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Dynamics of stony coral assemblages on patch reefs of the upper florida reef tract, including biscayne national park

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Title:
Dynamics of stony coral assemblages on patch reefs of the upper florida reef tract, including biscayne national park
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Wallace, Amy
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Agrra
Benthic Community
Photo-transect
Primer
Dissertations, Academic -- Biological Oceanography -- Masters -- USF   ( lcsh )
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bibliography   ( marcgt )
non-fiction   ( marcgt )

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ABSTRACT: The patch reefs located in Biscayne National Park (BNP) are some of the most northern reefs of the Florida reef system. The focus of my study is seven patch reefs that were first surveyed annually between 1977 and 1981, revealing 8% - 28% cover by scleractinian corals. An assessment of BNP patch reefs completed in 2000 reported that coral cover had decreased to approximately 0.4% - 10%. The once dominant species in the Florida reef tract, Acropora palmata and A. cervicornis, have rapidly declined over time and were not found in any transects during the 2000 survey. This study is a re-assessment of the BNP patch reefs surveyed in 1977-1981. In addition, one patch reef from BNP and three in upper keys region of the Florida Keys National Marine Sanctuary (FKNMS) have been included (a total of 11 patch reefs, all with historical data available). This study found 2% - 13% coral cover at these 11 reefs using a photographic survey (Point Count) and 4% - 21% coral cover using Atlantic and Gulf Rapid Reef Assessment (AGRRA) survey methods. These results are relatively similar to results reported for the same patch reefs in the 1990s and in 2002, indicating that the major changes occurred earlier with the extreme decline in Acropora spp. Montastraea annularis complex cover has also declined substantially at the BNP sites from 5.4% in 1977-81 to 1.3% in 2009. Although the number of species recoded on the seven resurveyed BNP patch reefs was only 23, compared with 28 recorded in the 1977-81 study, all species are still present in the region surveyed, indicating no actual loss of over all species richness.
Thesis:
Thesis (M.S.)--University of South Florida, 2011.
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Includes bibliographical references.
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by Amy Wallace.
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Dynamics of Stony Coral Assemblages on Patch Reefs of the Upper Florida Reef Tract, Including Biscayne National Park b y Amy A. Wallace A thesis s ubmitted in partial fulfillment of the requirements for the degree of Master of Science College of Marine Science University of South Florida Major Professor: Pamela Hallock Muller, Ph.D. Kendra Daly, Ph.D. Armando Hoare Ph.D. Walt er Jaap BS Date of Approval: March 28, 2011 Keywords: benthic community, AGRRA, photo transect PRIMER Copyr ight 2011, Amy A. Wallace

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i Table of Content s List of Tables ................................ ................................ ................................ ................... ii List of Figure s ................................ ................................ ................................ ................. iv Abstract ................................ ................................ ................................ .......................... v i Introduction ................................ ................................ ................................ ..................... 1 Methods ................................ ................................ ................................ .......................... 7 Survey S ites ................................ ................................ ................................ ......... 7 Photographic S urvey ................................ ................................ ............................ 7 Atlantic Gulf Rapid Reef Assessment Survey ................................ ....................... 8 Atlantic Gulf Rapid Reef Assessmen t versus Photographic Survey ..................... 9 Results ................................ ................................ ................................ .......................... 13 13 Photographic Survey ................................ ................................ .......................... 13 Atlantic Gulf Rapid Reef Assessment Survey ................................ ..................... 15 Atlantic Gulf Rapid Reef Assessment Survey versus Photographic Survey ........ 16 Discussion ................................ ................................ ................................ ..................... 55 Conclusions ................................ ................................ ................................ ................... 73 References Cited ................................ ................................ ................................ ........... 74

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ii Li st of Tables Table 1. Percent cover of the 28 species of coral observed between 1977 and 1981 at the BNP reefs (Dupont et al. 2008) ................................ ................................ ..... 4 Table 2. Coordinates and depth for Biscayne National Park sites ................................ 11 Table 3. Coo rdinates and depth for Florida K eys N ational Marine Sanctuary sites ....... 11 Table 4. CPCe data (percent cover) from transects photographed in June and July 2009, summarized into nine major categories ................................ ........................ 18 Table 5. Percent similarity among photo transects for each reef, determined using SIMPER an alysis ................................ ................................ ................................ 19 Table 6. Between reef comparisons based on CPCe analysis of photo transects calculated from the same data set as the similarities shown in Table 5 ......................... 21 Table 7. Percent cover of the 24 species of coral obse rved in 2009 at the BNP and FKNM S reef s; photo transect data ................................ ................................ .......... 26 Table 8. Percent cover data collected in eight benthic cover categories for each reef using AGRRA survey methods ................................ ................................ ............... 27 Table 9. Percent similarities among AGRRA transects for each reef determined using SIMPER analysis ................................ ................................ ................................ 28 Table 10. Between reef comparisons based on AGRRA analysis of transects calculated from the same data set as the similarities shown in Table 9 ......................... 30 Table 11. Percent cover by individual coral species for specimens larger than 10 cm in diameter ................................ ................................ ................................ ............... 35 Table 12. AG RRA coral cover percentage with M. annularis complex .......................... 37 Table 13. Comparison of data collected using AGRRA survey methods and those collected using CPCe analysis of photo transects combined into compatible categories ................................ ................................ ................................ .... 39 Table 14. Similarities and dissi milarities of data collected from the same transects using AGRRA and CPCe data from photo transects ................................ ...... 40 Table 15. Similarities and dissimilarities of data collected from the same transects using AGRRA and CPCe data from photo transects ................................ ...... 41 Table 16. Perc ent coral cover means for data sets collected over the past three decades from patch reefs of BNP and the upper Florida Keys ................................ ....... 62

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iii Table 17. CPCe coral cover percentage with M. annularis complex ............................. 63 Table 18. Mean percent coral cover by species ................................ ............................ 6 5

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iv Li st of Figures Figure 1. Locations of the original eight study sites in BNP ................................ ............. 5 Figure 2. Stony coral cover ( mean +/ SE) at 12 reefs in BNP ................................ ........ 6 Figure 3. Locations of the three study sites in FKNMS and one in BNP ........................ 12 Figure 4. A multidimensional scaling plot representing each transect for each reef, based on analysis of the 54 benthic cover cat egories using Coral Point Count ................................ ................................ ................................ ............................ 42 Figure 5. ANOSIM histogram comparing difference between reefs for benthic cover data collected from photo transects ................................ ................................ ..... 43 Figure 6. ANOSIM histogram comparing benthic cover data from photo transects, betwee n locations ................................ ................................ ......................... 44 Figure 7. A multidimensional scaling plot representing each transect for each reef, based on analysis of the six AGRRA categories of benthi c cover measured in cm /transect ................................ ................................ ................................ ................ 45 Figure 8. ANOSIM histogram comparing difference between reefs for benthic cover data collected from AGRRA survey ................................ ................................ ...... 46 Figure 9. ANOSIM histogram comparing benthic cover data from AGRRA survey, between locations ................................ ................................ ............................. 47 Figure 10 A multidimensi onal scaling plot comparing AGRRA benthic c over and the CPCe benthic cover ................................ ................................ ................................ 48 Figure 11. ANOSIM histogram comparing benthic cover data for both AGRRA and photo transect data ................................ ................................ ................................ 49 Figure 12 ANOSIM histogram comparing benthic cover data for both AGRRA and photo transect data ................................ ................................ ................................ 50 Figure 13. The dendrogram repres ents similarities between reefs ................................ 51 Figure 14 ANOSIM histogram based on coral cover data comparing results from AGRRA and photo transects methods ................................ ................................ ........... 52 Figure 15. ANOSIM histogram based on coral co ver from combined AGRRA and Photo transect data, comparing data from BNP reefs with those from FKNMS .............. 53 Figure 16. ANOSIM histogram comparing results between reefs based on the combined AGRRA and photo transect coral cover data ................................ ................. 54

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v Figure 17. Comparison between the mean coral cover of historic (Dupont et al 2008) and current data sets ................................ ................................ ........................... 66 Figure 18. Multidimensional scaling comparison of coral species data sets collected in 1977 1981 (Dupont et al 2008) and in 2009 (this study) ............................. 67 Figure 19. Compari son of coral species data sets collected in 1977 81 (Dupont et al. 2008) and in 2009 (this study) ................................ ................................ ............... 68 Figure 20. Comparison of top seve n coral species on Elkhorn Reef ............................. 69 Figure 21. Comparison of top s even coral species on Dome Reef ................................ 70 Figure 22. Compa rison of top seven coral species on Schooner Reef .......................... 71 Figure 23. Comparisons of study sites with AGRRA regional basel ines (modified from Kramer 2003, Fisher 2007) for corals >25 cm maximum diameter and data from Fisher (200 7), which was collected in 2002 ................................ ........................... 72

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vi Abstract The patch reefs located in Biscayne National Park (BNP) are some of the most northern reefs of the Florida reef system. The focus of my study is seven patch reefs that were first surveyed annually between 1977 and 1981, revealing 8% 28% cover by scleractinian corals. An assessment of BNP patch reefs completed in 2000 reported that coral cover had decreased to approximately 0.4% 10%. The once dominant species in the Florida reef tract, Acropora palmata and A cervicornis have rap idly declined over time and were not found in any transects during the 2000 survey. This study is a re assessment of the BNP patch reefs surveyed in 19 77 1981 In addition, one patch reef from BNP and three in upper keys region of the Florida Keys Natio nal Marine Sanctuary (FKNMS) have been included ( a total of 11 patch reefs, all with historical data available ) This study found 2% 13% coral cover at these 11 reefs using a photographic survey (Point Count) and 4% 21% coral cover using Atlantic and Gulf Rapid Reef Assessment (AGRRA) survey methods. These results are relatively similar to results reported for the same patch reefs in the 1990s and in 2002, indicating that the major changes occurred earlier with the extreme decline in Acropora spp Mo ntastraea annularis complex cover has also declined substantially at the BNP sites from 5.4% in 1977 81 to 1.3% in 2009. Although the number of species recoded on the seven resurveyed BNP patch reefs was only 23, compared with 28 recorded in the 1977 81 study, all species are still present in the region surveyed, indicating no actual loss of overall species richness.

