Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata)

Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) Item Type text; Electronic Dissertation Authors Lambert, Shea Maddock Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 07/10/2021 08:50:17 Link to Item http://hdl.handle.net/10150/630229 1 PHYLOGENETIC PERSPECTIVES ON VIVIPARITY, GENE-TREE DISCORDANCE, AND INTROGRESSION IN LIZARDS (SQUAMATA). by Shea Maddock Lambert ____________________________ Copyright © Shea Maddock Lambert 2018 A Dissertation Submitted to the Faculty of the DEPARTMENT OF ECOLOGY AND EVOLUTIONARY BIOLOGY In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2 THEUNIVERSITY OF ARIZONA GRADUATE COLLEGE Asmembers of the Dissertation Committee, we certify that we have read the dissertation prepared by Shea M. Lambert, titled "Phylogenetic perspectives on viviparity,gene-tree discordance, and introgressionin lizards {Squamata)" and recomme11dthat it be accepted as fulfillingthe dissertation requirem�t for the Degree of Doctor of Philosophy. _.c.---� ---------Date: May 21, 2018 _wJohn__ . �e� --�_:-_:-__:_ W_ -----�----'-------------------Date: May 21, 2018 Michael Barker M ichael ( s��t=t ��A". =----.�+o/-�i � -\.\----�--------._______ Date: May 21, 2018 Noa�man Final approval and acceptance· of this dissertation is contingent uporithe candidate's submission of the final copies of the· dissertation to the Graduate College. I hereby certify that I have read this dissertation prepared under my ditettion and recommend that it be accepted as fulfillin_;the �issertation requirement. V� _ Date: May 21, 2018 �Dissertation n1n1 ctor: John Wiens· 3 STATEMENT BY AUTHOR This dissertation has been submitted in partial fulfillment of the requirements for an advanced degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this dissertation are allowable without special permission, provided that an accurate acknowledgement of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the head of the major department of the Dean of the Graduate College when in his or her judgement the proposed use of the material is in the interests of scholarship. In all other instances, however, permission must be obtained from the author. SIGNED: Shea M. Lambert 4 ACKNOWLEDGEMENTS I first thank my doctoral committee, John Wiens, Michael Barker, Michael Sanderson, and Noah Whiteman, for their invaluable assistance and mentorship. I would also like to thank members of the UA EEB staff who have been incredibly helpful over the years, including Pennie Rabago, Lilian Schwartz, Lauren Harrison, Barry McCabe, and Vincente Leon. I would also like to thank all fellow scientists who have been friends, mentors, collaborators, and colleagues over the years, each of whom I am grateful to have known and learned from, including Anthony Baniaga, Evan Forsythe, Anthony Geneva, Julienne Ng, Daniel Scantlebury, Richard Glor, Tim O’Connor, Justin Shaffer, Kelsey Yule, Ryan Ruboyianes, Sarah Richman, Ben Weinstein, Leone Brown, Laurel Yohe, James Herrera, Carl Hutter, Uri Garcia, Tod Reeder, Noelle Bittner, Tereza Jezkova, Liz Miller, Cristian Roman-Palacios, Li Zheng, Alison Harrington, Caitlin Fisher-Reid, Xia Hua, Jeff Streicher, Doug Futuyma, John True, Peter Reinthal, Heather Lynch, and Adrian Nieto Montes de Oca. I would not be in this fortunate position without the support of my friends and family over the years. In particular, my parents Patrick and Joan Lambert, and sister, Nora Lambert, have always fostered and inspired my curiosity, and always been there when I needed them. I must also thank long- time friends from Rochester, NY for providing so much support and inspiration over so many years: Matthew Agone, Patrick Connelly, Zack Davis, Andrew Detty, Brian Kraftschik, Tom Segerson, and Robert Smith. Last but not least, I would like to thank close friends from Tucson: Evan Forsythe, Anthony Baniaga, Alex Ralston, Florence Durney, and Emily Xander. Finally, I would like to acknowledge my sources of funding, including an NSF Graduate Research Fellowship (2012), and research awards from the Society for the Study of Evolution (Rosemary Grant Student Research Award, 2012) and the Society of Systematic Biologists (Graduate Student Research Award, 2012). 5 TABLE OF CONTENTS ABSTRACT…………………………………………………………………………………. 6 INTRODUCTION…………………………………………………………………………… 8 REFERENCES………………………………………………………………………………. 14 APPENDIX A. EVOLUTION OF VIVIPARITY: A PHYLOGENETIC TEST OF THE COLD CLIMATE HYPOTHESIS IN PHRYNOSOMATID LIZARDS……………………………. 