Interspecific and intraspecific relationships, and biogeography of flap-footed geckos, Delma Gray 1831 (Squamata: Pygopodidae) A Thesis Presented to the Faculty of the Department of Biology, Villanova University In Partial Fulfillment of the Requirements for the Degree of Master of Science in Biology By Ian G. Brennan May 2014 Under the Direction of Aaron M. Bauer Table of Contents Dedication ...................................................................................................................................................... 3 Acknowledgments ......................................................................................................................................... 4 Biographical Sketch ....................................................................................................................................... 5 List of Figures ................................................................................................................................................ 6 List of Tables ................................................................................................................................................. 6 Abstract .......................................................................................................................................................... 7 I. Introduction to the Pygopodidae ................................................................................................................ 9 I.i—Historical biogeography of Australia ................................................................................................. 9 I.ii—An introduction to the Gekkota in Australia .................................................................................. 11 I.iii—Pygopodidae Boulenger 1884 ........................................................................................................ 13 I.iv—Delma Gray 1831 ........................................................................................................................... 18 I.v—Historical taxonomic position of the Pygopodidae within Squamata ............................................. 20 II. Materials and methods ............................................................................................................................ 21 II.i—Taxon Sampling ............................................................................................................................. 21 II.ii—Gene Selection .............................................................................................................................. 22 II.iii—Phylogenetic Analyses ................................................................................................................. 24 II.iv—Concatenation ............................................................................................................................... 27 II.v—Species Delimitation ..................................................................................................................... 28 II.vi—Divergence Dating ....................................................................................................................... 29 II.vii—Research Goals ............................................................................................................................ 30 III. Mito-nuclear discordance and speciation by aridification in flap-footed geckos, Delma Gray 1831 (Gekkota: Pygopodidae) ......................................................................................................................... 32 III.i—Abstract ......................................................................................................................................... 32 III.ii—Introduction ................................................................................................................................. 33 III.iii—Molecular Methods and Phylogenetic Analyses ........................................................................ 33 III.iv—Results ........................................................................................................................................ 37 III.v—Discussion .................................................................................................................................... 52 IV. Molecular and morphological evaluation of Delma australis (Squamata: Pygopodidae) with descriptions of two new species from biogeographically significant areas in Western Australia .......... 66 IV.ii—Introduction .................................................................................................................................. 67 IV.iii—Materials and Methods ............................................................................................................... 68 IV.iv—Taxonomy ................................................................................................................................... 72 IV.v—Delma australis Kluge, 1974 ....................................................................................................... 75 IV.vi—Delma australis S.WA sp. nov. .................................................................................................. 81 IV.ii—Delma australis N.SA sp. nov. .................................................................................................... 89 IV.viii—Results ...................................................................................................................................... 93 IV.ix—Discussion ................................................................................................................................... 98 V. Notes on hemipenial morphology of the Pygopodidae Boulenger 1884: a phylogenetic tool ............. 105 V.i—Abstract ........................................................................................................................................ 105 V.ii—Introduction: Diversity within a Divergent Lineage ................................................................... 105 V.iii—Monophyly of the Pygopodidae and Previous Phylogenetic Study ........................................... 106 V.iv—Hemipenial Morphology and Systematics ................................................................................. 108 V.v—Methods and Materials: Hemipenial Preparation ........................................................................ 110 V.vi—Characters and Hemipenial Descriptions ................................................................................... 111 V.vii.—Phylogenetic Discussion of Hemipenes in Pygopodidae ......................................................... 119 V.viii.—Cloacal Spurs and Reproductive Behavior ............................................................................. 125 VI.—Literature Cited ................................................................................................................................. 129 Appendix 1 ................................................................................................................................................. 140 Appendix 2 ................................................................................................................................................. 141 2 Dedication For my Aunt Irene, who taught me being weird was cool And to my parents and sister, for their unwavering support of a child herpetologist 3 Acknowledgments Without the unflinching support and guidance of my committee chair and advisor Dr. Aaron Bauer, and committee members, Dr. Todd Jackman and Dr. Adam Langley, this project, and my graduate student career at Villanova would never have been successful. Dr. Bauer’s savant-like herpetological knowledge, unparalleled library, and dark sense of humor have been an immense help throughout my career here. Dr. Jackman’s patience in helping to grow my understanding of phylogenetics, and eagerness to have a beer and talk systematics has been incredible. I’d like to thank the Bauer-Jackman lab post-docs, Dr. Matt Heinicke, and “Mr. Pinga Loca” Dr. Juan Daza, for their friendship, and help with navigating graduate life. Dr. Paul Doughty, who helped to shape this project—you’ve become a great mentor and friend—thank you for sharing your experiences, friends, and skull Mondays. Many thanks to my fellow graduate students and friends—and there have been plenty through my three years here—who have helped get me through long days and nights in the lab: Evan Kelemen, Sarah Baillie, Kevin Neal, Ben Karin, Michael Lough-Stevens, Jackie Childers, Katie Allen, Mikhail Chavis, Luke Musser, James Titus-McQuillan. I owe even more thanks to the Fire Island Gibbons: Arianna Kuhn, Andrew Kathriner, Rachel Skinner, and Elyse Freitas, who have made life in lab consistently fun—I hope your artistic skills continue to grow and swell as you erect your academic careers. Kate Freeman, thank you for your unwavering support and positivity as I whinged and moaned my way through writing this thesis. Happy reading. 4 Biographical Sketch Ian G. Brennan grew up in Montgomery, New Jersey, a central NJ suburb approximately equidistant from New York City and Philadelphia. Like most herpetologists, his interest in reptiles and amphibians started young, chasing frogs and turtles in backyard ponds, flipping rocks and logs for salamanders, and—like most northeastern kids—dreaming of lizards and snakes. As an undergraduate, Ian attended Union College in Upstate New York, where he split