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1 Introduction Coral reefs are one of the most biologically diverse ecosystems in the world. Heterogeneity supports the complex trophic we b The Florida reef tract is the most extensive living coral reef system in North American waters. accessible with many boat ramps and private tour companies located in close proximity to the reef s ystem Hundreds of thousands o f visitors vacation at Florida reefs each year, providing immense economical value for the South Florida area (Johns et al. 2003). Biscayne National Park (formerly Biscayne National Monument) is a 172,000 acre marine preserve hosting more t han 500,000 vi sitors each year. BNP is located southeast of t he large urban center of Miami, at the northern latitudinal fringe of th e Atlantic coral reef distribution ( Miller et al. 2000 Banks et al 200 5 Jaap et al. 2008 ). Corals generally grow between the 30N an d 30S latitudes. Florida is located at the northern edge, but the warm Gulf Stream flows along the east coast of Florida bringing warm water to higher latitudes. T he parameters supporting coral reef growth ( Wells 1957 www.floridakeys.noaa.gov ) are present in the waters off southeast Florida: High light surface irradiance of 2,000 E /sq m /s High oxygen: 5.0 7.0 mg/L Low turbidity: 0.01 0.10 mg/L Low nutrients: 0.01 0.10 M (Nitrogen or Phosphoru s) Temperature: 18 30 degrees Celsius

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2 Coral reefs are experiencing rapid declines around the world from local, regional, and even global causes (Dustan and Halas 1987 Bryant and Burke 1998 Dustan 1999, Hoegh Guldberg 1999 Wilkins on 1999 Gardner et al. 2003 many others). As of 2005, 80% of the Caribbean corals had disappeared; the rest of the world is not far behind because 58 70% of coral reefs are directly affected by anthropogenic activities (Bryant and Burke 1998 Hoegh Guld berg 1999 Wilkinson 1999 Goreau et al. 2000 Gardner et al. 2003). Reefs are experiencing persistent environmental disturbances (such as pollution and development along the coasts) causing a loss in species diversity, decreased growth, increased disease decreased fecundity, and overall mass mortality (Richmond 1993 Hoegh Guldberg 1999, Nystrom et al. 2000 Knowlton 2 001 CR E MP 2001 Porter and Tougas 2001 Patterson et al. 2002). Some of the historical documented anthropogenic disturbances specific to BNP are dredging (Hudson 1981 Marszalek 1982), sewage (Bright et al. 1981), boat groundings (Jaap 1984), anchor damage (Davis 1977), and fishing and diving activities (Tilmant and Schmahl 1982, Halas 1985 Glynn et al. 1989). Another potential disturban ce is coastal runoff loaded with fertilizers, pesticides, heavy metals, and hydrocarbon pollutants (Jaap 1984 Glynn et al. 1989). Further decline of the Florida reef system has the potential to be devastating to southeast Florida tourism as well as the e nvironment because of the multi billion dollar industries dependent upon it (www.boatflorida.org). A reef survey, carried out between 1977 and 1981, documented 28 species of stony corals (Milleporina and Scleractinia) on the eight patch reefs located withi n BNP (Fig. 1; Jaap and Wheaton unpublished, documented in Dupont et al. 2008). The percent coral cover ranged from 8 28% (Table 1). Stony coral cover at Elkhorn Reef declined from 27% in the 1977 1981 study to 9.5% in 1994 1996, as reported by Miller e t al. (2000). The decline continued further to 4.4% in the 2000 study ( Fig. 2 ) completed by

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3 Moulding and Patterson (2002), and further discussed by Dupont et al. (2008). Moulding and Patterson (2002) reported during 1998 2000 that coral cover was signifi cantly higher in on Elkhorn and Star reefs in 1977 1981, based on Kruskal Wallis tests. The principal species on the BNP patch reefs have also changed since 1981. Acropora palmata and A. cervicornis historically dominated Elkhorn and Elkhorn Control tran sects by 60% and 46% of coral cover respectively (Dupont et al. 2008). In 2000, Moulding and Patterson (2002) did not record either species on Elkhorn Reef in the video survey or during in situ belt census. This study reexamines seven BNP reefs surveyed in 1977 81 (Dupont et al 2008) as well as four reefs in the uppe r keys and BNP surveyed in 2002 (Fisher 2007). It describes benthic communities using photographic and Atlantic Gulf Rapid Reef Assessment survey methods. The goals are to quantify changes in percent coral cover and coral assemblages since the original surveys and to quantify percent cover of the other components of the benthic community. Results of the AGRRA methods surveys are c ompared with published results from other survey work along the Florida reef tract and the wider Caribbean. The working hypothesis is that reefs have decreased in coral cover since the original surveys, and that the dominant species have shifted from Acropora palmata and A. cervicornis to more stress tolerant spec ies The null hypothesis is that there has been no change on the studied reefs over the past three decades.

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4 Table 1. Percent cover of the 28 species of coral observed between 1977 and 1981 at the BNP reefs (Dupont et al. 2008). The denotes a differenc e from the publication. The table has been adjusted to correct a 1.9% coral cover miscalculation Coral Species Dome Dome Control Elkhorn Elkhorn Control Schooner Schooner Control* Star Star Control Acropora cervicornis 0 0 6.4 1.68 0.01 0 0.98 0.02 Acr opora palmata 0 0 10.6 6.67 0 0 0 0 Agaricia agaricites 0.26 0.28 0.33 0.72 0.1 0.25 1.16 0.14 Colpophyllia natans 2.6 0 0 0 0 0 0 2.18 Dichocoenia stellaris 0.3 0.98 0.01 0.11 0.56 0.31 0.1 0.02 Dichocoenia stokesii 0 0.08 0 0 0 0.01 0 0.04 Diploria clivosa 0.1 0.04 2.47 1.15 1.17 0.15 0.02 0 Diploria labyrinthiformis 0.06 0.36 0.08 0.05 0 0.04 0 0 Diploria strigosa 0 0 0.44 0 0.64 0 0.02 0 Eusmilia fastigiata 0.04 0.3 0 0 0 0.03 0.02 0 Favia fragum 0.04 0.04 0 0.04 0.04 0 0.02 0 Isophyllastrea r igida 0 0 0.01 0 0 0 0 0 Isophyllia sinuosa 0 0 0 0 0 0 0.02 0 Montastraea annularis (complex) 19.2 4.68 0 0.21 0.49 0.03 13.2 8.08 Montastraea cavernosa 0.34 0.28 0.09 0 0.44 0.58 0.16 0.42 Madracis deca c tics 0 0 0.03 0 0 0 0 0.02 Man icin a areolata 0 0 0.01 0 0 0.01 0 0.02 Millipora a l cicornis 2.88 0.94 0.33 1.25 2.31 3.89 1.42 2.38 Mi l lipora complanata 0 0 0.19 1.09 0 0 0 0 Mycetophyllia ferox 0.38 0 0 0 0 0 0.38 0.38 Mycetophyllia lamarckiana 0.18 0.32 0 0 0 0 0.04 0.16 Porites astreoides 0.06 0.36 2.25 3.93 0.7 0.62 0.76 0.6 Porites por it es 0.34 0.38 3.33 0.37 1.61 1.15 1.46 0.58 Siderastrea radians 0 0.04 0 0.05 0.01 0.03 0.02 0 Siderastrea siderea 1.02 4.9 0.48 0.77 3.36 2.8 1.82 0.4 Solenastrea bournoni 0 0 0 0 0 0.01 0 0 Solenastrea hy ades 0 0.04 0 0 0 0 0 0 Stephanocoenia michelini 0.06 0 0 0 0 0 0 0.2 Total (% cover) 27.8 14.0 27.0 18.1 11.5 9.9 0 21.6 15.6 Total (# of species) 16 15 16 14 13 15 17 16

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5 Figure 1. Locations of the original eight study sites in BNP. The GPS coord inates can be found in Table 2 (Dupont et al. 2008).

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6 Figure 2. Stony coral cover (mean +/ SE) at 12 reefs in BNP. Data are from three studies: 1. Historic data [1977 1981], 2. Miller et al. (2000) [1994 1996] and 3. Moulding and Patt erson (2002) [1998/1999 and 2000]. Bars with differ significantly from the others in the group (Kruskal Wallis p < 0.05) (Dupont et al. 2008).

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7 Methods Survey Sites In 1977, four experimental reef sites (Schooner, Elkhorn, Dome and Star) were chose n because of their accessibility to the public. All sites were marked with buoys and other visitor incentives during the historic 1977 1981 study. Four control sites (Schooner Control, Elkhorn Control, Dome Control, and Star Control) were chosen because they were close to the experimental sites but unmarked and therefore considered less accessible to visitors. The same sites from the original study were used for the assessment described here (Table 2), with the exception of Star Control, which could n ot were also surveyed (Fig. 3 ). These sites were chosen because of previous surveys conducted in 2002 by Fisher (2007). All of these sites were located within the FKNMS Photographic Survey Four to eight transects, 10 m in length, were placed in situ haphazardly on each of the eleven patch reefs. Photographs were taken at the height of 40 centimeters, cap turing a snapshot of a 0.1 2 m 2 (planar) quadrat using a Canon Sureshot 5 megapixel camera. Each site produced between 100 and 200 photographs for analysis. Thirty random points were sampled on each photograph using Coral Point Count v3.6 software (Kohle r and Gill 2006).

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8 The Coral Point Count program (CPCe) was used to compile data for each transect of each reef. The variables were tallied and mean, standard deviation, and standard error were computed by the program and placed in Microsoft Excel. Poin ts that fell on unknown or equipment (e.g. the transect line) were deleted. U nknown points represented areas that were too bright too dark, or blurry to interpret confidently. Octocorals were grouped by family because most species are difficult to ident if y in situ and combining by family added consistency to the identifications. E dited point count data were consolidated into a singl e spreadsheet and uploaded to PRIMER v6 for multivariate statistical analysis (Clark and Warwick 2001). Data were process ed multiple ways using the point sums. First, I compared all of the transects to one another using multidimensional scaling (MDS) plots, analysis of similarities (ANOSIM), and clustering functions. Similarity percentages (SIMPER) were used to evaluate ca uses of dissimilarity. The second step compared the reefs using assemblages to one another using MDS, cluster, and SIMPER functions. The factors used were Location (BNP vs. FKNM S) and Reef (Elkhorn, Dome, Three Sisters, etc.). Atlantic and Gulf Rapid Reef Assessment Survey The same transects were surveyed using the Atlantic and Gulf Rapid Reef Asse ssment (AGRRA) protocol (Fisher 2007; Ginsburg 2010 ). Three passes were made alon g each transect recording data on an underwater AGRRA Benthic Data sheet. Using a one meter measuring stick, marked in decimeters, the diver estimated the amount of sand, live stony coral less than 10 cm in size, crustose coralline algae, fleshy macroalga e, calcareous macroalgae, and other (sponges, gorgonians, etc.). M easurements were recorded to the nearest five centimeters on the first pass. AGRRA

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9 assumes any data that do not fit into one of these categories is turf covered hard bottom. During the se cond pass, the diver recorded the coral species greater than 10 cm in size located under the transect. The length, width, height, percent dead (old and new), and type of bleaching or disease (if identifiable) were recorded for each specimen. On the third and final pass, the diver dropped a 0.25 m by 0.25 m quadrat along the transect on the odd meters (1, 3, 5, 7, 9 ) and recorded the average height of fleshy and calcareous algae, type of substrate, maximum relief, and the number and species of coral recrui ts less than or equal to two centimeters. Diadema antillaru m located directly under the transect line during any pass were recorded Data were compiled into Excel spreadsheets available at www.agrra.org and were stati stically analyzed using Excel and PRIMER version 6. The data were processed using the same analyses as the photographic survey data. AGRRA survey vs. Photographic survey After describing each of the data sets, the AGRRA data set was compared to the pho tographic data set. The data compiled using Coral Point Count were more detailed than the AGRRA data. Therefore the photo transect data were simplified into six variables comparable to the AGRRA data: sand, crustose coralline algae, other live sessile in verts, total live coral, turf, and macroalgae. Turf algae is a multi specific assemblage of diminutive algae (often filamentous) usually having a canopy height of less than 10 cm (Steneck 1988). Total live coral consisted of the combined measurements for coral < 10 cm and coral > 10 cm from the AGRRA transect data. Macroalgae consisted of all fleshy and calcareous algae, excluding crustose coralline algae and turf.

