatom, diagonal stripes) for summer only assemblage data collected from the lower, middle and upper Keys in 2007 and 2006. Sites are listed from west to east (lef t to right). 49 Figure 23. Proportion of total assemblage for each symbiont type (Dinoflagellate, solid white, Rhodophyte, solid gray, Chlorophyte, crossbar pattern, and Diatom, diagonal strip es) for summer only assemblage data collected from the lower, middle and upper Keys in 1996 and 1995. Sites are listed from west to east (left to right). 50 Figure 24. MDS plot by reef type f or Keys wide data (summers only of 1995, 1996, 2D Stress: 0.1. 51 Figure 25. MDS plot by region for Keys wide data (summers only of 1995, 1996, 2006, 54 Figure 26. Mean percent coral cover and percent coral decline with standard er ror by region (lower, middle and upper Keys) and reef type (offshore deep, OD, offshore shallow, OS, and patch, P, reefs). ANOSIM results are given below the graphs. Starred R values are significant at p<0.05 and double starred values are significant at p<0.01. 59 Figure 27. Regressions of LBF species densities (per 100cm 2 ) from summer 2006 Keys wide and CREMP sites that were most correlated with percent coral cover (2005). When outliers for L. bradyi and C. compressa (circled) were removed, R 2 values increased to 0.2 for both species. Note: Scales vary. 62 Figure 28. Regressions of LBF species densities (per 100cm 2 ) from summer 2006 Keys wide and CREMP sites that were most correlated with percent coral decline (1996 2005). R 2 values increased to 0.3 for L. bradyi and 0.2 for C. compressa and B. pulchra when outliers (circled) were removed. Note: Scales vary. 64 Figure 29. Bray Curtis dendrogram of LBF assemblage across all depths sampled for all metadata sites. 66 Figure 30. MDS plot by region for meta 67

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ix hore shallow (OS, 71 Figure 32. Mean evenness ( E ) for summer only assemblage data (across all years) with standard error bars plotted by region: lower (solid white, N=36), middle (diagonal stripes, N=43) and upper (solid gray, N=84) Keys and Biscayne National Park (BNP, crossbar pattern, N=35). Significant differences between regions are indicated by different letters (two way ANOVA: F 3,188 = 6.1 8, p=0.0001). 74 Figure 33. Mean evenness ( E ) for summer only assemblage data (across all years) with standard error bars plotted by reef type: offshore deep (OD, solid gray, N=56), offshore s hallow (OS, solid white, N=48) and patch (P, crossbar pattern, N=96). Significant differences between reef types are indicated by different letters (two way ANOVA: F 2,188= 4.07, p=0.02). 75 Figure 34. Mean evenness ( E ) for summer only assemblage data with standard error bars plotted by reef type and region (across all years): lower (solid white), middle (diagonal stripes) and upper (solid gray) Keys and Biscayne National Park (BNP, crossbar pattern). The number of reefs sampled for each region by reef type (N) is listed below the corresponding bar. The interaction between region and reef type was not significant (two way ANOVA: F 4,188 = 1.2, p=0.31). 76 Figure 35. Mean evenness ( E ) for summer only assemblage data with standard error bars plotted by year and reef type (across all regions): offshore deep (OD, solid gray), offshore shallow (OS, solid white) and patch (P, crossbar p attern). The number of reefs sampled for each reef type (N) is listed below the corresponding bar. Significant differences between reef types are indicated by different letters (two way ANOVA: F 4,167 = 2.66, p=0.04). All values of E without letters are not significant from any other values (abc). 78 Figure 36. Mean evenness ( E ) for summer only assemblage data with standard error bars plotted by year and region (across all reef types): lower (solid white), middle (diagonal stripes) and upper (solid gray) Keys and Biscayne National Park (BNP, crossbar pattern). The number of reefs sampled within each region (N) is listed below the corresponding bar. Significant differences between regions are indicated by different letters (two way ANOVA: F 6,162 = 2.74, p=0.014). All values of E without letters are not significant from any other values (ab). 80

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x Distribution patterns of larger symbiont bearing Foraminifera of the Florida reef tract, USA Rebekah Duncan Baker ABSTRACT Studies of larger symbiont bearing foraminifers on reefs have revealed their potential as indicators of environmental stress because of their physiological analogies to corals (dependence on algal symbionts for growth and calcification) and relatively short life cycle (a few months to 2 years or more). The purpose of this study is to report distribution patterns and population densities of larger benthic foraminifers (LBF) of the Florida reef tract specifically reporting abundance data collected from offshore (1995 2000 2006, 2007 ) and patch reefs ( 1996, 2006 2007) Six years of quarterly data collected from two offshore reefs, Conch (10, 18 and 30m) and Tennessee (8 and 20m) revealed that LBF a ssemblages primarily varied with habita t depth, in turn reflecting available light and water motion. These assemblages were dominated by Amphistegina gibbosa r bigny and L a ev i penero p lis proteus which tended to occur together making up ~40 50 % of the assemblage s and up to 80% at the Tennessee 20m site Both overall abundance and evenness of the LBF assemblage structure exhibited the greatest variability at shallower depths. E venness was inversely related to densities of A. gibbosa which wer e typically higher at depth keeping evenness below 0.5. A cross the Keys, region ( location along the reef tract ), reef type (o ffshore s hallow, d eep or p atch reefs) and symbiont type strongly influenced LBF assemblage dynamics Upper Keys sites shared the h ighest degree of inter region similarity among assemblages (73%), while Biscayne National Park (BNP) and lower Keys sites had the lowest similarity (~60%). This likely reflects the greater variability of habitats found in the latter areas, mainly patch re efs

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xi C hlorophyte bearers were typically more ab undan t in shallower turbid waters, with diatom bearers more abundan t at depth. Additionally, I observed a significant two fold decrease in the proportion of chlorophyte bearers in the middle Keys likely due to light limitation by turbid Florida Bay outflow Finally, data comparisons revealed an inverse relationship between LBF abundances and percent coral cover Coral cover ( 2005 ) was staggeringly low on offshore reefs (5%) but was significantly higher on n earshore patch reefs (12%). Contrastingly, LBF species showed either no difference in abundance between reef types or a greater abundance on offshore reefs.

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1 INTRODUCTION Warm water larger foraminifers Foraminifera comprise a class of single celled micr oorganisms in the Phylum P rotoctist a that secrete an organic, agglutinated or mineralized shell which may have single or multiple chambers Foraminifers possess reticulating cytoplasmic pseudopods ( granulo reticulopodia) that extend through apertures in t he shell to form dense and extensively branched networks which are used in feeding and chamber construction The majority of Foraminifera are benthic; there are only about 40 50 planktonic species ( Sen Gupta, 1999). Vagile b enthic foraminifers are also able to use their reticulopodia to slowly crawl along a surface. Benthic Foraminifer s (LBF) describe a group that are larger in diameter ( typically >2mm) t han the majority of foraminifers and include representatives of several warm water porcelane ous and hyaline families ( Lee and Anderson 1991; Hallock, 1999; Murray 2006 ; others ). Algal symbiosis is prevalent in LBF that inhabit warm, clear, tropical waters, such as those found in the Florida Keys. In such environment s algal symbiosis is consi dered a form of mutualism because both the host and symbiont are thought to benefit from the association. The host provides physical protection, housing and nutrient rich metabolite s to the symbiont. Endosymbiotic algae capitalize on the recycled nutrien ts available from the host in nutrient limiting environments and fix carbon by photosynthesis (Hallock, 1981, 2000a) In turn, the symbiont passes up to 95% of its photosynthate to the host where it can be u sed for respiration, growth or calcification. U nder oligotrophic conditions, the enormous amount of energy supplied by algal symbiosis and algal productivity facilitates high rates of calcification and reef formation ( Hallock, 1981; Cowen, 1988 ; many others ). S tudies have found that growth to large si ze is

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2 primarily advantageous under relatively predictable conditions where resources are limiting, s uch as warm, shallow oligotrophic seas with favorable li ght conditions (Hallock 1985; Falkowski et al. 1993 ). High er nutrient flux support s more abundant phytoplankton and macroalgal growth, thereby promoting dominance by heterotrophic rather than mixotrophic foraminifers. F oraminifers hosting endosymbiotic algae are found within 1 2 families in the orders Miliolida, Rotaliida and Globigerinida (Lee and And erson 199 1 ; Hallock, 1999 ). Endosymbionts may be of several different algal types, including rhodophytes, chlorophytes, dinoflagellates diatoms and chrysophytes. H osts typically house one dominant algal taxon though other species may be present in muc h lower densities. Because bot h corals and LBF are sustained by their relationship with endosymbiotic algae and have similar water quality requirements Hallock (2000 a,b ) and Hallock et al. ( 2004) proposed the use of LBF to monitor the response of the bent hic community to environmental stress ors Foraminifers can be useful indicators in this way for several reasons. They are easily collected from reefs in high abundance with minimal impact on the reef itself. Also, they have relatively short life span s a s compared to hermatypic corals and thus can respond to chronic stress more quickly. In general, distribution s of LBF are constrained by a world wide climatic belt that exists along winter minimum isotherms between 15 and 20C. Thus, in shallow tropical seas, larger foramin if eral faunal provinces are defined latitudinally by winter isotherms and longitudinally by steep trophic gradients (Langer and Hottinger, 2000). Local influences on foraminiferal distributions include substrate availability turbidit y and nutrient flux Bleaching in Amphistegina & data set origin Bleaching is a stress response exhibited by bot h corals and larger foraminifers where endosymbionts lose their photosynthetic pigment, are expelled or are digested (e.g., Glynn, 1996)

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3 The l ack of algal cells or pigment reveal s the white calcium carbonate skeleton and transparent host tissu e, accounting for thei Bleaching was discovered in the Florida reef tract in Amphistegina gibbosa d'Orbigny in summer 1991 (Hallock et al ., 1993 ) This species is abundant in the Florida Keys and exhibits a when photo oxidative stress causes the degradation of its diatom endosymbionts (Talge and Hallock, 2003; Williams and Hallock, 2004) Williams et al. (1997) found significant bleaching in A gibbosa at Conch Reef in the Florida Keys that resulted in a population crash in late 1991 and low reproductive success through 1992. The discovery of e xtensive b leaching in field populations of A. gibbosa in 1991 prompted monthly sampling at Conch Reef beginning in 1992. Sampling was reduced to quarterly intervals, but broadened to inc lude sites at Tennessee Reef and all larger taxa (Table 1) in 1995 This effort contin ued through 2 000, providing a six year multi species data set. Following the discovery of bleaching in Amphistegina spp. worldwide (e.g., Hallock et al. 1995; Hallock, 2000a), combined with data documenting the long term decline of larger foraminiferal assemblages that paralleled th e decline of coral cover along the Florida ree f tract (Cockey et al. 1996), Hallock (2000b) proposed the development of environmental bioindicators using larger benthic foraminifers, both live and accumulating in the sediments (see also Hallock et al. 20 03, 2004). Seven patch reef sites were sampled quarterly in 2001 2003 by Fisher ( 2007) as part of a study comparing coral health as indicated by a suite of molecular biomarkers with the rate of recovery of the lesions created on the coral when the biomark er samples were collected. Foraminiferal assemblage samples were collected at the same sites and sample dates (Fisher, 2007). Keys wide sampling of foraminiferal assemblages at the Coral Reef Evaluation and Monitoring Program (CREMP) sites (e.g., Porter e t al. 2002) was conducted during the summers of 2006 2007. Finally, samples were collected at 32 patch and bank reef sites in Biscayne National Park as part of the thesis research of Ramirez (2008). Except for data from the Fisher

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4 sites (2001 2003) and the Ramirez sites, the resultant assemblage data were never analyzed. These multiple, and in most cases, multi year data sets provide the data sets for my study (Table 2) Calcification & projected climate change effects Larger f oraminifer s are well known for their prolific calcification, which is enhanced by their associat ion with algal symbionts. Several mechanism s for photosynthetically enhanced calcification have been proposed. Some suggest that photosynthesis promotes calcification by splitting bica rbonate and removing CO 2 (ter Kuile, 1991). Others have hypothesized just the opposite in that calcification converts bicarbonate to CO 2 and promotes photosynthesis (McConnaughey and Whelan, 1997). Under the latter explanation, a decreased ability to cal cify could have a negative impact on photosynthesis by the symbiont. I ncreased atmospheric CO 2 associated with fossil fuel burning, lower s carbonate saturation levels in seawater and makes precipitation of calcium carbonate more difficult (Kleypas et al. 1999 ) Currently, most temperate and tropical oceanic surface waters are supersaturated with respect to calcium carbonate. At higher degrees of saturation, Mg 2+ ions interfere with calcite formation. Some foraminifer s especially the Miliolida, secrete their shells in equilibrium with seawater and under higher carbonate saturation levels, incorporate more Mg 2 + The more Mg 2+ incorporated into the shell, the weaker the crystal structure (e.g. high Mg calcite). Other foraminifer s may actively exclude Mg 2+ to form low Mg calcite shells (e.g., many Rotalida and Globigerinida) Aragonite is much stronger than calcite and Mg 2+ does not interfere with crystal structure formation. However, aragonite is more energetically expensive to build and maintain at lower saturation levels than calcite (Hallock, 2000 a ). No larger foraminifers and very few smaller foraminifers secrete aragonite shells.

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5 This study will provide baseline information for larger f oraminifera l research and has implications for carbonate pro duction/calcification with increasing ocean acidification and global climate change (CO 2 increase). These changes could potentially alter foraminiferal distributions because high er atmospheric CO 2 will further decrease surface seawater pH and carbonate sa turation states, which will be less favorable for high Mg calc ite miliolid LBF than for the low Mg cal cite larger rotal i ids (Hallock 2000 a ). Aragonitic corals and calcareous green algae are also potentially at risk organisms whose loss precipitate s chang es at the ecosystem level (Hallock, 2005) Research Objectives 1. Map distrib utions of 12 LBF species (Table 1) along the Florida reef tract. 2. Determine if patterns of distribution are related to depth, reef type, algal symbiont taxa or seasonal, interannual o r spatial trends (e.g. depth or off shore reefs versus patch reefs). 3. Compare findings with other related data sets, including data comparing foraminifers with data on Biscayne and upper Keys patch reefs (Fisher, 2007 ), and with coral cover at Keys wide C o ral R eef E valuation and M onitoring P roject (CREMP) and Atlantic and Gulf Rapid Reef Assessment (AGRRA ) sites (Table 2).

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6 Table 1 Larger foraminiferal species are listed alphabetically by order with reference to species author, she ll composition and symbiont type. Order Species Reference Shell Composition Symbiont Miliolida Archaias angulatus Fichtel and Moll (1798) High Mg calcite, porcelaneous Chlorophyte Boreli s pulchra (1839) Diatom Broeckina orbitolitoides Hof ker (1930) Chlorophyte Cyclorbiculina compressa Chlorophyte Laevipeneroplis bradyi Cushman (1930) Chlorophyte Laevipeneroplis proteus Chlorophyte Peneroplis pertusus Forskl (1775) Rhodophyte Sorites margin alis Lamarck (1816) Dinoflagellate Rotaliida Amphistegina gibbosa Low Mg calcite, perforate wall Diatom Asterigerina carinata Diatom Gypsina sp. Unknown Heterostegina antillarium Diatom

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7 Tab le 2 Sampling sites are ordered by data set Reef type (Patch, P, Offshore Deep, OD, and Offshore Shallow, OS) is given along with respective locations in degrees and minutes, depth sampled (m), years sampled, sample source (or ne w unpublished data) and notes on the site history. Data Set Sites Type Latitude Longitude Depth (m) Years Sample source Site history Time series (quarterly) Conch Reef OS 24 57.369' N 80 27.443' W 10 1995 2000 Williams 2002 Foram bleaching Time serie s (quarterly) Conch Reef OD 24 57.113' N 80 27.082' W 18 1995 2000 Williams 2002 Foram bleaching Time series (quarterly) Conch Reef OD 24 57' N 80 27' W 30 1995 2000 Williams 2002 Foram bleaching Time series (quarterly) Tennessee Reef OS 24 44.6 99' N 80 46.87' W 8 1995 2000 Williams 2002 Foram bleaching Time series (quarterly) Tennessee Reef OD 20 1995 2000 Williams 2002 Foram bleaching Time series (quarterly) Alina's Reef P 25 23.185' N 80 09.775' W 6 8/2001 2/2003 Fisher 2007 Fisher 2007 Time series (quarterly) Algae Reef P 25 08.794' N 80 17.588' W 6 8/2001 2/2003 Fisher 2007 Fisher 2007 Time series (quarterly) White Banks P 25 02.243' N 80 22.513' W 6 8/2001 2/2003 Fisher 2007 Fisher 2007 Time series (quarterly) Three Sisters (KL 6m) P 25 01.105' N 80 23.852' W 6 8/2001 2/2003 Fisher 2007 Fisher 2007 Time series (quarterly) Rodriguez Key (KL3m) P 25 02.448' N 80 25.439' W 3 8/2001 2/2003 Fisher 2007 Fisher 2007 Time series (quarterly) Key Largo 9 m OS 25 00.146' N 80 23.626' W 9 8/2001 2/2003 Fisher 2007 Fisher 2007 Time series (quarterly) Key Largo 18 m OD 25 00.206' N 80 23.023' W 18 8/2001 2/2003 Fisher 2007 Fisher 2007 Summer only Alligator Reef OS 24 50.777' N 80 37.392 W 7.6 1996, 2006 07 Williams 2002 & new CREMP Summer only Alligator Reef OD 24 50.697' N 80 37.271' W 11.9 1996, 2006 07 Williams 2002 & new CREMP

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8 Summer only Carysfort Reef OS 25 13.282' N 80 12.603' W 4.3 1996, 2006 07 Williams 2002 & new CREMP Summer only Carysfort Reef OD 25 13.282' N 80 12.603' W 15.3 1996, 2006 07 Williams 2002 & new CREMP Summer only Conch Reef OS 24 57.369' N 80 27.443' W 6.7 1996, 2006 07 Williams 2002 & new CREMP Summer only Conch Reef OD 24 57.113' N 80 27.082 W 14.9 1996, 2006 07 Williams 2002 & new CREMP Summer only Looe Key Reef OS 24 32.687' N 81 24.484' W 8.2 1996, 2006 07 Williams 2002 & new CREMP Summer only Looe Key Reef OD 24 32.562' N 81 24.763' W 14.3 1996, 2006 07 Williams 2002 & new CREMP Summer only Molasses Reef OS 25 00.584' N 80 22.451' W 8.8 1996, 2006 07 Williams 2002 & new CREMP Summer only Molasses Reef OD 25 00.445' N 80 22.478' W 13.7 1996, 2006 07 Williams 2002 & new CREMP Summer only Sand Key Reef OS 24 27.111' N 81 52. 627' W 8.8 1996, 2006 07 Williams 2002 & new CREMP Summer only Sand Key Reef OD 24 27.083' N 81 52.781' W 11 1996, 2006 07 Williams 2002 & new CREMP Summer only Sombrero Reef OS 24 37.514' N 81 06.704' W 7.3 1996, 2006 07 Williams 2002 & new CREMP Summer only Sombrero Reef OD 24 37.373' N 81 06.640' W 16.2 1996, 2006 07 Williams 2002 & new CREMP Summer only Tennessee Reef OS 24 44.699' N 80 46.87' W 6.4 1996, 2006 07 Williams 2002 & new CREMP Summer only Tennessee Reef OD 24 45.166' N 80 4 5.456' W 13.7 1996, 2006 07 Williams 2002 & new CREMP Summer only Western Sambo Reef OS 24 28.750' N 81 43.041' W 7.3 1996, 2006 07 Williams 2002 & new CREMP Summer only Western Sambo Reef OD 24 28.750' N 81 43.041' W 12.8 1996, 2006 07 Williams 200 2 & new CREMP

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9 Summer only Eastern Sambo Reef OS 24 29.477' N 81 39.814' W 6.4 2006 2007 new CREMP Summer only Eastern Sambo Reef OD 24 29.293' N 81 39.955' W 15.3 2006 2007 new CREMP Summer only Rock Key OS 24 27.291' N 81 51.584' W 5.5 2006 2007 new CREMP Summer only Rock Key OD 24 27.193' N 81 51.408' W 13.3 2006 2007 new CREMP Summer only Grecian Rocks P 25 06.464' N 80 18.433' W 7 2006 2007 new CREMP Summer only Cliff Green P 24 30.208' N 81 46.073' W 6.7 2006 2007 new CREM P Summer only Dustan Rocks P 24 41.394' N 81 01.776' W 4 2006 2007 new CREMP Summer only East Washerwoman P 24 39.904' N 81 04.335' W 5.2 2006 2007 new CREMP Summer only Jaap Reef P 24 35.150' N 81 34.893' W 3.4 2006 2007 new CREMP Summer o nly Porter Patch P 25 06.199' N 80 19.459' W 5.5 2006 2007 new CREMP Summer only Turtle Patch P 25 17.757' N 80 13.048' W 5.2 2006 2007 new CREMP Summer only West Turtle Shoal P 24 41.960' N 80 58.025' W 7.6 2006 2007 new CREMP Summer only We st Washerwoman P 24 35.212' N 81 34.860' W 5.5 2006 2007 new CREMP Summer only Western Head P 24 29.863' N 81 48.337' W 9.2 2006 2007 new CREMP Summer only Admiral Patch P 25 02.730' N 80 23.654' W 4.3 2006 2007 new CREMP Summer only Long Ke y Patch P 24 47.832' N 80 47.047' W 4 2006 new CREMP Summer only Seagrass Patch P 24 29.465' N 81 40.711' W 5.2 2006 2007 new none Summer only Coral Gardens P 24 50.244' N 80 43.735' W 4.6 2006 new AGRRA Summer only Rodriguez Key P 25 02.448' N 80 25.439' W 3 2006 new Fisher 2007 Summer only Three Sisters P 25 01.105' N 80 23.852' W 6 2006 2007 new Fisher 2007 Summer only Algae Reef P 25 08.794' N 80 17.588' W 6 2006 2007 new Fisher 2007 Summer only White Banks P 25 02.243' N 80 22 .513' W 6 2006 2007 new Fisher 2007

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10 Questions & Hypotheses 1. Are there seasonal trends in LBF distribution s ? H o : There will be no seasonal trends in distribution. H 1 : I hypothesize that there will be seasonal trends in LBF distribution s correspond ing wi th reproductive cycles of individual species 2. Are there interannual trends in distribution? H o : There will be no interannual differences in LBF distributions. H 1 : There will be significant interannual differences. 3. Are there spatial trends in LBF distribut ion s ? H o : There will be no spatial trends in distribution. H 1 : I hypothesize that spatial distributions will be affected by the type of reef environment, such that groupings will depend on depth and distance from shore 4. Are there trends (spatial, depth, et c.) related to taxa of algal symbionts ? H o : There will be no distributional trends related to symbiont taxa. H 1 : I hypothesize that LBF distributional trends will be related to symbiont taxa.

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11 METHODS Sampling Data analyzed for this project were origina lly collected for several different studies at a variety of sites ( Table 2 ). The basic sample collection and processing methods are well established and previously described by Hallock et al ( 1995, 2006 ) Williams et al. ( 1997 ) Talge et al. ( 199 7 ) and o thers. To summarize, SCUBA divers collected three sets of three or four palm sized pieces of reef rubble into re sealable plastic bags at depth and brought them to the surface. The sealed plastic bags of rubble were placed into a covered bucket containin g ambient seawater to protect the specimens from exposure to high li ght intensities and temperature fluctuations until the samples could be processed. Each piece of rubble was carefully scrubbed with a toothbrush to remove microorganisms from the rock sur face. The resultant sediment organism slurry was decanted into a petri dish and placed into an incubator, maintained between 24 and 28 C depending on ambient seawater temperature, and on a 12 hour light/dark cycle. Taxa of interest ( Table 1 ) were isolat ed using forceps and placed into separate petri dishes containing seawater from the collection site. All living specimens were enumerated by species Densities for all species were calculated using the individual counts and area of bottom covered by rubb le samples which were estimated by analyzing digital images of each rock using Coral Point Count w/ Excel extensions (CPCe V3.4) software. Nearly quarterly from June 1995 to 2000, samples were collected at 10, 18 and 30m from Conch Reef, and 8m ( though a few samples were collected at 7 and 10m) and 20m from Tennessee Reef in the Florida Keys (Fig 1). Samples were a lso collected and processed during the summer of 1996 at nine offshore reefs each

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12 sampling site in the same manner as above. Sampling during the summers of 2006 and 2007 expanded on the number of offshore reefs as well as patch reefs surveyed (Table 2). The resulting data are hence referred to as Keys wide data. Data sets were similarly collected, processed and analyzed in 2001 03 from sites in Biscayne National Park and the upper Keys by Fisher ( 2007) and from Biscayne National Park by Ramirez (2008). Results from these studies also are inclu ded in my analyses. Limitations of the data set The data analyzed in this study were originally collected to assess bleaching responses in Amphistegina gibbosa Reef rubble, which typically provides suitable microhabitats for A. gibbosa was the only sub strate sampled and thus represents some degree of sampling bias. Rubble pieces were chosen as the sampling unit because they are easily collected with no damage to surrounding reef, and they provide a variety of microhabitats including turf algae, sedimen t and sometimes macroalgae on the upper surface, and coralline algae on the lower surface. The major substrates that this method undersamples are macrophytes, especially those that grow in sands such as seagrass. Thus, the data from this study provides no information on presence and abundance of LBF in seagrass, and is not representative of LBF abundances on other macrophytes or soft subst r ates.

