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EAGLES by MEGAN E. JUDKIN CONSERVATION GENOMICS OF NORTH AMERICAN BALD (HALIAEETUS LEUCOCEPHALUS) AND GOLDEN (AQUILA CHRYSAETOS) EAGLES By MEGAN E. JUDKINS Bachelor of Arts/Science in Natural Resources Ecology and Management Oklahoma State University Stillwater, OK 2005 Master of Business Administration Marylhurst University, Marylhurst, Oregon 2012. 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, 2017 CONSERVATION GENOMICS OF NORTH AMERICAN BALD (HALIAEETUS LEUCOCEPHALUS) AND GOLDEN (AQUILA CHRYSAETOS) EAGLES Dissertation Approved: Dr. Ronald A. Van Den Bussche Dissertation Adviser Dr. Jim Lish Dr. Meredith Hamilton Dr. Andrew Doust Outside Committee Member ii ACKNOWLEDGEMENTS There are a number of people that I must thank who made my dissertation possible and who supported me throughout this journey. To Victor Roubidoux who has supported all of my ideas in an effort to make the Grey Snow Eagle House the best it can be, thank you for allowing the bald and golden eagle conservation partnership between the Iowa Tribe of Oklahoma and the Van Den Bussche Lab to happen. Without your support, this project would have never been able to transform into the success that it is today. I also must express my deepest thanks and appreciation to Ron Van Den Bussche for taking a chance on this initially unfunded project that was fueled by the passion of three people who understand the importance of the conservation of eagles. I must also thank Ron for all the time, effort, and knowledge shared throughout the last six years that built me into the researcher and person I am today. To both Ron and Victor, I greatly appreciate that both of you trusted that I could handle both my management position at the aviary while I pursued this degree, so I did not have to choose between the two opportunities. I must also thank the many individuals that provided me with knowledge and a willingness to collaborate. My committee members Dr. Andrew Doust, Dr. Meredith Hamilton, Dr. Jim Lish have provided a wealth of knowledge gained through courses taken, teaching assistantship opportunities, and conversations that cannot be replaced. Your kind words and support, even with just a hello in the hall, helped me continue iii Acknowledgements reflect the views of the author and are not endorsed by committee members or Oklahoma State University. throughout my day. Furthermore, I am greatly appreciative of the overwhelming support from researchers, biologists, veterinarians, and wildlife rehabilitators from around the country who have provided their years of experience in eagle conversation as well as samples to my project. Without their help, my project would not have been able to have its range wide perspective. Throughout my PhD, my family, friends, and husband have seen me through the good days and the bad. My family and friends always provided an ear to listen when things were not going quite as planned and cheered me on throughout all of my successes. To my parents, thank you for instilling in me an appreciation for knowledge and support as I have worked hard to achieve my dreams. To my husband, Tell, thank you for being my backbone throughout the last six years when balancing my job and dissertation left little spare time for other things. I cannot express how grateful I am to have had you by my side through this roller coaster ride. Finally, I must include my dogs, Shadow, Hunter, and Mattie, who willingly lost many hours of sleep staying up with me every night to ensure the day’s goals were met and who excitedly got me up the next morning to begin the day on time, regardless of how sleep deprived we were. iv Acknowledgements reflect the views of the author and are not endorsed by committee members or Oklahoma State University. Name: Megan E. Judkins Date of Degree: DECEMBER 2017 Title of Study: CONSERVATION GENOMICS OF NORTH AMERICAN BALD (HALIAEETUS LEUCOCEPHALUS) AND GOLDEN (AQUILA CHRYSAETOS) EAGLES Major Field: Zoology Abstract: Although eagles play pivotal roles in most Native Americans, First Nations, and Mesoamericans cultures and represent many countries around the world as the national symbol, these ecologically important predators still face many anthropogenic stressors. Stressors currently affecting bald and golden eagle populations include electrocution, habitat loss and degradation, lead poisoning, wind turbines, and disturbances. Despite the number of stressors these species face, neither of these species have been thoroughly studied from a genetic standpoint causing concern about the long-term conservation of these ecologically and culturally important species. To begin addressing the lack of genetic information about these species, each chapter addressed critical information that is lacking for both species. In Chapter 1, the Holarctic phylogeographic patterns, genetic variation, and demographic history of golden eagles in North America were assessed. The results indicated that there are two genetic lineages of golden eagles with only one Holarctic haplotype, there is little to no modern day gene flow between Nearctic and Palearctic golden eagles, and that the current distribution of haplotypes in the Nearctic reveal a recent population expansion with moderate levels of gene flow. For Chapter 2 and 3, a custom 100K SNP array was designed and subsequently used to assess the levels of the partitioning of genetic variation, SNPs under putative selection, and to begin the development of biologically sound management units. The results of both of the chapters revealed significant levels of genetic structure within the population and a list of putative SNPs under selection was developed. Finally, in Chapter 4, a population of bald eagles in New Jersey was evaluated to determine the nest turnover rate and relatedness of hatchling individuals in the population. Results show the population has high rates of inbreeding, moderate levels of nest turnover rates, and the presence of half sibling and unrelated relationships between individuals raised in the same nest in the same year. The findings of my research provide a new baseline of data for the conservation of bald and golden eagles. This information will be critical in the development of conservation management plans. v TABLE OF CONTENTS Chapter Page I. HOLARCTIC PHYLOGEOGRAPHY OF GOLDEN EAGLES (AQUILA CHRYSAETOS) AND EVALUATION OF ALTERNATIVE NORTH AMERICAN MANAGEMENT APPROACHES ................................................1 Abstract ....................................................................................................................1 Introduction ..............................................................................................................2 Materials and Methods .............................................................................................6 DNA Isolation and Sequence Development .....................................................6 Data Analysis .....................................................................................................8 Results ....................................................................................................................10 Phylogeographic Structure ...............................................................................11 Genetic Diversity .............................................................................................11 Genetic Structure .............................................................................................12 Population Fluctuations ...................................................................................13 Discussion ..............................................................................................................14 Conclusion .............................................................................................................18 Acknowledgements ................................................................................................19 Literature Cited ......................................................................................................20 Figure Legends.......................................................................................................26 II. CHARACTERIZATION OF GENETIC STRUCTURE AND ADAPTATION USING A 37K SNP ARRAY FOR GOLDEN EAGLES (AQUILA CHRYSAETOS) .....37 Abstract ..................................................................................................................37 Introduction ............................................................................................................38 Methods..................................................................................................................43 SNP Chip Development ...................................................................................43 Sample Selection ..............................................................................................45 Population Structure Assessment .....................................................................46 Relatedness and Population Genetics ..............................................................47 Outlier Detection ..............................................................................................48 Results ....................................................................................................................49 SNP Chip Development, Samples Scoring, and Error Rate ............................49 Population Structure.........................................................................................50
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