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Genetic Connectivity of Octocorallia Across Abiotic Gradients in the Deep Gulf of Mexico

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Genetic Connectivity of Octocorallia Across Abiotic Gradients in the Deep Gulf of Mexico GENETIC CONNECTIVITY OF OCTOCORALLIA ACROSS ABIOTIC GRADIENTS IN THE DEEP GULF OF MEXICO A Dissertation Submitted to the Temple University Graduate Board In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY by Andrea M. Quattrini May 2014 Examining Committee Members: Dr. Erik E. Cordes, Advisory Chair, Biology Dr. Amy Freestone, Biology Dr. Rob Kulathinal, Biology Dr. Robert W. Sanders, Biology Dr. Timothy M. Shank, External Member, Woods Hole Oceanographic Institution © Copyright 2014 by Andrea M. Quattrini All rights reserved ABSTRACT Cold-water corals increase habitat heterogeneity and enhance biodiversity in deep waters worldwide. Despite the recognition of their importance in the deep sea, limited data exist on the ecology and evolution of deep-water corals. The overarching goal of this dissertation research was to integrate molecular, morphological, and ecological data to understand the degree to which populations are connected, species are distributed, and communities are assembled in the deep (250-2500 m) Gulf of Mexico (GoM). Specifically, several hypotheses were tested regarding the roles of environmental variables, particularly depth, influencing population and community structure. Combining phylogenetic and population genetic approaches with ecological data enabled species delimitations of many taxa while demonstrating that deep-water populations and communities diverge over short bathymetric distances. It appears that population isolation, congeneric species replacement and changes in community composition occur rapidly with depth, and these changes are likely due to a combination of both dispersal limitation and adaptive divergence with depth. Local self-recruitment may also be strong within any one site. Furthermore, results suggest that evolutionary history and neutral dynamics play a critical role in octocoral community assembly in the deep sea. This dissertation not only contributes a substantial amount of evolutionary and ecological information on a poorly studied group of foundation species in the deep sea, this research has broader implications for aiding in efforts to protect these long-lived, foundation species from anthropogenic disturbances. ii For the biggest supporters in my life Chris and Myadog who always know how to make me laugh at the end of the day iii ACKNOWLEDGEMENTS I thank my committee for their wisdom, guidance and willingness to help throughout this process: Erik Cordes, Robert Sanders, Amy Freestone, Rob Kulathinal, and Timothy Shank. I particularly thank my advisory chair Erik Cordes for his mentorship and friendship, and his willingness to allow me to pursue my own interests. He provided me unparalleled opportunities to grow as both a scientist and an explorer, while shaping my abilities to effectively communicate science. I am thankful that his door was always open, and am beyond impressed with his willingness to educate and share his knowledge about science and the world in general. He is a truly amazing mentor. I also thank Amy Freestone who sparked my interests in community ecology and provided statistical help, Robert Sanders for his enthusiastic support and sound advice, and Rob Kulathinal for pushing me beyond my comfort zone. I thank Tim Shank for sharing his knowledge, particularly in the ROV control van, for guiding me through my first Okeanos cruise as a Science Lead, and for being an inspiration as a public educator and leader in deep-sea biology. I also acknowledge several others for their invaluable guidance during my dissertation. I thank Katriina Ilves (Royal Ontario Museum) for being a sounding board and helping me to further understand phylogenetic methods. I also thank her for her friendship, for re-introducing me to SCUBA again, for the countless reviews, and for allowing me to continue my love of identifying fishes. I thank Cheryl Morrison (USGS) for her help with microsatellite development and for her advice over the past 11 years. Iliana Baums and Meghan Durante-Devlin (Penn State University) helped with initial iv microsatellite marker design and Matthew Hansen, Stephen Lengyel, and Craig Stanley (Temple University) guided me countless times with bioinformatics. I cannot adequately express the amount of gratitude that I feel towards my Temple peers, colleagues, and friends, particularly Jay Lunden and Erin Graham. I am thankful that I have made lifelong friends who will continue to support me throughout my professional and personal life. I am excited to see what the future holds. Thank you. Thank you. My gratitude also extends to all past and present members of the Cordes Lab, particularly my fellow graduate students Sam Georgian and Danielle