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13 Figure 1 Florida Keys sampling sites listed by reef type: patch (P, triangles), o ffshore shallow (OS, squares) and offshore deep (OD, circles) and set within the context of benthic habitat type (from Florida Fish and Wildlife Conservation Commission National Ocean Service, 1998 ) : bare substrate, seagrass, hardbottom with seagrass, hard bottom, platform mar gin reef and patch reef using ArcMap (v. 9.2) Some sites appear to overlap due to the map scale. Note: the original document contains color that is necessary for understanding the data presented here. The original thesis is on file with the USF library in Tampa, Florida.

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14 Statistical a nalysis The statistical methods used in this study are similar to those by Fisher (2007), i.e., two way analysis of similarities (ANOSIM2) to determine if LBF assemblages differ significantly among site s (averaged over the entire study period) and times (averaged across all sites). The ANOSIM procedure produces an R statistic between 1 and +1, where zero represents the null hypothesis or no difference among samples. Pairwise tests indicate the degree of sep aration between groups by the R statistic, which describes the difference between groups and ranges from 0 (indistinguishable) to 1 ( variation within groups is less than the variation between groups ), as well as the significance level. I interpreted both values when determining significant differences between groups according to the recommendations of Clarke & Gorley ( 200 6 ) In gen eral, comparisons with higher R values (>0.75 well separated ) and low er p values (<0.0 1 ) were recognized as str ong diff erences, while weaker R values (<0.25 not well distinguished ) and low p values (<0.05) were still considered significant, yet without full confidence. Intermediate R values (>0.5) indicated that groups were separate, but somewhat overlapping. Data from C onch and Tennessee reefs were analyzed by depth, season and year For Keys wide sites data were analyzed by region and reef type Bray Curtis similarity matrices were calculated for all log (x+1) tra nsformed LBF densities and multi dimensional scaling (M DS) plots were used to determine how sites cluster ed based on densities of all LBF species For an MDS plot, the proximity between sites represented similarity and a stress level of <0.2 was considered to be a useful representation of relationships (Clark e and Warwick 2001). S imilarity percentages (SIMPER) analyses allowed the species primarily responsible for site clustering to be determined (Clarke and Warwick, 2001). In addition, a metadata analysis of summer only data from the Conch and Tennessee ree fs, Keys wide, Fisher (2007) and Biscayne National Park (Ramirez, 2008 ) data sets was performed using this same procedure.

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15 Evenness ( E ) is a measure of biodiversity that expresses how numerically equal a community of species is giving a value between zero (very unequal) and one (numbers of all species are equal) I c alculated evenness from the Shannon Index (Shannon, 1948) using SSC Divers ity Index Calculator, an Excel a dd in script (see Appendix A for relevant equations), for Conch and Tennessee reefs to look at LBF assemblage structure over time from 1995 2000 as well as for Keys wide sites to look at LBF assemblage structure across the full extent of the Florida reef tract for 2006 and 2007. A mphistegina gibbosa density was regressed with evenness to e xamine how this dominant species might affect LBF assemblage structure. Also, normally distributed mean E values were analyzed using a two way analysis of variance ( ANOVA ) followed by the Tukey Kramer HSD multiple comparison test. Comparisons resulting i n a p value greater than 0.05 were considered non significant. Evenness means with three or fewer reefs sampled (i.e. low sample size) were excluded from analysis (e.g. offshore shallow and deep reefs in 2001, 2002 and in 2004). The BIOENV or BEST analy sis method (Clarke and Ainsworth, 1993) was implemented using PRIMER v 6 (Plymouth Routines in Multivariate Ecological Rese arch PRIMER E Ltd., Plymouth). This procedure all ows the matching of biotic datasets between the multivariat e patterns of the assemblage s The extent to which the patterns match reflects how well one dataset explain s the other I compared patterns in percent coral cover and decline (collected by the Coral Reef Evaluation and Monitoring Program, CREMP) with pat terns in LBF species density (from Keys wide sites corresponding to CREMP sites) and regression analysis to determine relationships. All ANOSIM2, ANOSIM, MDS and SIMPER analyses were performed using PRIMER ANOVA analysis was performed using XLSTAT softwa re (Addinsoft version 2008.3.01) Arc Map (v. 9.2) was used to visualize distribution patterns.

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16 R ESULTS Time series analysis Conch Reef LBF assemblages at Conch Reef (1995 2000) primarily varied with sa mpling depth ( averaged across all years; ANOSIM 2 : Global R= 0.64 p=0. 00 1) with significant differences at each depth ( Table 3 ). LBF densities also varied according to season (averaged across all years; ANOSIM 2 : Global R=0.07 p=0. 00 7) with significant differences between summer and winter assemblages (Ta ble 4 ). Table 3 ANOSIM2 results for differences between sampling depths based on LBF densities (across all years) for Conch Reef (1995 2000); Global R=0.644, starred values are significant at p < 0.0 01 10m 18m 30m 10m 18m 0.77 4 30m 0.783 0.376 Table 4 ANOSIM 2 results for differences between seasons based on LBF densities (across all years) for Conch Reef (1995 2000); Global R=0.073, starred values are significant at p<0.05. Non significant val ues are represented by n.s. Summer Fall Winter Spring Summer Fall 0.095* Winter 0.145* n.s Spring 0.087* 0.080* n.s. Bray Curtis an alysis of transformed (log x+1) LBF densities at C onch Reef (1995 2000) revealed that species tended to clus ter based on abundance with more dominant species grouping together and less abundant species forming a second cluster ( Fig. 2 ). The two most abundant

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17 species, A mphistegina gibbosa and L aevipeneroplis proteus were paired together with greater t han 80% similarity in the resultant Bray Curtis dendrogram. MDS analysis showed that LBF assemblages were distinct by sampling depth at 10m, 18m and 30m (Fig. 3). S a m p l e s A. angulatus A. gibbosa L. proteus A. carinata L. bradyi H. antillarium B. orbitol itoides C. compressa Gypsina S. marginalis P. pertusus B. pulchra 100 80 60 40 Similarity Figure 2 Bray Curtis dendrogram of LBF assemblage across all depths sampled (10m, 18m and 30m) at Conch Reef (1995 2000). More Abundant Less Abundant

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18 Figure 3 MDS plot for Conch Reef (1995 2D Stress: 0 16 SIMPER analysis by sampling depth showed that the 10m, 18m and 30m sites all exhibited about 81% within depth similarity (Table 5 ). The species most consistently responsible for the high degree of similarity within each depth were A. gibbosa and L. proteus which contributed 20 29% and 16 18% for all depths, respectively. The 10m and 18m sites were the most dissimilar (28%), while the 18m and 30m sites were least dissimilar ( 22 %, Table 6 ). The species most consistently responsible for the dissimilarity between depths were A rchaias angulatus Fichtel and Moll and C yclorbiculina compressa which contributed 16.5 25% and 12 18% across all depths, respectively.

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19 Table 5 SIMPER results by sampling depth (10m, 18m and 30m) at Conch Reef (1995 2000) showing average percent similarity for each depth, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity wi thin each depth. Gray shading indicates those species responsible for contributing greater than 10% to the similarity between each depth. 10m 18m 30m Average similarity: 82.9% Average similarity: 80.5% Average similarity: 81.8% Species Av.Abund %Con Spe cies Av.Abund %Con Species Av.Abund %Con A. gibbosa 4.74 19.6 A. gibbosa 4.68 28.2 A. gibbosa 5.45 29.5 L. proteus 3.94 16.0 L. proteus 3.12 17.6 L. proteus 3.48 18.0 A. angulatus 3.64 13.7 A. carinata 2.51 13.2 H. antillarium 2.08 10.3 C. compressa 3. 58 13.5 H. antillarium 1.74 9.4 C. compressa 2.49 9.68 A. carinata 2.2 8.06 L. bradyi 1.52 6.95 A. carinata 1.84 7.7 H. antillarium 1.7 6.22 P. pertusus 1.16 5.61 L. bradyi 1.65 7.61 B. orbitolitoides 1.93 5.73 C. compressa 1.19 5.38 B. orbitolitoides 1 .92 7.57 P. pertusus 1.35 4.35 B. orbitolitoides 1.02 3.55 S. marginalis 1.39 4.12 A. angulatus 0.87 3.21

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20 Table 6 SIMPER dissimilarity results by sampling depth (10m, 18m and 30m) at Conch Reef (1995 2000) showing ave rage percent dissimilarity between sampling depth s average abundances (count/100 cm 2 ), and percent contribution for species contributing to dissimilarity between each depth. Gray shading indicates those species responsible for contributing greater than 1 0% to the dissimilarity between each depth. 10m & 18m 10m & 30m 18m & 30m Average dissimilarity = 28% Average dissimilarity = 26.4% Average dissimilarity = 22.4% Species 10m 18m %Con Species 10m 30m %Con Species 18m 30m %Con A. angulatus 3.64 0.8 7 21.3 A. angulatus 3.64 0.42 24.9 C. compressa 1.19 2.49 16.5 C. compressa 3.58 1.19 18.7 C. compressa 3.58 2.49 12.0 B. orbitolitoides 1.02 1.92 13.2 B. orbitolitoides 1.93 1.02 9.66 S. marginalis 1.39 0.32 8.74 A. carinata 2.51 1.84 11.5 S. marginali s 1.39 0.41 8.05 B. orbitolitoides 1.93 1.92 8.62 A. gibbosa 4.68 5.45 9.76 L. proteus 3.94 3.12 7.65 A. carinata 2.2 1.84 7.01 L. proteus 3.12 3.48 7.71 A. carinata 2.2 2.51 6.66 A. gibbosa 4.74 5.45 6.92 L. bradyi 1.52 1.65 7.55 B. pulchra 1.18 0.61 5 .75 B. pulchra 1.18 0.58 6.16 A. angulatus 0.87 0.42 6.92 L. bradyi 1.16 1.52 5.44 P. pertusus 1.35 0.7 6.02 P. pertusus 1.16 0.7 6.64 A. gibbosa 4.74 4.68 5 L. proteus 3.94 3.48 5.66 H. antillarium 1.74 2.08 6.43 P. pertusus 1.35 1.16 4.81 L. bradyi 1. 16 1.65 5.25 B. pulchra 0.61 0.58 5.17

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21 Amphistegina gibbosa densities varied from < 100 to 650 per 100cm 2 from 1995 2000 (Fig. 4 ) At both 10m and 18m sites, densities were relatively low (0 200 per 100cm 2 ) from 1995 1996, but increased to 300 400 per 100cm 2 during 1997 only to crash again in mid 1998. Densities again remained low until the end of 1999 At 30m, A. gibbosa densities were generally higher than at the shallower sites, reaching the highest densities of 500 per 100cm 2 at the end of 1997 a nd declining by half in 1998, though densities did not go as low as populations in shallower waters (<100 per 100cm 2 )

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22 Figure 4 Amphistegina gibbosa density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 3 0m sites, N=2) with standard error bars at Conch Reef (CR): 10m ( ), 18m ( ) and 30m ( ) sites and Tennessee Reef (TN) : sites from 1995 2000. Laevipeneroplis proteus densities seemed to vary seasonally at Conch Reef, rarely dropping below 10 individuals per 100cm 2 and reaching mid summer highs of 70 to 110 per 1995 1996 1997 1998 1999 2000 CR TN A. gibbosa density (per 100cm 2 )

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23 100cm 2 for all depths from 1995 2000 (Fig. 5 ) The 18m site had lower densities (usually <50 per 100cm 2 ) than the 10m and 30m sites. A rchaias angulatus densities also varied seasonally at the Conch Reef 10m site with peaks occurring in Septemb er (usually 75 to 200 per 100cm 2 ) from 1995 2000 (Fig. 6 ) Populations at both 18m and 30m sites were extremely low at less than 5 individuals per 100cm 2 Cyclorbiculina compressa densities ranged from 20 to 80 per 100cm 2 at the Conch Reef 10m site with out a regular seasonal trend (Fig. 7 ) The highest peak was in 1996 with 160 per 100cm 2 Densities at the deeper 18m and 30m sites were generally lower than at the 10m site Densities at the 30m site were similar to the 10m site, but suddenly dropped in 1998 to less than 10 per 100cm 2 and did not recover by early 2000 The 18m site had the lowest densities overall (typically <5 per 100cm 2 ) from 1999 2000. Densities of A sterigerina carinata g n y were quite variable for all depths at Conch Reef (Fig. 8 ) Densities were highest for the 10m and 18m sites (10 40 per 100cm 2 ). Also, abundance peaks varied by season and depth. Densities of A. carinata peaked in spring at the 30m site, but in fall at the 18m site from 1997 2000 Densities at the 10m site tended to have very subtle peaks between the 18m and 30m peaks. The depth distribution of H eterostegina antillarium was similar to A mphistegina gibbosa in that densities were highest at the 30m site though no clear seasonal trend was observed ( Fig. 9 ) In general, d ensities varied between 5 and 15 per 100cm 2 for the 30m site, 2 and 15 per 100cm 2 for the 18m and 10m site Densities of B roeckina orbitolitoides Hofker were highest at the 30m site and densities for all sites were typically between 5 and 50 per 100cm 2 from 1995 1998 (Fig. 1 0 ). After 1998, densities did not exceed 15 per 100cm 2 L ess abundant species, including L aevipeneroplis bradyi Cushman P eneroplis pertusus Forsk l Sorites marginalis Lamarck B orelis pulchra g n y and Gy psina sp were typically present at less than 10 per 100 cm 2 (Appendi ces B and C ).

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24 Figure 5 Laevipeneroplis proteus density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard er ror bars at Conch Reef (CR): 10m ( ) sites and Tennessee Reef (TN) sites from 1995 2000 Note: scales are different. 1995 1996 1997 1998 1999 2000 CR TN L. proteus density (per 100cm 2 )

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25 Figure 6 Archaias angulatus density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m a nd 30m sites, N=2) with standard error bars at Conch Reef (CR): 18m ( ) sites and Tennessee Reef (TN) sites from 1995 2000 Note: scales are different. 1995 1996 1997 1998 1999 2000 CR TN A. angulatus density (per 100cm 2 )

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26 Figure 7 Cyclorbiculina comp ressa density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch Reef (CR): ) sites and Tennessee Reef (TN) sites from 1995 2000 Note: scales a re different. 1995 1996 1997 1998 1999 2000 CR TN C. compressa density (per 100cm 2 )

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27 Figure 8 Asterigerina carinata density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch Reef (CR): ) sites and Tenne ssee Reef (TN) sites from 1995 2000 199 5 1996 1997 1998 1999 2000 CR TN A. carinata density (per 100cm 2 )

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28 Figure 9 Heterostegina antillarium density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch Reef (C R): ) sites and Tennessee Reef (TN) sites from 1995 2000 1995 1996 1997 1998 1999 2000 CR TN H. antillarium density (per 100cm 2 )

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29 Figure 10 Broeckina orbitolitoides density means (per 100cm 2 N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch Reef (CR): ) sites and Tennessee Reef (TN) sites from 1995 2000 Note: scales are different. 1995 1996 1997 1998 1999 2000 CR TN B. orbitolitoides density (per 100cm 2 )

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30 Evenness ( E ) plots over time exhibited a somewhat cyclical pattern at all depths that did not seem to follow any strong linear trends (R 2 <0.25 for all depths, Fig. 11 ). Figure 11 Mean evenness ( E ) of LBF assemblage with standard error bars (N=3, except April 1997 for Conch Reef 18m and 30m sites, N=2) at Conch Reef (CR): ( ) sites and Tennessee Reef (TN) sites from 1995 2000 The overall mean trend show s that E was highly variable from 1995 to 2000. At the 30m site, the mean E decreased from about 0.5 to about 0.3 from 1995 19 99, but increased to 0.5 in 2000. 1995 1996 1997 1998 1999 2000 CR TN Mean evenness ( E )

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31 Meanwhile, the 10m and 18m sites seemed to decline slightly less, but had more dramatic changes in evenness. These sites were consistently higher in evenness than the 30m site with a few exceptions. Evenness and A. gibbo sa density at all depths were negatively related (R 2 =0. 36 Fig. 1 2 ). Figure 12 Evenness ( E ) plotted against A. gibbosa densities with linear regression for combined 10m, 18m and 30m depths at Conch Reef (R 2 = 0.36). Linear r eg ressions applied to individual depths (Fig. 13) showed a negative relationship at the 10m site (R 2 =0. 44 ) and the 18m site (R 2 =0.3 9 ). Amphistegina gibbosa densities at the 30m site had a weaker negative relationship to evenness (R 2 =0.1 8). No other speci es had a strong relationship with evenness. Furthermore, evenness was calculated excluding A. gibbosa densities. The evenness of the other taxa averaged about 0.72 and when regressed with A. gibbosa density, there was no relationship (r 2 = 0).

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32 Figure 13 Evenness ( E ) plotted against A. gibbosa densities with individual linear regressions for 10m, 18m and 30m depths at Conch Reef with R 2 = 0.44, 0.39 and 0.18, respectively. Tennessee Reef LBF assemblages at Tennessee Reef (1995 2000) primarily varied with sa mpling depth (averaged across all years; ANOSIM 2 : Global R=0. 9 p=0.001 ) with significant di fferences between depth s LBF densities did not var y with se ason (averaged across all years ). Bray Curtis analysis of transformed (l og x+1) LBF densities grouped species by abundance ( Fig. 1 4 ). Though still highly abundant A. gibbosa and L. proteus were not directly paired with each other in the resultant Bray Curtis dendrogram. Amphistegina gibbosa stood out alone with only about 4 5% similarity to the other species distributions.

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33 Figure 14 Bray Curtis dendrogram of LBF assemblage across all depths sampled ( 8 m and 20m) at Tennessee Reef (1995 2000). B. orbitolitoides P. pertusus S. marginalis B. pulchra L. bradyi Gypsina A. gibbo sa C. compressa A. carinata A. angulatus L. proteus H. antillarium S a m p l e s 100 80 60 40 20 0 Similarity More Abundant Less Abundant

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34 Further MDS analysis showed that LBF assemblages exhibited strong grouping by sampling depth ( Fig 1 5 ). Figure 15 MDS plot for Tennessee Reef (19 95 2000) by sampling depth: 8 2D Stress: 0 0 9. assemblages at both Conch and Tennessee reefs overlap each other while the deep (20m) Tennessee R eef sites are distinct from both the 18m and 30 m Conch Reef sites (Fi g 1 6 )

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35 Figure 16 MDS plot by sampling depth for Conch Reef (CR) sites and Tennessee Reef (TN) 8 m ( ) and 20m ( 1995 2000. 2D Stress: 0 12. SIMPER analysis by sampling depth further confirmed the MDS groupings and showed that the 8 m and 20m sites exhibited about 75% within depth similarity (Table 7 ). The taxa most consistently responsible for the high degree of similarity among depths were A. gibbosa and L. proteus which contributed 25 66% and 10 13% at both depths, respectively. The dissimilarity between the 8 m and 20m sites was nearly 50% and a result of diff erences in the densities of C compressa (18%) A sterigerina carinata (17%) A rchaias angulatus ( 16 %) and L. proteus (11 %) all of which were much less common at the deep site than at the shallow site.

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36 Table 7 SIMPER results by sampling depth (8m and 20m) at Tennessee Reef (1995 2000) showing average percent similarity (dissimilarity) within each depth average abundances (count/100 cm 2 ), and percent contribution for taxa contributing to similarity (dissimilarity) for each depth. Gray shading indicates those species responsible for contributing greater than 10% to the similarity (dissimilarity) between each depth. 8m 20m Average similarity: 74.6% Average similarity: 75.3% Species Av.Abund %Con Species Av.Abund %Con A. gibbosa 4.67 25.0 A. gibbosa 4.89 66.5 A. carinata 2.82 15.6 H. antillarium 1.2 12.4 L. proteus 2.55 13.0 L. proteus 1.24 10.7 C. c ompressa 2.79 12.4 Gypsina 0.52 4.33 A. angulatus 2.39 10.9 H. antillarium 1.77 8.95 P. pertusus 1.24 5.6 8m & 20m Average dissimilarity = 48.4% Species 8m 20m %Con C. compressa 2.79 0.1 18.1 A. carinata 2.82 0.37 17.1 A. angulatus 2 .39 0.08 15.7 L. proteus 2.55 1.24 10.5 A. gibbosa 4.67 4.89 9.53 P. pertusus 1.24 0.16 7.53 H. antillarium 1.77 1.2 5.62 B. pulchra 0.79 0.05 4.93 S. marginalis 0.59 0.09 3.9 In general, species densities were quite variable, particularly for the shallow site. Amphistegina gibbosa densities varied from <100 to 7 00 per 100cm 2 for the shallow site and <100 to 300 per 100cm 2 at the deep site ( Fig. 4 ). At the shallow site, d ensities were very low (<100 per 100cm 2 ) from 1995 1996 but then rapid ly incr ease d to 800 1000 per 100cm 2 in 1997. As at Conch Reef, the A. gibbosa population crash ed in 1998. Densities climbed to nearly 500 per 100cm 2 in 1999 and fell again, remain ing relatively low into 2000. At the deep site A. gibbosa densities were higher than at the shallow site until the summer of 1997, after which they

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37 followed a similar pattern as at the shallow site, though not to the same degree of intensity and maintained relatively low er densities Densities of L. proteus at the Tennessee Reef shall ow and deep sites were characterized by summer peaks and occasiona l winter peaks (Fig. 5 ). There were usually less than 30 per 100cm 2 with the 20m populations always smaller than the 8m populations. A seasonal trend was not observed for Archaias angulat us at Tennessee Reef ( Fig. 6 ). Densities at the shallow site were typically less than 20 per 100cm 2 but peaked in 1999 to 86 per 100cm 2 Archaias angulatus was nearly absent from the deep site and appeared only in six samples in extremely low densities (1 2 per 100cm 2 ) over the six year sampling period. Cyclorbiculina compressa tended to peak in abundance during winter at the Tennessee Reef shallow site, except for 1999 when abundanc e peaked in early summer (Fig. 7 ). Two very high peaks occurred in the winters of 1996 and 1998 and densities were just over 100 per 100cm 2 Excepting these two high peaks, abundances were generally below 40 per 100cm 2 At the deep site, C. compressa was absent or found in extremely low abundance (1 2 per 100cm 2 ). Asteriger ina carinata densities varied between 10 and 40 per 100cm 2 at the shallow site peaking in June from 1997 2000 (Fig. 8 ). The deep site densities were extremely low throughout (<5 per 100cm 2 ). Heterostegina antillarium did not have a consistent seasonal pa ttern of abundance at either the shallow or deep sites (Fig 9 ). Densities at the shallow site were typically less than 10 per 100cm 2 though a strong winter peak was observed in early 1998 of 23 per 100cm 2 Densities at the deep site were typically less than 5 per 100cm 2 Broeckina orbitolitoides was rare at both shallow and deep sites (Fig. 1 0 ). O ther less abundant taxa including L. bradyi P. pertusus S. marginali s Gypsina and B orelis pulchra were typically present in abundances of less than 5 per 100 cm 2 (Appendices B and C ).

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38 Evenness ( E ) plots ove r time for shallow ( 8 m) and deep (20m) depths did not seem to follow any strong linear trends (R 2 <0.08; Fig. 11 ). Evenness at the shallow site was consistently higher than at the deep site and maintained a high E of 0.7 to 0.8 from 1995 1996. Evenness dropped in 1997 to about 0.3 and steadily increased into 2000. At the deep site, evenness was low overall and varied between 0.1 and 0.4. In contrast with Conch Reef, e venness and A. gibbosa den sity across all depths were not related at Tennessee Reef (R 2 = 0.06, Fig. 1 7 ). Figure 17 Combined linear r egression for both shallow (8 m) and deep (20m) sites at Tennessee Reef (R 2 = 0.06). However, linear and log regression s applied to shallow and deep depths respectively showed negative relationships (shallow R 2 = 0.52, deep R 2 = 0.55; Fig. 18) on par with those observed at Conch Reef.