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10 An issue that influences comparisons between my data and both the 1977 81 and 2002 data sets is the identification of Montastraea spp. Although M. annularis M. faveolata, and M. franksi were originally identified as sibling species, they were generally all identified as M. annularis until Wiel and Knowlton (1994) revived the other two speci es based on morphological, molecular, and behavioral characte ristics (see also Szmant et al. 1997). T he three are still commonly lumped as M. annularis species complex in fi eld studies (e.g., Fisher et al. 2007). Thus, for comparison of my data set with previous data sets, it was necessary to combine data from M. faveolata and M. franksi into the M. annularis complex category.

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11 Table 2. Coordinates and depth for Biscayne National Park sites Reef Name Dome Dome Control Star Schooner Schooner Control Elkhorn Elkhorn Control Latitude (N) 25.26.888 25.26.977 25.24.092 25.23.935 25.23.831 25.21.705 25.21.550 Longitude (W) 80.09.516 80.09.513 80.09.102 80.09.632 80.09.622 80.09.846 80.09.960 Depth (m) 3 5 3 5 3 5 5 7 5 7 1 3 1 3 Table 3. Coordina tes and depth for Florida Keys National Marine Sanctuary sites Reef Name Alina's Reef Algae Reef White Banks Reef Three Sisters Reef Latitude (N) 25.23.185 25.08.794 25.02.243 25.01.105 Longitude (W) 80.09.775 80.17.588 80.22.513 80.23.852 Depth (m) 3 5 3 5 5 7 5 7

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12 (BNP), Algae Reef (AR), White Banks (WB), and Three Sisters Reef (KL 6m). The GPS coordinates are listed in Table 3 (Fisher 2007).

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13 Results All dat that still had a mooring ball for public use. Between four and eight transects were surveyed per reef; the number of transects varied with field conditions. Photographic Survey More than 1 5 00 photographs were collected and analyzed using CPCe from the 69 transects surveyed. Benthic cover data originally compiled for 54 categories for each reef are summarized in Table 4 Seven reefs were dominated by turf while the other four were co dominated by turf and macroalgae. Total coral cover ranged from 2% (Dome Control) to 13% (Elkhorn) a t BNP patch reefs data and 4% (Three Sisters) to 20% (Algae) at FKNMS reefs. The MDS plot of benthic cover data collected from photo transects ( Fig. 4) shows that transects generally grouped together by reef with two outliers. The plot stress level is 0.13 denoting that the relationships are well represented (Clarke and Warrick 2001 Clarke and Gorely 2006). Three Sisters 6 is the only transect not within 60% simi larity with another transect; t his transect had more sea grass than any of the other transects. Based on SIMPER analysis, the individual reefs have among transect similarities ranging from 64 82% (Table 5 ). At ten reefs, two of the t op three contributing factors to reef similarity were turf and Dictyota One reef (Schooner) did not have Dictyota as a top contributor, but turf contributed to 82% of the similarity at that reef. Transects located in BNP and FKNMS had similarities of 64 % for each transect within each

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14 location. The top three contributors to the similarity of this g roup were turf, Dictyota and Gorgoniidae. Although transects grouped by reef, there are differences between the reefs. Dome and Dome Control are at least 2 0% dissimilar when comparing reefs to each other (Table 6 ). White Banks and Schooner are most dis similar at 64% Between p atch reefs surveyed in BNP and FKNMS the dissimilarity is 40%. Turf, Dictyota and Gorgoniidae were the major contributors for ree f and location dissimilarity. An ANOSIM has a Global R scale of 1 to 1. The closer the Global R value is to zero, the more the test supports the null hypothesis. The Global R must also be located within the histogram distribution. The null hypothesis is that samples being compared are similar (Clark and Gorley 2006). The ANOSIM comparing reefs ha s an R = 0.651 confirming variability among the reefs (Fig 5 ) T he ANOSIM comparing BNP and FKNMS reefs has an R = 0.141 (Fig 6 ) showing there is little d ifference in variability between the locations of the reefs along the reef tract (i.e. BNP versus FKNMS) A total of 24 species of coral were identified in photographs collected during this survey (Table 7 ) The maximum number of coral species by reef wa s 16 at White Banks and the minimum was 7 species at Elkhorn Control and Three Sisters reefs. The overall coral cover for each reef ranged between 2% and 13%. Montastraea faveolata exhibited the highest coral cover on six of the reefs w hile Porites astr eoides and Siderastrea siderea had the highest cover on two reefs each. Porites porites was the species found to have the highest coral cover at Three Sisters Reef. The most abundant coral species across the study were S. siderea and M. faveolata attrib uting to 23% and 22% of the total coral cover. Porites astreoides contributed 19% of the total cover, while P. porites and Millepora alcicornis made up 13% and 9% of total cover respectively.

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15 Atlantic and Gulf Rapid Reef Assessment Survey AGRRA data w ere collected on each reef along the same transects. Benthic cover data and coral cover data for each reef are summarized in Table 8 The dominant benthic cover for all reefs, based on AGGRA data, was turf algae The MDS plot based on AGRRA data (Fig. 7 ) shows a relatively tight grouping of transects in the center of the plot with two outlying transects. The stress level is 0.12 indicating that the relationships on the plot are well represented. The first outlier is Three Sisters 4, where four to ten times more sand was recorded on this transect than any other in the data set. Most transects had less than 50 cm of sand and this particular transect had 500 cm of sand. The diver noted she ran her transect line completely off the reef. The second outli er, Star 3, had twice as much live coral cover as the next closest transect on Star R eef. When compared to transects from the other reefs, Star 3 has approximately three to five times more coral cover. Based on SIMPER analysis, within individ ual reefs tr ansect similarit ies rang ed from 58 83% (Table 9 ). In every reef, turf was the top contributor for the similarity among transects. The next most important contributors were the fleshy macroalgae and other live sessile invertebrates. Transects within B NP and FKNMS had an average similarity of 73% and 69% respectively. The top two contributors to the similarity were turf and fleshy macroalgae. When comparing the reefs to each other, Elkhorn and Schooner were only 18% dissimilar (Table 10 ). Schooner an d Star were most dissimilar at 40%. Reefs in BNP compared to those in FKNMS have a dissimilarity of 31%. Turf and fleshy macroalgae were the major contributors for location dissimilarity. The ANOSIM between reefs has an R=0.189 and the BNP FKNMS compari son has an R = 0.191 showing there is very little difference among the reefs based on AGRRA survey methods (Fig s. 8 and 9 )

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16 A total of 28 coral species were identified using AGGRA survey methods (Table 11 ) The overall coral cover for each reef ranged b etween 4 % and 21 % Montastraea annularis and Porites porites were the most common coral species on three reefs each. Porites astreoides was the next most abundant on two reefs. Montastraea faveolata M. franksi and Siderastrea siderea were m ost prevale nt on one reef each. The variability in abundance of different Montastraea spp can be attributed to different divers in AGRRA surveys. One diver identified most of the Montastraea she encountered as M. annularis while other divers distinguished between M. faveolata and M. franksi After combining the Montastraea spp into M. annularis complex, different results were observed Montastraea annularis complex was the most common coral at six reefs and the most abundant coral species overall accounting fo r 30% of the total coral cover (Table 1 2 ). Siderastrea siderea and Porites porites contributed 20% and 19% of the total cover respectively, while P. astreoides made up 10% total cover. AGRRA survey vs. Photographic survey To facilitate comparisons betwe en the photo transect and AGRRA data sets, the photo transect data were summarized two ways. F irst showing all categories responsible for at least 1% of cover at that r eef and then combining the photo transect data categories into AGRRA categories (Table 1 3 ). The MDS plot comparing benthic cover along the transects from each data set showed no distinction between patch reefs in BNP and FKNMS (Fig. 10 A ) The stress level of 0.08 indicates the MDS spatial pattern is an excellent preservation of the similari ty matrix. An ANOSIM testing the difference between BNP and FKNMS locations has an R = 0.089 (Fig 11 ) supporting the null hypothesis of no difference in sample sites When the sampling method is superimposed on the same MDS plot (Fig. 10B),

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17 distinct AG RRA and photo transect groups are evident. T he variance between AGRRA and photo transect data has an R = 0.496 (Fig. 12) indicating considerable difference between the sampling methods. SIMPER procedure was applied to identify the sources of the similari ty and differences between sampling methods (Table 1 4 ) Within methods, the AGRRA data are 84% similar while the CPCe data are 79% similar. Between methods, t he data sets are 27% dissimilar. The top two contributors for both similarities and dissimilar ities are turf and macroalgae. Cluster analysis revealed three different clusters of reefs (Fig. 1 3 ). One reef, Three Sisters (AGRRA), was an outlier of cluster 2 and differed by the amount of sand located along the transect s as noted previously. Thes e transects combined had four to five times more sand than any other reef or data set. A SIMPER evaluation based on coral species showed only 36 % among reef similar ity within the AGRRA data and 52 % similarity within the CPCe data. Moreover the two data se ts were 57 % dissimilarity ( Table 1 5 ). The ANOSIM shows that the high variability in these data sets precludes detecting differences between sampling methods ( R = 0.023, Fig 14 ) or between locations ( R = 0.029 Fig 15 ) However the variability between reefs is significant at R = 0.631 ( Fig 16 )

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18 Table 4. Photo transect data (percent cover) from transects photographed in June and July 2009, summarized into nine major categories

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19 Table 5. Percent similarity among photo transects for each reef, det ermined using SIMPER analysis. The final two entries show percent similarity among transects from patch reefs surveyed in BNP and FKNMS. The data set consisted of 54 variables; the octocorals were identified to family Reef/Location Similarity Top 3 Cont ributors Percent Contribution Dome 81. 8 Turf 40.0 Dictyota 25.3 Gorgoniidae 20.5 Dome Control 78.5 Turf 38.5 Dictyota 22.9 Gorgoniidae 16.3 Elkhorn 74.2 Turf 52.5 Gorgoniidae 12.9 Dictyota 11.5 Elkhorn Control 81.7 Turf 69.9 Dictyo ta 8.38 Plexauridae 5.46 Schooner 81.7 Turf 81.8 Plexauridae 3.37 Sea grass 1.39 Schooner Control 72.2 Turf 41.0 Dictyota 26.6 Gorgoniidae 7.54 Star 64.3 Turf 39.5 Dictyota 21.8 Gorgoniidae 14.0 Alina's 75.1 Turf 42.9 Dictyota 3 2.3 Halimeda 8.14 Three Sisters 79.4 Turf 51.3 Dictyota 35.6 Sponge 6.78 Algae 74.5 Turf 37.0 Dictyota 21.7 Gorgoniidae 17.8 White Banks 73.7 Dictyota 29.1 Turf 25.2 Gorgoniidae 24.3

