Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2014 Model-based Tests of Historical Demography and Species Delimitation in the Caribbean Coral Reef Sponge Callyspongia Melissa Barrett eBD iasse Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation DeBiasse, Melissa Barrett, "Model-based Tests of Historical Demography and Species Delimitation in the Caribbean Coral Reef Sponge Callyspongia" (2014). LSU Doctoral Dissertations. 3540. https://digitalcommons.lsu.edu/gradschool_dissertations/3540 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. MODEL-BASED TESTS OF HISTORICAL DEMOGRAPHY AND SPECIES DELIMITATION IN THE CARIBBEAN CORAL REEF SPONGE CALLYSPONGIA A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Melissa Barrett DeBiasse B.Sc., Indiana University, 2003 M.Sc., Nova Southeastern University, 2008 August 2014 Acknowledgements This document is years in the making and the effort of many people. First I would like to thank my advisor Dr. Michael Hellberg. From the very first email he sent in response to my inquiry about the availability of positions in his lab he has shown enthusiasm about my research and my development as a scientist. He gave me the freedom to pursue the projects that interested me but also guidance when my ideas needed to be reigned in. He never hovered but was always available. He has made me an infinitely better writer and helped me to think about the big picture questions that motivate my research. The Louisiana Boards of Regents, National Science Foundation, LSU Department of Biological Sciences, American Museum of Natural History (Lerner Gray Grant), Smithsonian Tropical Research Institute, and the LSU local and national chapters of Sigma Xi funded my research. My committee members Dr. Robb Brumfield, Dr. Bryan Carstens, Dr. Joseph Neigel, and Dr. Joseph Powers have been incredibly helpful and generous with their time. Robb and Bryan exponentially expanded my knowledge about evolutionary biology through the courses they taught and they were always happy to provide recommendation letters for my grant proposals (some of which were successful!). Joe Neigel provided insightful comments that greatly improved the first chapter of my dissertation and helped lead to its publication. I had the pleasure of working with my outside committee member Joe Powers through the EnvironMentors program at LSU. Volunteering with EnvironMentors was a wonderfully rewarding and I am grateful to have had that experience. Dr. Jeremy Brown provided advice and computational resources for the species delimitation chapter of my dissertation and graciously invited me to attend his lab’s weekly paper discussions. I am also grateful to Dr. Vinson Doyle and Dr. Tom Giarla for their professional advice and friendship. Dr. Carlos Prada was the best “lab brother” I could have hoped for. Over the last six years, Carlos and I have had countless discussions about ecology and evolution in marine systems. His unique perspective has challenged and expanded the way I think about science from basic, applied, and philosophical points of view. My interactions with Carlos have been integral to my development as a scientist and I consider him to be a valuable collaborator and friend. Tara Pelletier and Sarah Hird have been an incredible support system for me as a scientist generally and as a female scientist specifically. Their professional and personal encouragement helps me believe in myself when the going gets tough. Reid Brennan is my calm in the storm and always brings out the best in me. I have learned more from interacting with my fellow graduate students than I could have ever imagined was possible. They have provided advice on project ideas, analytical methods, weird results, grant proposals, and manuscripts. They have also been incredible friends and helped to create an environment of hard work and fun that makes the LSU SEE division so special: Dr. Lori Patrick, Dr. Noah Reid, Dr. Eric Rittmeyer, and Cesar Sanchez (members of my cohort), Dr. Verity Mathis, Dr. Meche Gavilanez, Caroline Judy (my running and crossfit buddies), Dr. Ron Eytan, Dr. Alice Dennis, Karine Posbic (past and present Hellholers), Mike Harvey, Clare Brown, Jordan Satler, Dr. John McVay, Cathy Newman, Glenn Seeholzer, John Mittermeier, Ryan Terrill, Matt Brady, ii Vivian Chua,Valerie Durouen, Bill Ludt, Caleb McMahon, and Maria Vozzo (great colleagues and friends). Finally I would like to thank my parents Tony and Martha DeBiasse and my sister Jaime DeBiasse for their unconditional support. They never questioned my career path and lived my (momentary) defeats and triumphs as if they were their own. I would not have made it this far had it not been for them. I dedicate my dissertation to the memory of my grandparents, Malcolm and Dorothy Watson and Anthony and Joanne DeBiasse. Their love and support stays with me and I think of them always. iii Table of Contents Acknowledgements……………………………………………………………………......ii Abstract………………………………………………………………...