University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 5-1-2013 EXPLORING SIGNALS OF HISTORICAL DEMOGRAPHY IN BOREAL MAMMALS THROUGH INTEGRATION OF STATISTICAL CONSERVATION PHYLOGENETICS, TAXONOMY, AND COMPARATIVE PHYLOGEOGRAPHY Jason Malaney Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Malaney, Jason. "EXPLORING SIGNALS OF HISTORICAL DEMOGRAPHY IN BOREAL MAMMALS THROUGH INTEGRATION OF STATISTICAL CONSERVATION PHYLOGENETICS, TAXONOMY, AND COMPARATIVE PHYLOGEOGRAPHY." (2013). https://digitalrepository.unm.edu/biol_etds/74 This Dissertation 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]. Jason L. Malaney Candidate Department of Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Dr. Joseph A. Cook , Chairperson Dr. Steve Poe Dr. Tom Turner Dr. Rob Guralnick EXPLORING SIGNALS OF HISTORICAL DEMOGRAPHY IN BOREAL MAMMALS THROUGH INTEGRATION OF STATISTICAL CONSERVATION PHYLOGENETICS, TAXONOMY, AND COMPARATIVE PHYLOGEOGRAPHY by JASON L. MALANEY B.S., Wildlife and Fisheries Sciences, ENMU, 2000 M.S., Applied Ecology, ENMU, 2003 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico May 2013 ACKNOWLEDGMENTS Dr. Joseph A. Cook supported all phases of my research and demonstrated a consistent zeal as a colleague. I thank him for this and providing unparalleled guidance and wisdom as my research adviser, dissertation committee chair, and friend. You have provided proper encouragement and I have benefited greatly from your tutelage. I thank my committee members, Dr. Steve Poe, Dr. Tom Turner, and Dr. Robert Guralnick, for their patience and guidance throughout my professional development. Each has contributed unique but significant perspectives that have enhanced this work. I acknowledge and appreciate the assistance of several individuals directly associated with this research. Fellow graduate students Andrew G. Hope, and Yadeeh Sawyer (Escobedo), and UnO (Undergraduate Opportunities) scholars Hiyatsi Bassett, Alys Jones, Randle McCain, Elisha K. Song, and Sophia Thompson helped with field work (2007 and 2010). Lab work was aided by Lena Moffitt and Ashley Montoya. Lab mates in the CUERVO lab have provided many thoughtful discussions. Special appreciation is extended to the curators and collections managers from several institutions that loaned valuable vouchers, including John Demboski, Jennifer Frey, Larry Heaney, Jim Kenagy, Link Olson, Eric Rickart, but especially Jim Patton. Most importantly, I thank the many natural history collectors over the years. Without your efforts, much of our understanding of the natural world would be absent. A special note of appreciation is extended my loved ones, especially my parents Jack and Evelyn Malaney for providing the necessary tools to realize and accomplish my goals. Finally, to Analiese, you have provided the truest inspiration – hopefully, one day, you will recognize your contributions. iii EXPLORING SIGNALS OF HISTORICAL DEMOGRAPHY IN BOREAL MAMMALS THROUGH INTEGRATION OF STATISTICAL CONSERVATION PHYLOGENETICS, TAXONOMY, AND COMPARATIVE PHYLOGEOGRAPHY by Jason L. Malaney B.S., Wildlife and Fisheries Sciences, Eastern New Mexico University M.S., Applied Ecology, Eastern New Mexico University Ph.D., Biology, University of New Mexico ABSTRACT Understanding how diversity is partitioned across the landscape can provide perspectives related to the environmental processes that have influenced the evolutionary history of organisms. This main idea, often termed phylogeography, serves as the backdrop to my research where I explore three broad concepts including historical biogeography, cryptic diversity and ecology, and conservation phylogenetics. I address various questions in each of these concepts by using a set of mammals that are associated with montane and mesic environments of North America. More specifically, I focus on the jumping mice (Zapodidae) to test hypotheses that scale to the broader community. This approach allows for a more refined understanding and interpretation of how species have responded to geophysical changes of the past that may be useful for predicting how future environmental pressures may influence geographically oriented lineages. By integrating across multiple disciplines of population genetics, phylogenetics, phylogeography, distribution modeling, and paleoclimatology, I assess how environmental change has left an imprint on the genetics and ecology of various organisms. Signatures of the past are useful to forecast conservation issues of the future. iv TABLE OF CONTENTS Introduction..........................................................................................................................1 Literature Cited........................................................................................................7 Chapter 1: The biogeographic legacy of an imperilled taxon provides a foundation for assessing lineage diversification, demography, and conservation genetics.......................12 Abstract..................................................................................................................13 Introduction............................................................................................................15 Methods..................................................................................................................21 Results....................................................................................................................28 Discussion..............................................................................................................32 Acknowledgments..................................................................................................38 Literature Cited......................................................................................................39 Appendix................................................................................................................56 Figures....................................................................................................................67 Tables.....................................................................................................................73 Chapter 2: Phylogeography of the Western Jumping Mouse (Zapus princeps) detects deep and persistent allopatry with expansion....................................................................75 Abstract..................................................................................................................76 v Introduction............................................................................................................77 Methods..................................................................................................................80 Results....................................................................................................................87 Discussion..............................................................................................................91 Acknowledgments..................................................................................................97 Literature Cited......................................................................................................98 Appendix..............................................................................................................120 Figures..................................................................................................................124 Tables...................................................................................................................130 Chapter 3: Using biogeographic history to inform conservation: the case of Preble’s meadow jumping mouse..................................................................................................133 Abstract................................................................................................................134 Introduction..........................................................................................................135 Methods................................................................................................................138 Results..................................................................................................................145 Discussion............................................................................................................148 Acknowledgments................................................................................................155 Literature Cited....................................................................................................156 vi Figures..................................................................................................................174 Tables...................................................................................................................179 Supplementary Information.................................................................................186 Conclusions......................................................................................................................205