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Fossils, Phylogeny, and Anatomical Regions: Insights Exemplified Through Turtles

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Fossils, Phylogeny, and Anatomical Regions: Insights Exemplified Through Turtles Copyright by Robert Wayne Burroughs 2013 The Thesis Committee for Robert Wayne Burroughs Certifies that this is the approved version of the following thesis: Fossils, Phylogeny, and Anatomical Regions: Insights Exemplified Through Turtles APPROVED BY SUPERVISING COMMITTEE: Christopher J. Bell, Supervisor Julia A. Clarke Travis J. LaDuc Fossils, Phylogeny, and Anatomical Regions: Insights Exemplified Through Turtles by Robert Wayne Burroughs, B. A. Thesis Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Master of Science in Geological Sciences The University of Texas at Austin August 2013 Dedication This work is dedicated to my family. To my parents Nora and Wayne Burroughs for teaching me that the only way to achieve dreams is through hard work, but through hard work dreams can be achieved. To my sister, Angela Macias-Armstrong, who many years ago encouraged me to come to Austin to attend UT-Austin, and encouraged me to take a course taught by Chris Bell. This dramatically changed my life by helping my realize what I wanted to do and what I could do. Finally, to my wife, Catherine Burroughs, who has tirelessly supported my endeavors and without who this work would never have been completed. Acknowledgements I first must thank Chris Bell, who’s guidance and mentorship helped me complete this work. Without the opportunities that Chris has given to me, this work would never have come to be. He has at every step of the way challenged me to think critically, helped me become a scientist, and helped me be a better person. For that I am truly grateful. I must acknowledge the efforts of the committee who supervised this research, who committed many hours of effort on their part to improve my education, writing, and thinking about matters associated with biology and paleontology. Julia Clarke challenged me to think deeply about how methods we use as scientists affect our thinking, perceptions, and communication. She was always there to discuss any issues I had during my thesis. Her work in evaluating and improving my writing and skills as a scientist has been invaluable. I owe a great debt to Travis LaDuc, he has carefully guided me throughout my undergraduate and graduate career. He has always been careful to listen and provide critical insights when I needed them most. Those insights helped me improve as a scientist and a person. I have no doubt that I would not be here today if it weren’t for his guidance and help. I acknowledge Dennis Trombatore, the Jackson School of Geosciences Librarian, for his help in gathering and editing resources and citations for this thesis. I acknowledge the faculty, graduate, and undergraduate students associated with The University of Texas at Austin Paleontology Research Group. All of who provided many hours of humor, support, communication, and education. I gratefully acknowledge the efforts of the many collections managers and curators who provided loan material and discussion. I acknowledge the Jackson School of Geosciences, The University of Texas at Austin, and the Texas Academy of Science for providing many of the funds that helped fund this v research. Each chapter holds a separate acknowledgments section where I have recognized my gratitude to those individuals who have helped bring this work to fruition. vi Preface Arguably, this work had its conception in 2008 when I began working with Chris Bell, Travis LaDuc, and Dean Hendrickson (all from UT-Austin) on a project involving the skeletal variation of the endangered Mexican box turtle, Terrapene coahuila. At the time, I was still an undergraduate, wandering through an Anthropology degree, but I became increasingly interested in issues associated with variation, and as a result in the biology and evolution of organisms. The impetus for evaluating Terrapene coahuila was two-fold. First, it was an understudied organism that continues to need attention drawn to it for conservation purposes. Second, I was after a greater understanding of box turtle morphology and variation. The latter point was because early on I had established the ultimate goal of this thesis, at least as originally conceived, to describe and name a distinct box turtle from the Eocene/Oligocene boundary of west Texas. That turtle is now described in Chapter 1 of this thesis. After I finished my work with Terrapene coahuila, I took up the work now housed in Chapter 1, but with a slightly different focus. My exposure to the ideas associated with how morphological variation can impact phylogenetic analyses plagued me from the beginning of my master’s work. I focused on evaluating not just the fossil, but understanding