Brigham Young University BYU ScholarsArchive Theses and Dissertations 2004-03-12 Phylogenetic Systematics and Evolution within the Family Scincidae Alison Swindle Whiting Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biology Commons BYU ScholarsArchive Citation Whiting, Alison Swindle, "Phylogenetic Systematics and Evolution within the Family Scincidae" (2004). Theses and Dissertations. 1133. https://scholarsarchive.byu.edu/etd/1133 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. PHYLOGENETIC SYSTEMATICS AND EVOLUTION WITHIN THE FAMILY SCINCIDAE by Alison Swindle Whiting A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Integrative Biology Brigham Young University April 2004 BRIGHAM YOUNG UNIVERSITY GRADUATE COMMITTEE APPROVAL of a dissertation submitted by Alison Swindle Whiting This dissertation has been read by each member of the following graduate committee and by majority vote has been found to be satisfactory. Date Jack W. Sites Jr., Chair Date Aaron M. Bauer Date Keith A. Crandall Date Leigh Johnson Date Duke S. Rogers BRIGHAM YOUNG UNIVERSITY As chair of the candidate’s graduate committee, I have read the dissertation of Alison Swindle Whiting in its final form and have found that (1) its format, citations, and bibliographical style are consistent and acceptable and fulfill university and department style requirements; (2) its illustrative materials including figures, tables, and charts are in place; and (3) the final manuscript is satisfactory to the graduate committee and is ready for submission to the university library. Date Jack W. Sites Jr. Chair, Graduate Committee Accepted for the Department Keith A. Crandall Graduate Coordinator Accepted for the College R. Kent Crookston Dean, College of Biology and Agriculture ABSTRACT PHYLOGENETIC SYSTEMATICS AND EVOLUTION WITHIN THE FAMILY SCINCIDAE Alison Swindle Whiting Department of Integrative Biology Doctor of Philosophy Scincidae (skinks) comprise one of the largest families of lizards, and the more than 1300 species show great variation in body size and form, and are found worldwide in a diversity of habitats. The group presents many interesting questions ranging from the colonization of oceanic islands, to the evolution of limb loss, yet most of these and other questions remain understudied. The purpose of this dissertation is to use multiple mitochonidrial and nuclear DNA markers in connection with current cladistic methods to address evolutionary questions at many levels within Scincidae. In chapter one, a molecular phylogenetic study, based on six genes and extensive analyses support Cordylidae+Xantusiidae as its sister group, and confirm the paraphyly of Scincinae. The Acontinae is the sister group to all remaining skinks, while Feylininae is nested within an otherwise monophyletic southern African scincine clade. Limited support for reversal of limb and digit loss is found. In chapter two, the monophyly and relationships of Malagasy scincines are investigated using data from seven gene regions. Malagasy scincines are monophyletic, and derived from a single colonization from southern Africa. Our analyses confirm the paraphyly of Amphiglossus, and support Madascincus as a valid genus. Madascincus is sister to a monophyletic Paracontias, while Voeltzkowia is basal to the remaining Amphiglossus and Pygomeles. Chapter three uses seven gene regions to infer relationships within South American Mabuya, and to test the hypothesis of two independent colonizations from Africa to the New World. Direct Optimization (DO) is compared with traditional alignment methods, and multilocus maximum likelihood and Bayesian methods are used to date divergence times within the group. Results show that DO consistently finds more optimal tree topologies regardless of the optimality criterion used, and provides the ability to use models throughout the alignment and tree reconstruction process. South American Mabuya are not monophyletic, and the two colonization hypothesis is confirmed with parametric bootstrapping. Within the mainland species of Mabuya, many taxonomic problems are uncovered including multiple species complexes. Due to the lack of reliable fossil information, dating methods differ greatly in their estimates of divergence dates within Mabuya. ACKNOWLEDGMENTS I would like to thank the members of my committee for all of the time and effort they have put into my graduate career, they have not only improved my dissertation greatly, but they have helped me to develop as a scientist. They have all been very easy to work with, making