University of Kentucky UKnowledge Theses and Dissertations--Biology Biology 2017 GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES Paul Michael Hime University of Kentucky, [email protected] Digital Object Identifier: https://doi.org/10.13023/ETD.2017.284 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Hime, Paul Michael, "GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES" (2017). Theses and Dissertations--Biology. 45. https://uknowledge.uky.edu/biology_etds/45 This Doctoral Dissertation is brought to you for free and open access by the Biology at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Biology by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. I agree that the document mentioned above may be made available immediately for worldwide access unless an embargo applies. I retain all other ownership rights to the copyright of my work. I also retain the right to use in future works (such as articles or books) all or part of my work. I understand that I am free to register the copyright to my work. REVIEW, APPROVAL AND ACCEPTANCE The document mentioned above has been reviewed and accepted by the student’s advisor, on behalf of the advisory committee, and by the Director of Graduate Studies (DGS), on behalf of the program; we verify that this is the final, approved version of the student’s thesis including all changes required by the advisory committee. The undersigned agree to abide by the statements above. Paul Michael Hime, Student Dr. David W. Weisrock, Major Professor Dr. David F. Westneat, Director of Graduate Studies GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Arts and Sciences at the University of Kentucky By Paul Michael Hime Lexington, Kentucky Director: Dr. David W. Weisrock, Professor of Biology Lexington, Kentucky 2017 Copyright Ó Paul Michael Hime 2017 ABSTRACT OF DISSERTATION GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in cryptobranchid salamanders, suggesting a conserved system of female heterogamety in this group. At much deeper scales, phylogenetic analyses of hundreds of protein-coding genes across all major amphibian lineages are employed to reveal the backbone topology and evolutionary timescales of the amphibian tree of life, suggesting a new set of hypotheses for relationships among extant amphibians. Yet, genomic data on their own are no panacea for the thorniest questions in evolutionary biology, and this work also demonstrates the power of a model testing framework to dissect support for different phylogenetic and population genetic hypotheses across different regions of the genome. KEYWORDS: Population Genomics, Molecular Evolution, Species Delimitation, Gene Tree - Species Tree Discordance, Lissamphibia Paul M. Hime 24 July, 2017 GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES By Paul Michael Hime Dr. David W. Weisrock Director of Dissertation Dr. David F. Westneat Director of Graduate Studies 24 July, 2017 DEDICATION This work is dedicated to my parents, Michael Stanley Hime and the late Elizabeth Ann Davis Hime, and to my brother, Keith Isaac Hime, for instilling in me a deep curiosity about the natural world; to my children, Charlotte Elizabeth Hime, Genevieve Nicole Hime, and Natalie Andrea Hime, with whom I am honored to share my curiosity about the natural world; and especially to my wife, Nicole Meredith Ratner Hime, without whose unwavering love, patience, and support none of this would have been remotely possible. ACKNOWLEDGMENTS First and foremost, incalculable gratitude and praise are due to my incredible wife, Nicole Hime, who has made immense personal and professional sacrifices for me to pursue this graduate degree. In addition to being a phenomenally dedicated stay-at-home mother with our three young children, holding down multiple jobs from home to help support our family, and temporarily deferring many of her own aspirations, Nicole has been a constant source of inspiration, positivity, and love for me. I sincerely thank my Ph.D. advisor, Dr. David W. Weisrock, for taking a big chance on me and for believing in a zookeeper who talked a big game about trying to use genomics to understand amphibian evolution. I also owe an immense debt of gratitude to my undergraduate advisor, Dr. Jonathan B. Losos, for his support and guidance throughout the years. I am also indebted to my doctoral committee members, Dr.'s Catherine R. Linnen, David F. Westneat, and Christopher L. Schardl at the University of Kentucky, and to my external examiner, Dr. Scott V. Edwards of Harvard University, for their shepherding, encouragement, and pointed critiques. I am also grateful for influential interactions during my undergraduate training with Richard E. Glor, D. Luke Mahler, Thomas J. Sanger, Joshua S. Reece, and Matthew E. Gifford, who each went out of their way to encourage and challenge me at critical moments. All of these scholars embody the characteristics to which I aspire as a scientist and I would not be where I am today without them. I also wish to thank the current and past members of the Weisrock-Linnen "SuperLab" at the University of Kentucky for setting the bar really high, and for their support and camaraderie over these past six years. Jeramiah J. Smith and his lab at the University of Kentucky also deserve many thanks for their mentorship, computational iii hand-holding, and for granting access to large numbers of CPU nodes on short notice. Additionally, I have been very fortunate to interact with and learn from the researchers at the UK Center for Computational Sciences, in particular, Mr. Vikram Gazula. When I entered graduate school I was a complete novice at computation, and the members of the UK CCS have been patient teachers and mentors while I learned to leverage supercomputing to address questions in the biological sciences. I also thank J. Alexander, J. Bridgeman, S. Clarke, A. A. Corea, W. J. Evans, K. Fareed, R. Glasper, H. Hancock, J. Haynes, T. Delvon Jones, T. S. Monk, J. Owens, E. R. Powell, J. Scofield, E. E. Spalding, M. Tyner, L. White III, and V. L. Wooten for constant inspiration. Although this dissertation is primarily my own work, four of these six chapters (Chapters 2-5) involve key collaborations with numerous collaborators (beyond my advisor, Dr. David W. Weisrock) whom I must acknowledge. Without the contributions of these individuals, none of these projects would have been possible in their present forms. These four chapters also benefitted greatly from the contributions of many individuals and institutions who provided tissue samples, genetic data, locality information, logistical support, and intellectual input. I also thank the University of Kentucky Information Technology Department and Center for Computational Sciences for computing time on the Lipscomb High Performance Computing Cluster. All work was conducted in accordance with applicable institutional guidelines for animal welfare under IACUC protocols SLZ- 2009-04 and SLZ-2010-07 to myself, UKY-2012-0952 to Dr. David W. Weisrock, and UKY-2013-1073 to Dr. Steven J. Price. In Chapter 2, I thank my collaborators Scott Hotaling, Richard Grewelle, Eric O'Neill, Brad Shaffer, and Randal Voss. I also thank Brian and Shonna Storz for their iv efforts in the field to sample A. ordinarium across its range. This study was greatly improved through discussions with participants of a Species Delimitation Workshop at the National Institute of Mathematical and Biological Synthesis, and through additional discussions with Laura Kubatko and Tara Pelletier. The design and implementation of PHRAPL analyses were greatly aided through discussions with PHRAPL workshop participants at the Ohio State University,