Western University Scholarship@Western Electronic Thesis and Dissertation Repository 9-5-2013 12:00 AM Genetic and morphological variation of butterflies in elictr habitats Lindsay A. Crawford The University of Western Ontario Supervisor Dr. Nusha Keyghobadi The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Doctor of Philosophy © Lindsay A. Crawford 2013 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Ecology and Evolutionary Biology Commons Recommended Citation Crawford, Lindsay A., "Genetic and morphological variation of butterflies in elictr habitats" (2013). Electronic Thesis and Dissertation Repository. 1600. https://ir.lib.uwo.ca/etd/1600 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Genetic and morphological variation of butterflies in relict habitats (Thesis format: Integrated Article) by Lindsay Ann Crawford Graduate Program in Biology with Environment & Sustainability A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy The School of Graduate and Postdoctoral Studies The University of Western Ontario London, Ontario, Canada © Lindsay A. Crawford 2013 Abstract Habitat fragmentation and loss are leading threats to global biodiversity and can alter patterns of dispersal, population dynamics, and genetics with implications for long-term species persistence. Most habitat fragmentation research has focused on recently fragmented species that historically occupied interconnected habitat patches. We know comparatively little about how naturally fragmented species may respond to habitat loss. For these species, local habitat patch quality may influence the dynamics and genetics of populations more than the structure of the surrounding landscape (e.g., degree of isolation of suitable habitat). I examined aspects of the ecology and evolution of populations inhabiting fragmented landscapes, using two butterfly species representing relict populations that are 1) recently fragmented by anthropogenic activities (Mormon metalmark, Apodemia mormo), and 2) naturally fragmented (bog copper, Lycaena epixanthe). I assessed patterns of genetic (amplified fragment length polymorphism, AFLP) and flight-related morphological variation, and their relationship to measures of surrounding landscape structure and local habitat quality. Population genetic analysis of the anthropogenically fragmented Mormon metalmark revealed a high degree of spatial genetic structure, indicating limited gene flow, despite a small geographic scale (<20 km). Management of this endangered population should focus on increasing connectivity among the most isolated sub-populations and through urban areas. For the naturally fragmented bog copper, genetic diversity was explained by variables related to patch quality rather than landscape structure. Movement ability in the bog copper (inferred by flight morphology) appeared to depend on both local habitat conditions and the surrounding landscape. Also, using an AFLP-based genome scan approach, I identified signatures of selection in the bog copper associated with fine-scale landscape heterogeneity. ii My work on the bog copper highlights the importance of considering the effects of local habitat conditions, in addition to habitat isolation, for conservation of fragmented populations. Finally, I also reviewed the current literature (470 articles) to evaluate the quality of AFLP data used in ecological and evolutionary research. I discovered a pervasive lack of consistency and transparency in both the methods used to assess data reproducibility, and in the details of methodology presented. This work has identified an important publishing gap in molecular ecology research. Keywords Amplified fragment length polymorphism, Adaptive genetic variation, Apodemia mormo, Conservation genetics, Flight morphology, Fragmented habitats, Genetic diversity, Genotyping error rate, Habitat fragmentation, Habitat quality, Host plant, Isolation, Landscape heterogeneity, Lepidoptera, Lycaena epixanthe, Mobility, Outlier loci, Population genetics, Relict, Specialist. iii Co-Authorship Statement A version of Chapter 2 was published in Molecular Ecology with Daria Koscinski and Nusha Keyghobadi as co-authors. Dr. Koscinski and Dr. Keyghobadi contributed to study design, helped with data interpretation and provided editorial comments on the manuscript. A version of Chapter 3 was published in Conservation Genetics with Sylvie Desjardins and Nusha Keyghobadi as co-authors. Dr. Desjardins provided logistical support in the field, and both co-authors contributed to study design, provided access to equipment, helped with data interpretation and provided editorial comments on the manuscript. Chapters 4 - 6 are co-authored with Nusha Keyghobadi who contributed to study design, provided equipment, helped interpret data and provided editorial comments on the manuscripts. iv Acknowledgments First and foremost I would like to thank my supervisor Dr. Nusha Keyghobadi for her invaluable support and guidance throughout my degree. You have been an influential mentor to me both academically and personally, and I consider your leadership something to aspire to. To all the members of my lab, past and present: Liam Frappe, Heidi Keller, Chung-Yung (Christina) Kim, Dr. Daria Koscinski, Sheri Maxwell, Katie Millette, John O’Leary, Dr. Gordana Rasic, Noah Shapiro, Jenna Siu, Eliot Winkler and Kristina Zilic, thank you for your friendship and support. You have made my graduate experience truly special and something that I will always look back on with fond memories. In particular I would like to thank Sheri for teaching me the ins and outs of working with AFLPs and Katie for helping me to learn how to navigate the daunting world of R and model selection analyses. As well, I am deeply grateful to Daria whose collaboration, mentorship and friendship has been central to all my successes throughout my degree. I would also like to thank the members of my advisory committee both past and present: Dr. Beth MacDougall-Shackleton, Dr. Brock Fenton, Dr. Cheryl Pearce and Dr. Adam Yates. Your valuable advice and expertise has greatly contributed to the development of my project. I have been very lucky to have had the chance to work with many wonderful people throughout my degree and would like to thank all of the volunteers and research assistants who have helped with my lab and field work: Wesley Chick, Amy Dang, Jenna Donald, Orville Dyer, Jared Hobbs, Curtis Irvine, Heidi Keller, Chung-Yung (Christina) Kim, Katie Millette, George Pang, Kevin Schreiber, Dennis St-John, Lucy Reiss, Sue Seddon, Katelyn Weaver and Katie White. As well I am also extremely appreciative to the following people v who offered technical and logistical support, service and access to equipment as well as provided valuable advice towards my project: Dr. Brian Branfireun, Jason Dromboskie, Aren Fischer, Jennifer Hillyer, Angela Marinas, Dr. Jeremy McNeil, Justin Peters, Alan Noon, Dr. Brent Sinclair, Rick Stronks and the staff at Harkness Laboratory for Fisheries Research. Financial support for myself and this research project was generously provided by The Centre for Environment and Sustainability, Canada Research Chairs Program, Government of Ontario, National Sciences and Engineering Research Council of Canada, The Xerces Society for Invertebrate Conservation, The University of Western University Department of Biology, Malcolm Ferguson Award in Life Science, and a partnership of the World Wildlife Fund and Environment Canada. Finally, thank you to my family especially my parents Rob and Debbie, my sister Katie, my brother Scott and my parents-in-law Ian and Dianna for their constant love and encouragement. As well, I am forever indebted to my parents who fostered my curiosity about the natural world and who have always encouraged and provided support for me to pursue an education and career that challenges and excites me. To my husband Ross, throughout the trials and tribulations of my project, you have provided me with unwavering support and motivation to face my challenges. You have helped me to find pride in my accomplishments and confidence in times of self-doubt. This thesis would not have been possible without you and I thank you for your love and support. vi Table of Contents Abstract ............................................................................................................................... ii Co-Authorship Statement................................................................................................... iv Acknowledgments............................................................................................................... v List of Tables .................................................................................................................... xii List of Figures .................................................................................................................. xvi List of Appendices ......................................................................................................... xviii List of Symbols and Abbreviations.................................................................................. xix List of Software