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39 Figure 18 Linear and logarithmic regression for Tennessee Ree f at shallow (8 m) and deep (20m) sites (R 2 = 0.52 and 0.55, respectively). Keys wide analysis LBF densities & symbiont analysis LBF assemblages among Keys wide sites (1995, 1996, 2006, 2007) primarily varied by reef type (averaged across all regions; ANOS IM2: Global R=0.24 p=0. 00 1) with significant differences between each type (Table 8 ). This in turn was largely affected by habitat depth. Table 8 ANOSIM2 results for differences between reef types (offshore shallow, OS, offshore deep, OD and patch, P) based on LBF densities (across all regions) for Keys wide sites (1995, 1996, 2006, 2007); Global R=0.236. Starred values are significant at p< 0.01. OS OD P OS OD 0.123* P 0.313* 0.306* A second factor affecting LBF densi ties was region (averaged across all reef types ; ANOSIM2: Global R=0. 13 p=0. 00 3 ; Table 9 ). Pairwise comparisons revealed the middle and upper Keys

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40 sites to be most significantly different, while the middle and lower Keys sites were not significantly d iff erent from each other (p=0.5 8) Table 9 ANOSIM2 results for differences between regions (upper, middle and lower Keys) based on LBF densities (across all reef types) for Keys wide sites (1995, 1996, 2006, 2007); Global R=0.132. St arred values are significant at p<0.05. Non significant values are represented by n.s. Lower Middle Upper Lower Middle n.s. Upper 0.098* 0.55* Bray Curtis analysis of transformed (log x+1) summer only data revealed that species tended to clus ter based on abundance ( Fig. 1 9 ). The four consistently most abundant species, Amphistegina gibbosa L. proteus Archaias angulatus and C. compressa formed the dominant cluster at >60% similarity. Cluster analysis also grouped the less abundant taxa at about < 60% similarity, except for Gypsina which represented an outlier. More Abundant Less Abundant

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41 Some species densities were significantly different between region s or reef type s (Table s 10 and 11 ). LBF densities were also highly variable by s ite and among replicates for 1995, 1996, 2006 and 2007 ( see Appendices D and E ). A series of one way ANOSIMs by year showed that, for many species, 2006 or 2007 proved to be years with significantly higher sum mer abundances than in 1995 or 1996, including A rchaias angulatus (ANOSIM2: Global R =0.1 6 p=0.001), B. orbitolitoides ( ANOSIM : Global R=0.1 3 p=0.004), C. compressa ( ANOSIM : Global R= 0.08 p=0.0 2 ), L. proteus ( ANOSIM : Global R= 0.06 p= 0.05 ), P. pertusus ( ANOSIM : Global R= 0.19 p= 0.001 ) and S. margina lis ( ANOSIM : Global R= 0.06 p= 0.04 ; Table 10) In general, LBF abundances in summer 2006 were not different from those in summer 2007, with the exception of A. gibbosa L. p roteus A. angulatus C. compressa B. pulchra B. orbitolitoides A. carinata L. bradyi S. marginalis P. pertusus H. antillarium Gypsina 100 80 60 40 20 Similarity Figure 19 Bray Curtis dendrogram of LBF assemblage across all years sampled at all Keys wide sites. More Abundant Less Abundant

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42 P. pertusus whose abundance declined significantly from 2006 to 2007. A series of two way ANOSIM s (reef type by year and region by year ) for each species showed few differences between reef types, with the exception of Asterigerina carinata (ANOSIM2: Global R=0.09, p=0.01) H. antillarium (ANOSIM2: Global R=0.06, p=0.04) and S. marginalis (ANOSIM2: G lobal R=0.15, p=0.001) whose abundances were significantly lower at patch reefs than at offshore shallow sites. Sorites marginalis was also lower at offshore deep sites than at offshore shallow sites (p=0.001)

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43 Table 10 Summary of analysis of similarity (ANOSIM) tests for Keys wide summer data by region (upper, middle and lower Keys, across all years) and reef type (offshore deep, OD, offshore shallow, OS, and patch, P, reefs, across all years) and by year (1995, 1996, 2006 and 2 007, across all sites). Tests that supported the null hypothesis, indicating that no differences were found between groups, are denoted by n.s. (not significant). Starred differences are significant at p<0.05 and double starred differences are significan t at p<0.01. Summary of Analysis of Similarity Species Region Reef Type Year Amphistegina gibbosa n.s. n.s. n.s. Archaias angulatus Middle
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44 Table 11 Summary of untransformed LBF density means SE across all years for Keys wide summer only data. Density Means Species Region Reef Type Upper Middle Lower OD OS P Amphisteg ina gibbosa 119.9 16.0 144.8 21.2 90.0 12.4 150.4 19.8 128.1 15.0 70.2 12.1 Archaias angulatus 32.0 8.3 8.2 1.9 20.1 5.6 6.2 2.4 21.1 4.1 33.4 8.8 Asterigerina carinata 7.1 1.9 13.6 3.8 3.2 0.9 7.5 2.1 13.6 3.5 2.0 0.7 Borelis pulchra 2.9 0.6 1.4 0.3 0. 7 0.2 1.6 0.5 2.2 0.4 1.1 0.3 Broeckina orbitolitoides 9.3 2.1 1.7 0.6 3.1 0.7 5.9 1.6 3.8 1.1 3.9 1.4 Cyclorbiculina compressa 15.4 4.9 1 1 3 3.0 22.6 6.2 20.7 6.4 19.0 3.3 9.4 4.4 Gypsina 1.2 0.3 0.8 0.1 0.6 0.1 0.8 0.1 0.7 0.2 1.0 0.2 Heterostegina a ntillarium 5.0 0.9 4.5 0.6 3.9 0.6 4.9 0.7 6.0 0.8 2.2 0.4 Laevipeneroplis bradyi 7.1 1.3 2.7 0.8 3.4 0.7 5.1 1.3 4.6 0.7 3.1 0.8 Laevipeneroplis proteus 45.0 4.8 28.3 4.8 26.9 4.9 33.5 5.4 40.4 4.6 24.3 4.5 Peneroplis pertusus 4.7 0.7 3.1 0.7 1.8 0.3 2 .7 0.6 3.7 0.7 3.0 0.5 Sorites marginalis 3.0 0.6 2.6 0.6 3.9 0.8 1.8 0.4 6.0 0.8 1.5 0.3

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45 Of the diatom bearing species, only B. pulchra densities were significantly different between regions, being more abundant in the upper Keys than the middle and lo wer Keys across all years (ANOSIM2 : Global R = 0.07, p= 0.04). Contrastingly, several chlorophyte bearing species seemed to be in lower abundance in the middle Keys and in higher abundance i n the lower or upper Keys, including Archaias angulatus (ANOSIM2: Global R = 0.08 p= 0.03), Broeckina orbitolitoides (ANOSIM2: Global R = 0. 11 p= 0.002) across all years (Appendix D ). Additionally P. pertusus was less abundant in the middle Keys than in the upper Keys (ANOSIM2: Global R = 0.06, p=0.04). A series of two way ANOSIM s revealed a significant effect of region for diatom ( Global R=0.0 8, p=0. 02) chlorophyte ( Global R=0. 18, p=0. 001) and dinoflagellate ( Global R=0.0 6, p=0. 04 ) bearing species across all years ( Fig. 20 Table 12 ) Pairwise comparisons showed t hat diatom bearing foraminifers comprised a significantly higher proportion of the total LBF assemblage in the middle Keys (0.770.03) than in the upper Keys (0.550.03). The proportion of diatom bearer s in the lower Keys (0.630.04) was not significantly different from either the middle or upper Keys. In contrast, the proportion of chlorophyte bearer s was significantly lower in the middle Keys ( 0.190.02 ) than in the upper ( 0.4 2 0.0 3 ) or lower Keys ( 0.34 0.0 4 ). Dinoflagellate bearer s consistently made u p a small proportion of the tot al assemblage, yet were significantly higher in the lower Keys ( 0.020.00 ) than in the upper Keys ( 0.010.00 ). The proportion of dinoflagellate bearer s in the middle Keys ( 0.010.00 ) was not significantly different from eith er the lower or upper Keys. Rhodophyte bearer s also constituted a small proportion of the total assemblage in the lower ( 0.010.00 ), middle ( 0.020.01 ) and upper ( 0.020.00 ) Keys. There was no significant effect of region for this symbiont type. Across all regions, there was no effect of year on the proportions for any of the symbiont types.

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46 Table 12 Mean proportion of total assemblage by symbiont type with standard error for Keys wide sites. Overall means are given as well as for each region and reef type in 1995 : lower (N=4) and middle (N=4) Keys, offshore deep, OD (N=4) and offshore shallow, OS (N=4); 1996 : lower (N=4), middle (N=6) and upper Keys (N=4), offshore deep, OD (N=7) and offshore shallow, OS (N=7) reefs; and 2006 a nd 2007 : lower (N=13), middle (N=9) and upper Keys (N=15), offshore deep, OD (N=11); offshore shallow, OS (N=11); and patch, P (N=15) reefs. Mean Proportion of Total Assemblage Region Reef Type Overall Lower Middle Upper OD OS P Diatom 2007 0.60 0.04 0.490.06 0.830.09 0.560.04 0.700.05 0.570.05 0.550.07 2006 0.610.04 0.640.08 0.700.08 0.520.05 0.660.05 0.560.04 0.600.08 1996 0.750.04 0.860.11 0.790.06 0.600.08 0.810.05 0.700.07 1995 0.790.04 0.790.08 0.790.08 0.870.03 0.710.06 all years 0.630.04 0.770.03 0.550.03 0.730.03 0.610.03 0.580.05 Chlorophyte 2007 0.370.04 0.470.07 0.140.08 0.410.04 0.280.05 0.390.05 0.410.07 2006 0.350.04 0.320.07 0.240.09 0.440.05 0.300.05 0.380.03 0.360.08 1996 0.230.04 0.120.11 0.200.06 0.390.08 0.180.05 0.280.07 1995 0.180.04 0.170.08 0.190.08 0.110.03 0.250.05 all years 0.340.04 0.190.02 0.420.03 0.250.03 0.350.03 0.380.05 Rhodophyte 2007 0.0110.002 0.0090.002 0.0080.002 0.0160 .003 0.0080.003 0.0110.003 0.0140.003 2006 0.0250.004 0.0130.004 0.0450.012 0.0240.003 0.0230.004 0.0210.005 0.0290.009 1996 0.0080.002 0.0070.007 0.0090.003 0.0080.004 0.0030.001 0.0130.003 1995 0.0150.005 0.0200.006 0.0110.006 0. 0090.004 0.0220.007 all years 0.0110.002 0.0200.005 0.0180.002 0.0120.002 0.0160.002 0.0220.005 Dinoflagellate 2007 0.0140.002 0.0170.003 0.0110.004 0.0130.005 0.0060.002 0.0270.005 0.0100.002 2006 0.0170.003 0.0240.007 0.0110.004 0.0140.003 0.0120.003 0.0350.007 0.0070.001 1996 0.0040.001 0.0070.004 0.0040.002 0.0020.002 0.0030.001 0.0060.002 1995 0.0150.004 0.0200.005 00.0110.005 0.0100.005 0.0210.006 all years 0.0190.003 0.0100.002 0.0120.002 0.0080. 001 0.0240.003 0.0080.001

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47 Symbiont Region Dinoflagellate Group Rhodophyte Group Chlorophyte Group Diatom Group Lower 0.020.00 a 0.010.00 a 0.340.04 a 0.630.04 ab Middle 0.010.00 ab 0.020.01 a 0.190.02 b 0.770.03 a Upper 0.010.00 b 0.0 20.00 a 0.420.03 a 0.550.03 b p level 0.038 n.s. 0.001 0.019 Figure 20 Mean proportion of total assemblage for each symbiont type with standard error bars for summer only assemblage data (across all years) plotted by re gion: lower (N=34) middle (N=28) and upper (N=34) Keys. Means SE are listed below the figure for each symbiont : D inoflagellate (solid white) and R hodophyte (solid gray), C hlorophyte (crossbar pattern) D iatom (diagonal stripes) Significant difference s between regions within each symbiont type are indicated by different group letters. Non significant results within a symbiont type are denoted by n.s. A series of two way ANOSIMs (reef type by year) revealed that the proportion of the total assemblage for each symbiont type did not significantly vary among reef types, with the exception of dinoflagellate bearer s ( Global R=0. 15 p=0. 001) (Fig. 21, Table 1 2 ). Pairwise comparisons showed that the proportion of dinoflagellate bearer s was significantly hig her at offshore shallow sites ( 0.020.0 0 ) than offshore deep ( 0.010.00 ) or patch ( 0.010.00 ) reefs. Proportion of t otal assemblage

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48 Symbiont Reef type Dinoflagellate Group Rhodophyte Group Chlorophyte Group Diatom Group OD 0.010.00 a 0.010.00 a 0.250.03 a 0.730.03 a OS 0.02 0.00 b 0.020.00 a 0.350.03 a 0.610.03 a P 0.010.00 a 0.020.01 a 0.380.05 a 0.580.05 a p level 0.001 n.s. n.s. n.s. Figure 21 Mean proportion of total assemblage for each symbiont type with standard error bars for s ummer only assemblage data (across all years ) plotted by reef type : offshore deep (OD, N=33), offshore shallow (OS, N= 33) and patch (P, N=30). Means SE are listed below the figure for each symbiont: D inoflagellate (solid white) and R hodophyte (solid gra y), C hlorophyte (crossbar pattern) D iatom (diagonal stripes) Significant differences between reef types within each symbiont type are indicated by different group letters. Non significant results within a symbiont type are denoted by n.s. In general, assemblage symbiont composition was highly variable by site, though primarily due to variation in diatom bearing and chlorophyte bearing species in 2006 and 2007 (Fig. 2 2 ) and in 1995 and 1996 (Fig. 2 3 ) ( see also Appendix F for individual sites ) Proportion of t otal assemblage

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49 Fig ure 22 Proportion of total assemblage for each symbiont type (Dinoflagellate, solid white R hodophyte solid gray, Chlorophyte, crossbar pattern, and Diatom, diagonal stripes ) for summer only assemblage data collected from the low er, middle and upper Keys in 2007 and 2006. Sites are listed from west to east (left to right). Proportion of t otal assemblage Lower Middle Upper 2007 2006 W E

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50 Figure 23 Proportion of total assemblage for each symbiont type (Dinoflagellate, solid white R hodophyte solid gray, Chlorophyte, crossbar pattern, and Diatom, diagonal stripes ) for summer only assemblage data collected from the lower, middle and upper Keys in 1996 and 1995 Sites are listed from west to east (left to right). W E Lower Middle Upper 1996 1995 Pr oportion of t otal assemblage

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51 MDS & SIMPER analysis MDS anal ysis by reef type showed that patch reefs were more loosely grouped than either offshore shallow or deep sites (Fig. 2 4 ). Figure 24 MDS plot by reef type for Keys wide data (summers only of 1995, 1996, 2006, OS, OD, *). 2D Stress: 0.1. SIMPER analysis by reef type confirmed that offshore shallow and deep reefs exhibited strong within reef type similarities of 76% and 69%, respectively, and patch reefs were more variable with only 56% similarity (Table 1 3 ). The dissimilarity between reef types ranged from 30 40% and resulted from differences in the densities of Archaias angulat us C. compressa Amphistegina gibbosa Asterigerina carinata and L. proteus (Table 1 4 ). Patch and offshore deep sites were most dissimilar (40%), with Archaias angulatus contributing most to that difference

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52 Table 13 SIMPER resul ts by reef type for all Keys wide sites including patch, offshore deep and offshore shallow reefs showing average percent similarity within each reef type, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each reef type. Gray shading indicates those species responsible for contributing greater than 10% to the similarity within each reef type. Patch Offshore Deep Offshore Shallow Average similarity: 55.6% Average similarity: 69.1% Average similarity : 75.9% Species Av.Abund %Con Species Av.Abund %Con Species Av.Abund %Con A. gibbosa 3.53 30.8 A. gibbosa 4.78 35.1 A. gibbosa 4.63 24.2 L. proteus 2.55 17.6 L. proteus 3.11 19.4 L. proteus 3.46 17.0 A. angulatus 2.39 13.1 H. antillarium 1.54 9.25 C. c ompressa 2.53 10 P. pertusus 1.22 8.37 C. compressa 1.89 6.72 A. angulatus 2.48 9.17 H. antillarium 0.94 7.1 L. bradyi 1.32 5.37 H. antillarium 1.73 8.23 C. compressa 1.2 4.79 B. orbitolitoides 1.3 4.71 A. carinata 2.11 7.99 B. orbitolitoides 0.99 4.62 A. carinata 1.38 4.57 S. marginalis 1.66 6.38 S. marginalis 0.69 3.39 P. pertusus 1 3.83 P. pertusus 1.33 5.31 Gypsina 0.56 3.37 A. angulatus 1.2 3.7 L. bradyi 1.43 5.17

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53 Table 1 4 SIMPER results by reef type for all Keys wide sites including patch (P), offshore deep (OD) and offshore shallow (OS) reefs showing average percent dissimilarity for each sampling reef type, average abundances (count/100 cm 2 ), and percent contribution for species contributing to dissimilarity be tween each reef type. Gray shading indicates those species responsible for contributing greater than 10% to the dissimilarity between each reef type. Patch & Offshore Deep Patch & Offshore Shallow Offshore Deep & Offshore Shallow Average dissimilarity = 40.3% Average dissimilarity = 38.7% Average dissimilarity = 30.2% Species P OD %Con Species P OS %Con Species OD OS %Con A. angulatus 2.39 1.2 13.6 C. compressa 1.2 2.53 12.6 A. angulatus 1.2 2.48 14.1 A. gibbosa 3.53 4.78 12.8 A. angulatus 2.39 2.48 1 2.1 C. compressa 1.89 2.53 13.5 C. compressa 1.2 1.89 11.5 A. gibbosa 3.53 4.63 11.0 A. carinata 1.38 2.11 11.7 L. proteus 2.55 3.11 11.5 A. carinata 0.7 2.11 11 S. marginalis 0.82 1.66 8.75 A. carinata 0.7 1.38 8.5 L. proteus 2.55 3.46 10.6 L. proteus 3.11 3.46 8.41 L. bradyi 0.83 1.32 8.19 S. marginalis 0.69 1.66 7.95 B. orbitolitoides 1.3 1.08 8.38 B. orbitolitoides 0.99 1.3 7.88 L. bradyi 0.83 1.43 7.91 L. bradyi 1.32 1.43 7.83 P. pertusus 1.22 1 6.52 B. orbitolitoides 0.99 1.08 6.73 P. pertusus 1 1.33 6.79 H. antillarium 0.94 1.54 6.38 H. antillarium 0.94 1.73 6.32 A. gibbosa 4.78 4.63 6.28 S. marginalis 0.69 0.82 4.92 P. pertusus 1.22 1.33 5.44 B. pulchra 0.64 0.9 5.97

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54 MDS analysis based on total LBF assemblages showed that the upper Keys s ites were more tightly grouped than either the middle or lower Keys sites ( Fig. 25 ). Figure 25 MDS plot by region for Keys wide data (summers o nly of 1995, 1996, 2006, (+). 2D Stress: 0.1 SIMPER analysis by region showed that the upper Keys were 76 % similar, while the middle and lower Keys were only 65 % and 61 % similar respectively (Table 1 5 ). A cross all regions, the most consistently abundant species responsible for the high degree of similarity were A. gibbosa and L. proteus which contributed 2 4 3 7 % and about 18% to overall similarity amo ng sites, respectively The dissimilarity betwe en regions ranged from 3 4 3 8 % and resulted from differences in the densities of A rchaias angulatus C. compressa Asterigerina carinata L. proteus, Amphistegina gibbosa and B roeckina orbitolitoides (Table 1 6 ). In particular, C. compressa is about twice a s abundant in upper Keys assemblages as it is in the middle Keys, with

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55 assemblages in the lower Keys intermediate (Table 1 6 ). On the other hand, Asterigerina carinata contributes about twice as much to the middle Keys assemblages as to the upper and lower Keys assemblages. Middle and lower Keys sites had the highest degree of dissimilarity (38 % ), though this was not significant.

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56 Table 15 SIMPER results by region for Keys wide sites within the upper, middle and lower Keys showing a verage percent similarity within each sampling region, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each region. Gray shading indicates those species responsible for contributing greater than 1 0% to the similarity within each region. U pper Keys M iddle Keys L ower Keys Average similarity: 75.8% Average similarity: 64.7% Average similarity: 60.6% Species Av.Abund %Con Species Av.Abund %Con Species Av.Abund %Con A. gibbosa 4.53 23.8 A. gibbosa 4. 55 36.9 A. gibbosa 4.13 32.0 L. proteus 3.58 18.4 L. proteus 2.79 18.2 L. proteus 2.79 17.8 A. angulatus 2.76 11.5 H. antillarium 1.42 8.65 H. antillarium 1.42 10.1 C. compressa 2.01 7.26 A. carinata 1.84 8.4 C. compressa 1.9 7.94 B. orbitolitoides 1.8 7.15 P. pertusus 1.06 5.18 A. angulatus 1.8 6.97 L. bradyi 1.69 6.23 C. compressa 1.66 4.88 S. marginalis 1.14 5.37 P. pertusus 1.51 6.11 A. angulatus 1.41 4.16 P. pertusus 0.98 5.33 H. antillarium 1.42 5.99 L. bradyi 0.91 3.98 L. bradyi 1.03 3.78 A. carinata 1.49 4.89 A. carinata 1.15 3.73

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57 Table 16 SIMPER results by region for Keys wide sites within the upper, middle and lower Keys showing average percent dissimilarity for each sampling region, average abundances (cou nt/100 cm 2 ), and percent contribution for species contributing to dissimilarity between each region. Gray shading indicates those species responsible for contributing greater than 10% to the dissimilarity between each region. M iddle Keys & U pper Keys L ower Keys & U pper Keys L ower Keys & M iddle Keys Average dissimilarity = 33.5% Average dissimilarity = 34.1% Average dissimilarity = 37.7% Species M iddle Keys U pper Keys %Con Species L ower Keys U pper Keys %Con Species L ower Keys M iddle Keys %Con A. angulatus 1.41 2.76 14.7 A. angulatus 1.8 2.76 13.9 C. compressa 1.9 1.66 13.1 C. compressa 1.66 2.01 12.2 C. compressa 1.9 2.01 11.5 A. angulatus 1.8 1.41 12.3 B. orbitolitoides 0.63 1.8 10.1 L. proteus 2.79 3.58 10.2 A. carinata 1.15 1.84 11.4 L. pro teus 2.79 3.58 9.82 A. carinata 1.15 1.49 9.25 L. proteus 2.79 2.79 11.3 A. carinata 1.84 1.49 9.43 A. gibbosa 4.13 4.53 9.19 A. gibbosa 4.13 4.55 11.1 L. bradyi 0.91 1.69 8.53 B. orbitolitoides 0.92 1.8 9.15 S. marginalis 1.14 0.93 7.03 P. pertusus 1.0 6 1.51 6.79 L. bradyi 1.03 1.69 8.97 L. bradyi 1.03 0.91 6.98 A. gibbosa 4.55 4.53 6.59 S. marginalis 1.14 1.07 6.49 B. orbitolitoides 0.92 0.63 6.39 S. marginalis 0.93 1.07 6.41 P. pertusus 0.98 1.51 6.43 P. pertusus 0.98 1.06 6.26 B. pulchra 0.62 1.08 6.24 B. pulchra 0.46 1.08 6.15 H. antillarium 1.42 1.42 6.04

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58 BEST analysis Mean p ercent coral cover (2005) and long term decline (1996 2005) which were obtained from the Coral Reef Evaluation and Monitoring Project data archives, were analyzed by bot h region and reef type. One way ANOSIMs showed that both variables were significantly different between reef types (percent coral cover: Global R = 0.3 0 p=0.001; percent coral decline: Global R = 0.39 p= 0.001 ), but not between regions (percent coral cov er: Global R = 0.03, p=0.8; percent coral decline: Global R = 0.06, p=0.96; Fig. 26). Specifically, percent coral cover in 2005 was significantly higher at patch reefs than at offshore reefs and the long term decline (averaged over 1996 2005) was greate st at offshore reefs. Further, decline was significantly greater at shallow sites than deep sites at offshore reefs.

