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Pattern and Process in the Radiation of Ground-Dwelling Squirrels. University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations Spring 4-15-2017 Pattern and Process in the Radiation of Ground- dwelling Squirrels Bryan S. McLean University of New Mexico - Main Campus Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Part of the Biology Commons, and the Ecology and Evolutionary Biology Commons Recommended Citation McLean, Bryan S.. "Pattern and Process in the Radiation of Ground-dwelling Squirrels." (2017). https://digitalrepository.unm.edu/ biol_etds/206 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]. Bryan Stephen McLean 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 Cook , Chairperson Dr. Steven Poe Dr. Felisa Smith Dr. James Degnan Dr. Kristofer Helgen i PATTERN AND PROCESS IN THE RADIATION OF GROUND-DWELLING SQUIRRELS by BRYAN STEPHEN MCLEAN B.S., Biology, Appalachian State University, 2004 M.S., Biology, University of North Carolina Wilmington, 2011 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, 2017 ii ACKNOWLEDGEMENTS This dissertation and the degree to which it contributes represent the culmination of six years of fieldwork, labwork, travels, ups and downs, life and love. I owe the largest debt of gratitude to my major advisor Joe Cook, who gave me the freedom to pursue my own ideas and interests about ground squirrels while keeping me from going too far astray. Joe excels as an advisor and leader, but over the past years I had the privilege to witness his talent as a mentor as well. I also thank the additional members of my committee, Drs. Steven Poe, Felisa Smith, James Degnan, and Kristofer Helgen, for their time, insight, and valuable criticisms on the research contained herein. Being part of the exceptionally rich history of mammalogy at University of New Mexico has been a highlight of my graduate career. I thank the staff, scientists, and recent students at Museum of Southwestern Biology Division of Mammals with whom I have interacted over the past several years, in particular Jon Dunnum, Adrienne Raniszewski, and Mariel Campbell. I thank my past and present labmates Kayce Bell, Donavan Jackson, Schuyler Liphardt, Dianna Krejsa, Steve Greiman, Jocie Colella, Carlos Carrion, Andrew Hope, Jason Malaney, Jessica Weber, and Yadeeh Sawyer for support and lots of great times, especially in the field. My development as a scientist in general also greatly benefitted from interactions with Kayce Bell, Grey Gustafson, Libby Beckman, Mason Ryan, Dan Colman, Chris Witt, Andy Johnson, and Levi Gray. I spent one of the past six years as a fellow at the National Museum of Natural History. I thank my coadvisors there, Drs. Kris Helgen and Gene Hunt, for that valuable and constructive opportunity. I thank staff in the NMNH Division of Mammals for additional help and guidance, particularly Al Gardner, Darrin Lunde, Esther Langan, and iii Nicole Edmison. While at NMNH, I was able to greatly expand my thinking about ground squirrel evolution and the amount of data included in this dissertation, and I benefitted from interactions with a wide array of resident and visiting researchers. Of course, this dissertation relied on specimens contained in many museums other than MSB and NMNH; in particular, I wish to thank Bob Timm (KU), Jim Patton, Eileen Lacey, and Chris Conroy (MVZ), Priscilla Tucker and Cody Thompson (UMMZ), and Sharlene Santana and Jeff Bradley (UWBM) for access to materials under their care. Finally, I thank my parents, Steve and Bonnie McLean, and my sister, Dara McLean, for their long-time support, but especially over these past six years. There were times when visits were few and far between, and when birthday wishes were one or two days late, but without your help this dissertation would not have been possible. I owe a special debt of gratitude to my wife, Sally, a Tennessee girl who I was lucky enough to meet in New Mexico. Sally has been a fellow adventurer, a constant source of support and advice, and a last-minute editor on too many drafts and proposals to remember. Finally, to the many people who contributed in intangible ways, but are not mentioned here, thank you. iv PATTERN AND PROCESS IN THE RADIATION OF GROUND-DWELLING SQUIRRELS Bryan S. McLean B.S. Biology, Appalachian State University M.S. Biology, University of North Carolina Wilmington Ph.D Biology, University of New Mexico ABSTRACT What causes biological diversity to be unevenly apportioned across the Tree of Life? The pattern is widespread and well-characterized; but our understanding of processes underlying the taxonomic, phenotypic, and ecological disparities of clades remains incomplete. At least some of this disparity is due to clade-specific differences in the ability to respond to ecological opportunity, whereby access to, and exploitation of, different resources in ecological time drives evolutionary divergence and adaptive radiation. However, not all clades respond equivalently to ecological opportunity, and considerable heterogeneity therefore exists in diversification patterns across radiations. This dissertation focuses on patterns and processes of diversification in ground- dwelling squirrels of the tribe Marmotini. It seeks to infer phylogeny and describe variation in ecological and phenotypic traits (patterns) and, ultimately, to relate those to the developmental, environmental, and evolutionary factors shaping them (processes). It integrates molecular, morphological, and environmental datasets derived from museum specimens at two taxonomic levels (across the entire tribe and within the genus Urocitellus). Results at each level are evaluated in the context of current evolutionary theory and practice, and these are used to determine whether evolutionary themes exist in marmotine radiation transcending taxonomic and phylogenetic scales. v INTRODUCTION .................................................................................................................1 References ..................................................................................................................6 CHAPTER 1: Impacts Of Inference Method And Dataset Filtering On Phylogenomic Resolution In A Rapid Mammalian Radiation .......................................................................9 Abstract ......................................................................................................................9 Introduction ................................................................................................................10 Methods......................................................................................................................11 Results ........................................................................................................................15 Discussion ..................................................................................................................17 Acknowledgements ....................................................................................................22 References ..................................................................................................................23 Figure Captions ..........................................................................................................30 Tables .........................................................................................................................31 Figures........................................................................................................................32 Supplementary Figure Captions .................................................................................38 Supplementary Figures ..............................................................................................39 CHAPTER 2: Heterogeneity in Evolutionary Mode and Macroevolutionary Dynamics Among Ground Squirrel Morphological Traits .....................................................................41 Abstract ......................................................................................................................41 Introduction ................................................................................................................42 Methods......................................................................................................................43 Results ........................................................................................................................49 Discussion ..................................................................................................................52 vi Acknowledgements ....................................................................................................57 References ..................................................................................................................58 Figure Captions ..........................................................................................................66 Tables .........................................................................................................................67
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