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Molecular Markers Such As Mitochondrial DNA and Microsatellite Alleles Have Been Used to Study Population Genetic Structure in Avian Taxa

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Molecular Markers Such As Mitochondrial DNA and Microsatellite Alleles Have Been Used to Study Population Genetic Structure in Avian Taxa PHYLOGEOGRAPHIC ANALYSIS OF PURPLE SANDPIPERS (CALIDRIS MARITIMA) AS REVEALED BY MITOCHONDRIAL DNA AND MICROSATELLITES by Nathalie M. LeBlanc Thesis submitted in partial fulfillment of the requirements for the Degree of Master of Science (Biology) Acadia University Fall Graduation 2015 © Copyright by Nathalie Marie LeBlanc, 2015 This thesis by Nathalie M. LeBlanc was defended successfully in an oral examination on September 15, 2015. The examining committee for the thesis was: __________________________ Dr. Michael Robertson, Chair __________________________ Dr. David Toews, External Reader __________________________ Dr. Marlene Snyder, Internal Reader __________________________ Dr. Mark Mallory, Co-supervisor __________________________ Dr. Don Stewart, Co-supervisor __________________________ Dr. Brian Wilson, Head This thesis is accepted in its present form by the Division of Research and Graduate Studies as satisfying the thesis requirements for the degree Master of Science (Biology). …………………………………………. ii I, Nathalie M. LeBlanc, grant permission to the University Librarian at Acadia University to reproduce, loan or distribute copies of my thesis in microform, paper or electronic formats on a non-profit basis. I, however, retain the copyright in my thesis. _________________________________ Nathalie LeBlanc, Author _________________________________ Dr. Don Stewart, Co-supervisor _________________________________ Dr. Mark Mallory, Co-supervisor _________________________________ Date iii Table of Contents Title.....................................................................................................................................i Approval of Thesis............................................................................................................ii Library release form.........................................................................................................iii Table of contents..............................................................................................................iv List of figures...................................................................................................................vi List of tables.....................................................................................................................vi Abstract...........................................................................................................................vii Acknowledgements........................................................................................................viii Chapter 1. Literature Review Overview.......................................................................................................................1 Application of biogeographic information data to the conservation biology of avian species................................................................................................................................1 The use of microsatellite DNA in phylogeographic studies.........................................6 Current trends in phylogeographic case studies............................................................8 Natural history of the Purple Sandpiper......................................................................12 Chapter 2. Genetic differentiation and phylogeography of Purple Sandpipers using mitochondrial markers. Introduction.................................................................................................................18 Methods.......................................................................................................................23 Results.........................................................................................................................33 Discussion...................................................................................................................41 iv Chapter 3. Genetic differentiation and phylogeography of Purple Sandpipers using nuclear microsatellite markers. Introduction.................................................................................................................62 Methods.......................................................................................................................66 Results.........................................................................................................................72 Discussion...................................................................................................................77 Chapter 4. General Discussion and Conclusions........................................................90 Literature Cited................................................................................................................91 v List of Figures (abbreviated captions) Figure 1. Range map of Purple Sandpipers................................................................54 Figure 2. Schematic diagram showing approximate annealing locations...................55 Figure 3. Maps of different breeding population groupings.......................................56 Figure 4. Rooted bayesian phylogenetic tree..............................................................57 Figure 5. Rooted maximum parsimony phylogenetic tree..........................................58 Figure 6. Rooted maximum likelihood phylogenetic tree..........................................59 Figure 7. Unrooted statistical parsimony haplotype network.....................................60 Figure 8. Mismatch distribution..................................................................................61 Figure 9. Mean Ln Likelihood values.........................................................................87 Figure 10. Below: Individual assignment...................................................................88 List of Tables (abbreviated captions) Table 1. List of primers...............................................................................................50 Table 2. Pairwise estimates of ΦST..............................................................................51 Table 3. Standard diversity estimates.........................................................................52 Table 4. Demographic statistics for breeding populations..........................................53 Table 5. Average success............................................................................................83 Table 6. Diversity estimates for 10 microsatellite loci...............................................84 Table 7. Pairwise estimates of FST...............................................................................85 Table 8. Pairwise estimates of Jost's D.......................................................................86 Table 9. P-values from Wilcoxon and mode-shift......................................................89 vi Abstract The Purple Sandpiper (Calidris maritima) is a medium-sized shorebird that breeds in the Arctic and winters along northern Atlantic coastlines. Due to difficulty in recapturing banded birds, migration routes and affiliations between breeding grounds and wintering grounds are poorly understood. Populations appear to be declining, and future conservation efforts for this species will benefit from a thorough understanding of their migration patterns. This study used two mitochondrial DNA markers and 10 microsatellite loci to analyze current population structure and demographic trends. Samples were taken from breeding locations in Nunavut, Iceland and Svalbard, representing all three putative subspecies, as well as wintering locations along the coast of Maine, Nova Scotia, New Brunswick, Newfoundland, and the United Kingdom. Mitochondrial haplotypes displayed low diversity, a shallow phylogeny and haplotype network. F-statistics show significant differentiation between Iceland, Svalbard, and Canada, as well as differentiation between Iceland/Svalbard and North American wintering populations. vii Acknowledgements This project would not have been possible without the generous contributions of Greg Robertson, Julie Paquet, Lindsay Tudor, Glen Mittelhauser, Mark Elderkin, Snaebjörn Pálsson, Ron Summers, Roger Bull, Michel Gosselin, and Pamela Mills, who provided the samples used in this study. Without their support we would not have been able to make use of such a large number of samples from such a wide variety of locations. I would like to thank my funding sources, NSERC and the STAGE program at Environment Canada. I would also like to thank the people who supported my research here at Acadia. My supervisors, Don Stewart and Mark Mallory, for funding and advice these past two years. My labmate Brent Robicheau for feedback and moral support, and Dr. Steve Mockford and Jose Lefebvre for lending their experience with microsatellite markers. I'd like to thank Lisa Taul for always being available for advice about administration and shipping, and my parents for supporting me through this venture. viii CHAPTER 1 Literature Review Overview This thesis is an analysis of the phylogeography and population genetic structure of breeding and wintering (migratory) populations of Purple Sandpipers, Calidris maritima Brunnich 1764. In this section of the thesis, I review how historical biogeographic information has been applied to questions of conservation biology in avian taxa and how various molecular markers such as mitochondrial DNA and microsatellite alleles have been used to study population genetic structure in avian taxa. More specifically, I also review the current state
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