Young, lab managers Natasha Remon, Leslie Wickes, and Veronica Radice, and undergraduates Cheryl Doughty, Rosie Falco, Alex Stevens, Lisa English, Luke Byrnes, and Connall McNicholl. Cheryl, in particular, was an asset to my work, and it was a pleasure mentoring her during her academic pursuits. I have to thank all of my past and current mentors for believing in me and inspiring me. I thank Martha Nizinski and Tom Munroe (NOAA Systematics Lab), who always know the right advice to give. Steve Ross provided (UNCW) me my first deep- sea experience that shaped my career path, and I will always be appreciative of his mentorship and his enthusiastic support of my capabilities. I also want to recognize the late David Lindquist (UNCW), who chose me to be his last Masters student during his final days. My gratitude goes to my extended friends and family for their unbelievable support and encouragement throughout my entire collegial experience. Every day, I am amazed at the love and support that I receive from Chris Payne. I also thank my friend Carrie Makoid and her family for incorporating me into their family during my time in v Philadelphia. Finally, I thank my late mother who was my biggest supporter and my father for taking me fishing at an early age, which ultimately influenced my passion for the water. I thank all additional members and leaders of the Lophelia II team, particularly Chuck Fisher, Jim Brooks, Bill Shedd, Peter Etnoyer, Amanda Demopoulos, and members of the Fisher and Shank Labs. Walter Cho, Santiago Herrera, Dannise Ruiz, Pen Yuan-Hsing and Taylor Heyl were invaluable at sea. It was a pleasure sailing with them. I also thank all of the people who provided taxonomic and phylogenetic expertise in the Octocorallia, particularly Catherine McFadden, Stephen Cairns, Leen van Ofwegen, Juan Sanchez, Les Watling, Scott France, and Jana Thoma. The Bureau of Ocean Energy and Management and NOAA-OER provided funding for this study through contract #M08PC20038 to TDI-Brooks International. Funding, also provided by the NSF RAPID program (award #1045079), and the NOAA Damage Assessment, Response, and Restoration Program. I received funding from the NOAA Nancy Foster Scholarship, Temple University Completion Grant, and the Lerner Gray Fund for Marine Research. vi TABLE OF CONTENTS Page ABSTRACT........................................................................................................................ii DEDICATION....................................................................................................................iii ACKNOWLEDGMENTS .................................................................................................. iv LIST OF TABLES ............................................................................................................ xii LIST OF FIGURES .......................................................................................................... xiii CHAPTER 1. INTRODUCTION ......................................................................................................... 1 1.1 Background ........................................................................................................ 1 1.2 Deep-Sea Evolution and Ecology ...................................................................... 2 1.3 Octocorallia (Phylum Cnidaria: Class Anthozoa) ............................................. 4 1.4 Octocorallia Phylogenetics ................................................................................ 5 1.5 Chapter Aims ..................................................................................................... 7 2. GENETIC, MORPHOLOGICAL, AND ECOLOGICAL DIVERGENCE IN THE GENUS CALLOGORGIA GRAY 1858 ...................................................................... 9 2.1 Abstract ............................................................................................................. 9 2.2 Introduction ..................................................................................................... 10 2.3 Methods ........................................................................................................... 13 2.3.1 Field methods ................................................................................... 13 2.3.2 Morphological identification.............................................................15 2.3.3 Phylogenetics ....................................................................................15 vii 2.3.4 Video analysis ...................................................................................18 2.3.5 Abundance-environmental data ........................................................18 2.4 Results .............................................................................................................19 2.4.1 Phylogenetic Relationships ....................................................................19
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