University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 5-1-2013 A Holarctic perspective on mammalian evolution: The evolutionary and biogeographic history of red- backed voles and their close relatives (Rodentia: Arvicolinae) Brooks Kohli Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Kohli, Brooks. "A Holarctic perspective on mammalian evolution: The ve olutionary and biogeographic history of red-backed voles and their close relatives (Rodentia: Arvicolinae)." (2013). https://digitalrepository.unm.edu/biol_etds/63 This Thesis is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. i Brooks A. Kohli Candidate Biology Department This thesis is approved, and it is acceptable in quality and form for publication. Approved by the Thesis Committee: Joseph A. Cook, Chairperson Steven Poe Christopher C. Witt ii A Holarctic perspective on mammalian evolution: The evolutionary and biogeographic history of red-backed voles and their close relatives (Rodentia: Arvicolinae) by BROOKS A. KOHLI B.S., Biological Sciences, Ohio University, 2010 THESIS Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science Biology The University of New Mexico Albuquerque, New Mexico May 2013 iii ACKNOWLEDGEMENTS A thesis focusing on a group of species found across the Northern Hemisphere and on three continents could not be successful without the help of many people at all stages of the research. First of all, I have to thank my advisor, Joe Cook, for his guidance and encouragement throughout the whole process and for giving me the invaluable experiences I enjoyed in New Mexico, Alaska, and beyond. I would also like to thank Chris Witt and Steve Poe for their commitment and insight that greatly improved the quality of this work. Many thanks are also due to the members and associates of the Cook lab, past and present, for their advice, encouragement, help with lab work and learning analysis programs, and especially their friendship. Special thanks to Kelly Speer for her enthusiasm and dedication in the lab that made it possible to collect such a large amount of data in a short period of time. I am indebted to all the collectors of voles, over decades of difficult field research in some of the most remote regions of the world that afforded me this wealth of samples, and the natural history museums that have preserved them and made them available to me. I am grateful to the generous funding sources that supported this research, especially the UNM Department of Biology, Graduate and Professional Student Association, and Biology Graduate Student Association. Finally, my deepest gratitude to Adrienne for her endless help, support, and understanding and for always pushing me to be my best in everything I do. iv A Holarctic perspective on mammalian evolution: The evolutionary and biogeographic history of red-backed voles and their close relatives (Rodentia: Arvicolinae) by Brooks A. Kohli B.S., Biology, Ohio University, 2010 M.S., Biology, University of New Mexico, 2013 ABSTRACT The influence of Quaternary environmental changes on demography and geographic distribution is paramount to understanding how contemporary genetic diversity is partitioned in high-latitude species. This history of change in northern ecosystems sets the stage for forecasting how species inhabiting tundra and boreal forest will respond to the ongoing shift in climate. Utilizing broad geographic and taxonomic sampling, a multilocus species tree approach, ecological niche models, and population genetic techniques, I investigate the evolutionary and biogeographic history of a Holarctic mammal, the northern red-backed vole (Clethrionomys rutilus) and the systematics of the tribe it belongs to, Clethrionomyini. This tribe of forest and alpine voles is distributed throughout the Holarctic and diversified in the Northern Hemisphere over the last 5 MY. The biogeographic history of C. rutilus is characterized by subdivision and subsequent expansion from multiple refugia, including previously v unidentified refugia in central Asia. Several taxonomic issues are resolved by the use of multilocus data, including support of a polyphyletic Clethrionomys, prompting the suggestion of splitting the genus into two. Diversification in the tribe is not characterized by pulses of diversification, as previously suggested. The dynamic geographic, genealogic, and demographic history of C. rutilus and Clethrionomyini provides insight into the Quaternary biogeography of the northern high-latitudes in Asia and North America. vi TABLE OF CONTENTS Chapter 1 Thesis Introduction ..........................................................................................1 References ......................................................................................................................3 Chapter 2 Phylogeography of a Holarctic rodent (Clethrionomys rutilus): Testing high-latitude biogeographic hypotheses and the dynamics of range shifts ..................5 Abstract ..........................................................................................................................5 1. Introduction ................................................................................................................6 1.1 Study species and hypotheses ............................................................................9 2. Methods....................................................................................................................12 2.1 Sampling and laboratory techniques ................................................................12 2.2 Phylogeny reconstruction.................................................................................15 2.3 Species tree estimation .....................................................................................15 2.4 Population genetic inference ............................................................................16 2.5 Divergence dates and demographic history .....................................................17 2.6 Species distribution modeling ..........................................................................18 3. Results ......................................................................................................................20 3.1 Phylogenies and phylogeographic structure ....................................................21 3.2 Species tree estimation .....................................................................................22 3.3 Population differentiation and demographic history ........................................23 3.4 Species distribution models .............................................................................25 4. Discussion ................................................................................................................27 4.1 Phylogeographic structure and biogeographic history of C. rutilus ................28 4.2 Demographic history ........................................................................................30 4.3 Contact zones ...................................................................................................32 4.4 Conclusion .......................................................................................................33 vii References ....................................................................................................................34 Figures and Tables .......................................................................................................43 Appendices ...................................................................................................................55 Chapter 3 Multilocus systematics and the characteristics of a recent radiation in a Holarctic tribe of rodents (Arvicolinae: Clethrionomyini) ..........................................68 Abstract ........................................................................................................................68 1. Introduction ..............................................................................................................69 1.1 Objectives ..............................................................................................................71 2. Methods....................................................................................................................71 2.1 Brief description of Clethrionomyini ...............................................................72 2.2 Sampling and laboratory techniques ................................................................74 2.3 Gene tree reconstruction ..................................................................................76 2.4 Species tree estimation and divergence dates ..................................................77 2.5 Sequence divergence and genetic diversity .....................................................78 2.6 Characterization of evolutionary patterns ........................................................79 3. Results ......................................................................................................................80 3.1 Gene tree reconstruction ..................................................................................81 3.2 Species tree estimation