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59 Region Reef Type % Coral Cover (2005) % Coral Decline (1996 2005) % Coral Cover (2005) % Coral Decline (1996 2005) Upper Middle Upper Middle P OD P OD Upper Upper P P Middle 0.0320 Middle 0.0709 OD 0.5885 ** OD 0.3204 ** Lower 0.0240 0.0234 Lower 0.0575 0.0577 OS 0.4760 ** 0.0533 OS 0.6909 ** 0.1791 Figure 26 Mean percent coral c over and percent coral decline with standard error by region (lower, middle and upper Keys) and reef type (offshore deep, OD, offshore shallow, OS, and patch, P, reefs). ANOSIM results are given below the graphs. Starred R values are significant at p<0.0 5 and double starred values are significant at p<0.01. Lower Middle Upper OD OS P Region Re ef Type

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60 The B IOENV or BEST analysis showed the combinations of LBF species whose spatial distribution in summer 2006 was most correlated with trends in the coral communities, mainly percent coral cover in 2 005 and percent coral decline from 1996 2005 (Table 1 7 ). Percent coral cover (2005) was best correlated with the density distributions of A. gibbosa L. bradyi and C. compress a Table 17 BEST results from 2006 LBF species density data from corresponding Keys wide and CREMP sites. The top ten correlation values are listed for each test. The highest correlations are significant at p< 0.0 1 (starred). BEST Analysis Test No.Vars. Correlation Selections % Coral Cover 2005 3 0.575* 1,3,10 4 0.572 1,3,6,10 4 0.570 1,3,10,12 5 0.570 1,3,6,10,12 5 0.564 1 3,6,10 6 0.562 1 3,6,10,12 4 0.562 1,3,9,10 4 0.559 1 3,10 5 0.557 1,3,9, 10,12 4 0.556 1,3,4,6 % Coral Decline 1996 2005 4 0.386* 3,8,10,11 3 0.383 3,8,10 6 0.380 2,3,7,8,10,11 3 0.380 8,10,11 5 0.379 3,7,8,10,11 4 0.378 3,7,8,10 6 0.377 3,7,8,10 12 5 0.376 2,3,7,8,10 2 0.376 8,10 7 0.375 2,3,7,8,10 12 Va riables 1 A. gibbosa 7 H. antillarium 2 A. carinata 8 S. marginalis 3 L. bradyi 9 A. angulatus 4 L. proteus 10 C. compressa 5 P. pertusus 11 B. pulchra 6 B. orbitolitoides 12 Gypsina

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61 Regression analysi s by species f urther revealed the nature of these relationships to be negative such that LBF density decreased with higher percent coral cover ( Fig. 2 7 ) The regressions were linear for L. bradyi and C. compressa with low R 2 values of 0.05 and 0.01, respectively, but with outliers removed, R 2 i ncreased to 0.2 for both species. Amphistegina gibbosa density had the strongest regression with an exponential trendline (R 2 =0.5) In general, there was high variability in LBF density when percent coral cover was low (usually less than ~10%) However, higher coral cover was associated with lower LBF densities and lower variability.

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62 Figure 27 Regressions of LBF species densities (per 100cm 2 ) from summer 2006 Keys wide and CREMP sites that were most correlated with percent coral cover (2005). When outliers for L. bradyi and C. compressa (circled) were removed, R 2 values increased to 0.2 for both species. Note: Scales vary. P ercent coral decline (1996 2005) was best correlated with the density distributions of L. bradyi S. marginalis C. compressa and B. pulchra Regression analysis by species further revealed the nature of these relationships to be linear and positive such that LBF species density in creased with higher percent coral decline ( Fig. 2 8 ). Sorites marginalis had the strongest relat ionship with percent coral decline with an R 2 of 0.4. Laevipeneroplis bradyi B. pulchra and C compressa had very weak regressions with R 2 values of 0.06 0.07 and 0.01

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63 respectively. A few extreme outliers were removed ( L. bradyi : Jaap Reef and Molasse s Deep; B. pulchra : Molasses Deep; C. compressa : Admiral Patch, Looe Key Deep and Molasses Deep), which resulted in relatively much stronger regressions for L. bradyi (R 2 = 0.3 ), B. pulchra and C. compressa (R 2 =0.2) In general, there was high variability i n LBF density when percent coral decline was high (usually greater than ~40%). However, lower coral decline was associated with lower LBF densities and lower variability.

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64 Figure 28 Regressions of LBF species densities (p er 100cm 2 ) from summer 2006 Keys wide and CREMP sites that were most correlated with percent coral decline (1996 2005). R 2 values increased to 0.3 for L. bradyi and 0.2 for C. compressa and B. pulchra when outliers (circled) were removed. Note: Scales va ry. Metadata analysis The metadata analysis combined summer only data from Conch Reef and Tennessee Reef, Keys wide sites, BNP sites (Ramirez, 2008 ) and patch reefs off Key Largo (Fisher, 2007). The primary correlate with LBF densities was region (average d across all reef types ; ANOSIM2: Global R=0. 3 6 p=0.001 ) with significant differences between each region (Table 1 8 ) Pairwise comparisons revealed that the middle and lower Keys sites had the least significa nt difference (p= 0.0 32)

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65 Table 18 ANOSIM2 results for differences between regions (Biscayne National Park (BNP) and upper, middle and lower Keys) based on LBF densities (across all reef types) for metadata analysis; Global R=0.358. Starred values are significant at p<0.05 and double starred values are significant at p < 0.001. BNP Upper Middle Lower BNP Upper 0.362** Middle 0.331* 0.482** Lower 0.444** 0.519** 0.079* A second factor affecting LBF densities was reef type (averaged across all regions ; ANOSIM2: Gl obal R=0. 2 3 p=0. 00 1 ) with significant differences between each type (Table 1 9 ). While both had a significant effect, a larger difference was observed in LBF assemblages due to region rather than reef type. Table 19 ANOSIM2 result s for differences between reef types (offshore shallow, OS, offshore deep, OD and patch, P) based on LBF densities (across all regions) for metadata analysis; Global R=0.227. Bold ed values are significant at p< 0.001, while star red values are significant a t p<0.05 P OD OS P OD 0.295** OS 0.118* 0.286** Bray Curtis analysis of transformed (log x+1) species density data again revealed that species still tended to cluster based on abundance ( Fig. 2 9 ) producing a dendrogram very similar to the K eys wide data alone (Fig. 1 9 )

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66 Figure 29 Bray Curtis dendrogram of LBF assemblage across all depths sampled for all metadata sites. MDS & SIMPER analysis MDS analysis by region showed that upper Ke ys sites were more tightly grouped than BNP, middle or lower Keys sites ( Fig. 30 ). Further SIMPER analysis showed that upper Keys sites were 74% similar, while middle Keys and BNP sites were only 66 % and 60 % similar, respectively (Table 20 ). The lower Ke ys sites had the lowest similarity (58%). Across all regions, the most consistently abundant species responsible for interregional similarity among sites are Amphistegina gibbosa and L. proteus which contributed 25 37% and 17 29% to overall similarity am ong sites, respectively. The dissimilarity between all regions ranged from 33 47% and resulted from differences in the densities of A. gibbosa Archaias angulatus Asterigerina A. gibbosa L. proteus A. angulatus C. compressa B. orbitolitoides S. marginalis B. pulchra A. carinata L. bradyi P. pertusus Gypsina 100 80 60 40 20 Similarity H. antillarium More Abundant Less Abundant

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67 carinata C. compressa and L. proteus (Table 21 ). BNP and lower Keys sites we re most dissimilar (47%). Figure 30 MDS plot by region for metadata analysis: Biscayne National Park ( BNP, ), 2D Stress: 0.14

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68 Table 20 SIMPER results by region for metadata analysis including Biscayne National Park (BNP) and upper, middle and lower Keys showing average percent similarity for each sampling region, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each region. Gray shading indicates those species responsible for contributing greater than 10% to the similarity between each region. BNP U pper Keys Average similarity: 60.1% Average similarity: 73.5% Species Av.Abund %Con Species Av.Abund %Con L. proteus 2.94 29.0 A. gibbosa 4.7 25.6 A. gibbosa 2.73 25.0 L. proteus 3.66 19.0 A. angulatus 2 16.5 A. a ngulatus 2.65 10.3 C. compressa 1.42 7.52 C. compressa 2.07 7.22 L. bradyi 1.25 7.08 H. antillarium 1.61 6.88 P. pertusus 0.86 5.44 L. bradyi 1.52 5.97 A. carinata 1.78 5.95 P. pertusus 1.38 5.66 B. orbitolitoides 1.45 4.67 M iddle Keys L ower Keys Average similarity: 66% Average similarity: 58.3% Species Av.Abund %Con Species Av.Abund %Con A. gibbosa 4.67 36.7 A. gibbosa 3.95 32.8 L. proteus 2.81 19.0 L. proteus 2.66 17.2 H. antillarium 1.46 9.53 H. antillarium 1.36 10.2 A. carinata 1.81 7.86 C. compressa 1.93 7.81 C. compressa 1.62 5.96 A. angulatus 1.81 6.88 P. pertusus 1.04 4.89 S. marginalis 1.14 5.42 A. angulatus 1.37 4.62 B. orbitolitoides 1.01 5.18 S. marginalis 0.86 3.48 P. pertusus 0.88 4.92

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69 Table 21 SIMPER results by region for metadata analysis including Biscayne National Park (BNP) and upper, middle and lower Keys showing average percent dissimilarity for each sampling region, average abundances (count/100 cm 2 ), and percent contribution for sp ecies contributing to dissimilarity between each region. Gray shading indicates those species responsible for contributing greater than 10% to the dissimilarity between each region. Note: Table continues on following page. U pper Keys M iddle Keys L ower Keys BNP Average dissimilarity = 40.4% Average dissimilarity = 43.9% Average dissimilarity = 46.5% Species BNP U pper Keys %Con Species BNP M iddle Keys %Con Species BNP L ower Keys %Con A. gibbosa 2.73 4.7 14.5 A. gibbosa 2.73 4.67 16.8 A gibbosa 2.73 3.95 14.7 A. angulatus 2 2.65 10.6 A. angulatus 2 1.37 11.1 A. angulatus 2 1.81 12.4 C. compressa 1.42 2.07 10.3 A. carinata 1 1.81 10.6 C. compressa 1.42 1.93 11.8 H. antillarium 0.24 1.61 9.93 C. compressa 1.42 1.62 10.6 L. proteus 2 .94 2.66 11.3 A. carinata 1 1.78 9.42 H. antillarium 0.24 1.46 9.87 H. antillarium 0.24 1.36 9.14 B. orbitolitoides 0.48 1.45 8.14 L. proteus 2.94 2.81 8.8 L. bradyi 1.25 1.01 8.15 L. proteus 2.94 3.66 8.02 L. bradyi 1.25 0.81 7.85 A. carinata 1 0.9 7.77 L. bradyi 1.25 1.52 7.46 P. pertusus 0.86 1.04 6.09 S. marginalis 0.57 1.14 6.72 S. marginalis 0.57 1.04 6 S. marginalis 0.57 0.86 5.74 B. orbitolitoides 0.48 1.01 6.36 B. pulchra 0.34 1.05 5.97 B. orbitolitoides 0.48 0.43 4.5 P. pertusus 0.86 0 .88 5.25

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70 U pper Keys M iddle Keys L ower Keys U pper Keys Average dissimilarity = 33.2% Average dissimilarity = 36.6% Species U pper Keys M iddle Keys %Con Species U pper Keys L ower Keys %Con A. angulatus 2.65 1.37 14.4 A. angulatus 2.65 1.81 14.0 C. compressa 2.07 1.62 11.8 C. compressa 2.07 1.93 12.0 A. carinata 1.78 1.81 10.9 L. proteus 3.66 2.66 11.2 L. proteus 3.66 2.81 9.63 A. carinata 1.78 0.9 10.2 B. orbitolitoides 1.45 0.43 9.27 A. gibbosa 4.7 3.95 9.8 1 L. bradyi 1.52 0.81 8.01 L. bradyi 1.52 1.01 7.83 A. gibbosa 4.7 4.67 7.65 B. orbitolitoides 1.45 1.01 7.47 P. pertusus 1.38 1.04 6.42 S. marginalis 1.04 1.14 6.51 S. marginalis 1.04 0.86 6.29 B. pulchra 1.05 0.37 5.98 B. pulchra 1.05 0.6 5.99 H. antillarium 1.61 1.36 5.91 M iddle Keys Average dissimilarity = 39.3% Species M iddle Keys L ower Keys %Con C. compressa 1.62 1.93 12.8 A. gibbosa 4.67 3.95 12.5 A. angulatus 1.37 1.81 12.2 A. carinata 1.81 0.9 11.4 L. proteus 2.81 2.66 11.2 L. bradyi 0.81 1.01 6.78 S. marginalis 0.86 1.14 6.78 B. orbitolitoides 0.43 1.01 6.77 P. pertusus 1 .04 0.88 6.17 H. antillarium 1.46 1.36 5.88

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71 MDS analysis by re ef type showed that patch reef assemblages had a greater degree of dissimilarity than either offshore shallow or de ep assemblages (Fig 31 ). Figure 31 OS, and offshore deep ( OD, ). 2D Stress: 0 14. SIMPER analysis by reef type confirmed that offshore shallow and deep reefs exhibited strong similarities of 7 7 % and 70 %, respect ively, while patch reefs were more variable with on ly 59 % similarity (Table 22 ). The species most consistently responsible for the similarity among s ites within each reef type were Amphistegina gibbosa and L. proteus which contributed 2 4 36% and 17 2 3 % t o the similarity among sites, respectively. The dissimilarity between reef types ranged from 3 1 40 % and resulted from differences in the densities of A rchaias angulatus Asterigerina carinata Amphistegina gibbosa and C. compressa (Table 2 3 ). Patch and o ffshore deep reefs were the most dissimilar ( 40% ) again, with differences in Archaias angulatus occurrence as the most important factor

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72 Table 22 SIMPER results by reef type for metadata analysis including patch, offshore deep an d offshore shallow reefs show ing average percent similarity for each reef type, average abundances (count/100 cm 2 ), and percent contribution for species contributing to similarity within each reef type. Gray shading indicates those species responsible for contributing greater than 10% to the similarity between each reef type. Patch Offshore Deep Offshore Shallow Average similarity: 58.7% Average similarity: 70.3% Average similarity: 76.9% Species Av.Abund %Con Species Av.Abund %Con Species Av.Abund %Con A. gibbosa 3.64 27.4 A. gibbosa 4.85 36.3 A. gibbosa 4.63 23.5 L. proteus 3.06 22.6 L. proteus 3.08 19.3 L. proteus 3.51 17.1 A. angulatus 2.58 15.6 H. antillarium 1.6 10.2 C. compressa 2.68 11.0 P. pertusus 1.18 6.78 L. bradyi 1.34 6.06 A. angulatus 2.5 9.63 C. compressa 1.46 5.97 C. compressa 1.67 5.96 A. carinata 2.2 8.69 L. bradyi 1.11 4.72 A. carinata 1.56 5.93 H. antillarium 1.66 7.8 A. carinata 1.07 3.72 P. pertusus 0.9 3.61 S. marginalis 1.57 5.9 H. antillarium 0.94 3.53 B. orbitolitoides 0 .99 3.14 P. pertusus 1.29 5.28 L. bradyi 1.32 4.64

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73 Table 23 SIMPER results by reef type for metadata analysis including patch (P), offshore deep (OD) and offshore shallow (OS) reefs showing average percent dissimila rity for each reef type, average abundances (count/100 cm 2 ), and percent contribution for species contributing to dissimilarity between each reef type. Gray shading indicates those species responsible for contributing greater than 10% to the dissimilarity between each reef type. Patch & Offshore Deep Patch & Offshore Shallow Offshore Deep & Offshore Shallow Average dissimilarity = 39.7% Average dissimilarity = 35.9% Average dissimilarity = 30.5% Species P OD %Con Species P OS %Con Species OD OS %Con A angulatus 2.58 0.92 14.0 C. compressa 1.46 2.68 12.9 A. angulatus 0.92 2.5 14.9 A. gibbosa 3.64 4.85 12.9 A. carinata 1.07 2.2 11.6 C. compressa 1.67 2.68 14.2 C. compressa 1.46 1.67 10.7 A. gibbosa 3.64 4.63 11.5 A. carinata 1.56 2.2 11.6 A. carinata 1.07 1.56 9.87 A. angulatus 2.58 2.5 10.9 S. marginalis 0.65 1.57 8.81 L. proteus 3.06 3.08 9.6 L. proteus 3.06 3.51 8.71 L. proteus 3.08 3.51 8.55 H. antillarium 0.94 1.6 8.4 H. antillarium 0.94 1.66 8.02 B. orbitolitoides 0.99 0.91 7.52 L. bradyi 1.1 1 1.34 7.67 S. marginalis 0.77 1.57 7.94 L. bradyi 1.34 1.32 7.23 B. orbitolitoides 0.99 0.99 7.35 L. bradyi 1.11 1.32 7.26 A. gibbosa 4.85 4.63 6.77 P. pertusus 1.18 0.9 6.01 B. orbitolitoides 0.99 0.91 6.93 P. pertusus 0.9 1.29 6.34 S. marginalis 0.77 0.65 5.11 B. pulchra 0.64 1.01 5.78 B. pulchra 0.57 1.01 6.24

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74 Evenness Mean e venness ( E across all years and reef types) was the lowest in the middle Keys sites (0.460.03SE N=43 ) and highest at the BNP sites (0.730.02SE N=35 ), while the lower and upper Keys sites showed mid range mean E values of 0.530.03SE (N=36) and 0.57 0.01SE (N=84) respectively ( two way ANOVA: F 3,188 = 6.18, p=0.0001, Fig. 32 ). ost hoc tests revealed that t here were significant differences between BNP and all other regions (p= 0.0001). The upper Keys sites had a significantly greater mean E than the middle Keys sites (p=0.0003), but the lower Keys mean E was not different from the mean E for the upper or middle Keys sites. Figure 32 Mean evenness ( E ) for summer only assemblage data (across all years) with standard error bars plotted by region: lower (solid white, N=36), middle (diagonal stripes, N=43) and upper (solid gray, N=84) Keys and Biscayne National Par k (BNP, crossbar pattern N=35). Significant differences between regions are indicated by different letters (two way ANOVA: F 3,188 = 6.18, p=0.0001). There was also a main effect of reef type (two way ANOVA: F 2,188 = 4.07, p=0.02; Fig. 33 ean E (across all years and regions) was lowe st at offshore deep reefs (0.440.02SE, N=56) and highest at offshore shallow (0.610.02SE, N=48) and patch reefs (0. 6 30.0 2 SE, N= 96 ). Offshore shallow and p atch reefs were not significantly different Evenness (E) a b bc c

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75 from each othe r, but were both significantly different than offshore deep reefs The interaction between region and reef type was not significant ( two way ANOVA: F 4,188 = 1.2, p=0.31; Fig. 34 ). Figure 33 Mean evenness ( E ) for summer only ass emblage data (across all years) with standard error bars plotted by reef type: offshore deep (OD, solid gray, N=56), offshore shallow (OS, solid white, N=48) and patch (P, crossbar pattern, N=96). Significant differences between reef types are indicated by different letters (two way ANOVA: F 2,188 = 4.07, p=0.02). Evenness (E) a a b

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76 N=13 13 10 18 18 7 25 17 42 35 Figure 34 Mean evenness ( E ) for summer only assemblage data with standard error bars plotted by reef type and region (across all year s): lower (solid white), middle (diagonal stripes) and upper (solid gray) Keys and Biscayne National Park (BNP, crossbar pattern). The number of reefs sampled for each region by reef type (N) is listed below the corresponding bar. The interaction between region and reef type was not significant (two way ANOVA: F 4,188 = 1.2, p=0.31) When E was examined across all years and regions a two way ANOVA revealed significant main effects of reef type ( F 2,167 = 5.38, p=0.01) and year ( F 6,167 = 3.17, p=0.01) as we ll as the interaction ( F 4,167 = 2.66 p=0. 04 ). showed that p atch reefs in 2007 had the highest mean E (0.690.02SE, N=47 ), which was only significantly greater than other patch reef mean E values in 2002 (0.520.04SE, N=14, p=0.004) and not in 2001 (0.610.04SE, N=10) 2004 (0.560.04SE, N=6) or 2006 (0.570.04SE, N=17; Fig. 3 5 ). In general, patch reef mean E values did not differ from offshore shallow mean E values and were significantly greater than offshore deep mean E values in 1995 ( 0.39 0.04SE, N=10, p<0.0001), 1996 ( 0.37 0.04SE, N=12, p<0.0001), and 2007 (0.480.05SE, N=11, p=0.006), but not in 2006 (0.560.05SE, N=11). Offshore shallow reefs did not differ significantly from each other across all years: 1995 (0.66 0.05SE, N=8), 1996( 0.56 0.05SE, N=10), 2006 (0.650.02SE, N=11), and 2007 (0.650.04SE, N=11). Offshore deep reefs did not differ significantly from each other Evenness (E)

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77 across all years. The only year in which offshore shallow and deep reefs were significantly different was in 1995 (p =0.028 ).

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78 N = 10 8 12 10 10 16 6 11 11 17 11 11 47 Figure 35 Mean evenness ( E ) for summer only assemblage data with standard error bars plotted by year and reef type (across all regions): offshore deep (OD, solid g ray), offshore shallow (OS, solid white) and patch (P, crossbar pattern). The number of reefs sampled for each reef type (N) is listed below the corresponding bar. Significant differences between reef types are indicat ed by different letters (two way ANO VA: F 4,167 = 2.66, p=0.04). All values of E without letters are not significant from any other values (abc). Evenness (E) b bc bc a bc ac ac bc ac bc

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79 A cross all years and reef types, a two way ANOVA revealed significant main effects of region ( F 3,162 = 10.2, p=0.0001) and year ( F 6,162 = 2.53, p =0.02) as well as the interaction ( F 6,162 = 2.74, p=0.01; Fig. 36 BNP reefs had the highest mean E ( 0.750.02SE, N=32 ), which was significantly higher than me an E values in lower (p=0.002) and middle (p=0.014) Keys sites in 1995, lower (p<0.0001), middle (p<0.0001) and upper (p=0.018) Keys sites in 1996 as well as upper Keys sites in 2002 (p=0.005), lower Keys sites in 2006 ( p=0.007 ), and middle Keys sites in 2007 ( p<0.0001 ) Upper Keys sites were not significantly differen t across all years sampled: 1995 ( 0.570.05SE, N=8 ), 1996 ( 0.540.02SE, N=10 ), 2001 ( 0.630.4SE, N=9 ), 2002 ( 0.540.04SE, N=12 ), 2004 ( 0.560.04SE, N=11 ), 2006 ( 0.610.04SE, N=14 ), 2007 ( 0.610.03SE, N=13 ). Middle Keys sites were not significantly differe nt across all years sampled: 1995 (0.490.10SE, N=6), 1996 (0.420.08SE, N=8), 2006 (0.61 0.04SE, N=12), 2007 (0.410.06SE, N=9). Finally, lower Keys sites were not significantly different across all years sampled: 1995 (0.400.09SE, N=4), 1996 (0.310.0 7SE, N=4), 2006 (0.540.05SE, N=13), 2007 (0.600.04SE, N=15). In general, u pper, m iddle and l ower Keys reefs did not differ significantly from each other across all years and mean E values for reefs within each of these geographic region s did not change significantly between sampling years.

