University of Central Florida STARS Electronic Theses and Dissertations, 2004-2019 2010 Biogeography And Diversification In The Neotropics: Testing Macroevolutionary Hypotheses Using Molecular Phylogenetic Data Juan Manuel Daza Rojas University of Central Florida Part of the Biology Commons Find similar works at: https://stars.library.ucf.edu/etd University of Central Florida Libraries http://library.ucf.edu This Doctoral Dissertation (Open Access) is brought to you for free and open access by STARS. It has been accepted for inclusion in Electronic Theses and Dissertations, 2004-2019 by an authorized administrator of STARS. For more information, please contact [email protected]. STARS Citation Daza Rojas, Juan Manuel, "Biogeography And Diversification In The Neotropics: Testing Macroevolutionary Hypotheses Using Molecular Phylogenetic Data" (2010). Electronic Theses and Dissertations, 2004-2019. 4182. https://stars.library.ucf.edu/etd/4182 BIOGEOGRAPHY AND DIVERSIFICATION IN THE NEOTROPICS: TESTING MACROEVOLUTIONARY HYPOTHESES USING MOLECULAR PHYLOGENETIC DATA by JUAN M. DAZA B.S. – Universidad de Antioquia, Medellín, Colombia, 1997 M.S. – Universidad de Antioquia, Medellín, Colombia, 2005 A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Conservation Biology in the Department of Biology in the College of Sciences at the University of Central Florida Orlando, Florida Spring Term 2010 Major Professor: Christopher L. Parkinson © 2010 Juan M. Daza ii ABSTRACT Lineage diversification in the Neotropics is an interesting topic in evolutionary biology and one of the least understood. The complexity of the region precludes generalizations regarding the historical and evolutionary processes responsible for the observed high diversity. Here, I use molecular data to infer evolutionary relationships and test hypotheses of current taxonomy, species boundaries, speciation and biogeographic history in several lineages of Neotropical snakes. I comprehensively sampled a widely distributed Neotropical colubrid snake and Middle American pitvipers and combined my data with published sequences. Within the colubrid genus Leptodeira, mitochondrial and nuclear markers revealed a phylogeograhic structure that disagrees with the taxonomy based only on morphology. Instead, the phylogenetic structure corresponds to specific biogeographic regions within the Neotropics. Molecular evidence combined with explicit divergence time estimates reject the hypothesis that highland pitvipers in Middle America originated during the climatic changes during the Pleistocene. My data, instead, shows that pitviper diversification occurred mainly during the Miocene, a period of active orogenic activity. Using multiple lineages of Neotropical snakes in a single phylogenetic tree, I describe how the closure of the Isthmus of Panama generated several episodes of diversification as opposed to the Motagua-Polochic fault in Guatemala where a single vicariant event may have led to diversification of snakes with different ecological requirements. This finding has implications for future biogeographic studies in the region as explicit temporal information can be readily incorporated in molecular clock analyses. Bridging the gap between the traditional goals of historical biogeography (i.e., area relationships) with robust statistical methods, my research can be applied to multiple levels of the biological hierarchy (i.e., above species level), other regional systems and other sub-disciplines in biology such as medical research, evolutionary ecology, taxonomy and conservation. iii To the one who left too early, my father And the one that came as a bless, my daugther iv ACKNOWLEDGMENTS Over the years, countless people guided my maturation as a scientist, and I hope that I continue to receive their help in the future. I reserve a special place in this paragraph for those who have patiently dealt with my personality, my (sometimes) unfounded criticisms, my own frustrations and, obviously, my Hispanic accent!. This dissertation is partially published and I’m in debt with the coauthors of the papers derived from this research. I thank Jonathan Campbell, Ulrich Kuch, Mahmood Sasa, Paul Chippindale and Vivian Paez for their active input to the papers. I owe much to my dissertation’s director, Chris Parkinson, for giving me a place in his lab, the chance to develop my own ideas (although many times they were wrong!) and the opportunity to hone my research skills. He helped me to become a more mature and integral, albeit still naïve, scientist. My own “evolution” during my doctoral research in phylogenetics and biogeography (two big words) was enormously accelerated by the brilliant scientist, Todd A. Castoe, with whom after hours and hours of discussions, disagreements and frustrations, we realized how much we enjoy science (we could even forget the rest of the world including our wives!). The result of this camaraderie, fortunately for me, is represented in every page on this manuscript. Todd became my mentor and friend, and beyond the scientific mentality that I learned from him, he made the years in the States a wonderful experience for this “Mexican!” I would like to thank Jill Castoe, a beautiful friend, for all her energy, enthusiasm and complicity that made feel at home…I also thank her for keeping Todd away from me!! v I’m forever indebted to Eric N. Smith for becoming more than a committee member by taking an active role in my research. He shared his amazing experience, knowledge and passion for Neotropical herpetology, a combination that definitively shaped and improved all my thoughts written in this text. I thank William Crampton, John Fauth, and Eric Hoffman for being part of my committee, giving me support and sharing their experience every time I needed it. They were definitely a good choice. I also want to thank Professor Pedro Quintana-Ascencio for his enormous contributions to my formation as a researcher. The University of Central Florida provided an excellent learning and research environment for me, and I owe many of its faculty and staff a debt of gratitude for making things easier. Thanks to Daren Caine, Michelle Ver Way, Sara Elliot, and Gayle Story for their willingness to provide help in all the boring paperwork. I thank the members of the Department of Biology at UCF for sharing their ideas and being continuous support in many areas outside of science. I thank Haakon Kalkvik for letting me share all of my frustrations and teaching me to be a more integral scientist. I hope that he does not get tired and disappointed with all my attacks on everyone else’s science!. Parkinson and Hoffman lab members were always willing to share their ideas, which helped me clarify my own thoughts. For this assistance, their corrections to my long manuscripts and for their company in an otherwise dry lab, I thank Mary Beth, Allyson Fenwick, Genevieve Metzger, Tyler Hether, Gregory Territo, Rosana Tursi, Jenna Evans and Sara Johnson. I thank the Single Malt Genomics Institute’s members: Jack Degner, Sam Fox, Robb Ruggiero and Josh Reece. With them, I enjoyed the pleasures of science, good music (except Tom Waits) and liquor, each individually and combined (the real philosophy of the SMGI). Their own research and vi tremendous skills in other fields of Biology are a motivation for me to continue in the field of science. All these years at UCF would not have been possible at all without the support of my beautiful wife, Angela. Her eternal and unconditional support gave me the strength I needed during the best and the worst times of my PhD. Thanks Angela for giving me the most beautiful human being, Manuela. Now she becomes the REAL project that we will pursue together for the rest of our lives! My perfect family, Nelsy, Aristides, Diana, Paulo and Cristian always supported and gave me the strength to survive the countless and lonely days in Orlando. Juan Daza September 28, 2009 vii TABLE OF CONTENTS ABSTRACT ....................................................................................................................................................... iii TABLE OF CONTENTS ............................................................................................................................ viii LIST OF TABLES ............................................................................................................................................ x LIST OF FIGURES ......................................................................................................................................... xi CHAPTER 1 – INTRODUCTION .............................................................................................................. 1 The role of molecular phylogenetics in historical biogeography ....................................................... 1 The Neotropics as an excellent setting .................................................................................................. 3 Snakes as model in evolutionary biology ............................................................................................... 4 Goals of this study .................................................................................................................................... 5 References .................................................................................................................................................. 7 CHAPTER 2 – COMPLEX EVOLUTION IN THE NEOTROPICS: THE ORIGIN AND DIVERSIFICATION