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Diversity and Diversification Across the Global Radiation of Extant Bats

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Diversity and Diversification Across the Global Radiation of Extant Bats Diversity and Diversification Across the Global Radiation of Extant Bats by Jeff J. Shi A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Ecology and Evolutionary Biology) in the University of Michigan 2018 Doctoral Committee: Professor Catherine Badgley, co-chair Assistant Professor and Assistant Curator Daniel Rabosky, co-chair Associate Professor Geoffrey Gerstner Associate Research Scientist Miriam Zelditch Kalong (Malay, traditional) Pteropus vampyrus (Linnaeus, 1758) Illustration by Gustav Mützel (Brehms Tierleben), 19271 1 Reproduced as a work in the public domain of the United States of America; accessible via the Wikimedia Commons repository. EPIGRAPHS “...one had to know the initial and final states to meet that goal; one needed knowledge of the effects before the causes could be initiated.” Ted Chiang; Story of Your Life (1998) “Dr. Eleven: What was it like for you, at the end? Captain Lonagan: It was exactly like waking up from a dream.” Emily St. John Mandel; Station Eleven (2014) Bill Watterson; Calvin & Hobbes (October 27, 1989)2 2 Reproduced according to the educational usage policies of, and direct correspondence with Andrews McMeel Syndication. © Jeff J. Shi 2018 [email protected] ORCID: 0000-0002-8529-7100 DEDICATION To the memory and life of Samantha Jade Wang. ii ACKNOWLEDGMENTS All of the research presented here was supported by a National Science Foundation (NSF) Graduate Research Fellowship, an Edwin H. Edwards Scholarship in Biology, and awards from the University of Michigan’s Rackham Graduate School and the Department of Ecology & Evolutionary Biology (EEB). A significant amount of computational work was funded by a Michigan Institute for Computational Discovery and Engineering fellowship; specimen scanning, loans, and research assistants were funded by the Museum of Zoology’s Hinsdale & Walker fund and an NSF Doctoral Dissertation Improvement Grant. This research would not have been possible without the continued support of my co- advisors and committee chairs, Dan Rabosky and Catherine Badgley. I cannot thank either of them enough for humoring the various dead ends, seemingly fruitless explorations, and detours that have colored these last six years. I would also like to thank the other members of my committee, Geoffrey Gerstner and Miriam Zelditch, for their support, input, and advice. Finally, I want to highlight the truly heroic efforts of the EEB office staff through the years - particularly those of Cindy Carl and Jane Sullivan - which should truly earn them all places on each and every thesis and dissertation committee coming out of this department. I would also like to acknowledge the many, many members of the Rabosky and Badgley labs over the past six years. Special thanks to Pascal Title, for being infallible in his assistance with visualization and spatial analyses, to Michael Grundler and Iris Holmes, for patiently listening to me argue and debate and ramble in the office, and to Erin Westeen, for the thankless and herculean feat of digitizing morphological data for this dissertation. Thanks as well to Sonal Singhal, Talia Moore, Katie Loughney, and Tara Smiley for inspiration and conversations they probably do not remember, but I very much do. More thanks go to Nathan Katlein and Heather Williams for also toiling away in the specimen collections. To everyone else in both labs: thank you for your support, especially through the times when I least appreciated it. I would also like to iii thank Stephen Smith, Cody Hinchcliff, Aaron King, Cody Thompson, Michelle Lynch, and Caroline Parins-Fukuchi for support and assistance through the years. My scientific inspirations and support extend well past EEB, UM, and the last six years. I must thank the Organization for Tropical Studies, SANParks, Laurence Kruger, and Corrie Schoeman for thinking it was a good idea to let me explore Kruger National Park at night, in search of bats, alongside my fellow amateur researchers, Matthew Minder and Amar Doshi. My deepest gratitude goes to Rytas Vilgalys, V. Louise Roth, Dan McShea, Kevin Wright, and Paul Manos at Duke University’s Department of Biology for their patience and hand in shaping my entire foundation for evolution and ecology. And, of course, thank you to Anne Yoder and Lauren Chan for taking me under their wings, and treating me like a colleague from the beginning. Thanks to the rest of the Yoder Lab c. 2010-2012, including Meredith Barrett, Sheena Faherty, Amy Heilman, and Megan Morikawa, for everything I know about research. Outside of Science Drive, I want to thank Annie Boehling, Jessie Tang, Sean Hyberg, Greg Bachman, Kelly Adamski, Erica Duh, and