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Clinostomus Elongatus) Conservation genetics of Redside Dace (Clinostomus elongatus): insights from environmental DNA and phylogeography A Thesis Submitted to the Committee on Graduate Studies in Partial Fulfillment of the Requirements for the Degree of Master of Science in the Faculty of Arts and Science TRENT UNIVERSITY Peterborough, Ontario, Canada © Copyright by Natasha R. Serrao 2016 Environmental and Life Sciences M.Sc. Graduate Program May 2016 Abstract Conservation genetics of Redside Dace (Clinostomus elongatus): insights from environmental DNA and phylogeography Natasha R. Serrao Recent range reductions of endangered species have been linked to urban development, increased agricultural activities, and introduction of non-native species. I used Redside Dace (Clinostomus elongatus) as a focal species to examine the utility of novel monitoring approaches, and to understand historical and contemporary processes that have influenced their present distribution. I tested the efficacy of environmental DNA (eDNA) to detect Redside Dace, and showed that eDNA was more sensitive for detecting species presence than traditional electrofishing. Parameters such as season, number of replicates, and spatial versus temporal sampling need to be accounted for when designing an eDNA monitoring program, as they influence detection effectiveness and power. I also assessed the species’ phylogeographic structure using both mitochondrial and microsatellite DNA analysis. The data from the microsatellite markers indicate that Redside Dace populations are genetically structured, with the exception of several populations from the Allegheny River basin. Combined sequence data from three mitochondrial genes (cytochrome b, ATPase 6 and ATPase 8) indicated that Redside Dace persisted within three Mississippian refugia during the last glaciation. Secondary contact between two lineages was indicated by both mitochondrial and microsatellite data. The combined results from the eDNA and conservation genetics studies can be used to inform Redside Dace recovery efforts, and provide a template for similar efforts for other aquatic endangered species. ii Keywords: Redside Dace (Clinostomus elongatus), endangered species, environmental DNA (eDNA), DNA, detection probability, conservation genetics, phylogeography iii Dedication This thesis is dedicated with love to my grandmother Rosy Serrao who passed away at the start of my degree. She was one of the most influential female figures in my life and I aspire to have her strength. I love you nana, and think about you all the time! iv Acknowledgements I am extremely grateful for all the amazing experiences and wonderful people I have had the opportunity to work with over the last three years. I have had the lab support and assistance from a number of talented individuals in the Fish Genetics Lab. I especially thank Maggie Boothroyd for being there to listen and offer advice during my entire degree, and being such a great friend to me. Kristyne Wozney has helped me with all aspects of my thesis, and has offered invaluable lab troubleshooting, as well as life advice along the way. I am grateful to Cait Nemeczek for teaching me how to do my first eDNA extraction, her friendship, and words of encouragement. I thank Caleigh Smith for help with everything microsatellite and mitochondrial, and always managing to put a smile on my face. I also thank Jenn Bronnenhuber and Anne Kidd for their insight and advice on various aspects of my project. I am very appreciative to Scott Reid’s Aquatic Endangered Species Research Team for all their help in the field, and collecting water samples for my project during Fall 2012. To Victoria Kopf, thank you for all your efforts for everything Redside Dace, teaching me to climb, and entertaining my terrible jokes. I wouldn’t have been able to survive this degree without your friendship and support. I would also like to thank Matt Sweeting for all his patience with me in the field; I could not have asked for a better person to have experienced my first field season with. I also thank Andrea Dunn and colleagues (Conservation Halton) for helping me collect buccal swabs at Sixteen Mile Creek. I would like to acknowledge all my American collaborators for going out into the field and collecting Redside Dace samples for my project. Douglas Carlson (New York v State Department of Environmental Conservation), Konrad Schmidt and Jenny Kruckenberg (North American Native Fishes Association), Holly Jennings (Forest Service) and John Pagel (Ottawa National Forest), Brant Fisher (Indiana Department of Natural Resources), Brian Zimmerman (Ohio State University), David Thorne and Isaac Gibson (West Virginia Division of Natural Resources), John Lyons (Wisconsin Department of Natural Resources), Nate Tessler (EnvironScience), and David Miko (Pennsylvania Fish and Boat Commission), Matthew R. Thomas (Kentucky Department of Fish and Wildlife Resources) generously provided samples that would otherwise have not been possible to collect. Additionally, Aaron Clauser (Clauser Environmental), Wayne Starnes (North Carolina State Museum of Natural Sciences), Aaron Snell (Streamside Ecological Services, Inc), and Douglas Fischer (Pennsylvania Fish and Boat Commission) also provided valuable advice during my project. I thank my mum and my dad for their unconditional love and support, and being there to help me with all four Peterborough moves! I wouldn’t be where I am without the values you have instilled in me. I thank my siblings Nicole and Daniel for providing comedic relief, and helping me through the final stretch of this degree. I am extremely grateful to Shannon Fera for her words of wisdom, and for taking me in under her wing and helping me through the initial rough patch of my graduate degree. I also thank Jessica Tomlin for her daily calls, editing thesis drafts, and 17 years of sustained friendship- I am so lucky to have you in my life! Lauren Banks, Tim Bartley, Ryan Franckowiak, Bob Hanner, Christine Terwissen, Spencer Walker, Cristen Watt also deserve special thanks for valuable insight into various aspects of my project. vi Lastly, I would like to thank my graduate committee for all their help and guidance over my three years. I thank Al Dextrase for his patience, hours of hands-on help with occupancy modelling, and always being there to help despite short notice. I thank Joanna Freeland for her speedy feedback, attention to details, and for her words of encouragement during my project. I am appreciative to Scott Reid for providing me with the field technical support, and teaching me the importance of being a professional. You are a brilliant research scientist and I am grateful to have had the opportunity to work with you. To Chris- thank you for your mentoring, life counselling, and for helping me grow. Your friendship has been one of my most valued ones at Trent and I have come to view you as my academic father. Thank you! vii Table of Contents Abstract ............................................................................................................................... ii Dedication .......................................................................................................................... iv Acknowledgements .............................................................................................................. v Table of Contents ............................................................................................................. viii List of Figures .................................................................................................................... xi Chapter 1: General introduction ........................................................................................... 1 References ............................................................................................................................ 8 Chapter 2 ............................................................................................................................ 15 Abstract .............................................................................................................................. 15 Introduction ........................................................................................................................ 16 Results ................................................................................................................................ 31 Discussion .......................................................................................................................... 35 References .......................................................................................................................... 40 Chapter 3 ............................................................................................................................ 57 Abstract .............................................................................................................................. 57 Introduction ........................................................................................................................ 58 Methods .............................................................................................................................. 63 Results ................................................................................................................................ 71 Discussion .......................................................................................................................... 78 References .........................................................................................................................
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