Instructions for Mac Users BIOGEOGRAPHY AND PHYLOGEOGRAPHY OF MAMMALS OF SOUTHEAST ASIA: A COMPARATIVE ANALYSIS UTILIZING MACRO AND MICROEVOLUTIONBY Melissa T.R. Hawkins A Dissertation Submitted to the Graduate Faculty of George Mason University in Partial Fulfillment of The Requirements for the Degree of Doctor of Philosophy Biology Committee: _________________________________________Dr. Larry L. Rockwood, Dissertation Director _________________________________________Dr. Jesús E. Maldonado, Committee Member _________________________________________Dr. Kristofer M. Helgen, Committee Member _________________________________________Dr. Elizabeth Freeman, Committee Member _________________________________________Dr. Lee Talbot, Committee Member _________________________________________Dr. Albert Torzilli, Graduate Program Director _________________________________________Dr. Robert Jonas, Department Chairperson _________________________________________Dr. Donna Fox, Associate Dean, Student Affairs & Special Programs, College of Science _________________________________________Dr. Peggy Agouris, Dean, College of Science Date: __________________________________Summer 2015 George Mason University Fairfax, VA Biogeography and Phylogeography of mammals of Southeast Asia: A comparative analysis utilizing macro and microevolution A Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at George Mason University by Melissa T.R. Hawkins Masters of Science Western Illinois University, 2009 Bachelors of Science Western Illinois University, 2007 Director: Larry L. Rockwood, Professor Department of Biology Summer Semester 2015 George Mason University Fairfax, VA This work is licensed under a creative commons attribution-noderivs 3.0 unported license. ii DEDICATION This is dedicated to my family, present and future, and to those who motivate me to explore and preserve where the wild things are. iii ACKNOWLEDGEMENTS The list of whom to thank for the tremendous amount of support I have received over the past six years is immense, and here I will try to recount each person. First and foremost, Dr. Jesus E. Maldonado has been an amazing mentor, ever present, and always encouraging me though thick and thin to do the best work possible. Without his support this dissertation would have had a very different outcome. He has believed in me more than almost any other person, and for this I will be forever grateful. Not only is Jesus an incredible advisor, but such a genuine and amazing person, and I will always aspire to be as caring a mentor as he. Dr. Larry Rockwood has also supported me since my first days at GMU. He took me under his wing my first semester, and allowed me to serve as the teaching assistant for his undergraduate ecology course. Larry has always been encouraging, interested in my ambitious dissertation plans, assisted with various technical and logistical situations through the university, and always happy to just catch up, and for all these reasons I’m very grateful. Dr. Kristofer M. Helgen has taught me about mammals, biodiversity, and so much more. I knew nothing about museums when I started at the National Museum of Natural History, and because of him I now have a deep appreciation and understanding of these incredible natural history repositories. Kris has an unrivaled knowledge of all things mammal, and I hope to have rubbed off just a fraction of that information and passion. I have learned more than I can recount from Kris, but some of the most obvious skills include professional presentation, educational outreach, social media communication, collaboration, and importantly field skills. He is the ultimate tour giver, and in my opinion, the Steve Jobs of mammalogy. Dr. Jennifer A. Leonard funded almost all the research for my dissertation, with several large grants from the Spanish government. She has allowed me to develop the different chapters of my dissertation however I wanted, and to focus on the groups most interesting to me. Jen has found a way to keep me on a research assistantship for five years, funded my attendance at workshops, and paid for two international field expeditions to Borneo, which were experiences I will forever cherish. I would like to thank my committee members; Dr. Elizabeth Freeman has been supportive of this research throughout my time at GMU. Dr. Lee Talbot has also been an inspiring instructor, who always has a great story to tell, and has been very supportive of my research. I have been fortunate to be part of several laboratory groups, including the Center for Conservation and Evolutionary Genetics (CCEG), the Smithsonian Institution National Museum of Natural History, Division of Mammals, and the Conservation and iv Evolutionary Genetics Group (CEGG), Sevilla, Spain. Each of these lab groups has given me support and advice on various aspects of my research. The CCEG has served as my home base for the tenure of my dissertation research. I have learned all aspects of high-throughput sequencing here, and have made many lasting friendships. Dr. Robert Fleischer and I met for the first time in 2008 (of all things, looking for a bilateral gynandromorph cardinal in Central Illinois), and supported my joining of the lab group. Nancy McInerney Rotzel, Taylor Callicrate, Carly Muletz Wolz, Anna Savage, Ellen Martinsen, Andreanna Welch, Heather Lerner, Frank Hailer, and Marissa Aherling have all helped me with some aspect of my research through my dissertation. Courtney Hofman and I started our dissertation tenure in fall 2009, and we have learned so many things together, and she has always been there for me. Tammy Wilbert, Lilly Parker, Molly McDonough, Rebecca Dikow, Mirian Tsuchiya, Klaus Koepfli, Eliecer Gutierrez, and Michael Campana have all participated in significant discussions or served as collaborators on a diversity of projects. I appreciate all the friendships and help I have received from so many of these amazing people. The Division of Mammals has long supported the field initiatives of my dissertation, especially Darrin Lunde, who is always ready to talk fieldwork. Esther Langan, Nicole Edmison, Maya Yamato, E. Grace Veatch, Suzy Peurach, Louise Emmons and many others have helped me in various ways. The CEGG group in Spain has also been supportive of this research, particularly Carles Vila, Anna Cornellas, and Violeta Munoz-Fuentes. Miguel Camacho-Sanchez has also done his PhD in parallel to mine, including both field expeditions; the expeditions would not have been possible without our combined efforts. The field work component of this dissertation would not have been possible without the support of Robert Stuebing, Fred Sheldon, Maklarin Lakin, Fred Tuh, Justin Sator, Paul Yambum, and all the hard working Malaysian porters and technicians. Rose Ragai was an amazing field assistant, and deserves special recognition. From GMU, Ryan Valdez, Jennifer Mickelberg, and Mike Hallworth are thanked for assistance and support. Several administrative staff have helped me with all the strange requests from the international funding, and I’d like to thank Rosslyn Cress and Joanne Andersen for their help. This research has been funded by the Spanish Government (CSIC), the Smithsonian Institution (Grand Challenges, Small Grants), the American Society of Mammalogists (Grants-in-aid, Travel), and George Mason University (Department of Biology, Graduate Student Travel Fund). My friends and family are a big reason for my success here, and although they may not fully understand what it is I do, they have constantly supported me. My parents Jan and Joe Roberts, and my sister Nikki Blaesing have always been proud of me, and always let me ramble on about genetics while patiently smiling and nodding, and I thank them for that! Rick and Marilyn Hawkins have also been very supportive of my research, even though it took their son far from home. I want to thank my high school AP biology teacher, Bill Donato, for sparking my interest in biology. Michael Romano also encouraged me to continue past my master’s degree, and I thank him for that. v Finally, my husband and best friend, Lyndon, has dealt with so much during the six years since I dragged him from the Midwest to Virginia, including me leaving for months at a time to do field work. Never once has he asked me to pass up an opportunity, even when he hasn’t been able to join. I’m incredibly lucky to have such an amazing person to spend my life with, and it has been a great adventure so far! I apologize to anyone I have forgotten, it is not from your lack of impact on my dissertation, solely a lack of memory on my part. I wouldn’t do anything different if given the opportunity to start over again, and am so lucky that I have countless amazing people in my life. This has been an incredibly experience, and I’ll forever cherish these years. vi TABLE OF CONTENTS Page List of Tables .................................................................................................................... xii List of Figures .................................................................................................................. xiii List of Abbreviations and/or Symbols .............................................................................. xv Abstract ............................................................................................................................ xvi Chapter 1 – Introduction ....................................................................................................