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20 Reef/Location Similarity To p 3 Contributors Percent Contribution BNP 63. 7 Turf 56.6 Dictyota 16.4 Gorgoniidae 8.45 FKNMS 64.3 Turf 38.0 Dictyota 31.6 Gorgoniidae 12.7

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21 Table 6. Between reef comparisons based on CPCe analysis of photo transects calculated from the sa me data set as the similarities shown in Table 5 Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Dome/Dome Control 19.5 Turf 26.1 Gorgoniidae 19.3 Dictyota 8.88 Dome/Star 30.3 Turf 16.8 Gorgoniidae 15.0 Dictyota 13.4 Dom e Control/Star 30.9 Turf 20.2 Gorgoniidae 13.0 Dictyota 12.7 Dome/Algae 25.4 Turf 16.3 Gorgoniidae 12.0 Dictyota 8.98 Dome Control/Algae 27.3 Turf 20.1 Gorgoniidae 12 .0 Dictyota 7.84 Star/Algae 30.6 Dictyota 13.0 Turf 11.3 Gorgon iidae 9.7 Dome/White Banks 26.9 Turf 26.8 Gorgoniidae 15.1 Dictyota 8.39 Dome Control/White Banks 29.8 Turf 27.4 Gorgoniidae 16.8 Dictyota 8.88 Star/White Banks 36.1 Gorgoniidae 16.2 Turf 15.0 Dictyota 12.8 Algae/White Banks 31.0 Turf 14.7 Gorgoniidae 13.8 Halimeda 10.5 Dome/Alina's 28.4 Gorgoniidae 23.0 Turf 13.8 Dictyota 9.81 Dome Control/Alina's 29.7 Gorgoniidae 18.2 Turf 16.9 Dictyota 11.8

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22 Reef/Location Dissimilarity Top 3 Contributors Percen t Contribution Star/Alina's 32.2 Turf 17.2 Dictyota 16.6 Gorgoniidae 9.91 Algae/Alina's 30.9 Turf 15.3 Gorgoniidae 15.0 Dictyota 13.2 White Banks/Alina's 36.4 Gorgoniidae 21.6 Turf 21.2 Halimeda 10.4 Dome/Elkhorn 29.3 Turf 20.0 Dic tyota 17.7 Gorgoniidae 14.4 Dome Control/Elkhorn 29.8 Turf 22.6 Dictyota 14.6 Gorgoniidae 12.6 Star/Elkhorn 37.1 Turf 23.5 Dictyota 13.0 Gorgoniidae 7.78 Algae/Elkhorn 33.4 Turf 24.6 Dictyota 11.9 Gorgoniidae 9.19 White Banks/Elkho rn 38.9 Turf 29.6 Dictyota 15.6 Gorgoniidae 14.1 Alina's/Elkhorn 35.7 Dictyota 21.1 Turf 16.3 Gorgoniidae 10.7 Dome/Schooner 52.2 Turf 35.4 Dictyota 20.2 Gorgoniidae 15.8 Dome Control/Schooner 50.8 Turf 35.1 Dictyota 18.9 Gorgoni idae 13.4 Star/Schooner 57.3 Turf 38. 6 Dictyota 16.0 Gorgoniidae 7.25

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23 Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Algae/Schooner 58.6 Turf 37.0 Dictyota 15.5 Gorgoniidae 10.6 White Banks/Schooner 64.2 Turf 39.0 Dictyota 17.9 Gorgoniidae 14.9 Alina's/Schooner 53.5 Turf 33.2 Dictyota 24.0 Halimeda 6.31 Elkhorn/Schooner 40.6 Turf 33.4 Dictyota 13.4 Gorgoniidae 12.2 Dome/Schooner Control 30.3 Gorgoniidae 20.2 Dictyota 16.2 Tu rf 14.3 Dome Control/Schooner Control 30.5 Turf 18.0 Dictyota 17.7 Gorgoniidae 15.5 Star/Schooner Control 36.9 Dictyota 17.5 Turf 16.5 Halimeda 8.29 Algae/Schooner Control 37.8 Dictyota 15.2 Turf 14.1 Gorgoniidae 10.9 White Banks/Scho oner Control 37.2 Turf 22.3 Gorgoniidae 19.8 Dictyota 12.6 Alina's/Schooner Control 31.2 Turf 14.7 Dictyota 12.9 Halimeda 10.5 Elkhorn/Schooner Control 35.7 Dictyota 22.9 Turf 15.9 Gorgoniidae 9.02 Schooner/Schooner Control 49.4 Turf 3 1.8 Dictyota 25.6 Sea grass 5.47

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24 Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Dome/ Three Sisters 37.5 Gorgoniidae 25.9 Dictyota 20.0 Turf 14.0 Dome Control/Three Sisters 37.0 Gorgoniidae 22.4 Di ctyota 21.8 Turf 15.2 Star/three Sisters 44.1 Dictyota 20.4 Turf 19.5 Gorgoniidae 12.6 Algae/Three Sisters 46.1 Dictyota 18.5 Turf 18.1 Gorgoniidae 16.6 White Banks/ Three Sisters 47.0 Turf 24.6 Gorgoniidae 23.4 Dictyota 14.9 Alina' s /Three Sisters 3 1.9 Dictyota 18.5 Turf 15.6 Sea grass 10.7 Elkhorn/ Three Sisters 40.4 Dictyota 28.4 Gorgoniidae 15.7 Turf 11.6 Schooner/Three Sisters 47.9 Dictyota 34.4 Turf 26.9 Sea grass 9.23 Schooner Control/ Three Sisters 32.6 Dict yota 17.8 Turf 15. 2 Sea grass 11.5 Dome/Elkhorn Control 41.4 Turf 35.3 Gorgoniidae 19.2 Dictyota 14.0 Dome Control/Elkhorn Control 39.0 Turf 35.9 Gorgoniidae 16.7 Dictyota 12.8 Star/Elkhorn Control 46.0 Turf 39.5 Dictyota 11.2 Go rgoniidae 8.54

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25 Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Algae/Elkhorn Control 45.7 Turf 39.1 Gorgoniidae 12.9 Dictyota 10 .0 White Banks/Elkhorn Control 53.8 Turf 39.3 Gorgoniidae 17.2 Dictyota 12 .5 Alina's/Elkhorn Control 41.5 Turf 33.7 Dictyota 19.3 Plexauridae 6.92 Elkhorn/Elkhorn Control 32.3 Turf 32.0 Gorgoniidae 14.7 Dictyota 8.45 Schooner/Elkhorn Control 24.6 Turf 19.4 Dictyota 18.6 Sea grass 10.0 Schooner Control/Elkho rn Control 40.8 Turf 30.2 Dictyota 20.7 Sea grass 4.91 Three Sisters/Elkhorn Control 40.1 Dictyota 29.6 Turf 23.6 Sea grass 9.43 BNP/FKNMS 39.9 Turf 25.6 Dictyota 16.1 Gorgoniidae 14.1

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26 Table 7. Percent cover of the 24 species of cor al observed in 2009 at the BNP and FKNMS reefs; photo transect data Coral Species Dome Dome Control Elkhorn Elkhorn Control Schooner Schooner Control Star Three Sisters Algae Alina's White Banks Acropora cervicornis 0 0 0 0 0 0.26 0 0 0 0.11 0.13 Agar icia agaricites 0 0 0.03 0 0 0.19 0.10 0.05 0.20 0 1.21 Colpophyllia natans 0 0 0.16 0 0 0 0 0 0 0 0 Coral (general) 0.03 0 0 0 0 0 0 0 0 0 0.02 Dichocoenia stokesi i 0 0 0.08 0.04 0.07 0.12 0.34 0 0.16 0.03 0.44 Diploria clivosa 0 0 0 0 0.07 0 0 0 0 0 0 Diploria labyrinthiformis 0.30 0.08 0 0 0 0 0 0 0 0 0.19 Diploria strigosa 0.16 0 0 0 1.69 0 0.02 0 0 0.03 0 Eusmilia fastigiata 0 0 0 0 0 0 0 0 0 0 0.04 Favia fragum 0 0 0 0 0.02 0 0 0 0 0 0 Madracis decactis 0 0 0 0 0 0 0 0 0.13 0 0 Meandrina mea ndrites 0 0 0 0 0 0 0 0 0.36 0 0 Millipora alcicornis 0.16 0.25 0.96 0.69 1.11 1.22 0.80 0.18 0.29 0.73 0.96 Millipora complanata 0 0 0 0 0 0 0 0 0.29 0 0.02 Montastraea cavernosa 0.41 0.08 0.08 0.29 0.35 0.62 0 0.44 0.07 0.03 0.13 Montastraea faveolat a 0.99 0.74 0 0 0 4.15 3.10 0.05 3.57 3.30 1.53 Montastraea franksi 0.05 0 0 0 0 0 0.07 0 0 0 0 Porites astreoides 0.11 0.04 4.88 2.44 0.04 0.33 0.80 0.15 3.08 1.78 1.17 Porites divaricata 0.03 0 0 0 0 0.10 0 0 0 0 0.15 Porites furcata 0 0 0 0 0 0 0 0 0 0 0.04 Porites porites 0.11 0.04 3.32 0.29 0.58 1.81 0.87 1.31 0.29 1.08 0.67 Siderastrea radians 0.05 0 0 0 0 0.02 0 0 0.03 0 0 Siderastrea siderea 0.93 0.94 3.43 0.88 3.68 0.91 2.54 1.16 1.70 1.32 0.44 Solenastrea bournoni 0 0 0 0 0 0 0.44 0 0 0.27 0.02 Stephanocoenia intersepta 0 0 0 0 0 0 0 0 0 0.00 0.02 Total Percent Cover 3.35% 2.17% 13.0 % 4.62% 7.61% 9.73% 9.09% 3.34% 10.2 % 8.67% 7.17% Total Number of Species 11 8 8 7 9 11 10 7 12 10 16

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27 Table 8. Percent cover data collected in eight ben thic cover categories for each reef using AGRRA survey methods. Key: Sp = Porifera, Gorg = Gorgonians, Paly = Palythoa, Octo = Oct ocorals

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28 Table 9. Percent similarities among AGRRA transects for each reef, determined using SIMPER analysis. The final two entries show percent similarity among transects from patch reefs surveyed in BNP and FKNMS. The data set consisted of eight variable s. Abbreviations as in Table 8 Reef/Location Similarity Top 3 Contributors Percent Contribution Dome 79.6 Turf 66.6 Fleshy Macro 10.8 Other Live Sessile 10.6 Dome Control 76.9 Turf 70.1 Fleshy Macro 13.5 Other Live Sessile 7.9 0 Elkhorn 83.1 Turf 76.4 Live Coral (> 10cm) 12.2 Other Live Sessile 4.57 Elkhorn Control 81.9 Turf 81.9 Fleshy Macro 6.56 Calc Macro 3.4 0 Schooner 80.4 Turf 83.2 Live Coral (> 10cm) 7.59 Schooner Control 67.7 Turf 67.1 Other Live Sessile 12.5 Live Coral (> 10cm) 10.2 Star 58.5 Turf 54.3 Fleshy Macro 18.9 Live Coral (> 10cm) 8.4 0 Alina's 72.5 Turf 7 2.8 Fleshy Macro 10.3 Calc Macro 7.08 Three Sisters 69.6 Turf 65.8 Fleshy Macro 22.2 Other Live Sessile 6.75 Algae 70.5 Turf 56.5 Live Coral (> 10cm) 12.4 Calc Macro 12.4 White Banks 75.7 Turf 65.5 Fleshy Macro 13.2 Other Live Se ssile 10.8

