PHYLOGEOGRAPHY AND GENETIC STRUCTURING OF MOOSE (ALCES ALCES) POPULATIONS IN ONTARIO, 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 © Copyright by Glynis N. R. Price 2016 Environmental and Life Sciences Ph.D. Graduate Program May 2016 Abstract Phylogeography and Genetic Structuring of Moose (Alces alces) populations in Ontario, Canada Glynis N. R. Price Moose are an iconic species, known for their large size and impressive antlers. Eight subspecies are classified in circumpolar regions of the planet - four in North America. Two subspecies are similar in shape and size, the north-western moose (Alces alces andersoni) and the eastern moose (Alces alces americana). It was previously believed that these two subspecies meet in northern Ontario. Earlier genetic population studies used a small number of samples from Ontario, primarily in broad studies covering all of North America. A comprehensive genetic study of moose populations in Ontario has not previously been conducted. We examined the genetic diversity and population structure at 10 polymorphic loci using 776 samples from Ontario, as well as outgroups from representative populations – Manitoba/Cape Breton, representing A. a. andersoni, and New Brunswick/Nova Scotia, representing A. a. americana. Results indicated three genetic populations in the province, in north-western Ontario, north-eastern Ontario and south-central Ontario. RST values, compared against both FST and Jost’s D values for phylogenetic analyses, indicated no phylogenetic pattern which suggests no subspeciation present in the province. ii Population movement patterns in Ontario were studied. Gene flow was estimated using genetic and spatial data. Isolation by distance was only seen within the first distance class of 100 kilometres and then not seen again at further distances, indicating that moose display philopatry. There were very few migrants travelling across the province, with a greater number moving gradually north and west, towards better habitat and food sources. A forensic database in the form of an allele frequency table was created. Three loci showed very low levels of heterozygosity across all three populations. Probability of identity was calculated for the three populations and quantified. Samples with known geographic origins were run against the database to test for sensitivity, with identification of origin occurring at an accuracy level between 87 and 100%. Within Ontario, there are not two different subspecies, as previously believed, but two different populations of the same subspecies meeting in northern Ontario. The genetic data does not support previous research performed in Ontario. The sample sizes in our research also provide a more comprehensive view of the entire province not seen in any previous studies. The comprehensive research enabled the building of a reliable forensic database that can be used for both management and forensic purposes for the entire province. Keywords: Moose, Ontario, phylogeography, subspecies, genetic diversity, Alces alces, migration, forensic database iii Preface This dissertation is written in article format. Chapters 2-4 are in preparation for peer- reviewed journals. Experimental design, analyses, and manuscript preparation were all carried out by the Ph.D. candidate. Dr. Cornelya Klutsch helped with the DAPC analyses. iv Acknowledgements “I can no other answer make but thanks, and thanks, and ever thanks.” William Shakespeare, Twelfth Night, Act 3, Scene 3 I am grateful to many people for supporting me through this journey. First, I would like to thank my supervisory committee, Jeff Bowman and Dennis Murray. Thanks to my supervisors: Barry Saville, for helping me finish my thesis; Paul Wilson, for providing me with this opportunity and for his financial contributions; and Marie-Josée Fortin, for her support, valuable feedback and courage along the way. Thanks to all of my funders, along with the many hunters and MNRF conservation officers who enthusiastically provided me with the numerous samples. I would also like to thank Cornelya Klutsch for her help with some of my statistical analyses. I would like to thank my parents for their endless support, patience, editing skills and understanding. It has been quite the journey, and they have made the entire trip with me. Thanks to Glen Hawkins and Joseph Warren for their interest and advice. A huge thankyou to Linda Cardwell for her support, as well as being a conscientious advocate for her students. I also want to acknowledge the Happy PhD Club: Eunice, Megan and Andrea - the final piece of our puzzle is now in place. To Karen McQuade Smith, Lindsay Thompson and Sharon Beaucage-Johnson - thanks to all of you for lending me your ears and giving me some great suggestions. There are many others to whom I owe thanks for their support over the years: to Brandie Bugiak for always being there, letting me vent and helping me laugh. Thanks to Mandy Juby-Livings and Bill Juby for v providing distractions and encouragement, both in person and across the country, and to my sisters, Adrienne and Megan, and my extended family and friends. Finally, a huge thankyou to Derek Winterhalt, for being my resident supporter, my sounding board, an avid fan of “Meese” . and for keeping me grounded. vi Funders NSERC Ontario Ministry of Natural Resources and Forestry Ontario Federation of Anglers and Hunters Trent University vii Table of Contents Abstract ..................................................................................................................................... ii Preface ..................................................................................................................................... iv Acknowledgements .................................................................................................................. v Funders ................................................................................................................................... vii List of Commonly used Abbreviations and Acronyms ........................................................... x List of Tables ........................................................................................................................... xi List of Figures ......................................................................................................................... xii Chapter 1: General Introduction .............................................................................................. 1 References .......................................................................................................................... 13 Chapter 2 - Genetic structure of moose (Alces alces) in Ontario, Canada ....................... 16 Abstract ............................................................................................................................... 16 Introduction ......................................................................................................................... 17 Methods ............................................................................................................................... 20 Results................................................................................................................................. 23 Discussion ........................................................................................................................... 26 Conclusion .......................................................................................................................... 29 References .......................................................................................................................... 31 Figure Legend ..................................................................................................................... 37 Chapter 3 – Spatial and genetic structure of moose (Alces alces) populations in Ontario, Canada: Implications for Management................................................................................. 42 Abstract ............................................................................................................................... 42 Introduction ......................................................................................................................... 43 Methods ............................................................................................................................... 50 Results................................................................................................................................. 53 Discussion and Conclusions.............................................................................................. 54 References .......................................................................................................................... 58 Figure Legend ..................................................................................................................... 63 Chapter 4 – Resolution of regional populations of moose (Alces alces) in Ontario - formation of forensic genetic database ................................................................................ 70 Abstract ............................................................................................................................... 70 Introduction ........................................................................................................................