its phylogenetic affinities. As I worked harder on this problem, it became obvious that I would need to account for variation in the form of polymorphisms. Thus, the phylogenetic analyses that form up a portion of Chapter 1 were borne out through my desires to build a robust phylogeny that accounted for variation. The body of vii Chapter 1 now represents not only a fossil description, but a broad phylogenetic analysis of testudinoid turtles, and brings to light real problems associated with working within this group. At the same time as I worked on Chapter 1, I had the great fortune to take a course taught by Julia Clarke. This course revolved around the application of phylogenetic methods to paleontology. In her course, I decided I would explore an additional problem associated with reconstructing the phylogeny of organisms. That problem is a systematic bias among researchers to focus only a few selected sets of characters for inferring phylogeny. I chose to exemplify my work with both morphology and turtles. Because many turtle paleontologists struggle with having fossil specimens represented by only skulls or shells. This exemplified my own frustration from having only a shell to describe the new fossil from, in my first chapter. After the course I realized I had built a second chapter that was intimately related to the first chapter. Because both attempt to address issues plaguing phylogenetic reconstruction. This work is now the body of Chapter 2. So, both chapters of this work were conceived somewhat independently, but are interrelated by virtue of being designed to address and attempt to solve issues associated with phylogenetic reconstruction, fossil identification, and evolutionary interpretations of testudinoid turtles. This work also reflects my evolution as a researcher from humble undergraduate beginnings to a more advanced understanding of biology, paleontology, and science in general. This work represents the conclusion of my Master of Science in Geosciences. The thesis contained hereafter was born, struggled through adolescence and viii is today, I hope, a mature vehicle that serves to enlighten the reader regarding this subject matter. ix Abstract Robert Wayne Burroughs, M.S.Geo.Sci. The University of Texas at Austin, 2013 Supervisor: Christopher J. Bell Fossils, Phylogeny, and Anatomical Regions: Insights Exemplified Through Turtles There are more than 300 species of extant turtles, the majority of which belong to the Testudinoidea. Here I describe a new box turtle from the Eocene-Oligocene boundary of west Texas. This specimen impacts the phylogeny of Testudinoid turtles by pulling the divergence of extant Testudinoid turtles back in time approximately 25 million years. This results in a need to refocus on paleontological research of Testudinoid turtles into the late Paleogene and early Neogene to identify fossil localities and specimens that can help further elucidate the evolution of the group. New work on the fossil record of turtles also requires a re-evaluation of methods used for identifying and evaluating the evolutionary history of turtles as a group. An implicit assumption over the last 150 years of turtle paleontology was that both turtle shells and turtle heads reveal congruent and complimentary evolutionary relationships. This assumption was never adequately tested. I utilized a series of methods to evaluate the congruency of phylogenetic hypotheses using disparate anatomical regions. Using a dataset of extant Emydid turtles, I evaluated whether turtle shells and turtle heads provided congruent and complimentary phylogenetic hypotheses. My methods employed parsimony-based reconstruction, maximum-likelihood-based reconstruction, and Bayesian-based reconstruction, including Bayesian-partition analyses. My conclusions are that heads and shells do not provide fully congruent topologies, and that in many cases there is a loss of phylogenetic resolution when only turtle sklls are used to generate phylogenies. The implication is that a focus on a robust and complete dataset of anatomical features will provide the best basis for further investigation of fossils. My work also provides a framework for dataset exploration by providing a method to identify the most robust phylogenetic signal found within a dataset. This framework will allow non-turtle paleontologists and systematists the ability to further investigate their own datasets and develop robust hypotheses of evolutionary relationships across the diversity of the tree of Life. x Table of Contents Preface................................................................................................................... vii Chapter 1: Description of a new functional box turtle from the Eocene/Oligocene boundary of west Texas and issues of testudinoid phylogeny ........................1 Introduction
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