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29 Reef/Location Similarity Top 3 Contributors Percent Contribution BNP 73. 0 Turf 74.5 Fleshy Macro 7.96 Live Coral (> 10cm) 5.94 FKNMS 69.3 Turf 65.9 Fleshy Macro 15.9 Other Live Sessile 7.19

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30 Table 10. Bet ween reef comparisons based on AGRRA analysis of transects calculated from the same data set as the similarities shown in Table 9. Abbreviations as in Table 8 Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Dome/Dome Control 20.7 Tur f 32.8 Fleshy Macro 32.7 Other Live Invert 11.2 Dome/Star 32.0 Turf 33.4 Fleshy Macro 16.6 Other Live Invert 12.8 Dome Control/Star 32.7 Turf 32.3 Fleshy Macro 17.5 Live Coral (>10 cm) 12.8 Dome/Algae 29.5 Turf 28.5 Fleshy Macro 27. 5 Sand 17.5 Dome Control/Algae 32.4 Turf 27.6 Fleshy Macro 18.6 Calc Macro 17.0 Star/Algae 33.9 Turf 28.4 Live Coral (>10 cm) 15.7 Live Coral (<10 cm) 13.6 Dome/White Banks 22.0 Turf 31.6 Fleshy Macro 23.0 Other Live Invert 15.5 Do me Control/White Banks 23.3 Turf 28.6 Fleshy Macro 26.0 Other Live Invert 15.2 Star/White Banks 32.6 Turf 30.4 Other Live Invert 14.0 Live Coral (>10 cm) 13.6 Algae/White Banks 30.0 Turf 24.4 Calc Macro 19.1 Other Live Invert 14.9 Dome /Alina's 26.3 Turf 30.7 Fleshy Macro 17.2 Other Live Invert 14.9

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31 Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Dome Control/Alina's 28.0 Turf 30.2 Fleshy Macro 22.5 Calc Macro 12.9 Star/Alina's 35 .8 Turf 35.2 Fleshy Macro 12.4 Live Coral (>10 cm) 12.3 Algae/Alina's 30.9 Turf 34.6 Live Coral (>10 cm) 13.5 Calc Macro 13.4 White Banks/Alina's 28.6 Turf 30.1 Other Live Invert 17.8 Fleshy Macro 14.6 Dome/Elkhorn 22.3 Turf 28.6 Fl eshy Macro 23.3 Live Coral (>10 cm) 16.0 Dome Control/Elkhorn 25.8 Fleshy Macro 28.3 Turf 26.2 Live Coral (>10 cm) 17.3 Star/Elkhorn 35.9 Turf 34.6 Fleshy Macro 15.6 Live Coral (>10 cm) 13.4 Algae/Elkhorn 30.6 Turf 37.4 Calc Macro 16.5 Fleshy Macro 12.8 White Banks/Elkhorn 25.0 Turf 32.0 Fleshy Macro 21.0 Other Live Invert 16.6 Alina's/Elkhorn 24.0 Turf 31.3 Fleshy Macro 15.5 Live Coral (>10 cm) 14.6 Dome/Schooner 25.9 Turf 34.6 Fleshy Macro 24.8 Other Live Inver t 11.9

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32 Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Dome Control/Schooner 27.9 Turf 31.8 Fleshy Macro 29.8 Other Live Invert 9.91 Star/Schooner 40.0 Turf 38.3 Fleshy Macro 17.0 Live Coral (>10 c m) 10.6 Algae/Schooner 36.1 Turf 39.0 Calc Macro 15.2 Fleshy Macro 14.0 White Banks/Schooner 29 .0 Turf 35.4 Fleshy Macro 22.5 Other Live Invert 15.1 Alina's/Schooner 26.5 Turf 34.1 Fleshy Macro 18.0 Calc Macro 13.7 Elkhorn/Schooner 18 .0 Turf 35.9 Live Coral (>10 cm) 15.1 Fleshy Macro 10.7 Dome/Schooner Control 25.0 Turf 39.6 Fleshy Macro 26.6 Other Live Invert 8.0 Dome Control/Schooner Control 26.1 Turf 38.7 Fleshy Macro 27.0 Other Live Invert 9.4 Star/Schooner Con trol 36.7 Turf 36.3 Fleshy Macro 16.2 Other Live Invert 11.2 Algae/Schooner Control 35.3 Turf 32.9 Calc Macro 16.8 Fleshy Macro 16.4 White Banks/Schooner Control 26.7 Turf 38.5 Fleshy Macro 22.5 Other Live Invert 11.7

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33 Table 10 (cont Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Alina's/Schooner Control 30.8 Turf 34.8 Fleshy Macro 18.9 Other Live Invert 13.00 Elkhorn/Schooner Control 27.8 Turf 37.7 Fleshy Macro 21.3 Other Live Invert 12.4 Schoo ner/Schooner Control 28.9 Turf 35.9 Live Coral (>10 cm) 15.1 Fleshy Macro 10.7 Dome/Three Sisters 28.4 Turf 28.5 Fleshy Macro 27.5 Sand 17.5 Dome Control/ Three Sisters 26.7 Turf 28.4 Fleshy Macro 27.3 Sand 18.5 Star/Three Sisters 39.2 Turf 25.7 Fleshy Macro 17.4 Sand 12.6 Algae/ Three Sisters 37.6 Fleshy Macro 19.8 Turf 19.7 Calc Macro 16.7 White Banks/ Three Sisters 28.5 Turf 38.3 Fleshy Macro 17.0 Sand 10.6 Alina's/Three Sisters 34.6 Turf 28.4 Fleshy Macro 22.2 Sand 14.3 Elkhorn/Three Sisters 33.8 Fleshy Macro 28.1 Turf 28 .0 Sand 14.8 Schooner/Three Sisters 36.3 Turf 31.9 Fleshy Macro 29.8 Sand 14.4

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34 Reef/Location Dissimilarity Top 3 Contributors Percent Contribution Schoone r Control/Three Sisters 32.2 Turf 34.2 Fleshy Macro 24.3 Sand 15.4 Dome/Elkhorn Control 22.7 Turf 35.2 Fleshy Macro 19.5 Other Live Invert 14.9 Dome Control/Elkhorn Control 24.9 Turf 33.5 Fleshy Macro 26.9 Other Live Invert 12.0 Star/E lkhorn Control 37.0 Turf 33.4 Fleshy Macro 16.6 Live Coral (>10 cm) 12.8 Algae/Elkhorn Control 33.7 Turf 40.2 Calc Macro 14.0 Live Coral (>10 cm) 13.6 White Banks/Elkhorn Control 26.6 Turf 36.0 Other Live Invert 17.5 Fleshy Macro 16.5 Alina's/Elkhorn Control 22.5 Turf 37.5 Calc Macro 14.5 Fleshy Macro 14.1 Elkhorn/Elkhorn Control 18.5 Turf 31.0 Live Coral (>10 cm) 21.6 Fleshy Macro 13.1 Schooner/Elkhorn Control 19.6 Turf 34.6 Fleshy Macro 24.8 Other Live Invert 11.9 Schooner Control/Elkhorn Control 27.8 Turf 37.7 Fleshy Macro 21.3 Other Live Invert 12.4 Three Sisters/Elkhorn Control 32.4 Turf 34.6 Fleshy Macro 26.5 Sand 15.6 BNP/FKNMS 30.7 Turf 32.3 Fleshy Macro 19.9 Other Live Invert 10.5

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35 Tabl e 11. Percent cover by individual coral species for specimens larger than 10 cm in diameter; data collected using AGRRA survey methods. A. BNP reefs Coral Species Dome Dome Control Elkhorn Elkhorn Control Schooner Schooner Control Star Acropora cervicornis 0 0 0 0 0 1.41 0 0.01 Agaricia agaricites 0.03 0 0 0 0 0.04 0 0 Colpophyllia natans 0 0 0 0 1.08 0 0 0 Dichocoenia stokesii 0.02 0.08 0 0 0 0.07 0.59 0 Diploria clivosa 0.03 0.03 0 0 0.97 0 0.16 0 Diploria labyrinthiformis 0 0 0 0 0 0 0 0 Diploria strigosa 0.22 0 0.56 0 0 0 0 0 Eusmilia fastigiata 0 0 0 0 0 0 0 0 Favia fragum 0.01 0 0 0 0 0 0 0 Helioseris cucullata 0 0 0 0 0 0 0 0 Madracis decactis 0 0 0 0 0 0 0 0.01 Madracis mirabilis 0 0 0 0 0 0.03 0 0 Meandrina meandrites 0 0 0 0 0 0 0.08 0 Millipora alcicornis 0.12 0.30 0.50 0.58 0.79 0.59 0.23 0 Millipora complanata 0.02 0 0 0 0 0 0 0 Montastraea annularis 0 0 0 0 0 0 4.90 1.13 Montastraea cavernosa 0 0.02 0.07 1.01 0.16 0.47 0 0.38 Montastraea faveolata 3.87 0.08 0 0 0 0 4. 12 1.67 Montastraea franksi 0 1.54 0 0 0 0 0 0 Porites astreoides 0 0 4.83 1.72 0 0.05 0.13 0 Porites divaricata 0.01 0 0 0 0 1.20 0 0 Porites furcata 0 0 0 0 0 0.03 0 0.01 Porites porites 0.15 0.09 4.28 0.03 0.07 2.60 0.17 2.17 Siderastrea radians 0 .01 0.09 0 0 0.07 0 0.01 0 Siderastrea siderea 0.54 1.16 2.16 1.67 5.66 0.37 0.95 0.91 Solenastrea bournoni 0 0.10 0 0 0 0 0.05 0.01 Solenastrea hyades 0.28 0.02 0 0 0 0.09 0 0 Stephanocoenia intersepta 0 0 0 0 0 0.05 0 0 Total Percent Cover 5.30 3.50 12.4 5.00 8.80 7.00 11.4 6.30 Total Number of Species 13 10 6 5 7 14 11 11

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36 B. FKNMS reefs Coral Species Three Sisters Algae White Banks Acropora cervicornis 0 0 0.31 Agaricia agaricites 0.01 0 0.22 Colpophyllia natans 0 0 0.1 0 Dichocoenia stokesii 0 0.36 0 Diploria clivosa 0 0 0 Diploria labyrinthiformis 0 0 0.16 Diploria strigosa 0 0.26 0.02 Eusmilia fastigiata 0 0.02 0 Favia fragum 0 0 0 Helioseris cucullata 0 0 0 Madracis decactis 0 0 0 Madracis mirabilis 0 0 0 Me andrina meandrites 0 0.09 0 Millipora alcicornis 0.02 1.04 0.44 Millipora complanata 0 0.05 0 Montastraea annularis 0 4.97 2.74 Montastraea cavernosa 0.08 0 0.21 Montastraea faveolata 0 0 1.20 Montastraea franksi 0 0 0.75 Porites astreoides 0 4.68 0 .65 Porites divaricata 0.01 0 0 Porites furcata 0 0 0 Porites porites 2.25 0.68 0.88 Siderastrea radians 0 0.02 0.08 Siderastrea siderea 0.62 1.14 0.03 Solenastrea bournoni 0 0 0.11 Solenastrea hyades 0 0 0.44 Stephanocoenia intersepta 0.01 0 0.26 Total Percent Cover 3.00 13.3 8.60 Total Number of Species 7 11 17