Alena Reich for their support through many years in and out of North Carolina as I found my way and place in science. I am also indebted to a truly spectacular group of North American bat biologists for years of collaboration, conversation, and good company: Betsy Dumont, Sharlene Santana, Liliana Dávalos, Nancy Simmons, Kelly Speer, Christine Avena, Laurel Yohe, Abigail Curtis, Jasmin Camacho, Leith Miller, Amy Wray, and Aja Marcato. I look forward to the next time I work with you all. My deepest thanks go to the unnamed scientists whose efforts, specimens, maps, and sequences have built more dissertations and research projects than they could have ever imagined, including this one. Though they may not realize it, this six-year journey would likely not have finished without the truly incredible staff, volunteers, and interns at 826michigan. Thank you Amanda Uhle, Frances Martin, Catherine Calabro, D’Real Graham, Kati Shanks, Megan Gilson, Lucy Huber, Matthew Beyersdorf, Hannah Rose Neuhauser, Tom Bianchi, Terra Reed, and so, so many more people through the years for their kindness, unyielding optimism, and invaluable support. In addition, thank you to the wonderful leadership and staff of the Center for Research on Learning and Teaching for lighting the way, especially Nicole Tuttle, Victoria Genetin, iv Stephanie Moody, Michelle Majeed, Ronit Ajlen, Matt Kaplan, and Tazin Daniels. I cannot imagine how this dissertation and budding career could exist without all of you. Finally, it sometimes felt like it took the city of Ann Arbor to drag and haul this dissertation to the finish line. Thank you to Kevin Bakker, Paul Glaum, Pascal Title (again), and Celia Miller for our hours of toiling and the (many more) hours of lounging. Thank you to Alison Gould, Tara Smiley (again), Micaela Martinez, Tommy Jenkinson for doing all of this first. Thank you to a long list of past and present friends both in and outside of Michigan that have been and will continue to be my entirely unearned support system: Ashleigh Bell, Kevin Boehnke, Mara Bollard, Sally Carson, Leslie Decker, Julie Deeke, Jason Dobkowski, Michelle Fearon, Tim Fortescue, Josh Gardner, Sarah Hoffman, Anneka Jankowiak, Lisa Jong, Peter Kirk, Leigh Korey, Jennifer Kron, Clifton Martin, Jeff May, Meghan Moynihan, Jillian Myers, Timothy Necamp, Elizabeth Pierce, Elizabeth Pringle, Kelly Riffer, Andrew Schwartz, Jay Smith, Alex Taylor, Paula Teichholtz, Lauren Trimble, Lizz Ultee, Annie Wang, and Isabelle Winer. I am eternally grateful to each and every one of you for the many person-years of time and energy. Thank you to the endless patience of my family in Los Angeles, Las Vegas, and Hong Kong, who I know are always there for me, even when I least deserve it. Above all, my eternal gratitude and appreciation to Dori Cross, sine qua non. v TABLE OF CONTENTS DEDICATION............................................................................................................................... ii ACKNOWLEDGMENTS ........................................................................................................... iii LIST OF TABLES ...................................................................................................................... vii LIST OF FIGURES ..................................................................................................................... ix ABSTRACT .................................................................................................................................. xi CHAPTER 1 Introduction: global patterns of bat spatial diversity and richness .......................... 1 CHAPTER 2 Speciation dynamics across the global radiation of extant bats ............................ 52 CHAPTER 3 Ecomorphological and phylogenetic constraints on sympatry across extant bats ................................................................................................ 106 CHAPTER 4 Digitizing extant bat diversity: an open-access repository of 3D μCT-scanned skulls for research and education ........................................................................ 145 CHAPTER 5 The omnivores' dilemma: decoupling of ecological and morphological evolution across New World bats ....................................................................................... 175 CHAPTER 6 Conclusion ........................................................................................................... 231 vi LIST OF TABLES Table 1.1 Metadata on bat diversity for major biogeographic realms ......................................... 35 Table S1.1 Palearctic bat families and species with IUCN range data ........................................ 42 Table S1.2a Afrotropical (mainland) bat families and species with IUCN range data ................ 43 Table S1.2b Afrotropical (Indian Ocean islands) bat
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