Phylogeography of the Spring Salamander, Gyrinophilus porphyriticus: Historic and Contemporary River System’s Influence on Phylogeographic History A thesis presented to the faculty of the College of Arts and Sciences of Ohio University In partial fulfillment of the requirements for the degree Master of Science Michael D. Haughey August 2015 © 2015 Michael D. Haughey. All Rights Reserved. 2 This thesis titled Phylogeography of the Spring Salamander, Gyrinophilus porphyriticus: Historic and Contemporary River System’s Influence on Phylogeographic History by MICHAEL D. HAUGHEY has been approved for the Department of Biological Sciences and the College of Arts and Sciences by Shawn R. Kuchta Professor of Biological Sciences Robert Frank Dean, College of Arts and Sciences 3 ABSTRACT HAUGHEY, MICHAEL D., M.S., August 2015, Biological Sciences Phylogeography of the Spring Salamander, Gyrinophilus porphyriticus: Historic and Contemporary River System’s Influence on Phylogeographic History Director of Thesis: Shawn R. Kuchta Climatic oscillations during the Pleistocene repeatedly formed glacial boundaries, shifted suitable habitat, and caused significant geological changes in the major drainage systems of Eastern North America. Contemporary drainage systems were heavily impacted by these cycles of glacial advancement and retreat. These impacts, in conjunction with ongoing stream capture, caused the fragmentation and fusion of many major pre-Pleistocene drainage systems. In this study, I investigated the contribution of historic and contemporary drainage systems in shaping the phylogeographic patterns of genetic diversity in the stream dwelling salamander Gyrinophilus porphyriticus. I used nucleotide sequence data from two protein coding genes, one nuclear (Rag-1) and one mitochondrial (Cytochrome b), to generate a phylogenetic hypothesis of population-level relationships and utilized both matrix and linear based approaches to test for the role of isolation by distance and drainage system connectivity on phylogenetic patterns. My results show that while both historic and contemporary river systems have played a role in structuring phylogeographic relationships, historic river systems have played a greater role. 4 DEDICATION This thesis is dedicated to the memory of my grandmother Evelyn Evans. May 4, 1922 – July 24, 2013 5 TABLE OF CONTENTS Page Abstract ............................................................................................................................... 3 Dedication ........................................................................................................................... 4 List of Tables ...................................................................................................................... 6 List of Figures ..................................................................................................................... 7 1. Introduction ..................................................................................................................... 8 1.1 Introduction and Appalachian Drainage History ..................................................... 8 1.2 Systematic Overview of the Genus Gyrinophilus .................................................. 13 1.3 Aims of Study ......................................................................................................... 17 2. Materials and Methods .................................................................................................. 19 2.1 Sampling ................................................................................................................. 19 2.2 Molecular Methods ................................................................................................. 19 2.3 Phylogenetic Analysis ............................................................................................. 21 2.4 Divergence Estimates ............................................................................................. 23 2.5 Historical Demography ........................................................................................... 24 2.6 River Influences on Phylogenetic Patterns of Genetic Diversity ........................... 25 3. Results ........................................................................................................................... 30 3.1 Sequence Diversity ................................................................................................. 30 3.2 Phylogenetic Analysis ............................................................................................. 31 3.3 Divergent Estimates ................................................................................................ 34 3.4 Historical Demography ........................................................................................... 35 3.5 Historical and Contemporary River System Influences on Genetic Diversity ....... 36 4. Discussion ..................................................................................................................... 38 4.1 Systematics and Distributions of Phylogenetic Clades ........................................... 38 4.2 Biogeography and Historic Drainage Influences on Genetic Diversity ................. 45 4.3 Northern Appalachia and the Teays River .............................................................. 48 4.4 Southern Appalachia and White’s River ................................................................ 52 5. Summary ....................................................................................................................... 57 References ......................................................................................................................... 71 Appendix A: Table of Samples ......................................................................................... 79 Appendix B: Rag1 Gene Tree ........................................................................................... 88 Appendix C: Proportion of Genetic Variance Explained Using Fine-scale Drainage Associations (Hydrologic Unit Code – 6) ......................................................................... 89 6 LIST OF TABLES Page Table 1. Models of evolution chosen by PartitionFinder .................................................. 58 Table 2. Molecular diversity indices for Cyt-b and Rag1 ................................................. 58 Table 3. Cyt-b mean corrected genetic distance within and between clades and within clades................................................................................................................................. 59 Table 4. AMOVA examining the distribution of the Cyt-b genetic variation within and between the major clades resolved in the phylogenetic analysis ...................................... 59 Table 5. Tests for recent population expansions ............................................................... 60 Table 6. Proportion of genetic variance explained by drainage associations ................... 60 7 LIST OF FIGURES Page Figure 1. Histortic and present-day river systems of eastern North America .................. 61 Figure 2. Distribution of Gyrinophilus porphyriticus, and localities sampled for molecular analyses ............................................................................................................ 62 Figure 3. The four different subspecies of Gyrinophilus porphyriticus ........................... 64 Figure 4. Bayesian analysis of Cytochrome b sequences. ................................................ 65 Figure 5 Time calibrated bayesian analysis generated by BEAST. ................................. 67 Figure 6. Distribution of Rag-1 haplotypes ...................................................................... 68 Figure 7. Missmatch Distributions of major clades and subclades .................................. 69 Figure 8. Biogeographic scenarios for Gyrinophilus porphyriticus ................................. 70 8 1. INTRODUCTION 1.1 Introduction and Appalachian Drainage History One of the fundamental endeavors in evolutionary biology is to understand the natural processes that promote divergence between populations of a single species, and how this divergence can ultimately lead to the formation of new evolutionary lineages. These natural processes include both historic and contemporary geological, hydrological, and climatic variables (Kuchta and Meyer 2001; Kuchta and Tan 2006b; Lee 2011), as well as biotic interactions within and between species (Schemske 2009). Of these, previous research has demonstrated that historic and contemporary environmental, geological, and hydrological variables play a significant role in the creation and maintenance of evolutionary lineages (Berendzen et al. 2003; Kuchta and Tan 2005; Kuchta and Tan 2006a,b; Kuchta et al. 2009a,b; Kozak et al. 2006; Hollingsworth and Near 2009). Within the Appalachian region of eastern North America climatic and geological history is both dynamic and complex. Repeated climatic oscillations have continually reshaped both the physical and biotic environment (Hocutt 1978, 1979; Ross 1969; Teller 1973; Thornbury 1965; Ver Steeg 1946). Examples of this dynamic history include the waxing and waning of glaciers during the Pleistocene, repeated uplifting and subsequent erosion of the Appalachian Mountains (Thornbury 1965; Gallen et al. 2013), and a period of extreme warming during the Paleocene-Eocene Thermal Maximum (Newman and Rissler 2011; Highton 1995; Bohme 2003; Prince et