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37 Table 12. AGRRA coral cover percentage with M. annularis complex. = Montastraea annularis complex including M. annularis M. faveolata and M. franksi A. BNP reefs Coral Species Do me Dome Control Elkhorn Elkhorn Control Schooner Schooner Control Star Acropora cervicornis 0 0 0 0 0 1.41 0 0.01 Agaricia agaricites 0.03 0 0 0 0 0.04 0 0 Colpophyllia natans 0 0 0 0 1.08 0 0 0 Dichocoenia stokesii 0.02 0.08 0 0 0 0.07 0.59 0 Diploria clivosa 0.03 0.03 0 0 0.97 0 0.16 0 Diploria labyrinthiformis 0 0 0 0 0 0 0 0 Diploria strigosa 0.22 0 0.56 0 0 0 0 0 Eusmilia fastigiata 0 0 0 0 0 0 0 0 Favia fragum 0.01 0 0 0 0 0 0 0 Helioseris cucullata 0 0 0 0 0 0.00 0 0 Madracis decac tis 0 0 0 0 0 0 0 0.01 Madracis mirabilis 0 0 0 0 0 0.03 0 0 Meandrina meandrites 0 0 0 0 0 0 0.08 0 Millipora alcicornis 0.12 0.30 0.50 0.58 0.79 0.59 0.23 0.00 Millipora complanata 0.02 0 0 0 0 0 0 0 Montastraea annularis complex 3.87 1.62 0 0 0 0 9.02 2.80 Montastraea cavernosa 0 0.02 0.07 1.01 0.16 0.47 0 0.38 Porites astreoides 0 0 4.83 1.72 0 0.05 0.13 0 Porites divaricata 0.01 0 0 0 0 1.20 0 0.00 Porites furcata 0 0 0 0 0 0.03 0 0.01 Porites porites 0.15 0.09 4.28 0.03 0.07 2.60 0.17 2.17 Siderastrea radians 0.01 0.09 0 0 0.07 0 0.01 0 Siderastrea siderea 0.54 1.16 2.16 1.67 5.66 0.37 0.95 0.91 Solenastrea bournoni 0 0.10 0 0 0 0 0.05 0.01 Solenastrea hyades 0.28 0.02 0 0 0 0.09 0 0 Stephanocoenia intersepta 0 0 0 0 0 0.05 0 0 Total P ercent Cover 5.30 3.50 12.40 5.00 8.80 7.00 11.40 6.30 Total Number of Species 13 10 6 5 7 14 11 11

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38 B. FKNMS reefs Coral Species 3 Sisters Algae White Banks Acropora cervicornis 0 0 0.31 Agaricia agaricites 0.01 0 0.22 Colpophy llia natans 0 0 0.10 Dichocoenia stokesii 0 0.36 0 Diploria clivosa 0 0 0 Diploria labyrinthiformis 0 0 0.16 Diploria strigosa 0 0.26 0.02 Eusmilia fastigiata 0 0.02 0 Favia fragum 0 0 0 Helioseris cucullata 0 0 0 Madracis decactis 0 0 0 Madracis mirabilis 0 0 0 Meandrina meandrites 0 0.09 0 Millipora alcicornis 0.02 1.04 0.44 Millipora complanata 0 0.05 0 Montastraea annularis complex 0 4.97 4.69 Montastraea cavernosa 0.08 0 0.21 Porites astreoides 0 4.68 0.65 Porites divaricata 0.01 0 0 Porites furcata 0 0 0 Porites porites 2.25 0.68 0.88 Siderastrea radians 0 0.02 0.08 Siderastrea siderea 0.62 1.14 0.03 Solenastrea bournoni 0 0 0.11 Solenastrea hyades 0 0 0.44 Stephanocoenia intersepta 0.01 0 0.26 Total Percent Cover 3.00 13.30 8. 60 Total Number of Species 7 11 17

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39 Table 13. Comparison of data collected using AGRRA survey methods and those collected using CPCe analysis of photo transects combined into compatible categories. Table 8

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40 Table 14. Similarities and dissimilarities of data collected from the same transects using AGRRA and CPCe data from photo transects. Ther e were six categories used for comparison Sampling Method Similarity Top 3 Contributors Percent Contribution AGRRA 83.9 Turf 65.3 Macro Algae 16.4 Total Live Coral 10 .0 CPCe 79.2 Turf 45.3 Macro Algae 28.1 Other Live Inverts 18.5 Sampling M ethod Dissimilarity Top 3 Contributors Percent Contribution CPCe/AGRRA 26.9 Turf 38.0 Macro Algae 24.8 Other Live Inverts 21.9

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41 Table 15. Similarities and dissimilarities of coral cover data collected from the same transects using AGRRA and photo transect data sets

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42 Figure 4. A multidimensional scaling plot representing each transect for each reef, based on analysis of the 54 benthic cover categories identified using Coral Point Count.

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43 Figure 5. ANOSIM histogram comparing difference between reefs for benthic cover data collected from photo transects; R = 0.651 indicating that significant differences were detected among reefs (see Table 6).

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44 Figure 6. ANOSIM histogram comparing benthic cover data from photo transects, between lo cations; R = 0.141 indicates no significant differences between locations surveyed in BNP and FKNMS.

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45 Figure 7. A multidimensional scaling plot representing each transect for each reef, based on analysis of the six AGRRA categories of benthic cover m easured in cm/transect.

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46 Figure 8. ANOSIM histogram comparing difference between reefs for benthic cover data collected from AGRRA survey; R = 0.189 indicating that significant differences were detected among reefs (see Table 10).

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47 Figure 9. ANOSIM histogram comparing benthic cover data from AGRRA survey, between locations; R = 0.191 indicates no significant differences between locations surveyed in BNP and FKNMS.

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48 A. Plot is coded by location of reefs B. Plot coded by sample method. Figure 10. A m ultidimensional scaling plot comparing data from AGRRA benthic cover and the photo transect benthic cover analyses.

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49 Figure 11. ANOSIM histogram comparing benthic cover data for both AGRRA and photo transect data; R = 0.089 indicating that no significant differences were detected among locations.

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50 Figure 12. ANOSIM histogram comparing benthic cover data for both AGRRA and photo transect data; R = 0.496 indicating that significant differences were detected among data sets.

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51 Figure 13. The den drogram represents similarities between reefs. Black lines represent significant differences between data.

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52 Figure 14. ANOSIM histogram based on coral cover data comparing results from AGRRA and photo transects methods; R = 0.023 indicates no significa nt differences.

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53 Figure 15. ANOSIM histogram based on coral cover from combined AGRRA and Photo transect data, comparing data from BNP reefs with those from FKNMS; R = 0.029 reveals no significant differences.

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54 Figure 16. ANOSIM histogram comparing results between reefs based on the combined AGRRA and photo transect coral cover data; R = 0.631 indicates significant differences among reefs.

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55 Discussion The original goal of my project was to compare coral cover at the time of my surveys with coral c over data collected at eight BNP patch reefs between 1977 and 1981 to determine how the coral cover had changed at those sites over approximately 30 years. The original data were collected using a line point transect method on ts (Dupont et al. 2008). The transects were annually surveyed from 1977 through 1981. Unfortunately, many of the stakes had either deteriorated or been removed in the intervening years, although a few transect stakes were seen during the 2009 field work. Because the transects could not be exactly repeated and because photo transects are now the method most used in benthic surveys, my primary data collection method was photographic. However, because AGRRA surveys are also common ly used and AGRRA data wer e available for a set of upper keys reefs from 2002 (Fisher 2007), I also used AGGRA survey methods as a comparison. The AGRRA sampling method estimates cover, +/ 5cm, along a 10 m underwater transect using only eight variables. The estimation i s subject ive and depends on the judgment and experience of the diver, potentially increasing variability among transects. Underwater conditions (currents, swells, etc.) also influence the prevente d t he transect lines from remaining taut. There were strong swells at various times of the day which moved the transect lines during data collection; sometimes movements were up to 0.5 m on either side of center. All of these factors cause d data variabi lity during the three passes along each transect. T here is a possibility that data may be collected

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56 along slightly different substrate during each of the three passes along a transect. On the other hand, AGRRA is useful for counting the number of colonie s and estimating total size and volume of individual coral colonies, something more difficult from photo transects. Photographic surveys clearly provide the potential for greater accuracy in compiling a data set for benthic cover If the compiler is unsure of a n identification one can always return to the photo, seek other opinions or delete a specific problem point The major problems with photographic data are resolution and focus. Parts of a photo may be out of focus because of relief. Shadows can be cast by the diver or sometimes equipment will float in front of the photo and be included in the random points. There is a small chance that areas will be duplicated when a video camera is not used. However, all of these problems can be noted and the pro blem data deleted. Thus photo transects analyzed using identification of randomly generated points provide more reliable summary of benthic cover, so I will focus on CPCe data for the rest of the discussion unless I specifically note that I am comparing A GRRA data sets. Many studies have documented coral decline along the Florida reef tract over the past se veral decades (Dustan and Halas 1987 Porter and Meier 1992 CREMP 2001 Dupont et al 2008 Somerfield et al. 2008). My results are consistent with th ose studies, revealing that m ean coral cover declined about 59 % between 1981 and 2009 on the seven BNP patch reefs surveyed dropping from 18% cover to 7% cover (Table 16 ). Some patch reefs, such as Dome and Elkhorn r eef s declined by 8 1 % and 52% respect ively in that time frame (Fig. 1 7 ) Other patch reefs such as Schooner and Schooner Control, which had only 11% and 10% coral cover respectively in 1977 1981, exhibited much less change over time, with a 33 % decline for Schooner and no significant change for Schooner Control.