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80 N= 4 6 8 4 8 10 9 12 11 13 12 14 15 9 13 32 Figure 36 Mean evenness ( E ) for summer only assemblage data with standard error bars plotted by year and region (across all reef types): lo wer (solid white), middle (diagonal stripes) and upper (solid gray) Keys and Biscayne National Park (BNP, crossbar pattern). The number of reefs sampled within each region (N) is listed below the corresponding bar. Significant differences between re gions are indicated by different letters (two way ANOVA: F 6,162 = 2.74, p=0.014). All values of E without letters are not significant from any other values (ab). a b b b b b b b b Evenness (E)

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81 DISCUSSION I analyzed LBF assemblage data collected from the Florida reef tract by multiple s tudies over a 12 year period (1996 2007) following the discovery of bleaching in field population s of A mphistegina gibbosa in the Florida Keys in 1991 (Hallock et al. 1993). Bleaching in A. gibbosa for 1994 1999 was addressed by Williams (2002) who disc ussed several plausible sources of b leaching (e.g. sea surface temperature, pollution and solar radiation ). She concluded that bleaching trends implicated solar radiation as the largest contributor since the prevalence of bleaching tended to increase in M arch, when sea surface temperatures were near their seasonal minima and peak near the summer solstice (Hallock et al. 1995; Williams et al. 1997). Although my study did not directly address bleaching it is important to note that solar radiation can pl ay a pivotal role in structuring LBF assemblages in that A. gibbosa is the most abundant LBF species across the Florida Keys, populations are shown to be susceptible to photo oxidative stress ( Hallock et al ., 1986 ; Williams and Hallock, 2004 ) and their rep roduction is strongly impacted by bleaching ( Williams et al. 1997; Williams, 2002 ) LBF assemblage density trends Depth & temporal trends The availability of solar radiation can act as a double edged sword for symbiont bearing foraminifers, depending on w ater transparency which is controlled by the presence of both inorganic particulates (i.e., sediments) and particulate organic matter (e.g., plankton and marine snow), as well as by th e presence and concentration of colored dissolved organic matter (CDOM) (Zepp, 2003a). Water alone preferentially absorbs the longer wavelengths, while p articulate matter tends to limit light penetration across the solar spectrum. However, CDOM plays a critical

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82 role in protection against photo oxidative stress in shallow wa ter because it absorbs most strongly in the shorter, highest energy wavelengths of light (280 490 nm, which includes ultraviolet and the blue end of visible spectrum) (Zepp, 2003b) Fitt and Warner ( 19 95 ) and Williams and Hallock (2004) found that exposur e to the blue wavelengths induced more bleaching in corals and symbiont bearing foraminifers respectively than the same total energy at longer wavelengths. While LBF species certainly benefit from the greater availability of light in shallow waters (great er potential for photosynthate production by symbionts ), they are at greater risk for bleaching caused by irradiation Williams (2002) reported that, at Conch Reef where CDOM is typically lower than at Tennessee Reef, intensity of bleaching in A. gibbosa was consistently greater and densities were typically lower at shallow sites than at deep sites. Deeper A. gibbosa populations likely experienced less photo oxidative stress and higher reproductive success than shallower populations and thus reached high er densities. On the other hand, i f CDOM is consistently present in sufficient quantity to effectively absorb harmful shorter wavelength solar radiation, then LBF densities may be quite high at shallower depths while lower in deeper water (due to less l ight penetration and thus, lower photosynthate production by symbionts ) as observed at Tennessee Reef from 1997 2000. Stabenau et al. (2004) found Florida Bay to be a significant source of CDOM produced by Thalassia testudinum and suggested that seagrasse s are an important source of UV protective compounds, along with ot her microbially derived CDOM ( e.g., from mangrove litter ) and terrestrially derived CDOM. Southward o utflow currents tend to dominate, mixing Florida Bay waters with the Atlantic Ocean thr ough major tidal channels located in the middle K eys ( Smith, 2002 ) and smaller, more numerous channels in the lower Keys, thus conveying CDOM out to the reef tract Because of its geographic proximity to this major source of CDOM and turbid Florida Bay ou tflow significantly higher CDOM nutrients and chlorophyll a concentrations have been observed at Tennessee Reef ( Szmant and Forrester, 1996 ) than at Conch Reef, which is largely

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83 blocked from water exchange with Florida Bay by Key Largo (Lidz and Shinn, 1 991) and typically has higher water transparency due to the influence of the Florida Current (Klein and Orlando, 1994; Szmant and Forrester, 1996) During summers of acute bleaching in A. gibbosa (e.g. summers of 1996 and 1998 Williams, 2002 ), I observe d a greater decline in A. gibbosa densities at shallower sites than at deeper sites for both Conch and Tennessee reefs Williams (2002) found that summer bleaching affected significantly more of A. gibbosa populations at Conch Reef (42%) than at Tennessee Reef (31%) It was also noted that these years had low er recruitment of juveniles, which partly accounts for the lower total densities observed. While this overall trend is consistent for years with high UV stress it should be noted that a hurricane ev ent additionally impacted population densities in the fall of 1998 at Tennessee Reef, which was sampled immediately after the event Conch Reef was sampled just before the same event and thus, a similar sharp decline is not observed for these samples. Het erostegina antillarium and B. orbito li toi des shared a similar depth trend as A. gibbosa with densities higher at depth than in shallow water. The opposite depth trend was observed for L. proteus Archaias angulatus C. compressa and A sterigerina carinata with densities higher in shallow water than at depth. Except for A. carinata the latter are all porcelaneous taxa with chlorophyte symbionts, which raises the question of whether different symbiont types are adapted to different light climates. Recent m olecular research has confirmed that the dinoflagellate Symbiodinium in corals is actually diversified into multiple genetically distinct clades ( e.g. Rowan and Powers, 1991; Stat et al ., 2006) that have different photosynthetic responses to the same li ght intensities in culture ( Iglesias Prieto and Trench, 199 4 ). Iglesias Prieto et al (2004) sugg ested that the differential use of light by specific symbiotic dinoflagellates is important for niche diversification, controlling the abundance and distribut ion of hermatypic corals. Furthermore, these associations would result in zonation and reduced competition for space along

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84 an irradiance gradient (Iglesias Prieto and Trench 1994, 1997 ). The symbionts of larger ben thic foraminifers are not well studied i n this way, but a similar argument might be made given their physiological commonalities with corals (i.e. hosting of symbiotic algae and the use of algal photosynthate in calcification ) that the vertical distribution of LBF species may be controlled by how well adapted their symbionts are to different light regimes However, it is generally understood that different symbionts use specific ranges of the light spectrum, limiting their foraminiferal ho st to a particular depth range. For example, chloroph ytes are restricted to the shallowest areas, while diatoms and dinoflagellates can live in the deepest areas ( Renema et al. 2001). Additionally shell composition and wall thickness both factor into how much light is able to reach the foraminiferan symbio nt (e.g., Hallock 1979, 1988a,b, 1999) The m iliolid shell is porcelaneous, which is more opaque to light than the hyaline r otaliid shell which has a perforate wall with radially oriented crystal structure that may help focus light by form ing chan Hallock, 1999). Within this context, m iliolid s with thicker and more opaque shells, might be expected to dominate the harsher light intensities at shallow sites, while thinner shelled r otaliids might be more abundant at deeper sites. This phenomen on of declining outer wall thickness with predominant habitat depth was demonstrated by Hallock and Peebles (1993) They found that Androsina lucasi a mangrove pond dweller (Levy 1977, 1994) had the thickest outer wall ; Archaias angulatus an intermediat e thickness ; and the somewhat deeper dwelling C. compressa the thinnest outer wall. I also observe d this pattern and my data include d the m iliolid B. orbitolitoides wh ich was more abundant at deeper than shallower sites. Broeckina orbitol it oides was no t included in the flattest, thinnest shells of all the chlorophyte bearing taxa, and, as my data show, the deepest habitat. However, even B. orbitol it oides was rare at the 20 m site at Tennessee Reef. These trends are consistent with assessments of Hallock (1988a,b), who concluded that chlorophyte

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85 bearing taxa had primarily adapted to a diversity of relatively shallow environments while the diatom bearing taxa have tended to dominate the deeper euphoti c habitats. Interestingly, the chlorophyte bearing taxa are far more diverse in the western Atlantic and Caribbean than in the Indo Pacific, while the diatom bearing taxa show the more typical trend of much higher diversity in the Indo Pacific. Several sp ecies had fairly consistent seasonal trends in abundance, though the timing of abundance peaks varied. This could be a strategy to reduce interspecific competition o r a result of varied light requirements for opti mal reproduction and growth. Amphistegina gibbosa densities did not show a seasonal trend which was unexpected considering this species usually reproduces by alternation of asexual and sexual generations. This was also noted by Williams (2002) who surmised that the lack of seasonality in popula tion abundance was a result of reduced fecundity by stressed populations, so that even recruitment from asexual reproduction did no t significantly raise abundance in years when bleaching stress was most acute. Regional trends In general, LBF assemblages we re more similar among sites from the upper Keys than among sites in the lower Keys. The lower Keys had the lowest degree of inter site similarity, which may be due to greater variability of environmental factors (e.g. salinity, temperature, nutrients, et c.) produced by the interaction of the Gulf of Mexico Loop Current and Florida Bay Also, the lower Keys are geologically different from the upper Keys The lower Keys are fossil oolite shoals, which are much wider, support extensive mangroves, and have many passes that carry water from Florida Bay to the reef tract. In contrast, the Upper Keys, which originated from fossil patch reefs, are long and narrow with few passes that carry water from Florida Bay to the reef tract. Samples taken from Biscayne N ati onal Park a lso had lower similarity (60%) The BNP reefs were mostly patch reefs, that ranged from small, protected patch reefs, to patch reefs tidally

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86 influenced by water from Biscayne Bay, to exposed, very high energy patch and bank reefs near the sh elf margins. This habitat variability likely contributed to the high variability among the LBF assemblages. The significant decrease in chlorophyte bearing LBF abundance in the middle Keys is likely a result of reduced water transparency Due to the stro ng influence of Florida Bay on the middle Keys sites, water transparency may be limiting to chlorophyte bearing species, even a t the shallower sites as t he proportion s of chlorophyte bearing species at middle K eys shallow sites are comparable to the propor tions of chlorophyte bearing species at deep sites elsewhere Diatom bearing species seemed less affected and better able to dominate the available substrate in the middle Keys than in the upper Keys The d inoflagellate bearing species ( S. marginalis ), though low in density overall, was significantly more abundant at offshore shallow reefs than patch reefs and offshore deep reefs. This finding is consistent with Fujita and Hallock (1999) who observed that nutrification would negatively impact Sorite s Patch reefs are generally located in nearshore areas and in less than 5 m of water, where they are more subject to land run off that may encourage eutrophication. Anthropogenic nutrification promotes epiphytic growth that may deter attachment of Sorites ma rginalis which normally prefer flat, bare surfaces such as blades of seagra ss (Fujita and Hallock, 1999). As for the greater abundance at shallow sites than deep sites on offshore reefs, light may be the more important factor. Other symbiont groups did not significantly vary in their proportions of the total assemblage between reef types. Though total densities were significantly different between years (mainly between 1996 and 2006) for several species, I did not observe a significant variation in the overall symbiont group proportions of LBF assemblages over time. Trend summar ies by species Amphistegina gibbosa was found nearly ubiquitously along the Florida reef tract and abundances were not significantly different between regions or reef types. Thi s species was more

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87 abundant at deep sites (>10m) than shallow sites (<10m) and had a strong presence at both Conch and Tennessee Reefs. Depth and temporal trends in A. gibbosa density support the experiments and observations of previous studies that this species is sensitive to photo oxidative stress. Laevipeneroplis proteus was also found in strong abundances along the reef tract without significant differences between regions or reef types. This species was the only chlorophyte bearer that maintained a population (though in low abundance) at the Tennessee deep site. Archaias angulatus and Peneroplis pertusus abundances were both higher in the upper Keys than the middle Keys, where populations were likely light limited by turbid outflow from Florida Bay. Cyclorbiculina compressa abundances were not significantly different between regions or reef types, though abundances were typically higher at shallow sites than deep sites. Like most other chlorophyte bearers, C. compressa was rarely present at the Ten nessee deep site. Asterigerina carinata was found throughout the Florida reef tract, but abundances were significantly higher at Sorites marginalis abundances were h igher at offshore shallow sites than deep sites or patch reefs This is consistent with previous observations that S. marginalis preferred clean seagrass blades to blades overgrown by epiphytes. Borelis pulchra abundances were highest in the upper Keys a nd did not vary by reef type. In general t hese species (excluding Amphistegina gibbosa ) all had higher abundances at the Conch Reef shallow site than both the deep site and Tennessee shallow site. Typically, these species were in very low abundance s at the Tennessee deep site, except for L. proteus The remaining taxa (i.e., Broeckina orbitolitoides Laevipeneroplis bradyi Heterostegina antillariu m and Gypsina ) all had higher abundances at the Conch Reef deep site than the shallow site and a very minima l presence (if at all) at the Tennessee deep site, except for H. antillarium Broeckina orbitolitoides abundances were significantly higher in the upper Keys than in the middle or lower Keys but were not significantly different between reef types Thi s species has

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88 the thinnest shell wall of the chlorophyte bearers and thus, tended to prefer deeper habitats in clear water. Laevipeneroplis bradyi abundances were not signific antly different between regions or reef types. Distribution patterns between Co nch and Tennessee reefs revealed higher abundances at depth in the clear waters at Conch Reef. Like most other chlorophyte bearers L. bradyi was rarely present at the Tennessee deep site. Heterostegina antillarium abundances did not vary between regions but were greater at offshore shallow sites than patch reefs Gypsina was present in low abundances across all regions and reef types Diversity & habitat type Evenness data at both Conch and Tennessee reefs demonstrated how much A. gibbosa can dominat e the LBF assemblages, as evenness was inversely related to A. gibbosa density This relationship was most striking when A. gibbosa density suddenly decreased in 1998 and evenness concurrently increased. At both sites, evenness was consistently lower at depth than at the shallow sites as A. gibbosa tended to be more abundant at the deeper sites while the c h lorophyte bearers declined in abundance with depth A likely explanation is that A. gibbosa densities are exposed to higher photo oxidative stress a t shallow sites, which negatively impacts their reproduction and thus total abundance When A. gibbosa densities were low, the result was a more even assemblage (higher E ), yet I did not observe any other species become dominant (or disappear). This obs ervation indicates that the densities of the other LBF are not likely controlled by competition with A. gibbosa and that A. gibbosa densities are not a function of changes in the other species. At deep sites, A. gibbosa densities experienced less photic s tress and thus could achieve higher densities, resulting in a lower evenness. At Conch Reef, the correlation between A. gibbosa density and evenness deteriorated with depth. Amphistegina gibbosa density explained 44% of the variability in evenness at 10m but only 18% at 30m as evenness was more variable at

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89 depth when A. gibbosa was less abundant T he relationship between A. gibbosa density and evenness at the Tennessee Reef 8m and 20m sites explained 52 and 55% of the variability in evenness, respectiv ely. Porcelaneous species did not appear to be as impacted by the photo oxidative stress that resulted in strong interannual differences in A. gibbosa densities. Densities of the chlorophyte bearing taxa except for B. orbitol it oides decreased with depth at all sites, indicating that diminishing light rather than competition was limiting those species. At the Tennessee 20m site, where light was most reduced by CDOM and particulates from Florida Bay (Williams 2002), A. gibbosa totally dominated, even thou gh its densities were not particularly high. This further indicates that habitat was not suitable for chlo rophyte bearers. Bottom sediments were more muddy at the Tennessee 20 m site, which may also be a factor in limiting the chlorophyte bearing taxa. R amirez (2008) found that A. gibbosa was more common in muddier samples from BNP patch reefs than the chlorophyte bearing taxa. Asterigerina carinata though diatom bearing, appears to flourish in relatively high energy environments, which accounts for its much greater abundance at the shallow Tennes see site than at the muddier 20 m site. In the summer of 2007, e venness was greatest at BNP and decreased down the reef tract to the middle Keys. The lower Keys, however, were not statistically different from th e upper Keys or BNP. This result i s best explained by the dominance of A. gibbosa in middle Keys offshore reefs in 2007 (see Appendix D ). In contrast, the difference in evenness between regions was not significant for the previous summer (2006), when A. gibbosa density was less variable between regions. This may provide further support for the inverse relationship between A. gibbosa density and evenness although it still may only be a reflection of sampling bias in the upper Keys toward patch reefs Onl y five patch reefs were sampled in the lower and middle Keys, while eight patch reefs were sampled in the upper Keys Since patch reefs had the same overall evenness as offshore shallow reefs, sampling more patch reefs would increase the overall

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90 E for the upper Keys region even if the same number of offshore deep and shallow sites were sampled as in the other regions. Furthermore, mostly patch reefs were sampled in Biscayne National Park, which resulted in a significantly greater mean E th an the neighbori ng upper Keys. Data set comparisons Like many coral reefs world wide the Florida reef tract has declined in coral cover and diversity in recent years Data from the Coral Reef Evaluation and Monitoring Program (CREMP) revealed that corals have declined i n cover across the Florida reef tract by abou t 40 50% since 1996 (e.g., Beaver et al. 2004). In recent years larger symbiont bearing foraminifers have been proposed as potential bioindicators of water quality that should support community dominance by ca lcifying organisms dependent upon algal symbioses, including the potential to distinguish between local stresses, which (ideally) can be locally managed, and regional to global stresses, which will require regional to global political action to ameliorate ( Hallock, 2000a, b; Hallock et al ., 2004 ) However, my comparisons of LBF assemblages and coral cover indicate that current conditions along the Florida reef tract have elicited quite different responses from coral s and symbiont bearing foraminifers I fou nd that LBF densities were actually inversely related to percent coral cover in 2005, especially A. gibbosa L. bradyi and C. compressa which had the strongest correlations Likewise, long term p ercent coral decline (1996 2005) was positively related wit h LBF species abundance, particularly L. bradyi S. marginalis C. compressa and B. pulchra which had the strongest correlations. These correlations indicate that certain LBF species have been able to maintain or recover their abundances in spite of the stressors contributing to coral decline and perhaps even further, that water quality is not the major contributor to coral decline on offshore reefs.

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91 Factors that may contribute to the inverse relationship between coral cover and LBF abundance include di fferences in longevity, degree of mobility and sensitivity to temperature Foraminifers are shorter lived (months to a year or two) and are vagile to a certain extent, while coral colonies are longer lived (years to centuries) and are permanently attached to the substrate. Corals produce natural sunscreens, i.e., mycosporine like amino acids (MAAs) that preferentially absorb shorter, higher energy wavelengths of solar radiation (e.g., Shick et al ., 1996). So, if a reef experiences prolonged photic stress foraminifers must retreat out of the sun using their reticulopodia to crawl to more shaded area s (Hallock et al ., 1995, 2006), while coral s can produce additional MAAs to protect themselves Amphistegina spp. appear to behaviorally respond only to visib le wavelengths of solar radiation and therefore are particularly susceptible to photic stress that induces bleaching when ratios of ultraviolet to visible radiation are higher than normal (Williams and Hallock, 2004; Hallock et al., 2006). For the corals, the production of MAAs is energetically costly and may compromise the energy reserves of the coral host, possibly making them more susceptible to disease and certainly more susceptible to temperature induced mass bleaching. A major contributor to coral dec line is likely their sensitivity to elevated temperatures ( Jokiel and Coles 1990 ; Hoegh Guldberg, 1999; Fitt et al ., 2001 and many others ). Corals may be subjected to photo inhibition by high solar radiation, including shorter wavelengths of solar radiati combination of light and temperature stress. In contrast, A. gibbosa has been experimentally shown to be much more tolerant of elevated temperature than corals (Talge and H allock, 2003 ). Thus, the fluctuating but overall continued abundance of LBF on the offshore reefs indicate that the water quality there is still supportive of calcifying organisms dependent upon algal endosymbionts. This indicates that global to regiona l factors are likely contributing more to offshore decline of coral cover than are local factors. Rising sea surface temperatures may be the

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92 most critical problem for corals, yet the chronic to acute bleaching exhibited by A. gibbosa since 1991 (reviewed by Hallock et al ., 2006) indicates that changes in ratios of UV to visible solar energy have also increased the photo inhibitory stress on benthic communities including corals especially in the clearest waters which are associated with the offshore reef s So, what has caused the increase in photic stress reflected by chronic and, in some years acute (1991 92, 1998), bleaching documented in A. gibbosa populations since 1991 on the Florida reef tract and worldwide in Amphistegina spp. (Hallock, 2000 a ; Wi lliams, 2002; Hallock et al ., 2006)? According to Shick et al (1996), there has been approximately 10 15% depletion of stratospheric ozone since the 1960s, such that intensities of the most biologically damaging wavelengths of UV radiation (i.e., UV B) r eaching the sea surface at Florida latitudes are as high from April to August as they formerly were only around the summer solstice. Furthermore, the eruption of the Mt. Pinatubo volcano in the Philippines in May and June 1991 resulted in a further 4% dec line in stratospheric ozone over the lower latitudes. Hallock et al (1993, 1995) documented the onset of bleaching in A. gibbosa along the Florida reef tract in late June 1991. They further argued that corals did not suffer the same degree of mass bleac hing in 1991 that occurred in, e.g., 1998, because the ash and aerosol injected into the stratosphere by Mt. Pinatubo Patch reefs represent a different set of possibilities that involve both local and regional/global environmental factors; at least the local factors provide some potential for resource management. C omparison s of long term coral decline between different reef types showed that the decline was significantly less severe on nearshore patch reefs (~35%) than on offshore shallow reefs (~55%). Likewise, coral cover is staggeringly low at 5% on offshore bank reefs, but significantly greater at 12% on nearshore patch reefs. Thus, some aspect(s) of patch reef conditions apparently has allowed c orals to persist in higher abundance s in nearshore reefs than on offshore reefs. One clue, indicated by the research of Anderson et al ( 2001 ), Fisher

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93 (2007), and my results, is that the lower water transparency on the inshore patch reefs probably reduces the potential for photo inhibition that can cascade into mass bleaching when temperatures rise. A second clue comes from the research of Grottoli et al ( 2006 ), which has shown that Hawaiian coral taxa with greater potential for heterotrophic feeding are more likely to survive mass bleaching events. While there is relativ ely little difference in the species composition of the patch and offshore reefs of the Florida reef tract ( Beaver et al ., 2004 ), there is generally more particulate carbon in the waters over the inshore patch reefs ( e.g., Szmant and Forrester, 1996 ), which would provide more food for corals when they need it ( i.e., when they bleach ) and therefore a higher potential for recovery from bleaching. This idea is also supported by the work of Anthony (2000) which revealed corals from inshore, turbid environments on the Great Barrier Reef to have a greater heterotrophic feeding capacity than conspecifics on midshelf oligotrophic reefs. Comparisons of coral lesion recovery, molecular and protein biomarkers, and ecological data including LBF assemblages and densities, as reported by Fisher (2007), provides additional evidence, when combined with my data set, of the importance of water transparency in deciphering the different responses of corals an d LBF, and the potential for intervention by management. When Fisher compared four patch reefs of similar depth, coral lesion recovery and LBF densities were both highest at the patch reef offshore from protected mangrove coastline of John Pennekamp State Park. Both parameters were lowest at patch reefs offshore from human population areas, which have the greatest potential for anthropogenic impact. My results support the hypothesis of Ramirez (2008), who postulated that the regional/global stressors ha ve greater impact on the offshore reefs, while local factors influence environmental conditions, including water quality, on the patch reefs. The LBF, with their shorter life spans and higher potential for population increase following an acute stress eve nt, continue to maintain substantial abundances on the offshore reefs, where mass bleaching events

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94 and disease outbreaks have decimated coral populations. Corals, with their greater longevity, have been unable to re build coral cover o n offshore reefs Ho wever, their ability to function heterotrophically when bleached if sufficient plankton densities are available for feeding, may provide higher rates of survival in the patch reef setting. Th us, th e best remaining environmental conditions for coral and LBF, have diverged under global environmental change. The LBF are typically most abundant under very high water quality, even under chronic photic stress, and able to rebuild substantial population densities wi thin one to a few years after acute photic str ess event s such as occurred in 1991 92 and 1998. Corals, which also previously thrived under very high water transparency, have been decimated by photic and thermal stress events, as well as diseases that are likely opportunistic to some degree. The patc h reef conditions under which they still persist in double digit cover percentages can survive. because rates of coral survival are hi gher than on the offshore reefs. My data also show that the LBF assemblages on patch reefs differ far more than assemblages on the offshore reefs. These differences probably reflect greater diversity of environmental conditions among patch reefs. Therein lies potential for further research with direct implications for resource management. I recommend that research be focused on determining why some patch reefs have minimal coral cover while others have maintained quite high coral cover. Defining the con ditions under which surviving coral populations are doing relatively well may provide resource managers with arguments and rationale for, e.g., limiting development of adjacent shorelines or requiring developers to design communities with minimal disruptio n of coastal hammocks, mangroves and seagrass beds that protect the patch reefs from excessive runoff from land while providing reef waters with continuous sources of photo protective CDOM.

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95 In light of these observations, I would strongly recommend the con tinuation of monitoring programs, such as CREMP that provide critical information to reef managers and increased protection of patch reefs, which may harbor some o f the healthiest reefs left in S outh Florida ( Lirman and Fong, 200 7 ) Current t rends of cor al decline and photo oxidative stress in foraminifers are only the beginning of what we may observe in a future with increased anthropogenic pollution and global warming. Continued ozone depletion and rising atmospheric CO 2 are certain to induce increased photic stress, warmer SSTs and lower pH levels all of which will negatively impact corals and LBF populations.

