GENETIC AND ENVIRONMENTAL CONSIDERATIONS FOR ACROPORID CORAL RESTORATION By KATHRYN ELAINE LOHR A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Kathryn Elaine Lohr To my family ACKNOWLEDGMENTS I would first like to thank my advisor, Dr. Joshua Patterson for giving me the opportunity to complete my studies at UF. The guidance and mentorship he has provided over the past four years have been invaluable, and his advice and support have been deeply rewarding for my studies and my career. Sincere thanks also go to my supervisory committee members, Drs. Matt DiMaggio, Tom Frazer, Lyn Gettys, and Margaret Miller, for providing constructive advice and direction that have greatly improved the quality of my work. I would also like to thank Dr. Mark Flint for offering valuable early feedback on my work. My graduate research would not have been possible without the assistance of a number of individuals and institutions. First, I would like to thank the Tampa Electric Company for providing me with office space at the Florida Conservation and Technology Center during my time as a student. Chapters 2-4 of this dissertation would not have been possible without the Coral Restoration Foundation (CRF), who allowed me to conduct research involving their nursery and corals. Nursery-based studies were conducted under permit FKNMS-2011-159-A3 issued to CRF (Chapter 2), and permit FKNMS-2016-129-A1 issued to Dr. Joshua Patterson (Chapter 3). I would particularly like to thank Kayla Ripple for organizing field logistics throughout and for collaborating on Chapter 4. I’d also like to thank CRF for providing supplementary outplant data for Chapter 4, and Amelia Moura for coordinating data sharing. The Florida Aquarium provided field and logistical support for the initial outplanting work in Chapter 4, and specific thanks go to Keri O’Neil, Tim Stripling, Chris O’Neil, and Scott Graves for their assistance. Outplanting for this study was conducted under permit FKNMS-2011-159- A4 issued to CRF. Sincere thanks also go to the University of Florida’s Southeast 4 Center for Integrated Metabolomics for funding the metabolomics work in Chapter 3, as well as Drs. Tim Garrett, Matt Merritt, Ram Khattri, and Joy Guingab-Cagmat for their collaboration and feedback on this work. A number of University of Florida, CRF, and Florida Aquarium volunteers also provided indispensable field support for Chapters 2-4 of this dissertation. Field work for Chapter 5 was conducted in collaboration with the Central Caribbean Marine Institute (CCMI) in Little Cayman. Thanks to Dr. Carrie Manfrino for assistance in coordinating this collaboration, and to a number of CCMI staff members and students for assistance with field work. Particular thanks go to Aimee Cook McNab and Lowell Forbes.This work was supported by the National Science Foundation Research Experiences for Undergraduates program (OCE-1358600), CCMI, and the University of Florida. I also thank Krystan Wilkinson of the Chicago Zoological Society c/o Mote Marine Laboratory and the University of Florida for creating Figure 5-2. I would like to sincerely thank Drs. Emma Camp, David Suggett, and Unnikrishnan Kuzhiumparambil from the University of Technology, Sydney and Dr. Bill Leggat from the University of Newcastle for providing intellectual guidance, logistical support, and the research experience of a lifetime on the Great Barrier Reef (the results of which are detailed in Chapter 6). I’d also like to thank the staff of the University of Queensland’s Heron Island Research Station and Gus Fordyce for field and lab assistance on this study. Finally, I’d like to thank Dr. Adrian Lutz of the University of Melbourne for providing critical input on the metabolomic data presented in Chapter 6. Funding for the work in Chapter 6 was provided by the Australian Research Council (ARC; DP160100271 issued to Drs. David Suggett and Bill Leggat), with additional 5 support from an ARC Future Fellowship to Dr. David Suggett (FT130100202) and the University of Florida Foundation through the Evelyn Timm Koenig Memorial Endowment Fund. Coral collections in Chapter 6 were performed under permits G15/37488.1 and G16/38534.1 issued to Dr. Bill Leggat. A vast number of University of Florida staff, interns, and volunteers have been key to the completion of my studies. I’d especially like to thank the SFRC team for administrative assistance throughout my time as a student, Cheryl Thacker for assistance with dive logistics, and all my JPL labmates – Kelli O’Donnell, Rebecca Lucas, Kailee Schulz, Joe Henry, and Aaron Pilnick – for helping out with everything from field work to figure preparation. My unique office location provided me with a number of other coworkers who have provided support, guidance, and friendship over the years, so thanks also go to the entire FCTC crew. I’d also like to thank all the incredible friends who provided advice and encouragement throughout my academic experience. In closing, I’d like to thank my parents, Richard and Jill, who have always supported me throughout my academic journey, my brother, Kevin, who has one last chance to show up to one of my graduation ceremonies, and of course, Stanley and Copernicus. Finally, I’d like to say a huge thank you to Luke Miller. He has gone above and beyond for me these past years, and I appreciate his love and support more than words can express. 6 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 9 LIST OF FIGURES ........................................................................................................ 10 LIST OF ABBREVIATIONS ........................................................................................... 12 ABSTRACT ................................................................................................................... 13 CHAPTER 1 GENERAL INTRODUCTION .................................................................................. 15 2 INTRASPECIFIC VARIATION IN PHENOTYPE AMONG NURSERY-REARED ACROPORA CERVICORNIS ................................................................................. 26 Introduction ............................................................................................................. 26 Methods .................................................................................................................. 28 Results .................................................................................................................... 31 Discussion .............................................................................................................. 37 3 METABOLOMIC PROFILES DIFFER AMONG UNIQUE ACROPORA CERVICORNIS GENOTYPES ................................................................................ 43 Introduction ............................................................................................................. 43 Methods .................................................................................................................. 46 Sample Collection and Extraction ..................................................................... 46 1H-NMR Profiling .............................................................................................. 48 LC-MS Global Metabolomics ............................................................................ 49 Statistical Analysis ............................................................................................ 50 Results .................................................................................................................... 51 1H-NMR Profiling ............................................................................................. 52 LC-MS Global Metabolomics ............................................................................ 52 Discussion .............................................................................................................. 63 4 DIFFERENTIAL DISTURBANCE EFFECTS AND PHENOTYPIC PLASTICITY AMONG RESTORED ACROPORA CERVICORNIS AT PATCH AND FORE REEF SITES ........................................................................................................... 72 Introduction ............................................................................................................. 72 Methods .................................................................................................................. 76 Outplanting Experiment .................................................................................... 76 Expanded Dataset ............................................................................................ 78 7 Data Analysis ................................................................................................... 78 Results .................................................................................................................... 81 Discussion .............................................................................................................. 87 5 ASSESSMENT OF WILD AND RESTORED ACROPORA CERVICORNIS ACROSS THREE REEF ZONES IN THE CAYMAN ISLANDS .............................. 95 Introduction ............................................................................................................