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Using Phylogenetic Comparative Methods to Understand Diversification and Geographic Range Evolution University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2017 Using Phylogenetic Comparative Methods To Understand Diversification and Geographic Range Evolution Kathryn Aurora Massana University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Biodiversity Commons, Computational Biology Commons, Evolution Commons, Integrative Biology Commons, and the Other Ecology and Evolutionary Biology Commons Recommended Citation Massana, Kathryn Aurora, "Using Phylogenetic Comparative Methods To Understand Diversification and Geographic Range Evolution. " PhD diss., University of Tennessee, 2017. https://trace.tennessee.edu/utk_graddiss/4481 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Kathryn Aurora Massana entitled "Using Phylogenetic Comparative Methods To Understand Diversification and Geographic Range Evolution." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Ecology and Evolutionary Biology. Brian C. O'Meara, Major Professor We have read this dissertation and recommend its acceptance: Daniel S. Simberloff, Sally P. Horn, James A. Fordyce, Haileab Hilafu Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Using Phylogenetic Comparative Methods To Understand Diversification and Geographic Range Evolution A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Kathryn Aurora Massana May 2017 Copyright © 2017 by Kathryn Aurora Massana All rights reserved. ii DEDICATION I dedicate my work to the loved ones that I lost during my time as a graduate student – my father and my beautiful parrot, Izze. You both left this world far too soon. Papi, gracias por siempre apoyarme cuando pequeña. Me diste los recursos para engendrar y motivar mis curiosidades científicas. Tu fé en mi me mantuvo enfocada. Izze, you were my strength. There was nothing I cared for more in this world. You gave me hope when there was none. You taught me how to fight. This world is a lonelier place without you. Your bouts of flight inspired my third chapter. iii ACKNOWLEDGEMENTS First and foremost, I would like to thank my family – for being supportive and helping me during the difficult times throughout my graduate career. Moms and Titi Linda, this thanks especially goes to you. Your encouragement helped me persevere through thick and thin. I could not have done it without you. You were both there when I most needed help and always offered me constant positivity, which helped me persevere through the difficult times I had during my graduate career. Thanks for always believing in me. Carlos y Maria Julia, los amo con todo mi corazón. Este doctorado lo hice para enseñarles que sus sueños si se pueden hacer realidad. I would like to thank my advisor, Brian O’Meara. Without him, none of this work would be possible. He devoted much time and patience to help me develop to the scientist I am today. To him, I am incredibly indebted. I would also like to thank my committee members, Sally Horn, Dan Simberloff, Jim Fordyce and Haileab Hilafu for always giving me excellent feedback to improve my work. The breadth of your knowledge helped me diversify my thoughts. I would also like to thank the members of the O’Meara lab that helped me formulate and improve my research: Jeremy Beaulieu, Nick Matzke, Nathan Jackson, Jenn Bosco, Rosana Zenil-Ferguson, Orlando Schwery and Sam Borstein. I would like to thank my collaborators for affording me the opportunity to improve my skills and share my ideas through lively discussions. Among these, Chuck Davis, Anouk van’t Padje, Fabiola Soto-Trejo, Jeremy Beaulieu and Nick Matzke. You guys are the best, I swear. I would like to acknowledge my fellowship sources, the Program for Excellence and Equity in Research, the National Institute for Mathematical and Biological Synthesis and the Department of Ecology and Evolutionary Biology at the University of Tennessee, which provided me with many professional development opportunities. I would also like to thank my iv numerous research funding sources: the Society for the Study of Evolution, the Society for Systematic Biology for funding my travel as an Invited Symposium Speaker to Evolution 2015 in Brazil, the National Science Foundation for several funds including the East Asia Pacific Summer Institutes Fellowship for travel to New Zealand, the University of Tennessee Chancellor’s Funds, the Graduate Researchers in Ecology, Behavior and Evolution for Travel Awards, the Tennessee Plant Research Center Travel Award to present my first talk at the Botany 2013 Conference and the Sharp Fund at the University of Tennessee. I would like to thank the Exotics Team and the rotation veterinary students at the University of Tennessee Veterinary Medical Center. They took excellent care of my beautiful parrot Izze while she was sick. Because of them, I got six more months to share with her. I’m confident that no other veterinary team could have done the same. Thank you all so much. In particular, I would like to recognize the following people: Jennilee Morrison, Carla Bernal, Michael Jones, Cheryl Greenacre, Patrick Sullivan, Julie Sheldon, Janet Jones and Lillian Gerhardt. Having you all there to care for Izze made all the difference in that period of my life. I also valued the interesting discussions we had about my graduate research with the team members (particularly with Drs. Jones and Morrison) while on my many visits. Lastly, I would like to thank my wonderful friends, in particular, Jenn Bosco, Sarah Sheffield and Camila Reyes. Jenn, you are my scientist and Statistics twin. We share many ideals and I wouldn’t change that for the world. You helped me get through. Without you I wouldn’t have been able to make it. For that I am eternally grateful. Thank you for always being there for me, I will miss you after graduation. Sarah, you are the kindest person I have ever met. You gave me advice and helped me persist through the hardest situations. Your humor helped me keep a positive outlook through any situation. You have no idea how much that helped me. I look up to v you in every sense. I’m jealous of your positivity. Camila, thank you for always being there for me. Don’t assume that because I mentioned you last that I care for you least. On the contrary, I hold a very high regard for you. I’m so happy I met you. Thank you, thank you, thank you for always being my rock. I can depend on you for anything. And for that, I will always be indebted to you. I’m also grateful for you always humoring my shenanigans. That’s hard to do. You are a special lady. I love you all. vi ABSTRACT Two key processes that have been modeled in a phylogenetic comparative framework are diversification and historical biogeography. Many questions arise on what process have shaped the abundance (or lack) of species we see today and what influences their survival and interconnectedness with other species. Many methods have been developed to answer these questions. Over the past several decades there has been a rise in parametric modeling and development of more adequate frameworks to answer biological questions of interest. However, many models still lack the incorporation of ecological, mainly biotic factors, which influence the evolution and ecology of species, while accounting for phylogenetic relatedness. In my dissertation, I studied a diverse set of questions in the realm of diversification and biogeography. I began my investigation by improving upon the widely used Dispersal-Extinction and Cladogenesis model and showing my method DEC* is a more adequate model that usually has better model fit and parameter estimation (Chapter 1). I then moved on to learn how a complex trait such a parasitism could influence the diversification of parasitic angiosperms with a wide array of diversification models in phylogenetics (Chapter 2). My results indicated that all parasitic flowering plants are not undergoing an evolutionary dead end, as many have postulated. In my final chapter, I merged trait and biogeographic evolution by assembling a model that would test the influence of body size in passerine birds. Additionally, I tested the influence of several traits upon the diversification of passerine birds (Chapter 3). The results showed that the larger body sizes are not associated with greater dispersal rates in passerines. According to the results, smaller birds have a greater rate of dispersal. I also show support for both body size and region of occurrence in the world (temperate versus tropical) as having an influence on vii diversification. For the diversification analyses in Chapter 2 and 3, I find evidence of underlying biological trait and/process influencing the diversification of these groups. viii TABLE OF CONTENTS INTRODUCTION ......................................................................................................................................
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