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Conservation Genetics of Woodland Caribou in The CONSERVATION GENETICS OF WOODLAND CARIBOU IN THE CENTRAL BOREAL FOREST OF CANADA A dissertation submitted to the Committee on Graduate Studies in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Faculty of Arts and Science TRENT UNIVERSITY Peterborough, Ontario, Canada (c) Copyright by Laura M. Thompson 2015 Environmental and Life Sciences Ph.D. Graduate Program May 2015 ABSTRACT CONSERVATION GENETICS OF WOODLAND CARIBOU IN THE CENTRAL BOREAL FOREST OF CANADA Laura M. Thompson Maintaining functional connectivity among wildlife populations is important to ensure genetic diversity and evolutionary potential of declining populations, particularly when managing species at risk. The Boreal Designatable Unit (DU) of woodland caribou (Rangifer tarandus caribou) in Ontario, Manitoba, and Saskatchewan has declined in southern portions of the range because of increased human activities and has been identified as 'threatened' by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). In this dissertation, I used ten microsatellite DNA markers primarily from winter-collected fecal samples to delineate genetic structure of boreal caribou in declining portions of the range and increase understanding of the potential influence of the non-threatened Eastern Migratory DU of woodland caribou on genetic differentiation. Eastern migratory caribou are characterized by large home ranges compared to boreal caribou and migrate seasonally into portions of the Boreal DU range. A regional- and local-scale analysis using the spatial Bayesian clustering algorithm in program TESS delineated four regional clusters and 11 local clusters, with the majority of local clusters occurring along the southern periphery of the range. One of those clusters in Ontario corresponded spatially with the seasonal overlap of boreal and eastern migratory caribou and was characterized by substantial admixture, suggesting that the two DUs could be interbreeding. Next, I decoupled the impacts of historical and contemporary processes on genetic structure and found that historical processes were an ii important factor contributing to genetic differentiation, which may be a result of historical patterns of isolation by distance or different ancestry. Moreover, I found evidence of introgression from a currently unsampled population in northern Ontario, presumably barren-ground caribou (R. t. groenlandicus). Finally, because our analysis suggested recent processes were also responsible for genetic structure, I used a landscape genetics analysis to identify factors affecting contemporary genetic structure. Water bodies, anthropogenic disturbance, and mobility differences between the two DUs were important factors describing caribou genetic differentiation. This study provides insights on where conservation and management of caribou herds should be prioritized in threatened portions of the boreal caribou range and may have implications for future delineation of evolutionarily significant units. Keywords: Approximate Bayesian computation, Bayesian clustering model, boreal forest, Canada, Designatable Unit, gene flow, genetic structure, microsatellite DNA, landscape genetics, landscape resistance, Rangifer tarandus, woodland caribou iii To my father, Robert M. Thompson, Jr. for teaching me that anything is possible iv PREFACE The chapters in this dissertation will be submitted to peer-reviewed journals and each has, therefore, been written in manuscript format. Some redundancy among chapters occurs, particularly in the introduction sections, and the use of "we" has been used where appropriate because the work was conducted in collaboration with others. The co-authors have been listed at the beginning of each chapter. v ACKNOWLEDGEMENTS I would like to thank my Ph.D. advisors Drs. Paul Wilson and Micheline Manseau for giving me the opportunity to come and study caribou in the "Great White North". It has been a wonderful experience and I have truly grown both professionally and personally as a result. My committee members Drs. Bruce Pond and Jim Schaefer provided valuable advice and support along the way and I am very grateful to them. I am also thankful for the many people who helped in the lab, including Taryne Chong, Marina Kerr, and Karen Smith. I would like to thank the other students, post docs, and research associates working on caribou, including Laura Finnegan, Paul Galpern, Peter Hettinga, Sones Keobouasone, and Cornelya Klütsch, for providing consultation and encouragement. The work by Mark Ball carved the path for my study and I am grateful for his contributions. Additionally, this study would not have been possible without the many people who provided caribou DNA samples, funds for this project, and expertise on caribou biology, including Ken Abraham, Glen Brown, Natasha Carr, Chris Chenier, Peter Davis, Steve Kingston, Gerry Racey, and Art Rodgers from Ontario Ministry of Natural Resources, Dennis Brannen, Dale Cross, Vicki Trim, and Kent Whaley from Manitoba Conservation, Al Arsenault, Gigi Pittoello, and Tim Trottier from Saskatchewan Ministry of the Environment, and Dan Frandsen, Fiona Moreland, Richard Pither, and Norman Stolle from Parks Canada. The Natural Sciences and Engineering Research Council of Canada and Manitoba Hydro were also important contributors. I would like to thank Natasha Carr and Steve Kingston for my first helicopter trip and allowing me to enjoy the beautiful Lake Superior coast scenery. Vicki Trim took me on my first ice-fishing expedition in Thompson, Manitoba and we enjoyed fantastic vi walleye (or pickerel?). Also, a big thanks goes out to Gerry Racey for the magical trip to Webequie. I owe a debt of gratitude to the wonderful people I met along the way, in addition to those mentioned above (in alphabetical order): John Benson, Jim Castle, Andrea Cee, Cindy Chu, Mark and Heather Dzurko, Danielle Ethier, Fritz Fischer, Tina Fridgen, Colin Garroway, Matt Harnden, Josh Holloway, Megan Hornseth, Karen Hussey, Eric Koen, Karen Loveless, Stacey Lowe, Andrea Maxie, Erica Newton, Agnes Pelletier, Jenn Paul, Lucy Poley, Stephen Petersen, Glynis Price, Erin Rees, Terin Robinson, Jeff Row, Chris Sharp, Lindsay Spenceley, Lindsay Thomson, Aaron Walpole, Kaitlin Wilson, and Joanna Zigouris. I would also like to thank my friends from the Peterborough Ultimate League. My previous mentor, Dr. Scott Schlarbaum, has been a guiding light along the way. I'm also thankful for my current supervisors Drs. Shawn Carter and Doug Beard who have provided a tremendous amount of support while I worked on my degree. A special thanks goes to Cindy Thatcher for reviewing earlier drafts of my dissertation chapters. Finally, I would not be at this stage in my career or in life without my wonderful family. I love you all so much! You too, Wayah! vii TABLE OF CONTENTS ABSTRACT ............................................................................................... ii PREFACE .................................................................................................. v ACKNOWLEDGEMENTS ...................................................................... vi LIST OF FIGURES ................................................................................. xii LIST OF TABLES .................................................................................. xiv CHAPTER 1. GENERAL INTRODUCTION ........................................ 1 1.1 Background ................................................................................................................ 1 1.2. General Problem Statement ..................................................................................... 4 1.3. Justification ............................................................................................................... 7 1.4. Objectives................................................................................................................... 8 1.5. References .................................................................................................................. 9 CHAPTER 2. DELINEATING GENETIC STRUCTURE OF WOODLAND CARIBOU IN THE CENTRAL BOREAL FOREST OF CANADA ...................................................................................................19 2.1. Abstract .................................................................................................................... 20 2.2. Introduction ............................................................................................................. 21 2.3. Methods .................................................................................................................... 24 2.3.1. Study area and sampling ................................................................................... 24 2.3.2. Genotyping ........................................................................................................ 26 2.3.3. Measuring genetic structure ............................................................................. 27 2.3.4. Analysis of genetic groups ................................................................................ 30 viii 2.4. Results ...................................................................................................................... 31 2.4.1. Study area, sampling, and genotyping .............................................................. 31 2.4.2. Measuring genetic structure ............................................................................. 32 2.4.3. Analysis of genetic
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