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Landscape Genetics of the New England Cottontail: Effects of Habitat Fragmentation on Population Genetic Structure and Dispersal

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Landscape Genetics of the New England Cottontail: Effects of Habitat Fragmentation on Population Genetic Structure and Dispersal University of New Hampshire University of New Hampshire Scholars' Repository Master's Theses and Capstones Student Scholarship Fall 2010 Landscape genetics of the New England cottontail: Effects of habitat fragmentation on population genetic structure and dispersal Lindsey E. Fenderson University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/thesis Recommended Citation Fenderson, Lindsey E., "Landscape genetics of the New England cottontail: Effects of habitat fragmentation on population genetic structure and dispersal" (2010). Master's Theses and Capstones. 565. https://scholars.unh.edu/thesis/565 This Thesis is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Master's Theses and Capstones by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. LANDSCAPE GENETICS OF THE NEW ENGLAND COTTONTAIL: EFFECTS OF HABITAT FRAGMENTATION ON POPULATION GENETIC STRUCTURE AND DISPERSAL BY LINDSEY E. FENDERSON Wildlife Ecology, B.S., University of Maine, Orono, 2006 THESIS Submitted to the University of New Hampshire in Partial Fulfillment of the Requirements for the Degree of Master of Science in Zoology September, 2010 UMI Number: 1486975 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI' Dissertation Publishing UMI 1486975 Copyright 2010 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 This thesis has been examined and approved. &-£- Adrienne Kovach, Research Assistant Professor of Biology and Natural Resources $L-CL Litvaitis, Professor of Wildlife Ecology Marian Litvaitis, Professor of Zoology / /& I In Date DEDICATION This thesis is dedicated to David Veverka. Dave was an incredibly supportive person in my life and I wish he had been there throughout this experience. He would have made a first-rate marine mammalogist, or researcher in any other field in which he decided to pursue; his dedication and passion were truly inspiring. He always made time for others and his selflessness in Iraq was so typical of his many admirable qualities. He was an amazing person and I am so glad for having had the opportunity to know him. iii ACKNOWLEDGEMENTS Funding for this research was provided by the United States Fish and Wildlife Service, Maine Department of Inland Fisheries and Wildlife, the Maine Outdoor Heritage Fund, the U.S. Fish and Wildlife Service, and the New Hampshire Agricultural Experiment Station. I am extremely grateful for all of the assistance I received from my advisor, Adrienne Kovach. Thank you for making this a challenging and rewarding experience. I certainly couldn't have completed this without your support and enthusiasm. Continually spoiling your graduate students with delicious baked goods and garden surplus undoubtedly didn't hurt either. My other committee members, John and Marian Litvaitis, gave assistance as needed and offered many helpful comments on manuscript drafts, of which I greatly appreciated. John provided my first opportunity to see a live New England cottontail, which for a "pasty-white lab rat" was a rare and memorable experience. Marian, I truly appreciated your words of encouragement and praise, especially toward the end of this extensive undertaking. Many agency biologists, volunteers, former students and technicians were invaluable for their assistance with trapping and pellet collection as well as providing other support. In particular I am grateful to Walter Jakubas with the Maine Department of Inland Fisheries and Wildlife, Kate O'Brien with Rachel Carson National Wildlife iv Refuge, and Kelly Boland with the Environmental Defense Fund for continued support throughout this process. Additionally, I received much support from Anthony Tur and the U.S. Fish and Wildlife Service, Steven Fuller and New Hampshire Fish and Game, Howard Kilpatrick and Connecticut Department of Environmental Protection, Paul Novak and New York Department of Environmental Conservation, Brian Tefft and Rhode Island Department of Environmental Management, David Tibbetts, Margaret Arbuthnot, John DePue, Mike Marchand, Brian Johnson, Robin Innes, Vanessa Johnson, Jim Panaccione and Jon Lanza. Many of the aforementioned people, especially Kelly Boland, were fellow bushwhackers, who braved impenetrable fortresses of thorny, skin-clawing thickets and brambles to help collect rabbit samples; this research could not