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Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E

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Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School November 2017 Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E. Hepner University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Biology Commons, Ecology and Evolutionary Biology Commons, and the Other Oceanography and Atmospheric Sciences and Meteorology Commons Scholar Commons Citation Hepner, Megan E., "Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary" (2017). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/7408 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary by Megan E. Hepner A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Marine Science with a concentration in Marine Resource Assessment College of Marine Science University of South Florida Major Professor: Frank Muller-Karger, Ph.D. Christopher Stallings, Ph.D. Steve Gittings, Ph.D. Date of Approval: October 31st, 2017 Keywords: Species richness, biodiversity, functional diversity, species traits Copyright © 2017, Megan E. Hepner ACKNOWLEDGMENTS I am indebted to my major advisor, Dr. Frank Muller-Karger, who provided opportunities for me to strengthen my skills as a researcher on research cruises, dive surveys, and in the laboratory, and as a communicator through oral and presentations at conferences, and for encouraging my participation as a full team member in various meetings of the Marine Biodiversity Observation Network (MBON) and other science meetings. Frank provided guidance, wisdom, and plenty of red ink. I am eternally grateful to Dr. Ben Best who helped me develop my R coding skills. He was patient with me as I struggled to resolve error after error, chasing bug after bug. Dr. Katie Shulzitski helped me through the statistical analysis and designing plots. Matt McCarthy introduced me to ArcGIS. I thank Dr. Enrique Montes and Dr. Anni Djurhuus, both of whom I have looked up to and who have mentored me throughout my graduate program. They are a joy to travel and toast drinks with. I thank Dr. Chris Stallings for his contributions to the literary portion of my research. Dr. Jeremiah Blondeau was extremely helpful as I pinged him regularly with questions about the Reef Visual Census survey design and package. Dr. Jon Lefcheck provided guidance and knowledge in all things related to biodiversity and he also helped resolve coding errors. Past and present members of the IMaRS lab were a pleasure to work alongside with, especially Abdiel Laureano-Rosario, Catherine J. Reynolds, Dr. Digna Rueda, Justin Saarinen, Kate Colna, and Tyler Murray. I thank the graduate students at the College of Marine Science for their comradery during late night study sessions and for their social time at the “Tavern”. I very much thank the NASA Earth Science Division Applications Program, the NOAA Ocean Exploration Program, NOAA National Marine Fisheries Service, the US Integrated Ocean Observing System (IOOS), and the National Ocean Partnership Program (NOPP) for supporting me morally and through funding for the Marine Biodiversity Observation Network (NASA grant NNX14AP62A ‘National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)’). I thank the University of South Florida and Drs. David Naar and Dean Jacqueline Dixon for their unwavering support and financial travel assistance. I’d also like to thank my friends and family, especially my boyfriend, Nicholas Medina, for constantly making me laugh and smile and encouraging me to never give up, and of course my parents Ray Hepner and Deb Hepner for their unwavering love and support since the day I entered this crazy world. And last, but not least, I express my deepest gratitude to Dr. Steve Gittings, without whom I would not be here today. Steve has been a mentor, friend, boss, colleague, and all-around role model. I appreciate his constant support, encouragement, and inspiration. TABLE OF CONTENTS LIST OF TABLES ............................................................................................................. iii LIST OF FIGURES ........................................................................................................... vi ABSTRACT ..................................................................................................................... viii INTRODUCTION ...............................................................................................................1 1. BACKGROUND ...............................................................................................1 2. SPECIES RICHNESS ........................................................................................2 3. SPECIES EVENNESS ......................................................................................3 4. SPECIES DIVERSITY ......................................................................................4 5. FUNCTIONAL DIVERSITY ............................................................................6 6. DIVERSITY AS “EFFECTIVE NUMBER OF SPECIES” ..............................9 CHAPTER 1: PATTERNS AND DRIVERS OF DEMERSAL REEF FISH COMMUNITY IN THE FLORIDA KEYS NATIONAL MARINE SANCTUARY FROM 1999 – 2016……………………………………………………………………... 11 1. INTRODUCTION ...........................................................................................11 2. METHODS ......................................................................................................14 2.1. STUDY SITE ............................................................................................14 2.2. REEF FISH SURVEYS ............................................................................16 2.3. CALCULATION OF INDICES ...............................................................18 2.4. STATISTICAL ANALYSIS ....................................................................21 3. RESULTS ........................................................................................................23 3.1.PATTERNS IN INDICES BY PROTECTION LEVEL ACROSS YEARS 3.2.PATTERNS IN INDICES BY STRATA ACROSS YEARS ...................23 3.2.1. ABUNDANCE ...............................................................................24 3.2.2. BIOMASS .......................................................................................25 3.2.3. EVENNESS ....................................................................................25 3.2.4. RICHNESS .....................................................................................26 3.2.5. SPECIES DIVERSITY ...................................................................26 3.2.6. FUNCTIONAL DIVERSITY .........................................................26 3.3. PATTERNS IN INDICES BY SUBREGION ..........................................28 3.4. POTENTIAL DRIVERS OF OBSERVED PATTERNS IN INDICES ...28 4. DISCUSSION ..................................................................................................29 4.1. NO-TAKE MARINE ZONES AND HABITAT CHARACTERISTICS 29 4.2. SPECIES DIVERSITY AND FUNCTIONAL DIVERSITY...................35 4.3. DISTURBANCES ....................................................................................41 i SUMMARY .......................................................................................................................44 TABLES AND FIGURES .................................................................................................46 REFERENCES ..................................................................................................................65 APPENDIX ....................................................................................................................... 83 ii LIST OF TABLES Table 1. Conversion of common indices to true diversities (Jost, 2006) ..........................46 Table 2. Reef Visual Census by number of Primary Sampling Units per year and stratum in the Florida Keys domain ..............................................................................47 Table 3. Functional traits of reef fish used to characterize functional niche (from Stuart Smith et al., 2013) ...........................................................................................48 Table 4. Disturbances between 1999 – 2016 in the Florida Keys (Office for Coastal Management, 2017) .........................................................................................49 Table A1. Listing of families ranked by percent of total abundance observed in the reef visual census from the Florida Keys domain between 1999 – 2016 ................83 Table A2. Listing of species ranked by percent of total abundance observed in reef visual census from the Florida Keys domain between 1999 – 2016 ..........................84 Table A3. Contributions of individual traits to patterns in functional diversity in the Florida Keys. ................................................................................................................92 Table A4. Tested for differences between level of protection using the nonparametric Kruskal-Wallis rank sum test ...........................................................................92
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