GENETIC STRUCTURE AND CONNECTIVITY OF THE ENDANGERED BUTLER’S GARTERSNAKE (THAMNOPHIS BUTLERI) ACROSS THE FRAGMENTED LANDSCAPE OF SOUTHWESTERN ONTARIO By Megan Elizabeth Snetsinger A thesis submitted to the Graduate Program in Biology in conformity with the requirements for the degree of Master of Science Queen’s University Kingston, Ontario, Canada (September, 2017) Copyright © Megan Elizabeth Snetsinger, 2017 Abstract Genetic patterns in many species are affected by environmental features that may enable or obstruct gene flow. Geographical isolation of conspecific individuals by uninhabitable expanses can lead to genetic separation. For species impacted by human activities, understanding how they interact with their environment can promote re-establishment of population connectivity and conservation. Thamnophis butleri (Butler’s gartersnake) is an Endangered species in Ontario, its range comprising three disjunct regional populations: Essex County, Lambton County, and Luther Marsh. Thamnophis butleri is a specialist of wetland-adjacent grassland-type habitat, thus its distribution is constrained by Southwestern Ontario’s largely agricultural landscape. Genetic differentiation among populations inhabiting these isolated regions was shown in a single previous study. I explored genetic structure more comprehensively, augmenting the geographic sampling and deploying landscape genetics approaches. In my first data chapter, I tested for population differentiation in both T. butleri and the generalist Thamnophis sirtalis sirtalis (eastern gartersnake) where the congeners occur sympatrically in Ontario. Assignment analyses revealed clear genetic structure within T. butleri, with clusters corresponding to geographical regions: one each in Lambton and Luther Marsh, and two in Essex, one along the shoreline and another in LaSalle, ON and the Ojibway Prairie Complex. Dispersal by river, either aquatically or along riparian corridors, may facilitate connection in the Lambton and Essex shoreline clusters, while the Ojibway/LaSalle cluster may have no need to disperse (occurring in good-quality habitat) or be impeded from dispersing by intervening urban areas. In contrast, I found that T. s. sirtalis comprises a single genetic ii population, implying that its generalist ecology allows for dispersal through this heavily altered landscape. In my second data chapter, I explored the relationship between patterns of T. butleri genetic differentiation and landscape composition across its Canadian range, using Mantel-based methods to test the correlation along either uniform or habitat-delineated distance matrices. The relationship between landscape and genetics varied among regional populations, from resistance- based in Lambton to distance-based in Essex. Treating open water as a potential impediment or facilitator of dispersal did not alter my conclusions, raising the possibility of aquatic dispersal that may occur at a different spatial scale than terrestrial dispersal. iii Co-authorship Authorship of data chapters: Comparing the population structure of the specialist Butler’s gartersnake (Thamnophis butleri) and the generalist eastern gartersnake (Thamnophis sirtalis sirtalis) in Ontario Snetsinger, Megan, Jeffrey R. Row, Megan E. Hazell, Dennis Plain, and Stephen C. Lougheed Landscape genetics of Butler’s gartersnake (Thamnophis butleri) in Ontario Snetsinger, Megan, Jeffrey R. Row, Megan E. Hazell, and Stephen C. Lougheed Co-authors: Megan Snetsinger Researched and wrote thesis document, planned and led 2015 & 2016 field seasons, performed lab work, ran analyses Dr. Stephen Lougheed Financial contribution: funded field visits, lab work Intellectual contribution: advised project progression, edited drafts Dr. Jeffrey R. Row Intellectual contribution: advised on project progression, designed R code for landscape analysis, edited drafts Megan E. Hazell Collection contribution: provided DNA samples from Amec project in Essex Intellectual contributions: advised project progression, edited drafts Dennis Plain Collection contribution: collected majority of Aamjiwnaang and other Lambton County samples, provided local information on Butler’s gartersnakes iv Acknowledgements Project design • Dr. Stephen Lougheed has been my supervisor through the long haul, and I must thank him for taking me on and giving me this opportunity to delve into this fantastic field of research. • Thanks to Jeff Row and Megan Hazell, my co-authors, for working with me on making this thesis what it is today. • I’d also like to thank the members of my committee, Dr. Vicki Friesen and Dr. Shelley Arnott, for making it to all my committee meetings, and for the suggestions that helped develop my project into a model piece of research. Field sampling • First and foremost, I must thank Aamjiwnaang First Nation