17 APPENDIX B. WHEN DO SPECIES-TREE AND CONCATENATED ESTIMATES DISAGREE? AN EMPIRICAL ANALYSIS WITH HIGHER-LEVEL SCINCID LIZARD PHYLOGENY…. 34 APPENDIX C. INFERRING INTROGRESSION USING RADSEQ AND DFOIL: POWER AND PITFALLS REVEALED IN A CASE STUDY OF SPINY LIZARDS (SCELOPORUS)….. 46 6 ABSTRACT This dissertation consists of three works of phylogenetic biology. In each case, my collaborators and I contribute to the field by providing novel empirical results germane to each topic and study system, but also in a broader sense by facilitating the use and understanding of modern phylogenetic methods. In appendix A, I investigate the evolution of viviparity in phylogenetic test of the cold-climate hypothesis. This long-standing hypothesis states that the evolution of viviparity is an adaptation that prevents egg and/or juvenile mortality in cold climates. I apply a suite of cutting-edge phylogenetic comparative methods to phylogenetic, climatic, and life history data from the lizard family Phrynosomatidae. The results strongly support the cold-climate hypothesis, and help to explain two counter-intuitive patterns in Phrynosomatidae. In appendix B, I examine discordance in phylogenetic reconstruction in order to answer an unresolved question with significant practical implications for phylogeneticists: can disagreement between concatenated and multi-species coalescent estimates be predicted? Using an empirical example in higher-level scincid lizard relationships, I find that discordance between these methods is related to short, weakly supported branches, and the presence of conflicting gene trees. These results suggest that concatenation may provide a reasonable approximation of theoretically preferable species- tree methods under most circumstances. Moreover, standard methods for incorporating phylogenetic uncertainty may be sufficient to account for disagreements by species-tree method estimates. In appendix C, I demonstrate a novel workflow for the detection of nuclear introgression in an empirical case study of closely related spiny lizard (Sceloporus) species. I first show that mitochondrial data independently suggests a repeated history of introgression between the focal taxa. I then show that an exhaustive application of the DFOIL method to double-digest RADseq data from many individuals is effective at identifying introgression in the nuclear genome. This novel approach also reveals intra- 7 specific geographic variation in in patterns of introgression, without the need to determine population structure. Finally, I find that that batch effects in ddRADseq data may mislead D-statistics (and DFOIL) under certain circumstances. 8 INTRODUCTION Phylogenetic trees and comparative methods have become the backbone of a large and growing body of research in biology (reviewed in Baum & Smith 2012; Pennell & Harmon 2013; Garamszegi 2014). Methodological advances beginning in the 1970s and 1980s (e.g., Felsenstein 1985), together with rapidly expanding computational power and access to genetic data, have helped drive the growth of phylogenetic biology. Nevertheless, significant room for growth exists for the understanding and application of this rapidly expanding toolkit of methods by researchers more broadly. Increasing the visibility and accessibility of phylogenetic methods is a major goal of modern research in phylogenetic biology, and the unifying concept of this dissertation. Explanation of the dissertation format This dissertation contains three appendices, each of which is a collaborative scientific work on which I am the lead author. Two of these are already published (Lambert & Wiens 2013, Evolution; Lambert et al. 2015, Molecular Phylogenetics and Evolution), while the third is currently in review at Molecular Ecology Resources. This chapter provides a summary of each appendix and their contributions to the literature (Dissertation aims and outcomes), and the appendices themselves follow. Supporting or supplemental information for each Appendix are available elsewhere (e.g., Dryad, GitHub), with accessibility described within each appendix. Contributions I am the first and corresponding author of each appendix presented herein, reflecting my primary role in the design, analyses, and writing of each appendix. My major advisor John J. Wiens (JJW) was a collaborator on all appendices, with particular influence on the design and revision of appendix B. I conducted all of the statistical analyses and created all figures

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