PHYLOGENETIC RELATIONSHIPS AND HISTORICAL BIOGEOGRAPHY OF THE GENUS AKODON (RODENTIA: CRICETIDAE) By BRANDI S. COYNER Bachelor of Science, Zoology University of Oklahoma Norman, OK 2005 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY December, 2010 PHYLOGENETIC RELATIONSHIPS AND HISTORICAL BIOGEOGRAPHY OF THE GENUS AKODON (RODENTIA: CRICETIDAE) Dissertation Approved: Dr. Ronald A. Van Den Bussche Dissertation Adviser Dr. Janet K. Braun Dr. Meredith J. Hamilton Dr. David M. Leslie, Jr. Outside Committee Member Dr. Mark E. Payton Dean of the Graduate College ii ACKNOWLEDGMENTS I thank my committee members (Dr. Janet K. Braun, Dr. Meredith J. Hamilton, Dr. David M. Leslie, Jr., and Dr. Ronald A. Van Den Bussche) for their guidance and patience during my time under their tutelage. I would like to thank Dr. Ronald J. Tyrl, who retired prior to completion of my degree, but who provided much assistance during his time as my committee member. It is also without hesitation that I thank Dr. Michael A. Mares for his continued presence and support of my research and career as a mammalogist and for serving as a mentor. I would like to thank my many lab mates that have come and gone during my time as a member of the Van Den Bussche lab. I also thank the many graduate students that I have shared my time with, especially those that I consider my closest friends despite the distance that careers will put between us. I also thank my family, who despite not always understanding what I do or why I do it, still support me in my endeavors. Without a number of entities, this research would not have been possible. The Departments of Zoology at Oklahoma State University and at the University of Oklahoma are thanked for providing facilities and logistic support, as is the Sam Noble Oklahoma Museum of Natural History. The Recombinant DNA/Protein Core Facility at Oklahoma State University allowed me access to their equipment; I especially thank Janet Rogers and Lisa Whitworth for their assistance while at the Core and their iii willingness to provide assistance with troubleshooting. I am grateful to the many curators and collections managers from the following institutions that have facilitated the loans of tissues and specimens included in this project: Oklahoma Center for iv Genomic Resources, Sam Noble Oklahoma Museum of Natural History, Norman, Oklahoma; Field Museum of Natural History, Chicago, Illinois; Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico; Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California; Museum of Texas Tech University, Texas Tech University, Lubbock, Texas; and the American Museum of Natural History, New York, New York. I would like to thank the following organizations and institutions for financial support of this research. Funding for this research was provided by the National Science Foundation Graduate Research Fellowship Program, the Albert M. and Alma Shadle Fellowship in Mammalogy from the Buffalo Foundation and the American Society of Mammalogists, the American Society of Mammalogists’ Grants-in-Aid program, and the Oklahoma State University Zoology Graduate Student Society. Additionally travel grants to present findings from this research at national and international meetings were provided by the Oklahoma State University Graduate and Professional Student Society, Alaska EPSCoR, and the University of Wyoming. Last, but definitely not least, I thank the many individuals that assisted in the field collection of these specimens. They risked loss of life and limb, gave up time with their families, and endured sometimes harsh conditions to collect these mice. Without them, this project would not have been possible. iv TABLE OF CONTENTS Chapter Page I. INTRODUCTION TO A STUDY OF AKODON PHYLOGENETICS AND BIOGEOGRAPHY ..................................................................................................1 Literature Cited ........................................................................................................7 Figure Legends.......................................................................................................18 II. PHYLOGENETIC RELATIONSHIPS OF SOUTH AMERICAN GRASS MICE OF THE GENUS AKODON (RODENTIA, CRICETIDAE) BASED UPON THE CYTOCHROME B GENE ....................................................................................20 Introduction ............................................................................................................21 Materials and Methods ...........................................................................................24 Taxon Sampling ...............................................................................................24 Extraction, Amplification, and Sequencing .....................................................25 Data Analyses ..................................................................................................26 Results ....................................................................................................................27 Discussion ..............................................................................................................29 Akodon cursor group ........................................................................................30 Akodon boliviensis group .................................................................................32 Akodon varius group ........................................................................................36 Akodon aerosus group......................................................................................38 Incertae sedis lineages .....................................................................................40 Concluding Remarks ..............................................................................................42 Acknowledgments..................................................................................................43 Literature Cited ......................................................................................................44 Figure Legends.......................................................................................................66 v Chapter Page III. PHYLOGENETIC RELATIONSHIPS AND HISTORICAL BIOEGEOGRAPHY OF THE GENUS AKODON (RODENTIA, MURIDAE) USING A MULTI- GENE APPROACH...............................................................................................74 Introduction ............................................................................................................75 Material and Methods ............................................................................................79 Taxon Sampling ...............................................................................................79 Extraction, Amplification, and Sequencing .....................................................80 Data Analyses ..................................................................................................82 Results ....................................................................................................................85 Discussion ..............................................................................................................90 Akodon cursor group ........................................................................................92 Akodon boliviensis group .................................................................................94 Akodon aerosus group....................................................................................100 Akodon varius group ......................................................................................104 Incertae sedis lineages ...................................................................................106 Previously proposed biogeographic hypothesis of Akodon ...........................108 Concluding Remarks ............................................................................................109 Acknowledgments................................................................................................110 Literature Cited ....................................................................................................111 Figure Legends.....................................................................................................135 IV. CONCLUSIONS ON A PHYLOGENETIC AND BIOGEOGRAPHIC STUDY OF AKODON .......................................................................................................141 Future Research ...................................................................................................143 APPENDIX 1 .............................................................................................................145 vi LIST OF TABLES Table Page 1.1 Species of Akodon divided into the four species groups (Braun et al. 2008; Musser and Carleton 2005; Myers 1989; Myers et al. 1989; Patton and Smith 1992a; Rieger et al. 1995; Smith and Patton 2007) and taxa considered incertae sedis..................................................................................................................17 2.1 Species of Akodon divided into the four species groups (Braun et al. 2008; Musser and Carleton 2005; Myers 1989; Myers et al. 1989; Patton and Smith 1992a; Rieger et al. 1995; Smith and Patton 1992a, 2007) and taxa considered incertae sedis ...................................................................................................54