for the continued collaboration on this project: Dennis Plain and Justin Waters for running most of the 2014 field season and for helping us collect samples in 2015, and Sharilyn Johnston for the coordination that made all this possible. • Thank you to my field assistants Tori Brown (who kept me sane), Mary Alice Snetsinger (best mom ever), Henry Wang, Louisa Kennett, and Mark Szenteczki for being fast on your feet and subjecting your pants to grass stains in the pursuit of the snakes. • Thank you to everyone who provided me with supplementary DNA samples: Erin Carroll from St. Clair Region Conservation Authority (SCRCA) for sharing a small piece of the demo Butler’s gartersnake, Dan Noble and Jon Choquette for the leftover samples from their study, Megan Hazell and her team at Amec Foster Wheler for the many Windsor samples, Steve Lougheed and Jeff Row for doing quick field runs, and the anonymous researchers who collected the samples in the Lougheed Lab tissue database. • Thanks also go to Dan Choquette, Steve Marks, Nick Scobel, and the folks who put together the NHIC database for the help figuring out where to look for snakes. • Thank you to Sarah Fraser, Kathy Richardson, Anne Marie Laurence, Erin Hellinga, Emilee Hines, and Catherine Jong at the Ontario Ministry of Natural Resources and Forestry (OMNRF) for helping me acquire permission to catch and sample my snakes. Thank to Thomas Goniea at the Michigan Department of Natural Resources (MDNR) for the same. • Thank you to everyone who gave me permission to access public and private lands to look for snakes: Laura McLean (OMNRF), Crystal Allen, Tony Zammit, and Derek Strub (Grand River Conservation Authority), Erin Carroll, Kelli Smith, and Shane White (SCRCA), Sharilyn Johnston and Dennis Plain (Aamjiwnaang First Nation), Dan Lebedyk and Kathryn Arthur (Essex Region Conservation Authority), Greg Norwood and Jody DeMeyere (Detroit River International Wildlife Refuge), Paul Muelle and Paul Cypher (Huron-Clinton Metroparks), v Alicia Ihnken (MDNR), and Jim Kroetsch, Jeff Currier, and Adam Armaly (CH2M), Jim Gallaway, Jon Choquette, and Eric Jolin (private property access). • I’d also like to thank all the people who helped out here and there with the field work: Kelli Smith and the rest of the field team at SCRCA, Jared Fedora, and Christopher Moser-Purdy for joining in on one-off field visits; and Dr. Oliver Love from the University of Windsor, for giving me extra collection tubes when I ran out in the field. Lab work and analysis • I would like to thank everyone in the Lougheed lab who gave me advice and guidance in the lab, particularly Mark Szenteczki who taught me the essentials from the ground up when I began my project. • Thank you to all the assistants who helped me streamline the lab process, mainly Erin Suenaga and Tori Brown. • A big thanks to Zhengxin Sun for genotyping my thousands of PCR runs, and for troubleshooting the problem areas. • And thank you to those who gave me advice on what analyses to do and how to do them, particularly to Mark Szenteczki for showing me how to read my microsatellite results, Becky Taylor for her advice and help with Arlequin, and Jeff Row for getting me through the landscape analysis R code. Funding • Thank you to the folks at the Species at Risk Research Fund for Ontario for funding the first year of my research. • And thank you to my supervisor Dr. Lougheed for making up the rest with his grant from the Natural Science and Engineering Research Council of Canada. Emotional support • I really appreciate the love and support from all my friends and family – it really helped me drag myself through the three years of this project. Shout-outs go to Jen, Dionne, Austin, Steve M., Jake, and Hayley. And especially to my parents, who (almost) never thought I’d end up a career student. • I want to give a final recognition to Patt Austin, who just passed away this summer. Despite being deathly afraid of snakes, she supported my passion for them throughout my whole life. • And at last, thanks to our friend the Butler’s gartersnake! vi Table of Contents Abstract ........................................................................................................................................... ii Co-authorship ................................................................................................................................. iv Acknowledgements ......................................................................................................................... v Table of Contents .......................................................................................................................... vii List of Figures ...............................................................................................................................