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Where Mountain Lions Traverse: Insights from Landscape Genetics in Southwestern United States and Northwestern Mexico

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Where Mountain Lions Traverse: Insights from Landscape Genetics in Southwestern United States and Northwestern Mexico Where Mountain Lions Traverse: Insights from Landscape Genetics in Southwestern United States and Northwestern Mexico Item Type text; Electronic Dissertation Authors Naidu, Ashwin Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 08/10/2021 19:55:01 Link to Item http://hdl.handle.net/10150/578431 WHERE MOUNTAIN LIONS TRAVERSE: INSIGHTS FROM LANDSCAPE GENETICS IN SOUTHWESTERN UNITED STATES AND NORTHWESTERN MEXICO by Ashwin Naidu __________________________ Copyright © Ashwin Naidu 2015 A Dissertation Submitted to the Faculty of the SCHOOL OF NATURAL RESOURCES AND THE ENVIRONMENT In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY WITH A MAJOR IN NATURAL RESOURCES In the Graduate College THE UNIVERSITY OF ARIZONA 2015 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by Ashwin Naidu, titled Where Mountain Lions Traverse: Insights from Landscape Genetics in Southwestern United States and Northwestern Mexico and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy. _________________________________________________ Date: November 21, 2014 Melanie Culver _________________________________________________ Date: November 21, 2014 David Christianson _________________________________________________ Date: November 21, 2014 Craig Wissler Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copies of the dissertation to the Graduate College. I hereby certify that I have read this dissertation prepared under my direction and recommend that it be accepted as fulfilling the dissertation requirement. _________________________________________________ Date: November 21, 2014 Dissertation Director: Melanie Culver 2 STATEMENT BY AUTHOR This dissertation has been submitted in partial fulfillment of the requirements for an advanced degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this dissertation are allowable without special permission, provided that an accurate acknowledgment of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the copyright holder. SIGNED: Ashwin Naidu 3 ACKNOWLEDGMENTS Projects of a lifetime such as this dissertation require teamwork, collaborations, support and enthusiasm. All of the people and organizations that were involved in enabling the successful completion of this project deserve a lifetime of gratitude. My biggest thanks to Dr. Melanie Culver for bringing me on as her student while I was in India and providing all the impetus for my formal education in wildlife conservation. On the same level, I thank Ron Thompson, Lisa Haynes and Jim Sanderson for inspiring me in the field for wild cat conservation, and for being the best mentors in my life. I thank my co-advisors Dr. John Koprowski, Bob Henry, Craig Wissler and Dr. Dave Christianson for serving on my doctoral committee and providing me with incredibly important advice on moving forward in wildlife science, conservation and management. A big thank you to Robert Fitak and Sophia Amirsultan, my best graduate school buddies who helped me through thick and thin, for giving me my two cats Monster and Kutty, and for fixing my cars’ engines whenever they ditched me. I thank Lindsay Smythe, Susanna Henry, Sarah Rinkevich, and Grant Harris of the United States Fish and Wildlife Service (USFWS) for providing Dr. Melanie Culver and myself with the preliminary information and incentive to conduct this study, and financial support from the USFWS to start this project. I deeply appreciate Ron Thompson’s and Reuben Terán’s efforts toward facilitating the major portion of funding for this project through the Arizona Game and Fish Department (AGFD) – Habitat Partnership Committee (HPC) in partnership with the Arizona Desert Bighorn Sheep Society (ADBSS). Many thanks to the AGFD Game Branch for their collection of hunter harvested samples, to Jeff Cole for sending samples from the Navajo Nation, and to Ron Thompson and Ron Day for delivering these samples to the Culver Conservation Genetics Laboratory at the School of Natural Resources and the Environment. I thank Bob Henry, Brian Jansen, and Dave Conrad from the AGFD for providing me with the necessary insight on mountain lion biology and for scat sample collection in southwestern Arizona. I also thank Lindsay Smythe, Matthew Overstreet, Bobby Law and Jeremy Pennell, who helped with collecting mountain lion scat samples during our fieldwork. 4 I am extremely grateful for Dr. Ryan Perkl’s enthusiastic and unrestricted guidance on GIS modeling during 2014–2015, and several members of the Culver Conservation Genetics Laboratory for critically reviewing this project during its course and in its final stages. My deepest thanks to Sophia Amirsultan, Robert Fitak and Alex Ochoa for their assistance with data analyses, and to John Clemons, President of the ADBSS, who spent nearly three years learning conservation genetics and performing laboratory work with me as his retirement occupation. I also thank John Clemons for facilitating scholarship funds through the ADBSS, and providing me with the much-needed moral support for my dissertation. Support from my old and always best friends, Pratik Agrawal and Harish Damodaran, also came to me at the ‘right’ times, and I can never thank them enough for it. I am indebted to the School of Natural Resources and the Environment for hosting me as a master’s and doctoral student, to the Carson Scholars program, and to the many scholarship donors for the funding I received during the course of my studentship at the University of Arizona (2008–2014). Drs. Rafe Sagarin and Christopher Cokinos, mentors in the Carson Scholars program, strongly encouraged and supported my aspirations. Above all, I could not have accomplished this project without the undying support of my parents, my loving late grandmother, Amma, her descendants – my beloved extended family in India, my parents’ in-law, and the biggest love of my life and daily motivation for the last five years, Abhipsha Chatterjee. 5 DEDICATION This dissertation is dedicated to my parents, my wife, and the many biologists and conservationists who spend lives understanding and protecting wildlife. 6 TABLE OF CONTENTS LIST OF TABLES ............................................................................................................. 8 LIST OF FIGURES ........................................................................................................... 9 ABSTRACT .................................................................................................................... 11 INTRODUCTION ......................................................................................................... 12 Landscape genetics and study context ................................................................ 12 Dissertation goals .................................................................................................... 14 Description of the dissertation format ................................................................. 14 PRESENT STUDIES ...................................................................................................... 17 Focal species: mountain lion (Puma concolor) ....................................................... 17 Spatially explicit population structure analyses reveal major barriers to gene flow among mountain lions ......................................................................... 18 Linking GIS-based models of habitat connectivity with genetic relatedness among mountain lions ...................................................................... 20 Conclusions .............................................................................................................. 21 REFERENCES ................................................................................................................ 23 APPENDIX A: LANDSCAPE GENETICS FOR WILDLIFE MANAGEMENT AND CONSERVATION ........................................................ 26 APPENDIX B: SPATIALLY EXPLICIT POPULATION STRUCTURE ANALYSES REVEAL POTENTIAL BARRIERS TO GENE FLOW AMONG MOUNTAIN LIONS ............................................................................. 58 APPENDIX C: LINKING GIS-BASED MODELS OF HABITAT CONNECTIVITY WITH GENETIC RELATEDNESS AMONG MOUNTAIN LIONS ............................................................................................. 104 APPENDIX D: EXAMINATION OF HISTORICAL VERSUS RECENT POPULATION STRUCTURE FOR SOUTHWESTERN MOUNTAIN LIONS ..................................................................................................................... 135 APPENDIX E: SUPPLEMENTARY MATERIAL ................................................... 142 7 LIST OF TABLES Table A.1: Reviews published on landscape genetics to date ................................ 49 Table A.2: A summary of downloadable software packages used in landscape genetic studies ................................................................................
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