Squamata: Gymnophthalmidae): the Diversity in Southern Ecuador Revisited
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Philosophy, practice and implications of phylogenetic inference as exemplified by Neotropical microteiid lizards (Reptilia: Gymnophthalmidae, Alopoglossidae) by Santiago J. Sánchez-Pacheco A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Ecology and Evolutionary Biology University of Toronto © Copyright Santiago J. Sánchez-Pacheco, 2017 Philosophy, practice and implications of phylogenetic inference as exemplified by Neotropical microteiid lizards (Reptilia: Gymnophthalmidae, Alopoglossidae) Santiago J. Sánchez-Pacheco Doctor of Philosophy Department of Ecology and Evolutionary Biology University of Toronto 2017 Abstract Understanding evolutionary processes involved in the diversity of life first requires knowledge of phylogeny. This knowledge is necessary to explain the evolutionary origins of features and provides a predictive framework to guide research. Biodiversity demands explanation, and heritable variation provides the evidential basis for formulating and testing phylogenetic hypotheses. My goal herein is to advance understanding of phylogenetic inference by addressing theoretical, analytical and empirical problems, and the rationale behind my approaches to solving them. To this end, I use a combination of approaches both to make phylogenetic inferences and to advance the field. Consequently, I present a collection of broadly overlapping contributions. I begin with a review of median-joining (MJ), a method for phylogeographic analysis. I show that MJ networks are theoretically untenable for phylogenetic inference. I also discuss the concept of phylogenetic network. Given the confusion that afflicts the implementation of concepts in some methods, I explore the concept of cladogram and argue that cladograms do not necessarily require ii synapomorphies, but synapomorphies are required to test and ultimately falsify cladograms. I conclude that both cladograms and synapomorphies are required to achieve phylogenetic explanation. I continue with an evaluation of the impact of phenotypic evidence on molecular datasets. I show that inclusion of phenotypic evidence can alter both topologies and support values in phylogenetic analyses. I use an optimal phylogenetic hypothesis to formulate and test biogeographic hypotheses involving Neotropical montane regions, and to analyze character evolution. I finish with the development of a theory of outgroup sampling, a fundamental step in phylogenetic analysis, grounded in the logic of scientific discovery. Its objective is to test hypotheses of ingroup topology and homology as severely as possible. This framework provides a logical basis for sampling and successively increases severity of hypothesis-testing, but it does not provide any grounds for limiting the sample. I then propose a heuristic procedure that provides an empirical basis to limit sampling. For most projects, I use Neotropical microteiid lizards. Finally, biodiversity also demands documentation, and my research often results in taxonomic novelties. Herein, I describe three new species and erect two new genera of microteiid lizards. iii Dedication Being a woman with a master’s degree in mathematics and teaching in a Colombian university in the late 70’s and in the 80’s was an extreme rarity due to strong cultural barriers. Stella Pacheco not only pursued an academic career under such circumstances, but also managed to raise a family at the same time. I dedicate this work to Stella Pacheco, my mother, who passed away while I was completing my master’s degree in Brazil. She evidently shaped my life by giving me the opportunity to grow up amidst stacks of papers, books and exams, and often on campus. I will always be grateful for her early influence, unrelenting encouragement, and guidance by word, teaching and example, without which I surely would not have pursued a career in science. Her mathematics lessons made their way into this PhD thesis (Chapter 2). iv Acknowledgments My first acknowledgement goes to my supervisor Robert W. Murphy. I thank him for his encouragement, advice and friendship, and continued financial support. I am indebted to him for letting me follow my interests as they developed, and for constantly challenging me. He has greatly shaped the kind of scientist I strive to be. For her unrelenting encouragement and patience, countless sacrifices, unconditional support, and never-ending love I am deeply grateful to Paola Pulido-Santacruz, my precious wife, without whom my graduate studies would not have been possible. My father, Luis F. Sánchez, and my siblings, Victoria E. Sánchez-Pacheco and Juan F. Sánchez-Pacheco, have always provided encouragement in all my endeavors, often abroad. I thank my Committee members for their numerous insights that greatly improved this dissertation: Deborah McLennan and David C. Evans. Douglas Currie, Nathan Lovejoy, Sebastian Kvist and Michael Caldwell generously took part in my appraisal and final examinations. My approach to phylogenetics has been influenced heavily by Robert W. Murphy and Taran Grant, and I acknowledge them for sharing their knowledge and causing me to question my assumptions. I am grateful to my friends and colleagues—no one mentioned no one forgotten— who facilitated all aspects of my graduate studies. Collaborators on my PhD projects are included in the relevant chapters. The Royal Ontario Museum and the Department of Ecology and Evolutionary Biology at the University of Toronto (EEB) provided intellectual, stimulating environments and friendships during my five years as a PhD student. v Throughout my PhD, I was financially supported by a COLCIENCIAS doctoral fellowship (Becas Francisco José de Caldas) from the Colombian Department of Science, Technology and Innovation, an Ontario Graduate Scholarship at the University of Toronto, and a number of grants provided by EEB. The research in this thesis was funded through a grant from the Natural Sciences and Engineering Research Council (NSERC) to Robert W. Murphy. vi Table of Contents Dedication ............................................................................................................................. iv Acknowledgments ................................................................................................................ v Table of Contents .............................................................................................................. vii List of Tables ........................................................................................................................ x List of Figures ...................................................................................................................... xi Chapter 1 GENERAL INTRODUCTION .................................................................... 1 1.1 Phylogenetic analysis and research objective ................................................... 1 1.2 Study group .................................................................................................................... 2 1.3 Research outline .......................................................................................................... 3 1.3.1 Chapter 2. On the use of median-joining networks in evolutionary biology. 4 1.3.2 Chapter 3. Cladograms do not necessarily entail synapomorphies, but synapomorphies falsify cladograms. ............................................................................................... 4 1.3.3 Chapter 4. Lizards of the genus Riama (Squamata: Gymnophthalmidae): The diversity in southern Ecuador revisited. .............................................................................. 5 1.3.4 Chapter 5. Phylogeny of Riama (Squamata: Gymnophthalmidae), impact of phenotypic evidence on molecular datasets, and the origin of the Sierra Nevada de Santa Marta endemic fauna. ................................................................................................................ 6 1.3.5 Chapter 6. Formal recognition of the species of Oreosaurus (Squamata: Gymnophthalmidae) from the Sierra Nevada de Santa Marta, Colombia. ...................... 7 1.3.6 Chapter 7. Outgroup sampling criteria: severity of test, expansion, stability, and alopoglossid lizards. ....................................................................................................................... 7 Chapter 2 ON THE USE OF MEDIAN-JOINING NETWORKS IN EVOLUTIONARY BIOLOGY ........................................................................................ 9 2 Abstract .............................................................................................................................. 10 2.1 Introduction ................................................................................................................ 11 2.2 Theoretical overview ............................................................................................... 12 2.3 MJNs in the literature ............................................................................................... 23 2.4 Conclusions .................................................................................................................. 26 2.5 Acknowledgements ................................................................................................... 26 2.6 Figures ........................................................................................................................... 28 Chapter 3 CLADOGRAMS DO NOT NECESSARILY ENTAIL SYNAPOMORPHIES, BUT SYNAPOMORPHIES FALSIFY CLADOGRAMS