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96 CONCLUSIONS 1. Amphistegina gibbosa was found nearly ubiquitously along the Florida reef tract ranging from 25% of the total LBF assemblage i n Biscayne National Park and the upper Keys to 37% in the middle Keys and 33% in the lower Keys Depth and temporal trends in A. gibbosa density support the experiments and observations of previous studies that this species declines in response to acute p hoto oxidative stress (e.g., ~60 % decline at Conch Reef 10m and ~98% decline at Tennessee Reef 8m in 1998) 2. Archaias angulatus comprised a higher proportion of the total LBF assemblage in the upper Keys (12%) than the middle Keys (4%) wher e populations we re likely light limited by turbid outflow from Florida Bay. At patch reefs, A. angulatus (thicker shelled) was twice as abundant as C. compressa (thinner shelled) but at the deep offshore sites C. compressa was twice as abundant at A. angulatus This co nfirms depth trends noted by previous studies. 3. Asterigerina carinata was found throughout the Florida reef tract, but abundances were significantly higher at offshore shallow sites ( 13.6 3.5 per 100cm 2 ) compared to patch reefs ( 2 0.7 per 100cm 2 ), indicatin energy environments. 4. Borelis pulchra abundances were highest in the upper Keys (2.9 0.6 per 100cm 2 ) compared to the middle (1.4 0.3 per 100cm 2 ) and lower ( 0.7 0.2 per 100cm 2 ) Keys. This species did not vary by reef type 5. Broeckina orbitolitoides abundances were significantly higher in the upper Keys ( 9.3 2.1 per 100cm 2 ) tha n in the middle ( 1.7 0.6 per 100cm 2 ) or lower (3.1 0.7 per 100cm 2 ) Keys. This species has the thinnest shell wall of the chlorophyte bearers and thus tended

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97 to prefer deeper habitats in clear water There were no significant differences in B. orbitolitoides densities between reef types. 6. Cyclorbiculina compressa abundances were not significantly different between regions or reef types although a bunda nces were typically higher at shallow sites than deep sites. Like most other chlorophyte bearers C. compressa was rarely present at the Tennessee deep site. 7. Gypsina was present in low abundances ( typically <2 per 100cm 2 but occasionally 10 per 100cm 2 ) a cross all regions and reef types. 8. Heterostegina antillarium abundances did not vary between regions, but were greater at offshore shallow sites ( 6 0.8 per 100cm 2 ) than patch reefs (2 .2 0.4 per 100cm 2 ) 9. Laevipeneroplis bradyi abundances were not significant ly different between regions, reef types or years. D istribution patterns between Conch and Tennessee reefs revealed higher abundances at depth in the clear waters at Conch Reef. L ike most other chlorophyte bearers L. bradyi was rarely present at the Ten nessee deep site. 10. Laevipeneroplis proteus abundances ( up to 45 4.8 per 100cm 2 ) were not significantly different between regions or reef types. This species was the only chlorophyte bearer that maintain ed a population (though in low abundance) at the Tenne ssee deep site 11. Peneroplis pertusus abundances were higher in the upper Keys ( 4.7 0.7 per 100cm 2 ) than in the middle ( 3.1 0.7 per 100cm 2 ) Keys 12. Sorites marginalis abundances were higher at offshore shallow sites ( 6 0.8 per 100cm 2 ) than deep sites ( 1.8 0.4 per 100cm 2 ) or patch reefs ( 1.5 0.3 per 100cm 2 ) The latter observation is consistent with previous observations that S. marginalis preferred clean seagrass blades to blades overgrown b y epiphytes 13. Evenness was significantly higher on patch ( 0.630.02 ) an d offshore shallow ( 0.610.02 ) reefs than offshore deep reefs ( 0.440.02 )

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98 14. Evenness of LBF assemblages decreased down the reef tract with Biscayne National Park (BNP) having the greatest evenness ( 0.730.02 ) followed by the upper Keys reefs ( 0.570.01 ) This was attributed to the sampling primarily of patch reefs in BNP and of more patch reefs in the upper Keys than in the middle and lower Keys. 15. Evenness was strongly influenced by variations in A. gibbosa density. A s A. gibbosa density increase d, evennes s tended to decline ( e.g., Conch 10m : r 2 = 0.44 Tennessee 8m : r 2 = 0.52 ) Further analyses revealed that changes in evenness resulted from habitat differences rather than from competitive exclusion. 16. LBF species assemblages were distinct by depth at both Con ch and Tennessee Reefs. The Tennessee 20m assemblage was most dissimilar from other assemblages with minimal contribution by chlorophyte bearing taxa. 17. Chlorophyte bearers were typically in higher abundance in shallower waters, while diatom bearers were mo re a bundan t at depth. Additionally, I observed a significant two fold decrease in the proportion of chlorophyte bearers in the middle Keys likely due to light limitation by turbid Florida Bay outflow. 18. Abundances of LBF and percent coral cover are inversel y related at CREMP reef sites (r 2 =0.58, p<0.01) Environmental conditions on patch reefs, possibly mechanisms that reduce photo oxidative stress or provide more heterotrophic resources for coral feeding when light is limiting or bleaching occurs, have sup ported higher rates of coral survival on patch reefs than on offshore reefs In contrast, LBF species continue to thrive in the high water quality of offshore reefs, and even when populations are impacted by photic stress events, population densities can recover within a few years 19. My results indicate a) that the decline of coral cover on the offshore reefs is most likely the result of regional to global environmental change (e.g., stratospheric ozone depletion, increased frequency and intensity of thermal events, and regional disease outbreaks), and

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99 b) that local environmental conditions (e.g., greater concentration of CDOM, more frequent turbidity events) on patch reefs may ameliorate the impact of regional global change factors, thereby increasing coral survival rates. Therein lies the potential for research to better define the ameliorating conditions and for management actions to increase the potential for local reduction of global stressors.

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100 REFERENCES ANDERSON, S., ZEPP, R., MACHULA, J., SANTAVY D., HANSEN, L., MUELLER, E., 2001, Indicators of UV exposure in corals and their relevance to global climate change and coral bleaching: Human and Ecological Risk Assessment, v. 7, p. 1271 1282. ANTHONY, K. R. N., 2000, Enhanced particle feeding capacity of corals on turbid reefs (Great Barrier Reef, Australia): Coral Reefs, v. 19, p. 59 67. BEAVER, C R JAAP, W C PORTER, J W WHEATON, J CALLAHAN, M KIDNEY, J. KUPFNER, S TORRES, C. WADE, S JOHNSTON, D. (2005) Coral Reef Evaluation and Mon itoring Project, 2004 CREMP Executive Summary. Fish and Wildlife Research Institute, St Petersburg 12 p. CLARKE, K. R., and AINSWORTH, M., 1993, A method of linking multivariate community structure to environmental variables: Marine Ecology Progress Serie s, v. 92, p. 205 219. -----, and GORLEY, R. N., 2006, PRIMER v6: User Manual/Tutorial, PRIMER E: Plymouth, UK, 190 p. -----, and WARWICK, R. M ., 2001, Changes in marine communities: an approach to statisti cal analysis and interpretation, 2nd Edition PRI MER E Plymouth, UK, 172 p. COCKEY, E. M., HALLOCK, P., LIDZ, B. 1996, Decadal scale changes in benthic foraminiferal ass emblages off Key Largo, Florida: Coral Reefs, v. 15 p. 237 248. COWEN R., 1988, The role of algal symbiosis in reefs through time: P alaios, v. 3, p. 221 227. CUSHMAN, J. A., 1930, The Foraminiferida of the Atlantic Ocean, Part 7. Nonionidae, Camerinidae, Peneroplidae and Alveolinellidae, U.S. Nat iona l Mus eum Bull etin 104, 79 p. FALKOWSKI P. G., DUBINSKY, Z., MUSCATINE, L., and McCLOS KEY, L. 1993, Population control in symbiotic corals: BioScience v. 43, p. 606 611. FICHTEL, L. von, and von MOLL, J. P. C., 1798, Testacea microscopica, aliaque minuta ex generibus Argonauta et Nautilus ad naturam delineata et descripta (Mikroskopische und andere klein Schalthiere aus den geschlechtern Agonaute und Schiffer, nach der Natur gezeichnet und beschrieben.) Camesina, Wein, 123 p. FISHER, E. M., 2007, Assessing the Health of Coral Reef Ecosystems in the Florida Keys at Community, Individual, a nd Cellular Scales Ph.D. dissertation, University of South Florida, 267 p. FITT, W. K., and WARNER, M. E., 1995 Bleaching patterns of four species of Caribbean reef corals: The Biological Bulletin, v. 189, p. 298 307. -----, BROWN, B. E., WARNER, M. E., DUNNE, R. P., 2001, Coral bleaching: interpretation of thermal tolerance limits and thermal thresholds in tropical corals: Coral Reefs, v. 20, p. 51 65. FORSK L P. 1775 Descriptiones Animalium : Copenhagen Hauniae, Carsten Niebuhr.

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101 FUJITA, K., and HALL OCK, P., 1999, A comparison of phytal substrate preferences of Archaias angulatus and Sorites orbiculus in mixed macroalgal seagrass beds in Florida Bay : Journal of Foraminiferal Research, v. 29, p. 143 151. GLYNN, P, 1996, Coral reef bleaching: facts, hyp otheses and implications: Global Change Biology, v. 2, p. 495 510. GROTTOLI, A. G., RODRIGUES, L. J., PALARDY, J. E., 2006, Heterotrophic plasticity and resilience in bleached corals: Nature, v. 440, p. 1186 1189. HALLOCK, P., 1979, Trends in test shape wi th depth in large, symbiont bearing Foraminifera, Journal of Foraminiferal Research, v. 9, p. 61 69. -----, 1981 Light dependence in Amphistegina : Journal of Foraminiferal Research v. 11 p. 42 48. -----, 1985, Why are larger Foraminifera large?: Paleob iology, v. 11, p. 195 208. -----, 1988 a, Diversification in algal symbiont bearing foraminifera: a response to oligotrophy? : Revue de Paleobiologie, v. 2 (Benthos '86), p. 789 797. -----, 1988 b, Interoceanic differences in fora minifera with symbiotic alg ae: A result of nutrient supplies?: Proceedings of the Sixth International Coral Reef Symposium,Townsville, Australia, 8 th 12th August 1988, v. 3, p. 251 255. -----, 1999, Chapter 8. Symbiont bearing Foraminifera. In Sen Gupta, B. (ed) Modern Foraminifera Kluwer Press, Amsterdam, p. 123 139. (R) -----, 2000a, Symbiont bearing Foraminifera: harbingers of global change?: Micropaleontology, v. 46, p. 95 104. -----2000b, Larger Foraminifers as Indicators of Coral Reef Vitality in Martin, R. (ed.), Environm ental Micropaleontology, Plenum Press Topics in Geobiology, p. 121 150. -----2005 Global change and modern coral reefs: New opportunities to understand shallow water c arbonate depositional processes: Sedimentary Geology v. 175, p. 19 33. -----, and PE EBLES, M. W., 1993, Foraminifera with chlorophyte endosymbionts: Habitats of six species in the Florida Keys: Marine Micropaleontology, v. 20, p. 277 292. -----, BARNES, K., FISHER, E. M., 2004, From satellites to molecules: A multiscale approach to envir onmental monitoring and risk assessment of coral reefs: Journal of Environmental Micropaleontology, Microbiology, and Meiobenthology, v. 1, p. 11 39. -----, FORWARD, L. B., HANSEN, H. J., 1986, Environmental influence of test shape in Amphistegina : Jo urna l of Foraminiferal Research, v. 16 p. 224 231. -----, LIDZ, B. H., COCKEY BURKHARD, E. M., DONNELLY, K. B., 2003a, Foraminifera as bioindicators in coral reef assessment an d monitoring: The FORAM Index: Environmental Monitoring and Assessment v. 81 p. 221 238. -----, TALGE, H.K., SMITH, K., COCKEY, E. M., 1993, Bleaching in a Reef Dwelling Foraminifer, Amphistegina gibbosa : Proceedings of the 7th International Coral Reef Symposium, Guam, June 1992 p 42 47. (R) -----, TALGE, H. K., COCKEY, E. M., MU LLER, R. G., 1995 A new disease in reef dwelling foraminifera: Implicati ons for coastal sedimentation, Journal of Foraminiferal Research v. 25 p. 280 286.

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102 -----, WILLIAMS, D. E., FISHER, E. M., TOLER, S. K., 2006 Bleaching in Foraminifera with algal sy mbionts: implications for reef monitor ing and risk assessment: Anurio do Instituto de Geoscincias UFRJ, v. 29 p. 108 128. HOEGH GULDBERG, O., 1999, Climate change, coral bleaching and the future of the world s coral reefs : Marine and Freshwater Resear ch, v. 50, p. 839 866. HOFKER, J., 1930, Foraminifera of the Siboga Expedition, Part 2. Families Astrorhizidae, Rhizaminidae, Reophacid ae, Amomalinidae, Peneroplidae, in Siboga Expeditie, Monographie Iva. Leiden: E. J. Brill, p. 79 170. IGLESIAS PRIETO, R. and TRENCH, R. K., 1994, Acclimation and adaptation to irradiance in symbiotic dinoflagellates. I. Responses of the photosynthetic unit to changes in photon flux density: Marine Ecology Progress Series, v. 113, p. 163 175. -----, and TRENCH, R. K., 1997 Acclimation and adaptation to irradiance in symbiotic dinoflagellates. II. Responses of chlorophyll protein complexes to different light regimes: Marine Biology, v. 130, p. 23 33. -----, BELTRN, V. H., LAJEUNESSE, T. C., REYES BONILLA, H., THOM, P. E. 2004, Different algal symbionts explain the vertical distribution of dominant reef corals in the eastern Pacific: Proceedings of the Royal Society of London, v. 271, p. 1757 1763. JOKIEL, P. L., and COLES, S. L., 1990, Response of Hawaiian and other Indo Pacific reef corals to elevated temperature : Coral Reefs, v. 8, p. 155 162. KLEIN, C. J. III, and ORLANDO, S. P. JR., 1994, A spatial framework for water quality management in the Florida Keys national Marine Sanctuary: Bulletin of Marine Science, v. 54, p. 1036 1044. KLEYPAS, J. A., BUDDEMEIER, R. W., ARCHER, D., GATTUSO, J P., LANGDON, C., OPDYKE, B. N., 1999, Geochemical Consequences of Increased Atmospheric Carbon Dioxide on Coral Reefs : Science, v. 284, p. 118 120. KUILE, B. TER, 1991, Mechanisms for calcification and carbon cycling in algal symbiont bearing Foraminifera in LEE, J. J., and ANDERSON, O.R. (e ds. ), Biology of Foraminifera: Academic Press, New York p. 73 89. LAMARCK, J. B., 1816, Histoire natur elle des animaux sans vertbres, v. 2 : Verdi re, Paris, 568 p LANGER, M. R. Micropaleontology, v. 46, p. 105 126. LEE J. J. and ANDERSON, O. R. 199 1 Symbiosis in Foraminifera, in LEE, J. J., and ANDERSON, O.R. (eds.), B iology of Foraminifera: Academic Press, London, p. 157 220. LEVY, 1977, R vision micropleontologique des Soritidae actuels Bahamiens, Un nouveau genre: Androsina : Bulletin des Centres de Recherches Exploration Production Elf Aquitaine, v. 1, p. 393 449. ----, 1994, Sur un phnomne de spciation induit par l'environnement chez les Soritidae actuels (foraminifres): Oceanologica acta, v. 17, p. 33 41. LIDZ, B. H., and SHINN, E. A., 1991, Paleoshorelines, reefs and a rising sea: South Florida, U.S.A.: Journ al of Coastal Research, v. 7, p. 203 229.

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103 LIRMAN, D., and FONG, P., 2007, Is proximity to land based sources of coral stressors an appropriate measure of risk to coral reefs? An example from the Florida Reef Tract: Marine Pollution Bulletin, v. 54, p. 779 791. MCCONNAUGHEY, T. A., and WHELAN, J. F., 1997, Calcification generates protons for nutrient and bicarbonate uptake: Earth Science Reviews, v. 42, p. 95 1 17. MURRAY, J., 2006, Ecology and Appli cations of Benthic Foraminifera: Cambridge University Press New York. Paris: Arthus Bertrand. PORTER, J. W., KOSMYNIN, V., PATTERSON, K. L., PORTER, K. G., JAAP, W. C., WHEATON, J. ., HACKETT, K LYBOLT, M., TSOKOS, C. P., YANEV, G., MARCINEK, D. M., DOTTEN, J., EAKEN, D., PATTERSON, M., MEIER, O. W. BRILL, M., DUSTAN, P., 2002, Detection of coral reef change by the Florida Keys coral reef monitoring program. In: Porter JW, Porter KG (eds), The Everglades, Florida Bay, and Coral Reefs of the Florida Keys: an ecosystem sourcebook, CRC Press, Boca Raton, p. 749 769. RAMIREZ, A., 2008, Patch Reefs in Biscayne National Park, FL: Sediments, Foraminiferal Distributions, and a Comparison of Three Biotic Indicators of Reef Health M.S. thesis, University of South Florida 134 p. RENEMA, W., HOEKSEMA, B. W. VAN HINTE, J. E. 2001, Larger benthic foraminifera and their distribution patterns on the Spermonde shelf, South Sulawesi: Zoologische Verhandelingen v. 334, p. 115 149. ROWAN, R., and POWERS, D. A., 1991, A molecular genetic classification of zooxanthellae and evolution of animal algal symbioses: Science, v. 251, p. 1348 1351. SEN GUPTA, B. K. (ed.), 1999 Modern Foraminifera: Kluwer Academic Publish ers, Great Britain, 371 p. SHANNON, C. E., 1948, A mathe matical theory of communication: Bell System Technical Journal v. 27 p. 379 423 and 623 656 SHICK, J. M., LESSER, M. P., JOKIEL, P. L, 1996, Effects of ultraviolet radiation on corals and other cor al reef organisms: Global Change Biology, v. 2, p. 527 545. SMITH, N. P. 2002, Tidal, low frequency and long term mean transport through two channels in the Florida Keys: Continental Shelf Research, v. 22, p. 1643 1650. STABENAU, E. R. ZEPP, R. G., BART ELS, E., ZIKA, R. G., 2004, Role of the seagrass Thalassia testudinum as a source of chromophoric dissolved organic matter in coastal south Florida: Marine Ecology Progress Series, v. 282, p. 59 72. STAT M., CARTER, D., HOEGH GULDBERG, O., 2006, The evolu tionary history of Symbiodinium and scleractinian hosts Symbiosis, diversity, and the effect of climate change : Perspectives in Plant Ecology, Evolution and Systematics v. 8 p. 23 43 SZMANT, A. M., and FORRESTER, A., 1996, Water column and sediment nit rogen and phosphorous distribution patterns in the Florida Keys, USA.: Coral Reefs, v. 15, p. 21 41. TALGE, H. K., WILLIAMS, D. E., HALLOCK, P., HARNEY, J. N., 1997, Symbiont loss in reef foraminifera: Consequences for affected populations: Proceedings of the 8th International Coral Reef Symposium, Panama, v. 1, p. 589 594.

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105 APPENDICES

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106 Appendix A Calculation of the Shannon Index ( ), H max and evenness ( E ), where S is the total number of species and p i is defined as the relative abundance of each species or the number of individuals of a given species over the total number of individuals in the community. (a) (b) (c) (Shannon, 1948)

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107 Appendix B Species density means (per 100cm 2 N=3 except April 1997 for Conch Reef 18m and 30m sites, N=2) with standard error bars at Conch Reef (CR): ( ) sites and Tennessee Reef (TN) sites from 1995 2000 1995 1996 1997 1998 1999 2000 CR TN L. bradyi density (per 100cm 2 )

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108 1995 1996 1997 1998 1999 2000 CR TN P. pertusus density (per 100cm 2 ) Appendix B. Continued.

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109 1995 1996 1997 1998 1999 2000 CR TN S. marginalis density (per 100cm 2 ) Appendix B. Continued.

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110 B. pulchra density (per 100cm 2 ) 1995 1996 1997 1998 1999 2000 CR TN Appendix B. Continued.

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111 1995 1996 1997 1998 1999 2000 CR TN Gypsina density (per 100cm 2 ) Appendix B. Continued.

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112 Appendix C Mean species density (per 100cm 2 ) with standard error (N=3 except where starred, N=2). Sites are listed by site (Conch and Tennessee reefs), year (1995 2000), depth (Conch: 10m, 18m, 30m; Tennessee 8 m, 20m) and month. Note: Table continues on multiple pages. Site Year Depth (m) Month A. gibbosa A. angulatus A carinata B. pulchra B. orbitolitoides C. compressa Conch 1995 10 6 45.47 22.35.6 9.22.7 4.30.7 0.40.2 1.20.3 7 46.217.7 23.45.3 7.12.4 3.10.8 0.60.3 24.68 8 67.329.1 63.19.6 2.51.1 2.81.7 0.60.6 74.571.1 9 100.622.5 19542 .2 4.22.5 5.41.1 91 68.66.7 10 163.254.9 150.413.7 70.9 6.92.1 29.85 77.620.2 11 54.632.2 52.638.1 7.43.7 0.90.5 12.49.8 15.38.6 18 6 105.830.2 5.42.3 12.84.5 2.20.3 0.30.1 21 7 87.525.3 1.20.5 7.23 0.30.2 00 0.60 .1 8 64.327.1 1.10.7 10.32.9 1.40.7 0.30.3 2.21.6 9 128.253.2 20.6 1.80.8 0.70.4 1.40.5 1.40.4 10 132.924.5 2.20.5 40.5 1.20.5 2.51.2 20.6 11 60.87.2 1.50.8 16.85.9 0.40.4 5.92.6 2.20.6 30 6 173.615 0.70.7 6.63 .7 0.40.2 1.10.5 7.60.8 7 227.423 3.81.3 3.51.8 1.60.8 10.4 30.16.7 9 286.5100.4 0.40.4 4.10.8 0.50.5 5.60.8 7215.7 10 475.662.6 6.15.6 4.90.5 3.70.9 47.724.6 81.612 11 158.159.8 0.70.7 22.37.1 3.10.5 10.12.1 40 .917.4 1996 10 1 165.733.2 83.912 16.73.1 50.5 61.514.2 122.618.2 2 93.127.2 111.417.1 12.60.6 3.60.6 12.92.6 160.514.7 3 90.34.6 30.22.1 5.21.6 0.50.3 6.13.5 72.638 6 66.132.5 8.82.5 1.90.9 0.70.5 3.53.5 58.58.6 8 94.812.6 38.99.9 0.90.2 30.7 7.83.9 43.513 9 57.212.6 44.73.5 8.43.9 5.51.1 12.82.2 35.73.2

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113 Conch 1996 10 11 108.530.5 435.5 3.40.6 1.30.5 588.8 25.44.9 18 1 88.519.5 10.7 16.31.5 0.30.3 3.92 2.30.5 2 143.443.1 2.90 .6 17.74.2 2.31.2 6.20.9 7.93.8 3 78.310 0.60.4 27.49.6 10.6 3.30.4 4.60.7 6 52.121.3 0.30.2 1.90.8 0.80.5 0.40.4 30.4 8 63.116.9 0.30.1 22.518.6 20.4 0.60.4 1.90.8 9 78.94.3 2.51.8 4.70.2 0.90.5 3.30.2 5.20.9 11 109.912.5 40.7 3.50.4 10.3 24.63.2 3.90.6 30 1 32581.4 00 16.52.1 1.10.6 16.12.7 32.88.6 2 122.640.6 00 163 0.70.4 4.11.4 10.6 3 223.233.6 00 6.72.3 0.20.2 81.9 5.72.5 6 163.423.5 1.41.2 19.78.2 0.20.2 2.10. 8 4.22.1 8 430.376.1 00 2.70.8 2.70.9 5.11.8 56.416.8 9 150.158.4 00 1.90.9 0.90.3 84.1 26.412.2 11 237.624.1 0.20.2 1.30.7 00 28.68.4 29.56.3 1997 10 3 147.424.3 15.91.4 9.33.7 2.61.3 7.11 44.812.2 6 221.539. 2 17.20.9 205.6 10.13.5 0.70.3 333.6 9 293.853.2 120.421.6 4.21 2.20.9 2.70.3 42.713.5 18 3 95.429.7 0.50.3 13.34.9 20.8 1.90.5 6.93.5 4 193.324 0.40.2 13.23.1 2.71 3.41 21.319.1 6 19036.3 1.20.9 23.45.9 2.70 .9 0.70.4 6.80.8 9 24180.8 3.72.3 21.54.5 10.8 0.20.2 2.41 30 3 217.928.5 0.30.2 6.12 10.1 40.6 26.613 4 192.117.5 0.20.2 6.53 4.62.7 6.25.9 15.87.1 6 234.722.6 0.60.3 1.60.4 0.80.8 2.81.2 47.48.1 9 440 .4124.4 0.80.2 1.90.7 1.50.9 18.54.3 23.18.9 1998 10 1 383.543.9 40.38.2 152.4 1.30.7 18.75.3 5613.8 Appendix C Continued.

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114 Conch 1998 10 4 126.914.1 7.30.7 8.63.6 0.20.2 3.41.8 24.16.5 6 69.716.4 12.22.3 7.33.6 6.61.5 2.50.5 39.410.2 9 7718. 2 71.76.3 2.90.1 1.70.2 2.21.3 234.4 12 81.116.4 20.46.4 8.91.7 0.60.3 5.31 111.9 1 8 1 342.961.9 5.21.5 9.21.4 0.70.1 14.24.4 6.43.5 4 158.624.1 0.60.4 8.62.9 00 1.50.5 0.60.4 6 63.515.1 00 23.38 0.40.4 00 0.70.4 9 41.32.8 0.20.2 4.51.5 0.80.5 0.70.4 0.80.5 12 55.513.5 0.40.4 145.1 00 2.31 1.40.5 30 1 509.813.2 0.30.3 1.80.5 0.60.3 563.6 50.56 4 260.117.4 0.60.6 9.30.3 0.20.2 13.76.3 4.52.1 6 301.348.1 1.10.7 4.61.5 0. 80.1 6.40.6 10.41.3 9 237.355.5 00 0.20.2 0.20.2 1.60.6 3.32.3 12 21118.6 0.40.4 4.71 0.10.1 6.41 20.7 1999 10 3 90.713.2 5.70.4 11.31.4 0.30.2 2.21.1 24.17.3 6 135.522.8 20.22.9 17.95.6 3.93.4 1.30.9 134.2 9 165.551.7 163.732.7 18.62.3 1.90.5 15.97.3 678.2 12 189.350.6 61.121.6 12.83.9 0.50.5 6.53.3 6.42.5 18 3 1329.1 0.50.1 3.81.7 0.40.4 0.60.1 3.10.6 6 90.132.6 1.80.7 43.425.7 00 0.50.3 0.80.8 9 365.3127 8.53.4 15.3 1.9 0.40.2 1.60.8 0.40.2 12 16172 1.71 11.33.6 1.10.6 4.31.9 0.40.4 30 3 246.691.6 0.20.2 10.94.3 0.10.1 0.80.5 2.12.1 6 27254.4 0.50.5 10.95.7 10.5 1.60.1 2.70.6 9 383.960.4 0.50.5 51.9 0.80.4 8.15.2 3.61 1 2 211.481.3 0.70.7 11.21.2 00 7.90.9 41.5 2000 10 4 531.352.6 32.511.4 508.7 1.30.1 60.1 77.828.1 Appendix C Continued.