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57 Patch reefs in BNP and the entire Upper Keys have witnessed decline in coral cover (Table 1 6 ). According to the Coral Reef Evaluation and Monitoring Program (CREMP) executive summary of 1996 2000, there has been a decline of stony c oral cover across FKNMS. CREMP specifically reported a decrease in coral cover on patch reefs from 20% to approximately 15% during that time. Between the years 1999 and 2000, the trend appeared to halt as 109 out of 144 stations remained statistically un changed. Twenty four reefs showed an increase and only 11 showed a significant decrease. Twenty seven of the unchanged reefs were located in the Upper Keys. The CREMP executive summary of 2007 confirm ed the majority of coral loss (approximately 5 % in p ercent cover ) occurred between 1996 and 1999. B etween 1999 and 2006 only another 1.5% cover has been lost, on average Out of the five most common species Sanctuary wide, the group continually declining is M. annularis complex. The other four species s eem to be maintaining their cover C oral cover has declined so much over the past 30 years that it is difficult to detect further decline s The number of species I recorded was slightly lower than what was recorded in the 1977 81 study. In the earlier study Jaap et al (as reported by Dupont et al. 2008) observed 28 species of coral at the eight BNP reefs studied. In 2009, I recorded 24 species in the photo transects which must be corrected to 23 species because of the Montastraea spp. issues noted previously. Species found in 1977 81 but not in 2009 included Acropora palmata Isophyllastrea rigida Isophyllia sinuosa Mycetophyllia ferox M. lamarkiana Manicina areolata and Solenastrea hyades With the exception of A. palmata which was only f ound on Elkhorn and Elkhorn Control but in significant quantities in 1977 81, these species each covered less than one percent of the reef and were considered rare species. Porter and Meier (1992) contended that rare species do not contribute significantl y to the overall percent cover loss. Species that I found that

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58 were not recorded in the 1977 81 study included Meandrina meandrites Porties divaricata and P. furcata These species also contributed less than one percent of the coral cover on each reef and are considered rare. Moreover, I did record 26 species during the AGGRA surveys. Overall, my findings for species richness are consistent with those reported by Dupont et al. (2008) Therefore, the number of species that can be found on Biscayne pat ch reefs apparently has not changed, although taxa, notably Acropora spp ., that were abundant 30 years ago are now not commonly encountered Acropora palmata originally was so abundant on Elkhorn Reef that its common name is the reef name. Yet I found no ne on either Elkhorn or Elkhorn Control. The decline of Acropora spp has previously been reported throughout the Florida reef tract (Jaap and Sargent 1993 Porter and Meier 1992 Boulon et al 2005 Dupont et al 2008). In 1881, A. palmata populations co vered approximately 44 hectares (Agassiz 1882 Davis 1982) of the Dry Tortugas. The cover drastically decreased to 600 to 800 m 2 by 1993 according to Jaap and Sargent (1993). The cause of this decrease cannot be attributed to one thing but likely many factors includ ing disease, prolonged cold weather events, hurricanes, and bleaching (Jaap and Sargent 1993). Moulding and Patterson (2002) also recorded no Acropora spp. on Elkhorn R eef. The only A. cervicornis cover that I recorded was 0.3% on Schooner Control; the 1977 81 study did not record it on their transects at this reef. Montastraea annularis complex is the other group that sharply declined in coral cover between the 1977 81 and 2009 surveys. In 1977 81, M. annularis complex dominated coral co ver at Dome and Star reefs. In 2009, it was the dominant at both, but cover by this taxon had declined by nearly 90%. Interestingly, M. annularis complex increased from 0.49% to 4.15% over the same time frame at Schooner Control the only site showing a notable increase. Siderastrea spp and Porites spp have maintained

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59 their abundances on the reefs while other species of coral have been declining. In most cases, coral appears to have been replaced primarily by turf and Dictyota based on their current dominance of benthic cover. However, in this respect, I cannot directly compare my data with that collected from 1977 to 1981. There are three types of patch reefs observed in this study, those that decreased in Acropora spp ., those that decreased in Mon tastraea spp ., and those where coral cover was initially not very high and has remained relatively consistent ( Fig. 1 8 and 1 9 ). Elkhorn Reef is an example of a historically Acropora spp dominated reef. Figure 20 shows the decline of Acropora spp Dome R eef exemplifies a reef that decreased in Montastraea spp cover (Fig. 2 1) and Schooner Reef is a case where the overall coral cover has not changed as dramatically (Fig. 22 ) N either Acropora nor Montastraea were abundant there in 1977 81, and the coral cover has remai ned low and relatively stable. Thus, the decline in Acropora spp and Montastraea spp has resulted in relative low coral cover on all BNP patch reefs examined (Table 17 and 18 ) The variability among patch reefs, regardless of location o r sampling method, was a dominant feature in my data sets. Both Kuffner et al (2010), also studying patch reef benthos, and Baker et al. (2009), studying larger foraminiferal assemblages, noted that variability among patch reefs characterized their data sets. The AGRRA data indicate slightly higher coral cover in 2009 at each of the reefs assessed seven years earlier by Fisher (2007). However, given the difficulties with AGRRA data collection discussed earlier, one can question if those differences are m ostly observer issues about identification Moreover, the values still remained below the Caribbean wide means reported by Kramer (2003). Coral reef baselines are difficult to establish because of natural variation, but using the mean, best, and worst va lues for the Caribbean as comparison values can provide an indication of differences from the

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60 Caribbean normal (Kramer 2003, Fisher 2007). Large coral density consists of colonies with a measured diameter greater than 25 cm (Fig. 2 3 ). Although the percen t live coral cover is below the Caribbean wide means, the number of large coral colonies is above colonies). There seems to be a decrea se in the fleshy and calcareous macro a lgae cover as turf was dominant on my transects. Algae covered more than 50% of every reef. Fisher et al. (2007) discussed coral cover and other indicators of coral health at Lesions were induced quart erly over two years on five Montastraea colonies at each site as a consequence of cellular biomarker sampling Coral colonies at Algae R eef exhibited the fastest regeneration rates and t h is reef also had the highest coral cover in the study. Coral cover at White Banks was intermediate and coral colonies also regenerated relatively quickly while those at Three Sisters Reef failed to regenerate and the study colonies exhibited partial mortality. Three Sisters Reef also had the lowest coral cover in the st udy was more enigmatic, as it had relatively high coral cover and large colonies but very low lesion recovery rates, indicating that the stress that was preventing lesion recovery had not decimated coral cover (Fisher et al. 2007). Since I found comparable coral cover at between 2002 and 2009, despite the lesion and biomarker findings that indicated serious stress in the Montastraea colonies. Overall, my finding are consistent with other s tudies showing that inshore patch reefs are healthier with higher coral cover than the offshore reefs (Beaver et al 2005) The Florida reef tract overall has experienced the decline in coral cover that the rest of the Caribbean and reefs worldwide are recording (Bryant and Burke 1998

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61 Wilkinson 1999 Hoegh Guldberg 1999 Goreau et al 2000 Gardner et al 2003). While the FKNMS patch reefs have experienced decline in coral cover, in many cases the coral loss has been much less dramatic than that recorded on the hard bottom, deep, and shallow reefs (CR E MP 2001). At present coral cover, the only significant detectable changes may be increases, based on the fact that it is hard to detect a significant decrease if there i s less than 5 % cover to begin with. In the case of BNP patch reefs, the major decline apparently occurred in the 1970s and 1980s with the nearly complete loss of Acropora spp Loss of Montastraea spp apparently has occurred more sporadically over this p eriod, with substantial loss occurring in 1997 1999. Fisher et al. (2007) recorded mortality in some of the experimental coral during the 2001 2003 study noting that M. annularis complex colonies on inshore patch reefs regenerated faster and more consist ently than deeper, offshore reefs. S urveys over the past decade mostly show some variability but little or no significant decline I must note that results from my study might be quite different if my field work had been conducted in summer of 2010, af ter the mortality event associated with the record cold in January 2010 Previous cold events have been particularly hard on pat ch reefs and A. cervicornis thickets ( Hudson et al. 1976 Davis 1982 Porter et al. 1982 Roberts et al. 1982 Jaap et al. 2008 Soto et al. in review).

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62 Table 16. Percent coral cover means for data sets collected over the past three decades from patch reefs of BNP and the upper Florida Keys

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63 Table 17. CPCe coral cover percentage with M. annularis complex*. A. BNP reefs Cora l Species Dome Dome Control Elkhorn Elkhorn Control Schooner Schooner Control Star Alina's Acropora cervicornis 0 0 0 0 0 0.26 0 0.11 Agaricia agaricites 0 0 0.03 0 0 0.19 0.1 0 Colpophyllia natans 0 0 0.16 0 0 0 0 0 Coral (general) 0.03 0 0 0 0 0 0 0 Dichocoenia stokesii 0 0 0.08 0.04 0.07 0.12 0.34 0.03 Diploria clivosa 0 0 0 0 0.07 0 0 0 Diploria labyrinthiformis 0.3 0.08 0 0 0 0 0 0 Diploria strigosa 0.16 0 0 0 1.69 0 0.02 0.03 Eusmilia fastigiata 0 0 0 0 0 0 0 0 Favia fragum 0 0 0 0 0.02 0 0 0 Madracis decactis 0 0 0 0 0 0 0 0 Meandrina meandrites 0 0 0 0 0 0 0 0 Millipora alcicornis 0.16 0.25 0.96 0.69 1.11 1.22 0.8 0.73 Millipora complanata 0 0 0 0 0 0 0 0 Montastraea annularis 1.04 0.74 0 0 0 4.15 3.17 3.3 complex* Montastrae a cavernosa 0.41 0.08 0.08 0.29 0.35 0.62 0 0.03 Porites astreoides 0.11 0.04 4.88 2.44 0.04 0.33 0.8 1.78 Porites divaricata 0.03 0 0 0 0 0.1 0 0 Porites furcata 0 0 0 0 0 0 0 0 Porites porites 0.11 0.04 3.32 0.29 0.58 1.81 0.87 1.08 Siderastrea radi ans 0.05 0 0 0 0 0.02 0 0 Siderastrea siderea 0.93 0.94 3.43 0.88 3.68 0.91 2.54 1.32 Solenastrea bournoni 0 0 0 0 0 0 0.44 0.27 Stephanocoenia intersepta 0 0 0 0 0 0 0 0 Total Percent Cover 3.35 2.17 13.0 4.62 7.61 9.73 9.09 8.67 Total Number of Spec ies 11 8 8 7 9 11 10 10

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64 B. FKNMS reefs Coral Species Three Sisters Algae White Banks Acropora cervicornis 0 0 0.13 Agaricia agaricites 0.05 0.2 1.21 Colpophyllia natans 0 0 0 Coral (general) 0 0 0.02 Dichocoenia stokesii 0 0.16 0.44 Diploria clivosa 0 0 0 Diploria labyrinthiformis 0 0 0.19 Diploria strigosa 0 0 0 Eusmilia fastigiata 0 0 0.04 Favia fragum 0 0 0 Madracis decactis 0 0.13 0 Meandrina meandrites 0 0.36 0 Millipora alcicornis 0.18 0.29 0.96 Millipora complanata 0 0.29 0.02 Montastraea annularis 0.05 3.57 1.53 complex* Montastraea cavernosa 0.44 0.07 0.13 Porites astreoides 0.15 3.08 1.17 Porites divaricate 0 0 0.15 Porites furcate 0 0 0.04 Porites porites 1.31 0.29 0.67 Siderastrea radians 0 0.03 0 Side rastrea siderea 1.16 1.7 0.44 Solenastrea bournoni 0 0 0.02 Stephanocoenia intersepta 0 0 0.02 Total Percent Cover 3.34 10.2 7.17 Total Number of Species 7 12 16