……………....….v Chapter 1. Introduction……………………………………………………………………1 Chapter 2. Evaluating Summary Statistics Used to Test for Incomplete Lineage Sorting: Mito-nuclear Discordance in the Coral Reef Sponge Callyspongia vaginalis………………………………………………………………………………...…4 Chapter 3. Phylogeography of the Coral Reef Sponge Callyspongia vaginalis Across the Caribbean……...………………………………………………….………….22 Chapter 4. Species Delimitation in the Caribbean Coral Reef Sponge Genus Callyspongia……………………………………………………………......……………38 Chapter 5. Conclusions………………………………………………………..…………51 References………………………………………………………………………………..53 Appendix A. Supplementary Text, Tables, and Figures for Chapter 2….…...…………..73 Appendix B. Supplementary Tables and Figures for Chapter 3……………………..…..87 Appendix C. Supplementary Tables and Figures for Chapter 4…………..…………....106 Appendix D. Permission to Reproduce Chapter 2……………………………………...111 Vita………………………………………………………………..……………….……118 iv Abstract Coral reefs are the most productive and species rich ecosystems in the ocean yet we lack knowledge about the distribution of genetic variation the within and among reef species, particularly for the sponges (Porifera). My dissertation describes how genetic variation at mitochondrial and nuclear genes is partitioned among and within species in the sponge genus Callyspongia. I compared patterns of genetic diversity and population subdivision in the mitochondrial and nuclear genomes of one species, C. vaginalis, in Florida (Chapter 2). Previous work revealed three divergent mitochondrial lineages, but nuclear alleles did not correspond to either mitochondrial clade or geography. Coalescent simulations showed mito-nuclear discordance was not the result of incomplete lineage sorting. Instead, patterns in mitochondrial and nuclear DNA were consistent with changes in population size and sperm-mediated gene flow. Across the Caribbean, I found subdivision in C. vaginalis for mitochondrial and nuclear DNA was concordant, suggesting geographic features and habitat discontinuity are important for structuring populations at large spatial scales (Chapter 3). Clustering analyses found C. vaginalis populations were divided west-east and model-based tests of species boundaries supported a cryptic lineage in Central America. Phylogeographic patterns for three invertebrate sponge commensals also showed a west-east split between Florida and the Bahamas. I tested for mismatches between morphological and molecular species boundaries for seven Caribbean Callyspongia species (Chapter 4). Genetic distances calculated within and among species support C. fallax, C. tenerrima, and C. plicifera as distinct species. However, C. armigera, C. longissima, C. ?eschrichtii and C. vaginalis shared alleles across loci and genetic distances among these taxa overlapped distances within them. Model-based species delimitation supported the hypothesis that these latter four taxa represent one evolutionarily significant unit. This dissertation demonstrates that in the common reef sponge Callyspongia vaginalis, demographic processes and geography influence population structure at small and large spatial scales, respectively, and genetic markers from different genomes can show contrasting patterns. My work also shows the relationship between morphology and evolutionary history is not straightforward in sponges and points to the importance of inter- and intraspecific genetic data for a thorough documentation of biodiversity in marine invertebrates. v Chapter 1. Introduction Coral reefs are the most species rich habitats in the ocean (Odum & Odum 1955; Connell 1978) and play an important role in global ecosystem function (Mumby et al. 2008). Coral reefs act as breeding and nursery areas for a multitude of taxa (Nagelkerken et al. 2000). The heterogeneity and complex three-dimensional structure of coral reefs creates habitat and promotes species diversification (Paulay 1997). Coral reefs connect other important