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1 15 Conch 2000 18 4 107.724.5 1.30.5 50.95.4 0.30.3 0.60.1 1.80.2 30 4 149.126.5 0.50.3 234.5 0.50.3 1.10.8 0.60.3 Tennessee 199 5 7 9 26.66.4 6.91.8 2.80.5 10.7 00 0.20.2 8 6 40.519.8 61.1 7.11.1 0.70.6 0.10.1 4.54.2 20 6 125.647.1 00 0.40.4 00 00 0.40.4 20 9 32.811.1 00 00 00 00 00 1996 7 9 37.13.5 9.84.6 6.72.2 1.60.4 00 5.50.7 8 3 18 .31.5 10.91.7 7.80.7 0.30.1 0.30.1 97.617 8 6 14.96 1.30.1 7.71.2 0.50.3 00 10.24.8 10 1 75.832.5 00 10.52.4 2.21.7 0.10.1 103.735.5 20 1 98.25.4 00 0.10.1 00 0.30.3 00 20 3 127.516.4 00 0.60.6 0.20.2 0.20.2 0.20.1 20 6 80.826.8 00 0.20.2 00 0.50.3 0.10.1 20 9 302109.8 00 0.10.1 0.30.2 00 00 1997 8 3 65.728.4 8.74.8 8.54.6 1.50.2 0.10.1 33.716.9 6 443.4149.8 20.7 20.62.2 1.61.1 00 10.42.1 9 308.885.1 13.97.6 10.92.2 1.31 .3 00 6.13.6 20 3 286.84.1 0.10.1 00 0.10.1 0.80.5 0.40.3 6 219.190.5 0.10.1 0.20.2 00 0.30.2 0.40.2 9 181.531.7 00 0.40.2 00 00 0.10.1 1998 8 1 676.4161.5 21.71 30.93.8 71.3 0.20.2 117.112.8 4 444.7199.9 8.3 4.2 22.14.5 0.50.3 0.80.5 47.516.5 6 475.337.7 19.86.7 51.59.5 3.22.1 00 23.75.5 10 10.33.7 10.5 11.26.1 00 00 0.40.4 20 1 284.454.4 00 0.70.4 00 0.70.4 00 4 151.541.6 00 0.20.2 00 00 00 6 233.970.8 0.30.3 0 .50.5 00 00 0.30.3 Appendix C Continued.

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116 Tennessee 1998 20 10 31.715 0.70.7 44 0.20.2 00 00 1999 8 3 140.340.4 201.6 25.40.4 0.10.1 00 13.14.4 6 231.384.7 18.13.6 36.16.6 1.60.9 00 30.312.6 9 444.6182.7 86.712.8 28.46 2.30.8 00 22.75.7 1999 20 12 86.412.1 34.77.3 15.74.2 0.60.6 0.30.3 4.82.5 3 98.940.6 00 00 00 00 0.20.2 6 64.725.3 0.20.2 0.40.4 0.20.2 00 00 9 22742.9 00 1.20.5 00 00 00 12 76.921.3 0.40.4 0.50.5 00 00 00 2000 8 4 134.83 2.7 55.79.2 84.35.2 1.10.3 0.20.2 37.711 20 4 213.751.2 00 0.70.7 00 00 00 Appendix C Continued.

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117 Site Year Depth (m) Month Gypsina H. antillarium L. bradyi L. proteus P. pertusus S. marginalis Conch 1995 10 6 0.20.2 2.80.4 1.60.4 24.64.1 0.90.4 4.30.4 7 0.20.2 2.80.5 2.30.8 40.16.2 1.60.3 5.62.8 8 00 50.2 3.52.3 53.121.6 4.52.3 178 9 0.20.2 10.34.1 3.41.8 109.335 7.43.4 9.15 10 0.70.7 14.77 3.21.9 104.117.4 5.51.5 8.81.9 11 0.70.4 21.7 5.44.4 42.127.7 0.6 0.3 4.42.6 18 6 0.60.6 6.51.4 6.21.3 37.213.2 3.50.6 10.3 7 10.1 2.60.8 4.51.3 17.62.1 1.20.5 0.70.7 8 1.80.2 2.81.2 6.31.3 20.86.5 3.41.8 1.10.2 9 0.30.3 7.11.5 2.51.1 18.36.5 2.50.7 0.10.1 10 0.30.2 7.61.6 3 .60.3 16.43.3 1.30.2 0.20.2 11 0.80.3 3.50.9 4.51.1 18.31.1 1.80.5 0.80.5 30 6 0.40.4 5.61.2 6.21 49.38.4 0.80.3 1.20.3 7 0.50 7.51.8 3.51.5 31.44.8 0.40.3 0.30.3 9 0.20.2 5.92 2.61.3 16.22.3 1.20.7 0.80.4 10 1.81 16.83.5 7.22.8 56.521.3 6.21.5 2.41.7 11 1.60.3 6.83.8 4.82 34.88.5 2.22.2 0.40.4 1996 10 1 0.70.2 4.90.9 3.60.5 108.810.1 5.31.1 7.32.1 2 0.80.4 81.5 3.50.3 34.91.2 4.11.3 3.30.2 3 2.61.4 5.21.5 3.60.8 32.2 7.2 0.70.1 1.41.4 6 0.20.2 2.71.6 2.11 46.117.1 1.20.5 3.91.2 8 0.50.3 4.30.2 1.50.4 81.919.1 2.81.1 5.71.4 9 0.90.5 4.80.2 4.21.5 74.612.2 7.31.6 7.75.3 11 0.90.5 5.82.4 2.80.7 71.610.6 2.70.7 0.70.1 18 1 0.8 0.4 5.11.3 3.72.2 15.53.7 2.60.9 0.50.3 Appendix C Continued.

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118 Conch 1996 18 2 1.10.6 7.83.3 30.410.4 68.411.5 2.50.5 0.20.2 3 1.60.1 7.23.2 9.82.5 41.810.6 2.81.4 0.20.2 6 0.60.3 3.50.9 1.50.6 140.8 1.30.2 0.30.3 8 0.70.4 4.61.8 4.21.7 24 .32.8 2.80.6 0.90.5 9 0.50.3 8.11.1 6.72.7 28.33.9 31.2 10.6 11 1.40.5 9.82.4 3.91.2 43.16.5 4.31.4 21 30 1 1.10.5 4.91.9 5.62.3 48.13.9 1.20.8 21 2 1.31.2 10.45.1 14.68.4 20.10.5 1.50.7 0.50.2 3 1.61 7.92.9 13.23 38.28.3 2.20.9 00 6 0.60.4 7.22.6 6.61.8 52.91.7 1.20.7 0.50 8 1.40.5 144.2 4.72.1 71.18.2 1.10.6 0.70.4 9 1.10.8 4.63.8 2.71.5 30.612.4 1.10.7 00 11 0.30.3 8.72.3 4.71.8 37.69.6 0.80.8 0.30.3 1997 10 3 1.71.2 3.50.9 2.50.2 38.57.6 2.61.6 41.5 6 1.10.7 1.90.8 4.60.9 114.67.8 4.71.6 2.60.6 9 00 20.5 0.20.2 40.111.2 111.6 0.30.3 18 3 2.81 7.72.5 3.81.7 30.512.3 1.91 0.90.5 4 1.50.4 71.5 8.64.9 65.528.6 2.21. 4 0.50 6 0.80.5 4.91.6 6.51.1 34.92.4 3.70.7 0.90.1 9 0.50.3 2.50.8 0.70.5 202.1 10.61.6 0.60.4 30 3 1.91.1 5.40.6 3.10.4 31.96.4 0.80.1 0.20.2 4 1.90.2 4.52.8 9.14.3 79.310.6 1.51.8 0.10.2 6 0.30.3 7.3 1.9 41.2 45.99.5 2.31.2 00 9 1.30.4 4.60.9 1.60.9 26.38.7 1.80.9 2.41.5 1998 10 1 0.20.2 4.80.3 1.71 58.38.7 3.92 2.90.9 4 10.2 2.51 0.40.4 11.61.3 0.60.3 0.40.2 6 11 4.90.6 3.21.5 88.328.2 3.11.3 7.75.2 Appendix C Continued.

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119 Conch 1998 10 9 0.30.3 4.21.5 1.20.6 59.92.7 8.50.1 0.80.5 12 0.50.2 6.61.2 0.90.5 34.16.4 2.61.1 0.50.2 18 1 0.90.1 8.20.4 62 36.45 2.20 00 4 10.2 2.80.5 10.1 9.50.7 0.40.4 0.20.2 6 1.90.8 2.31.6 1.50.4 21.98.9 0.80. 8 00 9 0.40.4 2.91.2 00 5.91.9 1.90.7 00 12 0.50.1 1.60.4 1.30.4 6.91 1.10.6 00 30 1 2.92 10.41.5 7.92.1 423.2 0.90.6 0.30.3 4 3.81.6 11.92.6 2.80.4 16.41.6 00 00 6 3.11.4 12.92.2 5.71.4 67.28.9 1.91 0.30.3 9 1.70.5 4.71.1 2.41.3 21.13.1 0.20.2 00 12 1.30.5 7.60.5 1.60.3 192.7 2.10.9 0.20.2 1999 10 3 0.40 1.60.8 10.5 16.54.9 1.10.7 1.30.5 6 0.60.4 2.91 2.70.5 65.411.3 2.21.4 2.70.5 9 11 13.30.7 0.70.7 104.911. 8 5.21.3 0.30.3 12 10.1 2.90.4 1.40.6 24.96.9 1.30.6 0.70.2 18 3 0.80.3 3.70.6 10.6 9.80.3 0.70.3 0.50.3 6 2.41.2 2.92.5 5.43 3313.6 21.3 1.60.7 9 0.90.6 15.65.9 2.71.5 28.15.3 5.72.2 1.10.8 12 1.51.1 3.92.1 1 .60.3 8.73.2 1.20.4 00 30 3 1.30.7 8.74.7 1.51.2 18.74.8 0.50.3 0.70.5 6 0.80.8 4.30.5 6.62.1 41.713.3 1.30.5 0.50.3 9 30.2 11.81.6 2.50.6 20.74.7 1.10.8 00 12 1.41 16.98.1 4.10.5 184.7 0.70.7 00 2000 10 4 1. 20.6 8.71.6 3.42 499.2 1.10.3 5.71.4 18 4 0.50.5 2.50.6 3.40.9 24.23.5 1.10.4 0.80.4 30 4 1.91.9 4.92.5 4.30.9 25.32.5 0.30.3 00 Appendix C Continued.

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120 Tennessee 1995 7 9 00 7.21.5 0.70.4 5.91.4 21.2 0.50.3 8 6 0.10.1 2.10.6 0.90.5 10.71. 9 2.81.3 0.50.3 20 6 0.40.2 4.41 00 3.91.1 00 0.20.2 20 9 0.60.3 0.40.4 1.60.6 3.20.5 00 00 1996 7 9 0.30.3 4.91.6 00 17.92.3 4.61.1 0.60.3 8 3 0.70.3 3.61 0.30.1 123.9 0.50.1 0.40 8 6 0.60.4 2.30 0.30.3 13.24 1. 71.3 1.30.6 10 1 0.60.4 7.74.4 1.91 22.26.6 1.81.1 0.40.4 20 1 1.20.3 4.31.5 0.80.5 1.20.3 00 00 20 3 1.80.3 5.50.6 0.50.2 0.90.6 00 00 20 6 0.30.1 1.70.9 0.10.1 1.40.7 0.10.1 00 20 9 1.20.2 4.61 00 7.12.5 0.3 0.2 1.70.9 1997 8 3 1.61.5 1.30.7 0.10.1 10.35.4 2.90.6 1.50.8 6 1.61.4 3.20.7 0.60.4 19.87.3 10.3 10.5 9 00 3.41.4 00 10.92.4 7.82 2.11.8 20 3 1.70.3 41.3 0.60.6 7.32.6 00 00 6 1.10.4 4.12.6 0.60.6 12.66 00 00 9 0.50.3 2.51.4 0.90.6 3.70.3 1.20.9 00 1998 8 1 2.61 23.95.6 0.20.2 28.81.6 7.61.7 1.31.1 4 10.4 10.24.7 0.30.3 2.71.2 1.10.2 0.20.2 6 0.40.4 6.32.1 00 270.4 2.61.1 1.61.6 10 00 10.5 00 0.30.2 0.70.5 0 .20.2 20 1 0.30.3 2.30.9 0.80.8 5.63 1.30.5 00 4 0.20.2 1.60.2 00 0.20.2 00 00 6 00 5.52.1 0.30.3 1.61.2 00 00 10 00 0.10.1 0.10.1 0.10.1 00 00 1999 8 3 0.50.2 3.71.5 0.50.4 4.92.2 1.60.5 0.30.2 Appendix C Co ntinued.

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121 Tennessee 1 999 8 6 1.10.4 9.44.6 2.30.8 25.77.1 3.61.9 2.51.7 9 3.21.6 14.35.8 5.62.6 53.915.8 18.86.9 00 12 0.60.3 2.80.9 0.30.3 51 0.70.7 0.60.3 20 3 1.50.8 1.30.9 00 0.40.2 00 00 6 0.50.5 0.70.4 10.2 62.8 0.70.7 0.20.2 9 00 2.10.3 00 0.30.3 0.20.2 00 12 1.10.7 0.50.2 0.70.4 1.50.3 00 00 2000 8 4 0.20.2 5.21.5 0.50.5 24.511.4 1.91.1 1.40.5 20 4 1.80.9 3.21.7 00 7.33.7 00 00 Appendix C Continued.

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122 Appendix D Species den sity means (per 100cm 2 N=3) with standard error bars for lower, middle and upper Keys sites from summers of 1995, 1996, 2006 and 2007 by reef type: offshore deep (gray fill), offshore shallow (white fill) and patch (crossbar pattern). Sites are listed fr om west to east (left to right). ANOSIM2 results by region and reef type across all years and ANOSIM results by year are presented below with starred R values significant at p<0.05 and double starred R values significant at p<0.01. Note: scales may diffe r. Lower Middle Upper 2007 2006 A. gibbosa density (per 100cm 2 ) W E

PAGE 136

123 A. gibbosa Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0805 OD 0.0217 Upper 0.0248 0.0397 P 0.0174 0.0212 Year 1995 1996 2006 2007 1995 1996 0.1044 2006 0.016 5 0.1121 2007 0.0830 0.1415 0.0073 W E A. gibbosa density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 137

124 Lower Middle Upper 2007 2006 A. angulatus density (per 100cm 2 ) W E Appendix D Continued.

PAGE 138

125 A. angulatus Region Reef type Lower Middle Upper OS OD P Lower OS Middle 0.0695 OD 0.1996 Upper 0.0179 0.2712 ** P 0.0391 0.0184 Year 1995 1996 200 6 2007 1995 1996 0.0553 2006 0.3388 ** 0.3273 ** 2007 0.3122 0.2973 ** 0.0137 W E A. angulatus density (per 100cm 2 ) Lower Middl e Upper 1996 1995 Appendix D Continued.

PAGE 139

126 Lower Middle Upper 2007 2006 A. carinata density (per 100cm 2 ) W E Appendix D Continued.

PAGE 140

127 A. carinata Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0858 OD 0.0542 Upper 0.00 48 0.0096 P 0.1862 ** 0.0091 Year 1995 1996 2006 2007 1995 1996 0.0890 2006 0.0473 0.0031 2007 0.0979 0.0190 0.0107 W E A. carinata density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 141

128 Lower Middle Upper 2007 2006 B. pulchra density (per 100cm 2 ) W E Appendix D Continued.

PAGE 142

129 B. pulchra Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0326 OD 0.0278 Upper 0.0672 0.2000 ** P 0.0353 0.0279 Year 1995 1996 2006 2007 1995 1996 0.0539 2006 0.0383 0.0443 2007 0.1475 0.1197 0.0071 W E B. pulchra density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 143

130 Lower Middle Upper 2007 2006 B. orbitolitoides density (per 100cm 2 ) W E Appendix D Continued.

PAGE 144

131 B. orbitolitoid es Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0497 OD 0.0212 Upper 0.0777 0.3175 ** P 0.0450 0.0019 Year 1995 1996 2006 2007 1995 1996 0.1275 2006 0.3624 ** 0.0962 2007 0.5305 * 0.1994 0.0028 W E B. orbitolitoides density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continu ed.

PAGE 145

132 Lower Middle Upper 2007 2006 C. compressa density (pe r 100cm 2 ) W E Appendix D Continued.

PAGE 146

133 C. compressa Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0630 OD 0.0678 Upper 0.0371 0.1127 P 0.0934 0.0259 Year 1995 1996 2006 2007 1995 1996 0.2402 2006 0.4445 ** 0.0566 2007 0.3278 0.0254 0.0032 W E C. compressa density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 147

134 Lower Middle Upper 2007 2006 Gypsina density (per 100cm 2 ) W E Appendix D Continued.

PAGE 148

135 Gypsina Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0017 OD 0.0435 Upper 0.0130 0.0686 P 0.0327 0.0428 Year 1995 1996 2006 2007 1995 1996 0.2595 2006 0.0516 0.0647 2007 0.5622 0.1323 0.1000 W E Gypsina density (per 10 0cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 149

136 Lower Middle Upper 2007 2006 H. antillarium density (per 100cm 2 ) W E Appendix D Continued.

PAGE 150

137 H. antillarium Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0137 OD 0.0232 Upper 0.0282 0.0401 P 0.1626 ** 0.0085 Year 1995 1996 2006 2007 1995 1996 0.0906 2006 0.1689 0.1099 2007 0.1432 0.1079 0.0143 W E H. antillarium density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 151

138 Lower Middle Upper 2007 2006 L. bradyi density (per 100cm 2 ) W E Appendix D Continued.

PAGE 152

139 L. bradyi Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0299 OD 0.0218 Upper 0.0284 0.1978 P 0.0495 0.0074 Year 1995 1996 2006 2007 1995 1996 0.0858 2006 0.0979 0.0811 2007 0.0315 0.0077 0.0032 W E L. bradyi density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 153

140 Lower Middle Upper 2007 2006 L. proteus density (per 100cm 2 ) W E Appendix D Continued.

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141 L. proteus Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0309 OD 0.0524 Upper 0.0203 0.1916 P 0.0284 0.0574 Year 1995 1996 2006 2007 1995 1996 0.0242 2006 0.2417 0.0616 2007 0 .2507 0.0441 0.0048 W E L. proteus density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 155

142 Lower Middle Upper 2 007 2006 P. pertusus density (per 100cm 2 ) W E A ppendix D Continued.

PAGE 156

143 P. pertusus Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0256 OD 0.0124 Upper 0.0494 0.1269 P 0.0365 0.0284 Year 1995 1996 2006 2007 1995 1 996 0.0566 2006 0.3309 0.3740 ** 2007 0.1574 0.1767 0.1219 ** W E P. pertusus density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

PAGE 157

144 Lower Middle Upper 2007 2006 S. marginalis density (per 100cm 2 ) W E Appendix D Continued.

PAGE 158

145 S. marginalis Region Reef Type Lower Middle Upper OS OD P Lower OS Middle 0.0353 OD 0.3122 ** Upper 0.0063 0.0822 P 0.2348 ** 0.0 524 Year 1995 1996 2006 2007 1995 1996 0.0130 2006 0.0060 0.2281 ** 2007 0.0345 0.1829 0.0145 W E S. marginalis density (per 100cm 2 ) Lower Middle Upper 1996 1995 Appendix D Continued.

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146 Appendix E Mean species density (per 100cm 2 ) with standard error (N=3, except where starred, N=2). Sites are listed alphabetically by year (2007, 2006, 1996, 1995) and region (upper, middle and lower Keys). Inter region means SE are highlighted in gray Note: Table continues on multiple pages. Year Region Site A. gibbosa A. angula tus A. carinata B. pulchra B. orbitolitoides C. compressa 2007 Upper Admiral Patch 82.147.3 23.716.2 0.80.8 0.90.5 1.21.2 3.23.2 Algae Reef 57.419.1 83.7 1.70.6 0.50.3 4.52 1.10.6 Carysfort Deep 126.732.5 2.10.7 1.10.7 1.30.9 5.63 .3 3.51.4 Carysfort Shallow 157.320 19.65.1 7.42.1 1.10.7 13.32.5 33.410.8 Conch Reef Deep 332.9113 11.33.8 19.76.7 9.32 31.825.9 5.72.3 Conch Reef Shallow 70.136.5 11.18.4 5.43.1 3.22.1 1.41.4 10.76.9 Grecian Rocks 83.125. 8 15.73.7 0.60.3 1.70.7 4.40.3 2.91.1 Molasses Deep 7113.1 6.31.9 12.52.9 20.6 6.52 31.58.5 Molasses Shallow 45.98.8 22.58.3 20.412.6 2.91.2 1.80.8 9.23.2 Porter Patch 24.215 86.819.5 1.91.2 1.91.5 2.71.2 0.60.3 Three Si sters 59.816.7 6.93.1 0.40.4 2.20.5 3.72.3 0.20.2 Turtle Patch 49.25.7 84.2 1.11.1 1.11.1 0.80.8 12.610.8 White Banks 50.15.5 3.90.7 2.51.4 00 0.70.4 0.50.3 93.1 22.2 17.4 6.1 5.8 2 2.2 0.6 6 2.3 8.9 3.1 Middle Alligator De ep 252.9107.5 22.313.6 17.97.1 4.42.1 14.16.2 56.232.1 Alligator Shallow 401.9187.8 11.15 11.74.2 1.90.5 11 17.84.2 Dustan Rocks 57.718.6 00 00 00 00 00 East Washerwoman 146.427 9.81.2 00 0.50.5 00 6.71.7 Looe Key Deep 561.3166.5 7.54.7 6.82.4 2.12.1 11.54.8 2.10.2 Looe Key Shallow 132.849.4 18.65.5 30.77.5 3.20.7 5.61.2 7.10.5 Sombrero Deep 55.511.7 00 0.90.5 00 1.61.6 00 Sombrero Shallow 13585.8 6.70.3 6.63.3 1.40.5 20.2 2.70.6 Tenn essee Reef Deep 287.371.6 0.50.5 2.20.3 0.90.5 11 3.10.6

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147 Tennessee Reef Shallow 377.531.9 50.114.8 112.732.4 5.50 1.11.1 47.210.8 West Turtle Shoal 53.242.2 00 1.11.1 00 0.30.3 00 223.8 50.6 11.5 4.5 17.3 10 1.8 0.6 3.5 1.5 13 6 2007 Lower Cliff Green 8.15.3 0.50.5 00 00 0.70.3 0.20.2 Eastern Sambo Deep 31.913.5 00 00 00 2.81.9 0.50.2 Eastern Sambo Shallow 75.18.6 44.36.3 13.22 4.31.8 9.22.4 25.29.5 Jaap Reef 0.20.2 48.94.9 0.20.2 1.50.5 6.61. 5 69.913.1 Rock Key Deep 303.768.8 7.92.8 30.3 0.40.4 17.57.5 145.961.5 Rock Key Shallow 61.614.7 55.319 18.63.7 1.40.9 0.30.3 112.9 Sand Key Deep 13642 13.54.8 7.84.2 0.40.4 13.49.6 73.525.6 Sand Key Shallow 19074.7 184.7 6.21.6 2.21.2 12.91.7 93.122.3 Seagrass Patch 11.82.1 144.926 6.81.4 0.50.5 00 16.44.3 West Washerwoman 78.131.4 12.81 0.70.3 00 0.90.5 00 Western Head 0.60.3 00 00 00 0.50.2 00 Western Sambo Deep 80.19.4 1.10.4 0.40 .4 00 2.60.7 1.70.4 Western Sambo Shallow 94.638.9 8532.4 16.411.8 2.31.2 2.90.6 30.313.1 82.4 24.1 33.2 11.9 5.6 1.8 1 0.4 5.4 1.6 36 12.8 2006 Upper Admiral Patch 42.613.2 221.740.5 0.50.5 1.91 2.51.5 6.81 Algae Reef 128.371 59.526.9 41.2 2.81.5 37.726.1 3.51.6 Carysfort Deep 344.887.1 7.84.1 1.21.2 30.6 4.81.1 9.13.6 Carysfort Shallow 227.671.5 9211.3 10.62.7 3.93 359.2 36.813.7 Conch Reef Deep 92.731.7 61.4 7.22.3 3.31 158.3 25.15.2 Conch Reef Shallow 133.132.8 15.74.4 91.6 51.1 4.22.6 10.41.8 Grecian Rocks 38.94.4 76.41.3 17.83.7 2.71.1 21.73 3.20.8 Molasses Deep 203.221.7 75.417 49.412.5 13.96.8 40.611.9 130.949.6 Molasses Shallow 136.129.1 19.612.2 20.64 8. 14.9 6.53.4 5.72.4 Porter Patch 40.921.8 72.913.3 20.4 0.50.5 9.52.1 1.50.8 Appendix E Continued.