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65 Table 18. Mean percent coral cover by species. The difference shows overall increase o r decrease in cover. Stephanocoenia michelini has been renamed S. intersepta (Humann, 2008 ) Coral Species Mean 1977 1981 Mean 2009 Difference Percent Change Acropora cervicornis 1.3 0.04 1.26 96.9 Acropora palmata 2.46 0 2.46 100 Agaricia agarici tes 0.44 0.04 0.4 90.9 Colpophyllia natans 0.37 0.02 0.35 94.6 Dichocoenia stellaris 0.34 0 0.34 100 Dichocoenia stokesii 0.01 0.09 0.08 800 Diploria clivosa 0.73 0.01 0.72 98.6 Diploria labyrinthiformis 0.08 0.05 0.03 37.5 Diploria strigos a 0.16 0.27 0.11 68.8 Eusmilia fastigiata 0.06 0 0.06 100 Favia fragum 0.03 0 0.03 100 Isophyllastrea rigida 0 0 0 No change Isophyllia sinuosa 0 0 0 No change Madracis decactis 0 0 0 No change Manicina areolata 0 0 0 No change Meandrina meandri tes 0 0 0 No change Millipora alcicornis 1.86 0.74 1.12 60.2 Millipora complanata 0.18 0 0.18 100 Montastraea annularis* 5.4 1.3 4.1 75.9 Montastraea cavernosa 0.27 0.26 0.01 3.7 Mycetophyllia ferox 0.11 0 0.11 100 Mycetophyllia lamar c kiana 0.08 0 0.08 100 Porites astreoides 1.24 1.24 0 No change Porites divaricata 0 0.02 0.02 100 Porites furcata 0 0 0 No change Porites porites 1.23 1 0.23 18.7 Siderastrea radians 0.02 0.01 0.01 50 Siderastrea siderea 2.16 1.9 0.26 12.0 Solena strea bournoni 0 0.06 0.06 100 Solenastrea hyades 0.01 0 0.01 100 Stephanocoenia intersepta** 0.01 0 0.01 100

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66 Figure 17. Comparison between the mean coral cover of historic (Dupont et al. 2008) and current data sets. 0 5 10 15 20 25 30 Dome Dome Control Elkhorn Elkhorn Control Schooner Schooner Control Star Star Control Coral Cover (%) Reef Mean Coral Cover: 1977 81 vs. 2009 1977-81 2009

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67 A. B. Figure 18. A. Multidimensional scaling comparison of coral species data sets collected in 1977 81 (Dupont et al. 2008) and in 2009 (this study). B. interpretation of changes responsible for pattern seen in A. Decreasing Montastraea spp. Decreasing coral cover Decreasing Acropora spp.

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68 Figure 19. Comparison of coral cover data sets collected in 1977 81 (Dupont et al. 2008) and in 2009 (this study).

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69 Figure 20. Comparison of top seven coral species on Elkhorn Reef. Elkhorn (1977 1981) 27.03% Porites astreoides Siderastrea siderea Porites porites Millipora alcicornis Acropora palmata Acropora cervicornis Diploria clivosa Other Elkhorn (2009) 12.95% Porites astreoides Siderastrea siderea Porites porites Millipora alcicornis Acropora palmata Acropora cervicornis Diploria clivosa Other

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70 Figure 21. Comparison of top seven coral species on Dome Reef. Dome (1977 1981) 27.82% Montastraea annularis Siderastrea siderea Montastraea cavernosa Diploria labrynthiformis Millipora alcicornis Colpophyllia natans Mycetophyllia ferox Other Dome (2009) 3.35% Montastraea annularis Siderastrea siderea Montastraea cavernosa Diploria labrynthiformis Millipora alcicornis Colpophyllia natans Mycetophyllia ferox Other

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71 Figu re 22. Comparison of top seven coral species on Schooner Reef. Schooner (1977 1981) 11.46% Siderastrea siderea Millipora alcicornis Porites porites Montastraea cavernosa Diploria strigosa Diploria clivosa Dichocoenia stellaris Other Schooner (2009) 7.61% Siderastrea siderea Millipora alcicornis Porites porites Montastraea cavernosa Diploria strigosa Diploria clivosa Dichocoenia stellaris Other

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72 Figure 23. Comparisons of study sites with AGRRA regional baselines (modified from Kramer 2003, Fisher 2007) for corals >25 cm maximum diameter and data from Fisher (2007), which was c ollected in 2002. 0 10 20 30 40 50 60 Percent Cover/Number of Colonies Reef Data (Year) AGRRA Comparisons Live Coral Cover (%) Large Coral Density (>25 cm)

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73 Conclusions 1. Turf and Dictyota currently dominate benthic cover on the patch reefs surveyed 2. Coral cover has declined by approximately 59 % between 1981 and 2009 on BNP patch reefs surveyed 3. Acropora palmata was not found and A. cervicorn is was rare on the reefs surveyed in 2009 4. Montastraea spp have also declined, though are still the most common taxa on six of the patch reefs 5. Siderastrea spp ., Porites spp ., and Solenastrea spp ., have not noticeably changed in their percent cover. 6. Altho ugh species have changed in relative or absolute abundances, the species identified in 2009 are very similar to those seen in 1977 81.

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74 References Cited Agassiz A.1882. Explorations of the surface fauna of the Gulf Stream under the auspices of the United States Coast Survey II. The Tortugas and Florida Reefs. Mem. Acad. Arts Sci. Centennial 2(1): 107 134. Baker RD, Hallock P, Moses EF, Williams DE, and Ramirez A. 2009 Larger foraminifers of the Florida reef tract, USA: distribution patterns of reef rub ble habitats. Journal of Foraminiferal Research 39(4): 267 277. Banks KW, Riegl BM, Richards VP, Walker BK, Helmle KP, Jordan LKB, Phipps J, Shivji MS, Spieler RE, and Dodge RE 2008. The Reef Tract of Continental Southeast Florida (Miami Dade, Broward and Palm Beach Counties, USA). In: Riegl BM and Dodge RE, editors. Coral Reefs of the USA. Springer Science, Business Media B.V. p. 175 220 Beaver CR, Jaap WC, Porter JW, Wheaton J and 6 others 2005 Coral reef evaluation and m onitoring program, 2 004 executive summary. Florida Fish and Wildlife Conservation Commission and University of Georgia, St. Petersburg Boulon R, Chiappone M, Halley R, Jaap W, Keller B, Kruczynski B, Miller M, Rogers C. 2005 Atlantic Acropora Status Review. Report to N ational Marine Fisheries Service, Southeast Regional Office. Bright T, Jaap W and Cashman C 1981. Ecology and management of coral reefs and organic banks. U.S. Department of Commerce, NOAA, ERL, Miami, Florida. Proceedings of Environmental Research needs in the Gulf of Mexico. p. 53 160. Bryant D and Burke L 1998. Reefs at risk: a Map based Indicator of Potential Threats p. 56. Callahan M, Wheaton J, Beaver C, Brooke S, Johnson D, Kidney J, Kupfner S, Porter JW, Meyers M, Wade S, et al. 2007. Coral Reef Evaluation and Monitoring Project: 2006 Executive Summary EPA Steering Committee Meeting, July 2007. Clarke KR. 1993. Non parametric multivariate analyses of changes in community structure. Australian Journal of Ecology 18: 117 143. Clarke KR and Gorley RN 2006. PRIMER v6: User Manual/Tutorial. PRIMER E, Plymouth. Clarke KR and Warwick RM 2001. Change in marine communities: an approach to statistical analysis an d interpretation, 2nd edition. PRIMER E, Plymouth.

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75 Davis GE. 1977. Anchor damage to a coral reef on the coast of Florida. Biology Conservation 11 : 29 34. Davis GE. 1982. A century of natural change in coral distribution at the Dry Tortugas: a compar ison of reef maps from 1881 1976. Bulletin of marine Science 32: 608 623. Dupont J M, Jaap WC and Hallock P 2008. A Retrospective Analysis and Comparative Study of Stony Coral Assemblages in Biscayne National Park, FL (1977 2000). Caribbean Journal o f Science 44 : 334 344. Dustan P. 1999. Coral reefs under stress: Sources of mortality in the Florida Keys. Natural Research Forum 23 : 147 155. Dustan P and Halas JC 1997. Changes in the reef coral community of Carysfort Reef, Key Largo, Flo rida: 19 74 1982. Coral Reefs 6: 91 106. Fisher E 2007. Assessing the health of coral reef ecosystems in the Florida Keys at community, individual, and cellular scales. Ph.D. Dissertation. University of South Florida, Tampa, FL. Fisher E M, Fauth JE Hallock P, and Woodley CM 2007. Legion regeneration rates in reef building corals Montastraea spp. as indicators of colony condition. Marine Ecology Progress Series 339: 61 71. Florida Keys National Marine Sanctuary. Sanctuary Resources. http://floridakeys.noaa.gov/sanctuary_resources/welcome.html accessed 20 February 2010. Gardner T A Cote IM Gill JA Grant A and Watkinson AR 2003. Long term region wide declines in Caribbea n corals. Science 301 : 958 960. Ginsburg, RN Atlantic Gulf Rapid Reef Assessment. www.agrra.org accessed 20 February 2010 Glynn P W, Szmant AM Corcoran EF and Cofer Shabica SV 1989. Condition of Coral Reef Cn idarians from the Northern Florida Reef Tract: Pesticides, Heavy Metals, and Histopathological Examination Marine Pollution Bulletin 20: 586 576. Goreau T J McClananhan T Hayes R and Strong AE 2000. Conservation of coral reefs after the 1998 global bleaching event. Conservation Biology 14 : 5 15. Halas J C. 1985. A unique mooring system for reef management in the Key Largo National Marine Sanctuary Proc. 5 th Internatio nal Coral Reef Congr. Tahiti 4: 237 242. Hoegh Guldberg O. 1999. Climate cha coral reefs. Marine Freshwater Research 50: 839 866. Hudson J H. 1981. Growth rates in Montastraea annularis : a record of environmental change in Key Largo coral reef marine sanctuary, Florida. Bull of Mar Sci 31: 444 459.

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Dynamics of stony coral assemblages on patch reefs of the upper florida reef tract, including biscayne national park
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ABSTRACT: The patch reefs located in Biscayne National Park (BNP) are some of the most northern reefs of the Florida reef system. The focus of my study is seven patch reefs that were first surveyed annually between 1977 and 1981, revealing 8% 28% cover by scleractinian corals. An assessment of BNP patch reefs completed in 2000 reported that coral cover had decreased to approximately 0.4% 10%. The once dominant species in the Florida reef tract, Acropora palmata and A. cervicornis, have rapidly declined over time and were not found in any transects during the 2000 survey. This study is a re-assessment of the BNP patch reefs surveyed in 1977-1981. In addition, one patch reef from BNP and three in upper keys region of the Florida Keys National Marine Sanctuary (FKNMS) have been included (a total of 11 patch reefs, all with historical data available). This study found 2% 13% coral cover at these 11 reefs using a photographic survey (Point Count) and 4% 21% coral cover using Atlantic and Gulf Rapid Reef Assessment (AGRRA) survey methods. These results are relatively similar to results reported for the same patch reefs in the 1990s and in 2002, indicating that the major changes occurred earlier with the extreme decline in Acropora spp. Montastraea annularis complex cover has also declined substantially at the BNP sites from 5.4% in 1977-81 to 1.3% in 2009. Although the number of species recoded on the seven resurveyed BNP patch reefs was only 23, compared with 28 recorded in the 1977-81 study, all species are still present in the region surveyed, indicating no actual loss of over all species richness.
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