have been completed without their complete disregard for their protective epithelial cells. David Berlinsky helpfully provided laboratory space. I thank Jobriah Anderson at the University of New Hampshire Hubbard Center for Genome Studies for putting up with all of my convoluted sample names as he ran plate after plate of my samples. I also greatly appreciate Barbara Charry and Maine Audubon for providing GIS data for use in additional research. Melanie Schroer, Elisha Allan, Grace Smarsh, Samantha Petren, Cynthia Sirois and Allison Citro helped significantly with the endless DNA extractions and species identifications. Fellow graduate students Stephanie Coster, Jen Walsh, Tim Breton, Elisha Allen, Daniel Brubaker and Charlotte Gabrielsen helped along the way with various support, ranging from helping with occasional lab and GIS procedures, to providing helpful comments on manuscripts or presentations, to listening to my v 'traumatic'(albeit slightly exaggerated) or just plain ridiculous (corpse acting?) teaching experiences, or for simply providing a laugh over shared war stories from the trenches of the graduate school experience. Finally, I also appreciate the support of my family throughout this endeavor. Even despite the peanut-gallery comments about my career as a professional student, studying 'rabbit poo' and chasing 'wascally wabbits', each of you enrich my life in your own way and I'm lucky to have you all. vi TABLE OF CONTENTS DEDICATION iii ACKNOWLEDGEMENTS iv LIST OF TABLES xi LIST OF FIGURES xiii ABSTRACT xv INTRODUCTION 1 Landscape Genetics - Evaluating Landscape Impacts on Genetic Structure and Dispersal 2 New England Cottontails as a Case Study 4 Management Questions 7 Broad-scale 7 Fine-scale 7 Research Objectives 8 Broad-scale 8 Fine-scale 8 CHAPTER 1 POPULATION GENETIC STRUCTURE AND HISTORY OF FRAGMENTED REMNANT POPULATIONS OF THE NEW ENGLAND COTTONTAIL 9 Abstract 9 Introduction 10 vii Methods 15 Sample Collection and DNA Extraction 15 Microsatellite Genotyping 15 Descriptive Statistics 19 Population Differentiation and Structure 20 Detection of Migrants and Recent Gene Flow 21 Population History and Genetic Diversity 22 Results 23 Descriptive Statistics 23 Population Differentiation and Structure 31 Detection of Migrants and Recent Gene Flow 36 Population History and Genetic Diversity 39 Discussion 44 Population Structure 44 Population History and Genetic Diversity 47 Null Alleles and Deviations from Hardy Weinberg Equilibrium 49 Conservation Implications 51 CHAPTER 2 LANDSCAPE GENETICS AND DISPERSAL PATTERNS OF THE NEW ENGLAND COTTONTAIL 55 Abstract 55 Introduction 56 Hypotheses 60 Methods 62 viii Study System and Sample Collection 62 Microsatellite Genotyping 66 Population Genetic Structure, Diversity and Effective Size 67 Dispersal Barriers 69 Fine-scale Spatial Genetic Structure and Dispersal 69 Sex-biased Dispersal 70 Results 71 Population Genetic Structure, Diversity and Effective Size 74 Dispersal Barriers 86 Fine-scale Spatial Genetic Structure and Dispersal 91 Sex-biased Dispersal 99 Discussion 104 Population Genetic Structure and Diversity 104 Dispersal Barriers 106 Fine-scale Spatial Genetic Structure and Dispersal 108 Sex-biased Dispersal 109 Conservation Implications 113 CHAPTER 3 CONCLUSION 117 Broad-scale Management Questions 118 What is the current genetic structure of remnant cottontail populations and how genetically differentiated are those populations? 118 How has fragmentation at a range-wide scale influenced remaining cottontail populations? 119 ix How will current effective population size and genetic diversity affect cottontail persistence across the region? 121 What are the conservation genetic implications for future management practices? E.g. Should cottontails be translocated among populations? 122 Fine-scale Management Questions 123 Is current gene flow and genetic diversity sufficient to sustain cottontail populations in southern Maine and seacoast New Hampshire? 123 Are there landscape barriers to gene flow that will require mitigation? 125 How does fragmentation at a landscape scale affect cottontail dispersal and genetic structure? 126 Is dispersal sex-biased, and how will that affect management? 128 APPENDICES 131 Appendix I: Additional considerations for the genetic conservation of the New England cottontail 132 Reintroductions 133 Translocations 134 Captive Breeding 135 Appendix II: Additional information for non-geneticicsts: summary of genetic programs terms 138 Summary of genetic programs 138 Explanation of genetic terms 146 LITERATURE CITED 150 x LIST OF TABLES Table 1.1
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