themselves available and contributing excellent ideas and suggestions. I especially want to thank Jack Sites, as my committee chair he has always been the first person to offer help and suggestions. Aaron Bauer also deserves a great deal of credit, while he was not a committee chair on paper, he certainly contributed of his time as if he were. Without Aaron’s incredible expertise and input, not to mention the field work, this project would not have been possible. One of the most critical aspects of research is money, and access to the necessary resources. This research was supported by a National Science Foundation graduate student fellowship, a Brigham Young University graduate fellowship, a Society for Systematic Biologists award for graduate student research, and an NSF doctoral dissertation improvement grant (DEB02-00362). I also need to thank Brigham Young University, the Department of Integrative Biology, and the BYU Office of Graduate Studies for their support and terrific laboratory facilities. Lastly and most importantly, I would like to thank my family for their continued help and support throughout the last five years. Countless hours of free child care have made it possible for me to complete the work presented here without having to worry about my daughter, and the constant emotional support from family members has been priceless. The contributions of my husband, Mike, have been critical throughout my graduate career. Without his support and encouragement, this work would never have begun. Mike and Adalyn have made tremendous sacrifices to ensure that I could continue my research, and their love and happiness is paramount in my life. TABLE OF CONTENTS Title Page ………………………………………………………………….. i Graduate Committee Approval……………………………………………. ii Final Reading Approval and Acceptance………………………………….. iii Abstract……………………………………………………………………. iv Acknowledgments…………………………………………………………. vi Table of Contents………………………………………………………….. viii Chapter 1: Phylogenetic relationships and limb loss in southern African scicine lizards (Squamata: Scincidae)…………………………………………………….. 1 Introduction…………………………………………………………1 Materials and Methods…………………………………………….. 2 Results………………………………………………………………6 Discussion…………………………………………………………..9 Acknowledgments…………………………………………………. 12 Literature Cited…………………………………………………….. 15 Chapter 2: Malagasy skinks (Squamata: Scincidae) and the phylogenetic utility of Gapdh ……………………………………………………... 18 Introduction…………………………………………………………19 Materials and Methods…………………………………………….. 23 Results………………………………………………………………27 viii Discussion…………………………………………………………. 30 Acknowledgements…………………………………………………35 Literature Cited…………………………………………………….. 36 Table 1…………………………………………………………….. 45 Table 2…………………………………………………………….. 50 Figures…………………………………………………………….. 51 Chapter 3: Maximum likelihood alignment in South American Mabuya: testing for and dating a second colonization………………………………………………..56 Introduction…………………………………………………………58 Materials and Methods…………………………………………….. 63 Results and Discussion…………………………………………….. 68 Acknowledgments…………………………………………………. 73 References…………………………………………………………. 75 Table 1…………………………………………………………….. 81 Table 2…………………………………………………………….. 82 Table 3…………………………………………………………….. 84 Figures…………………………………………………………….. 86 Appendix 1……………………………………………………….... 70 ix MOLECULAR PHYLOGENETICS AND EVOLUTION Molecular Phylogenetics and Evolution 29 (2003) 582–598 www.elsevier.com/locate/ympev Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata: Scincidae) Alison S. Whiting,a,* Aaron M. Bauer,b and Jack W. Sites Jr.a a Department of Integrative Biology and M.L. Bean Museum, Brigham Young University, Provo, UT 84602, USA b Department of Biology, Villanova University, Villanova, PA 19085, USA Received 30 August 2002; revised 17 February 2003 Abstract Skinks are the largest family of lizards and are found worldwide in a diversity of habitats. One of the larger and more poorly studied groups of skinks includes members of the subfamily Scincinae distributed in sub-Saharan Africa. Sub-Saharan African scincines are one of the many groups of lizards that show limb reduction and loss, and the genus Scelotes offers an excellent op- portunity to look at limb loss in a phylogenetic context. Phylogenetic relationships were reconstructed for a total of 52 taxa rep- resenting all subfamilies of skinks as well as other Autarchoglossan families using sequence from six gene regions including; 12S, 16S, and cytochrome b (mitochondrial), as well as a-Enolase, 18S, and C-mos (nuclear). The family Scincidae is recovered as monophyletic