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148 Three Sisters 119.943.7 18.94 1.51.5 21.5 3.40.9 0.40.4 Turtle Patch 293.541.1 21.312 0.60.6 0.80.8 3.23.2 2.61.3 White Banks 137.66.3 38.47 .8 1.51.5 8.61.6 8.62.6 22 149.2 26.4 55.8 16.1 9.7 3.8 4.4 1.1 14.8 3.9 18.3 9.8 2006 Middle Alligator Deep 210.799.8 165.2 12.14.4 0.40.4 3.21.9 52.34.6 Alligator Shallow 71.313.7 19.85.8 10.42.6 0.50.5 0.90.5 15.24.5 Dustan Ro cks 52.632.8 0.50.5 00 00 00 0.50.5 East Washerwoman 21830.1 10.43.1 1.51.5 00 00 11.82.2 Looe Key Deep 58.414 3.82.3 19.14.4 2.61.5 1.50.4 13.66.5 Looe Key Shallow 176.525.5 9.15 24.52.3 1.91 00 8.81.7 Sombrero Deep 1 16.844.8 0.40.4 49.424.7 00 0.90.9 53.9 Sombrero Shallow 131.530.3 15.26.8 32.21.5 5.83.4 3.41.3 19.73 Tennessee Reef Deep 94.229.4 00 5.32.6 10.5 00 5.73.9 Tennessee Reef Shallow 142.587.8 21.811.1 31.62.6 1.50.5 0.30.3 57 19.2 West Turtle Shoal 14.38.8 00 5.42.1 00 00 00 117 20 8.8 2.5 17.4 4.7 1.3 0.5 0.9 0.4 17.2 5.9 Lower Cliff Green 151.632.2 0.50.5 00 00 1.30.7 00 Eastern Sambo Deep 160.921.8 10.5 00 00 0.60.6 1.61.2 Eastern Sambo Sha llow 225.266.2 19.91.5 5.14.5 3.71.3 1.70.3 24.15.7 Jaap Reef 1.31.3 74.814.6 00 00 3.12.3 124.659.5 Rock Key Deep 164.669.9 4.32.7 0.80.8 0.80.8 7.73.4 18.310.8 Rock Key Shallow 179.645.1 65.621.6 3.51.9 00 30.7 19.75 Sand Key Deep 43.617.5 7.61.2 12.63.5 0.50.5 2.92.9 7.82.6 Sand Key Shallow 138.116.8 90.8 1.20.6 0.60.6 3.30.8 29.71.8 Seagrass Patch 8427.2 3710 7.62.2 3.12 00 11.54.7 West Washerwoman 18.14.1 00 00 00 0.60.6 00 West ern Head 1.10.6 00 00 00 00 00 Appendix E Continued.

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149 Western Sambo Deep 104.618.6 2.60.8 00 0.60.6 2.11.7 4.70.9 Western Sambo Shallow 46.415.4 20.67.1 0.50.5 00 1.40.8 20.37.3 101.5 20.7 18.7 7 2.4 1.1 0.7 0.3 2.1 0.6 20.2 9.1 1996 Upper Carysfo rt Deep 88.236.3 0.60.4 0.20.2 0.10.1 3.21.1 5.43.5 Carysfort Shallow 7214 11 10.6 2.31.2 42 23.611.1 Molasses Deep 218.926.5 0.50.5 5.91.7 0.60.4 1.20.4 72.365.4 Molasses Shallow 69.628.7 6.32 5.52.3 0.30.3 0.20.2 9.21.7 112.2 35.8 2.1 1.4 3.1 1.5 0.8 0.5 2.2 0.9 27.6 15.4 Middle Alligator Deep 96.718.1 0.30.1 0.30.1 00 00 00 Alligator Shallow 64.516.9 204.8 3.51 5.81.4 5.32.4 14.53.6 Looe Key Deep 118.13.1 0.10.1 3.51.1 1.50.8 0.50.3 2.10.5 Looe Key Shallow 47.216.8 00 13.74.8 00 00 0.70.1 Sombrero Deep 108.813.9 00 1.20.8 0.40.2 0.80.4 0.20.2 Sombrero Shallow 13555.4 21.2 5.11.8 1.30.9 0.10.1 8.96.2 95 13.6 3.7 3.3 4.5 2 1.5 0.9 1.1 0.8 4.4 2.4 Lower Sand Key D eep 43.111.4 0.90.3 0.10.1 0.20.2 0.80.1 1.40.5 Sand Key Shallow 173.666.8 3.21.6 20.2 00 3.91.4 18.72 Western Sambo Deep 115.835.3 0.10.2 0.30.2 00 00 0.70.4 Western Sambo Shallow 8941.3 00 0.20.2 00 00 0.60.4 105.4 2 7.3 1 0.7 0.7 0.5 0 0 1.2 0.9 5.4 4.4 1995 Middle Looe Key Deep 147.828.5 0.30.2 5.63.8 0.90.5 0.20.2 0.60.6 Looe Key Shallow 61.939.7 10.96.2 16.89.8 0.70.2 00 0.80.6 Sombrero Deep 60.65.6 1.10.3 1.70.6 0.30.3 00 00 Sombr ero Shallow 4542.2 3.42.1 2.20.7 11.3 00 11.3 78.8 23.3 3.9 2.4 6.6 3.5 0.7 0.2 0 0 0.6 0.2 Lower Sand Key Deep 64.97.1 2.21.3 00 0.30.3 10.3 1.40.9 Sand Key Shallow 46.27.3 00 0.40.2 0.30.2 1.61.1 14.43.7 Appendix E Continued.

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150 Western Sambo Deep 65.332.1 0.20.2 00 0.10.1 00 00 Western Sambo Shallow 73.116.2 0.30.2 0.50.3 0.20.2 00 00 62.4 5.7 0.7 0.5 0.2 0.1 0.2 0 0.7 0.4 3.9 3.5 Appendix E Continued.

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151 Year Region Site Gypsina H. antillarium L. bradyi L. proteus P. pertusus S. marginal is 2007 Upper Admiral Patch 3.11.5 0.30.3 5.33.1 7425.4 2.91.1 2.31.5 Algae Reef 4.82.5 3.21.9 0.30.3 22.36.4 1.21.2 0.60.3 Carysfort Deep 0.30.3 11.34.5 0.60.3 37.58.4 00 0.50.5 Carysfort Shallow 00 3.11.2 11.32.2 84.119. 7 3.70.8 3.12.4 Conch Reef Deep 1.40.7 1.51.5 14.33.9 112.98.6 3.31.4 21.3 Conch Reef Shallow 0.40.4 6.84.8 3.61.9 24.213.9 3.23.2 10.36.7 Grecian Rocks 0.50.3 2.90.6 00 37.28.8 2.10.7 0.30.3 Molasses Deep 1.70.5 5.81.8 3 .90.8 48.81.8 5.72.4 1.10.8 Molasses Shallow 0.70.1 12.45.9 6.22.2 52.120.6 6.63.1 7.63 Porter Patch 0.30.3 1.81.1 00 34.610.8 1.10.3 0.80.4 Three Sisters 0.70.7 2.40.6 6.11.1 33.317.1 50.9 20.8 Turtle Patch 0.80.4 1.4 0.2 1.40.2 30.914.1 1.11.1 00 White Banks 2.10.9 20.6 3.42.3 10.64.7 1.91 00 1.3 0.4 4.2 1.1 4.3 1.2 46.3 7.9 2.9 0.5 2.4 0.9 Middle Alligator Deep 2.11.5 4.42.1 8.93.7 66.629.7 2.91.8 2.40.8 Alligator Shallow 0.80.4 7.71.6 20.5 31.810 1.40.8 9.33.8 Dustan Rocks 1.91 2.20.4 00 1.70.3 0.50.2 0.90.6 East Washerwoman 1.10.7 42 0.30.3 13.23.2 1.40.7 2.60.5 Looe Key Deep 0.70.4 11.63.4 6.51.8 46.77.4 3.42.3 10.5 Looe Key Shallow 0.30.3 5.92.3 1.41 43.57.5 3.21.1 4.90.9 Sombrero Deep 0.90.6 1.60.7 00 4.82.1 0.60.6 0.30.3 Sombrero Shallow 0.80.1 6.11.4 0.80.8 23.36.9 20.2 42.6 Tennessee Reef Deep 22 12.55.7 1.11.1 11.13 0.40.4 2.41.1 Tennessee Reef Shallow 2.60. 4 16.10.4 8.83.3 94.88.2 3.71.3 13.51.4 West Turtle Shoal 0.90.5 1.11.1 1.30.2 3.80.8 0.70.4 00 1.3 0.2 6.7 1.5 2.8 1 31 8.9 1.8 0.4 3.8 1.3 Appendix E Continued.

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152 Lower Cliff Green 11 0.90.6 00 0.80.4 0.20.2 0.30.3 Eastern Sambo Deep 0.30.3 2.8 1.1 0.30.3 9.15.8 1.10.7 0.30.3 Eastern Sambo Shallow 0.60.3 12.44.6 8.32.1 48.95.6 2.20.6 101.8 Jaap Reef 0.60.3 00 00 116.655 4.21.7 63 Rock Key Deep 0.80.8 188 12.87.2 11124.3 2.61.8 4.10.5 Rock Key Shallow 0.90.9 6.7 3 10.86.6 32.711.9 1.81.3 6.22.1 Sand Key Deep 1.70.4 4.81.8 8.74.9 5212.7 2.31.2 6.83 Sand Key Shallow 1.20.6 4.82.5 5.71.4 69.66.7 1.80.7 6.42.9 Seagrass Patch 2.61.3 0.40.4 1.81.3 19.84.3 0.90.4 3.21.9 West Washerwoma n 21.2 4.52 0.70.3 24.53.8 20.6 1.30.8 Western Head 00 0.50.5 00 00 00 00 Western Sambo Deep 0.80.1 20.9 1.71 130.5 00 10.2 Western Sambo Shallow 0.40.4 4.84.8 6.41.7 286.7 1.71 4.90.7 1 0.2 4.8 1.4 4.4 1.3 40.5 10.6 1.6 0.3 3.9 0.9 2006 Upper Admiral Patch 1.11.1 1.70.9 162.9 39.28.1 3.71.1 42.5 Algae Reef 0.60.6 86.1 6.93.4 42.617.6 9.16.4 3.31.6 Carysfort Deep 3.13.1 7.22.7 7.83.2 46.214.1 5.41 1.81 Carysfort Shallow 0.60.6 2.20.6 15 .84.5 41.47.4 4.42.3 8.31.3 Conch Reef Deep 00 3.21.6 13.55.1 54.512 5.21.1 8.41.5 Conch Reef Shallow 00 3.61.4 3.51.4 15.40.2 8.52.2 4.61.1 Grecian Rocks 00 2.30.8 10.43.1 40.66.8 5.92.3 1.20.6 Molasses Deep 11 6.13.1 35.915.2 64.212.4 19.51.1 7.53.4 Molasses Shallow 8.28.2 25.220.8 12.32.6 91.446.8 84.2 11.32.8 Porter Patch 10.5 2.51.4 0.50.5 10.91.6 4.92.5 1.50.9 Three Sisters 00 1.10.5 7.15 34.816.3 4.22.9 1.11.1 Turtle Patch 0.8 0.8 3.40.3 5.92.2 40.57 7.65.1 2.11.1 White Banks 0.50.5 10.5 9.52.8 17.15.3 12.82.8 1.50.9 Appendix E Continued.

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153 1.3 0.6 5.2 1.8 11.2 2.4 41.5 5.9 7.6 1.2 4.4 0.9 Middle Alligator Deep 1.70.9 41.3 3.21.7 40.87 0.80.8 2.20.4 Alligator Shallow 0.4 0.4 2.91 4.42 32.46.3 4.60.8 31.4 Dustan Rocks 1.20.9 1.91.3 00 3.81 4.42.5 0.50.5 East Washerwoman 10.5 3.81.7 00 20.52.4 4.32.3 5.10.4 Looe Key Deep 0.40.4 3.42 21.94.9 55.310.9 5.93.7 2.11.2 Looe Key Shallow 00 5.8 0 0.60.6 50.25.3 61 3.92.6 Sombrero Deep 00 1.71.1 2.31.2 12.33.8 42.7 00 Sombrero Shallow 0.40.4 9.13.6 6.23.1 117.910.4 22.68.8 5.52.2 Tennessee Reef Deep 00 1.60.5 00 14.32.8 5.22 0.30.3 Tennessee Reef Shallow 0.40.4 4 .93.1 1.21.2 47.515.6 3.10.4 11.55.4 West Turtle Shoal 1.40.7 00 00 21.4 3.62.3 00 0.6 0.2 3.6 0.7 3.6 1.9 36.1 10 5.9 1.7 3.1 1 Lower Cliff Green 00 7.73.1 00 00 1.71 1.61.6 Eastern Sambo Deep 00 2.20.9 1.30.7 30.26.1 1. 91 0.60.6 Eastern Sambo Shallow 0.70.4 3.70.9 8.65.9 42.212.4 4.51.9 12.65.2 Jaap Reef 00 0.60.6 00 5.81.3 2.22.2 00 Rock Key Deep 1.10.7 4.61.9 3.61 20.25.7 1.61 3.81.7 Rock Key Shallow 00 2.70.6 42.3 42.88.9 0.70.7 1 7.16.5 Sand Key Deep 0.80.8 0.50.5 1.90.3 14.98.4 3.62.1 2.42.4 Sand Key Shallow 0.50.5 4.61.3 8.81.9 33.85.3 2.71.6 13.25 Seagrass Patch 00 1.90.7 14.93.6 47.712.3 1.71 1.71.7 West Washerwoman 00 1.90.2 00 0.60.6 00 0 0 Western Head 00 0.40.4 00 00 00 00 Western Sambo Deep 1.10.6 2.31.2 2.11 29.32 6.95.5 3.42.5 Western Sambo Shallow 00 0.80.4 7.22.5 45.113.6 2.21.1 14.29.5 0.3 0.1 2.6 0.6 4 1.3 24.1 5.1 2.3 0.5 5.4 1.8 Appendix E Continued.

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154 1996 Upper Cary sfort Deep 0.40.4 10.33.2 0.70.5 17.85.6 00 00 Carysfort Shallow 0.10.1 40.4 2.40.8 57.97.1 1.50.5 0.70.2 Molasses Deep 0.70.4 9.30.7 5.21.2 103.96 0.70.2 00 Molasses Shallow 0.20.2 2.60.6 4.51.6 29.15.8 2.90 0.60.6 0.4 0.1 6.6 1.9 3.2 1 52.2 19.2 1.3 0.6 0.3 0.2 Middle Alligator Deep 0.10.1 0.80.4 1.90.5 9.35.3 0.20.2 0.50.5 Alligator Shallow 0.30.1 4.32 1.20.7 38.17.4 3.91.8 1.10.3 Looe Key Deep 10.3 31.2 1.50.4 16.52.7 1.10 0.70.2 Looe Key Shallow 0.40.2 3.11.1 0.20.2 7.90.9 0.30.1 00 Sombrero Deep 0.80.2 20.6 1.70.5 14.22.3 0.40.2 0.40.2 Sombrero Shallow 0.30.3 61.9 0.50.5 269.8 3.11.4 1.10.9 0.5 0.1 3.2 0.7 1.2 0.3 18.7 4.7 1.5 0.7 0.6 0.2 Lower Sand Key Deep 0.70.4 3.21.1 0.50.5 6.12.4 0.50.3 0.10.1 Sand Key Shallow 1.20.5 92 0.50 24.50.9 4.32.4 0.70.2 Western Sambo Deep 0.90.1 2.41.2 0.10.2 5.62 0.10.2 0.80.6 Western Sambo Shallow 0.50.4 3.10.4 0.40.5 2.82.4 00 1.60.5 0. 8 0.2 4.4 1.5 0.4 0.1 9.8 5 1.2 1 0.8 0.3 1995 Middle Looe Key Deep 0.20.2 4.21.7 3.62 21.95.5 3.42 1.51 Looe Key Shallow 0.20.3 4.62.1 00 16.49.5 2.42.2 2.91.8 Sombrero Deep 00 2.51 1.20.2 3.81.3 00 0.30.3 Sombrero Shallo w 0.50.6 2.31.2 2.30.9 13.36.2 0.40.5 0.50.1 0.2 0.1 3.4 0.6 1.8 0.8 13.8 3.8 1.6 0.8 1.3 0.6 Lower Sand Key Deep 0.20.2 71.4 1.31.1 9.12.3 1.31.3 0.30.2 Sand Key Shallow 0.40.4 51.3 0.90.1 16.51.5 3.81.9 31.2 Western Sa mbo Deep 0.10.2 2.80.8 00 2.10.8 0.20.2 1.91.2 Western Sambo Shallow 0.50.5 2.60.6 1.61.3 7.32.2 1.91.4 1.60.9 0.3 0.1 4.3 1 0.9 0.3 8.8 3 1.8 0.8 1.7 0.6 Appendi x E Continued.

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155 Appendix F Proportion of total assemblage by symbiont type for Keys wide sites in 2007, 2006, 1996 and 1995. Sites are listed alphabetically by year starting with the most recent data. Note: Table continues on multiple pages. Symbiont Year Site Diatom Chlorophyte Rhodophyte Dinoflagellate 2 007 Admiral Patch 0.421 0.537 0.014 0.011 2007 Algae Reef 0.595 0.343 0.011 0.005 2007 Alligator Deep 0.614 0.369 0.006 0.005 2007 Alligator Shallow 0.849 0.128 0.003 0.019 2007 Carysfort Deep 0.737 0.259 0.000 0.003 2007 Carysfort Shallow 0.501 0.479 0.011 0.009 2007 Cliff Green 0.706 0.173 0.019 0.026 2007 Conch Reef Deep 0.665 0.322 0.006 0.004 2007 Conch Reef Shallow 0.569 0.339 0.021 0.069 2007 Dustan Rocks 0.922 0.027 0.007 0.014 2007 East Washerwoman 0.811 0.161 0.008 0.014 2007 Ea stern Sambo Deep 0.707 0.258 0.023 0.006 2007 Eastern Sambo Shallow 0.414 0.536 0.009 0.040 2007 Grecian Rocks 0.583 0.398 0.014 0.002 2007 Jaap Reef 0.008 0.950 0.016 0.024 2007 Looe Key Deep 0.880 0.112 0.005 0.001 2007 Looe Key Shallow 0.671 0.29 6 0.013 0.019 2007 Molasses Deep 0.464 0.493 0.029 0.006 2007 Molasses Shallow 0.433 0.487 0.035 0.040 2007 Porter Patch 0.190 0.796 0.007 0.005 2007 Rock Key Deep 0.518 0.470 0.004 0.007 2007 Rock Key Shallow 0.426 0.531 0.009 0.030 2007 Sand Key D eep 0.464 0.502 0.007 0.021 2007 Sand Key Shallow 0.494 0.484 0.004 0.016 2007 Seagrass Patch 0.093 0.876 0.004 0.015 2007 Sombrero Deep 0.876 0.097 0.010 0.004 2007 Sombrero Shallow 0.779 0.185 0.010 0.021 2007 Tennessee Reef Deep 0.933 0.052 0.001 0.007 2007 Tennessee Reef Shallow 0.698 0.275 0.005 0.018 2007 Three Sisters 0.528 0.409 0.041 0.017 2007 Turtle Patch 0.488 0.495 0.010 0.000 2007 West Turtle Shoal 0.888 0.086 0.012 0.000 2007 West Washerwoman 0.653 0.305 0.016 0.010 2007 Weste rn Head 0.684 0.316 0.000 0.000 2007 Western Sambo Deep 0.791 0.192 0.000 0.009 2007 Western Sambo Shallow 0.425 0.549 0.006 0.018

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156 2007 White Banks 0.703 0.245 0.025 0.000 2006 Admiral Patch 0.137 0.838 0.011 0.012 2006 Algae Reef 0.467 0.490 0.0 30 0.011 2006 Alligator Deep 0.654 0.333 0.002 0.006 2006 Alligator Shallow 0.513 0.438 0.028 0.018 2006 Carysfort Deep 0.806 0.171 0.012 0.004 2006 Carysfort Shallow 0.510 0.462 0.009 0.017 2006 Cliff Green 0.969 0.011 0.010 0.010 2006 Conch Reef D eep 0.454 0.488 0.022 0.036 2006 Conch Reef Shallow 0.707 0.231 0.040 0.022 2006 Dustan Rocks 0.835 0.073 0.067 0.007 2006 East Washerwoman 0.808 0.154 0.016 0.018 2006 Eastern Sambo Deep 0.814 0.173 0.010 0.003 2006 Eastern Sambo Shallow 0.675 0.27 4 0.013 0.036 2006 Grecian Rocks 0.279 0.689 0.027 0.005 2006 Jaap Reef 0.009 0.981 0.010 0.000 2006 Looe Key Deep 0.444 0.511 0.031 0.011 2006 Looe Key Shallow 0.726 0.239 0.021 0.014 2006 Molasses Deep 0.421 0.536 0.030 0.012 2006 Molasses Shallo w 0.538 0.384 0.023 0.032 2006 Porter Patch 0.309 0.642 0.033 0.010 2006 Rock Key Deep 0.738 0.234 0.007 0.016 2006 Rock Key Shallow 0.549 0.399 0.002 0.050 2006 Sand Key Deep 0.577 0.354 0.036 0.024 2006 Sand Key Shallow 0.589 0.345 0.011 0.054 200 6 Seagrass Patch 0.458 0.526 0.008 0.008 2006 Sombrero Deep 0.871 0.108 0.021 0.000 2006 Sombrero Shallow 0.483 0.440 0.061 0.015 2006 Tennessee Reef Deep 0.800 0.157 0.040 0.002 2006 Tennessee Reef Shallow 0.558 0.395 0.010 0.035 2006 Three Sisters 0.640 0.332 0.022 0.006 2006 Turtle Patch 0.780 0.192 0.020 0.006 2006 West Turtle Shoal 0.739 0.075 0.135 0.000 2006 West Washerwoman 0.943 0.057 0.000 0.000 2006 Western Head 1.000 0.000 0.000 0.000 2006 Western Sambo Deep 0.673 0.255 0.043 0.0 21 2006 Western Sambo Shallow 0.300 0.596 0.014 0.090 2006 White Banks 0.622 0.316 0.053 0.006 1996 Alligator Deep 0.888 0.105 0.002 0.004 1996 Alligator Shallow 0.481 0.487 0.024 0.007 1996 Carysfort Deep 0.779 0.218 0.000 0.000 1996 Carysfort Shal low 0.465 0.521 0.009 0.004 Appendix F Continued.

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157 1996 Looe Key Deep 0.843 0.139 0.007 0.004 1996 Looe Key Shallow 0.871 0.120 0.004 0.000 1996 Molasses Deep 0.560 0.437 0.002 0.000 1996 Molasses Shallow 0.596 0.376 0.022 0.005 1996 Sand Key Deep 0.808 0.168 0.009 0.002 1996 Sand Key Shallow 0.764 0.210 0.018 0.003 1996 Sombrero Deep 0.859 0.129 0.003 0.003 1996 Sombrero Shallow 0.778 0.198 0.016 0.006 1996 Western Sambo Deep 0.933 0.052 0.001 0.007 1996 Western Sambo Shallow 0.940 0.039 0.000 0.016 1995 Looe Key Dee p 0.833 0.140 0.018 0.008 1995 Looe Key Shallow 0.715 0.238 0.021 0.024 1995 Sand Key Deep 0.812 0.168 0.015 0.004 1995 Sand Key Shallow 0.561 0.361 0.041 0.033 1995 Sombrero Deep 0.910 0.086 0.000 0.004 1995 Sombrero Shallow 0.703 0.278 0.005 0.007 1995 Western Sambo Deep 0.939 0.032 0.002 0.025 1995 Western Sambo Shallow 0.852 0.103 0.021 0.018 Appendix F Continued.