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Template: Front Matter PHYLOGENETIC RELATIONSHIPS, DIVERGENCE AND RADIATION WITHIN THE SUBFAMILY NEOTOMINAE (RODENTIA: CRICETIDAE) by Megan S. Keith, B.S. A Dissertation In Biology Submitted to the Graduate Faculty of Texas Tech University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Approved Robert D. Bradley Chair of Committee Robert J. Baker Llewellyn D. Densmore III David A. Ray Darin S. Carroll Mark Sheridan Dean of the Graduate School December, 2015 Copyright 2015 by Megan S. Keith Texas Tech University, Megan S. Keith, December 2015 ACKNOWLEDGMENTS There are several people that I would like to thank for their support throughout the course of my degree. First, I would like to thank my major advisor, Dr. Robert D. Bradley, for mentoring me beginning as an undergraduate researcher and through my pursuit of a doctorate degree. I would also like to thank the remaining members of my advisory committee for their knowledge and support: Drs. Robert J. Baker, Llewellyn D. Densmore, David A. Ray, and Darin S. Carroll. There are numerous friends and colleagues that I would like to thank for their advice and support both personally and professionally. Thank you to Dr. R. Neal Platt II, Dr. John D. Hanson, and Dr. Cody W. Thompson for being mentors to me in both my undergraduate and graduate research and for your continued collaboration on several projects. Several peers gave advice, support and friendship throughout the process of working toward my PhD: Dr. Matthew R. Mauldin, Dr. Faisal Ali Anawarli Khan, Juan P. Carrera-Estupiñán, Dr. Tyla Holsombeck, Dr. Adam W. Ferguson, Kenneth Griffith, Narayan Kandel, Dr. Molly M. McDonough, Nicté Ordóñez-Garza, Dr. Julie A. Parlos, Dr. Caleb D. Phillips, Emma Roberts, Dr. Lizette Siles-Mendoza, Dr. Cibele Sotero-Caio, Dr. Courtney A. Thomason, Christopher Dunn, Dr. Miryam Venegas-Anaya, Elise Wagley, and Sheri Westerman-Ayers. In addition, I would like to thank several people that I met through field trips or through attendance at scientific meetings that also offered their support and encouragement: Dr. Ralph Eckerlin, Dr. Walter Bulmer, Dr. John Matson and his wife Sharon, and Dr. ii Texas Tech University, Megan S. Keith, December 2015 Michelle Haynie. Without all of you, my graduate school experience would not have been as exciting and rewarding. Thank you to Heath Garner, Kathy MacDonald, and the Natural Science Research Laboratory (Museum of Texas Tech University) staff for assistance with tissue loans. I would also like to thank the following professional and academic societies from which research funding was acquired: the Association of Biologist at Texas Tech University and the Texas Academy of Science. Additionally, thank you to the Department of Biological Sciences and Graduate School of Texas Tech University for travel funding to attend and present my research at numerous state and national scientific meetings. Finally I would like to thank my family for their unwavering support and encouragement throughout my academic career: my parents, Mike and Patricia Corley, my grandmother, Betty Ebarb, my brother Craig Corley as well as my extended family, and my in-laws Lonnie and Yolanda Keith, Tiffany and Noahh Dorris, and Patrick and Mellissa Killingsworth. Most importantly, I want to thank my husband, Eric, for his support and encouragement, and for being there through all stages in the pursuit of my graduate degree. Without the love and support of these very special people, I would not have endured the trials and pressures of research and graduate school. iii Texas Tech University, Megan S. Keith, December 2015 TABLE OF CONTENTS ACKNOWLEDGMENTS .................................................................................... ii LIST OF TABLES ............................................................................................... vi LIST OF FIGURES ............................................................................................. ix ABSTRACT ......................................................................................................... xii I. INTRODUCTION ............................................................................................. 1 BACKGROUND INFORMATION ............................................................................. 1 OBJECTIVES ....................................................................................................... 6 ORGANIZATION OF CHAPTERS ............................................................................ 7 LITERATURE CITED ............................................................................................ 8 II. WHAT IS PEROMYSCUS? EVIDENCE FROM NUCLEAR AND MITOCHONDRIAL DNA SEQUENCES SUGGESTS THE NEED FOR A NEW CLASSIFICATION ............................................................................................ 16 ABSTRACT ........................................................................................................ 16 INTRODUCTION................................................................................................. 17 MATERIALS AND METHODS ............................................................................. 19 RESULTS .......................................................................................................... 24 DISCUSSION ..................................................................................................... 27 ACKNOWLEDGMENTS ....................................................................................... 36 LITERATURE CITED .......................................................................................... 37 III. MOLECULAR DATA INDICATE THAT ISTHMOMYS IS NOT ALIGNED WITH PEROMYSCUS ........................................................................................ 59 ABSTRACT ........................................................................................................ 59 INTRODUCTION................................................................................................. 60 MATERIALS AND METHODS ............................................................................. 63 RESULTS .......................................................................................................... 67 DISCUSSION ..................................................................................................... 69 ACKNOWLEDGMENTS ....................................................................................... 72 LITERATURE CITED .......................................................................................... 73 iv Texas Tech University, Megan S. Keith, December 2015 IV. PHYLOGENETIC RELATIONSHIPS AND DIVERGENCE OF THE SUBFAMILY TYLOMYINAE (RODENTIA: CRICETIDAE) AS DETERMINED BY A MULTILOCUS DATASET ........................................ 94 ABSTRACT ........................................................................................................ 94 INTRODUCTION................................................................................................. 95 MATERIALS AND METHODS ............................................................................. 98 RESULTS ........................................................................................................ 102 DISCUSSION ................................................................................................... 103 ACKNOWLEDGMENTS ..................................................................................... 106 LITERATURE CITED ........................................................................................ 107 V. UTILIZATION OF MULTIPLE MOLECULAR MARKERS TO RESOLVE TRIBAL AFFILIATIONS WITHIN THE SUBFAMILY NEOTOMINAE 128 ABSTRACT ...................................................................................................... 128 INTRODUCTION............................................................................................... 129 MATERIALS AND METHODS ........................................................................... 132 RESULTS ........................................................................................................ 135 DISCUSSION ................................................................................................... 136 ACKNOWLEDGMENTS ..................................................................................... 138 LITERATURE CITED ........................................................................................ 139 VI. CONCLUSIONS ......................................................................................... 157 PROJECT SUMMARY ....................................................................................... 157 FUTURE DIRECTIONS ...................................................................................... 162 LITERATURE CITED ........................................................................................ 164 v Texas Tech University, Megan S. Keith, December 2015 LIST OF TABLES 2.1 Specimens examined in this study are listed by taxon and genetic marker (Adh1- I2 - intron 2 of alcohol dehydrogenase, Cytb - cytochrome-b, Fgb-I7 - intron of the beta-fibrinogen, and Rbp3 - interphotoreceptor retinoid binding protein) and grouped by tribe, genus, and species group. GenBank accession (left of slash) and museum catalog (right of slash) numbers are given for each specimen. Museum acronyms are as follows: ASNHC (Angelo State Natural History Collection), BYU (Brigham Young University), CNMA (Colección Nacional de Mamíferos, Universidad Nacional Autónoma de México),
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