Conservation Genetic Implications of Microsatellite Variation in The
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Conservation Genetic Implications of Microsatellite Variation in the Muskox Ovibos moschatus: the Effect of Refugial Isolation and the Arctic Ocean on Genetic Structure Peter J. van Coeverden de Groot A thesis submitted to the Department of Bioiogy in conformity with the requirements for the degree of Doctor of Philosophy Queen's University Kingston, Ontario, Canada May, 2001 copyright O Peter J. van Coeverden de Groot, 2001 National Library Bibliothèque natiode of Canada du Canada Acquisitions and Acquisitions et Bibliographie Services services bibliographiques 395 Wellington Street 395, nie Wellington OttawaON KtAON4 OttawaON KiAW CaMda Canada The author has granted a non- L'auteur a accordé une licence non exclasive licence allowing the exclusive permettant à la National Lïbrary of Canada to Bibliothèque nationale du Canada de reproduce, loan, distribute or sell reproduite, prêter, distriiuer ou copies of this thesis in microfom, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/nlm, de reproduction sur papier ou sur format électronique. The author retains ownmhip of the L'auteur conserve la propriété du copyxight in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantial extracts Erom it Ni la thèse ni des extraits substantiels may be printed or othefwise de ceiie-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. To investigate the role Arctic Ocean water gaps play in impeding genetic exchange in muskoxen Ovibos moschatus and to conduct a genetic evaluation of current conservation and management plans for these animals, microsatellite polymorphism was examined across the range of the species. The low genetic variability in muskoxen meant that additional variable loci had to be cloned. Of 8 perfect and 9 hperfect di-nucleotide loci studied, pe~ectloci were found to be significantly more heterozygous than imperfect loci in this species. Thus average heterozygosity calculated from my increased sample of microsatellite loci was substantially higher than earlier estimates. Polymorphism at a subset of 14 microsatellite loci in 1 1 different muskox populations sampled across the Arctic showed that in spite of their larger numbers, Arctic Island muskoxen are much less variable than mainland conspecifics. In addition geneaiogical analyses suggest that mainland muskoxen constitute the sister group of two Arctic Island muskox lineages - the Northem Arctic Island (NAI) and Southem Arctic Island (SN) lineages. Refugial isolation on Banks Island during the Last Glacial Maximum of the Wisconsin may explain this pattern. Regression analyses of interindividual shared allele distance and geographic distance shows the Arctic Ocean does not consistently impede island muskoxen movement relative to mainland muskoxen. Multiple regession analysis suggests that Arctic Ocean watergaps generally expedite muskoxen movement in the more northem NAI muskcxen, while Generalized Mantel Analysis indicated different waterways can either retard or expedite muskoxen movement. This reflects ice conditions or width of individual watergaps. An evaluation of cumnt conservation practices found: 1) populations of the three major muskoxen lineages are conserved; 2) the most genetically diverse populations of Mainland and SAI muskoxen receive some protection; and 3) conservation areas are large enough to conserve the process of natural dispersal in NA1 and mainland muskoxen but perhaps not in SA1 muskoxen. The area of positive autocomlatiun frorn the autocorrelation of intenndividual genetic distance on geographic distance was used to estimate dispersa1 indirectly for the latter analysis. This thesis would not have been completed without the support and love of my wife Margaret - thank you. Many members of the Boag lab have helped in completing this project particularly Denise Michaud, Chad Davis, Linsey Mutch and Candace Scott. Steve Lougheed, Jim Austen and Andrew Check made the late evening work more enjoyable. The collection of samples was a large undertaking and in this regard Anne Gunn needs the heartiest of thanks for her expeditious charm in securing many samples. 1 would also like to thank S. Akeeagok, P. Aastmp, L. Coady, E. Coleman, M. Forchhammer, J. Hunter, J. Kuneyuna, T. Lockhardt, R. Mulder, J. Nishi, A. Williams for assistance with sarnple collection in Canada and Greenland. My field trips were funded by gants from the Northem Students Training Program (NTSP) with substantial support from the Polar Continental Shelf Project (PCSP) and by Peter Boag's NSERC grant. The substantial cos& of lab work was covered by Peter Boag's NSERC grant. Queen's University funded me through a Queen's Graduate Award and a Queen's Graduate Fellowship with additional support from Peter Boag's NSERC grant, Resources Wildlife and Economic Development (RWED) of the Northwest Temtories and Department of Sustainable Development in Nunavut. My parents Frans and Adrienne v. C. de Groot also helped me pursue this work. Thanks to Peter Boag who thought these were good ideas, helped me formulate them more precisely, and let me go after them - 1could not have asked for anymore. Also thanks to Tim Birt, Chris Eckert, Dolf Harmsen and Rowland Tinline for being on my cornmittee, Table of Contents Abstract Achwledgements iii Table of Contents List of Figures viii List of Tables Chapter 1 GENERAL INTRODUCTION AND LITERATURE REVIEW Two Conservation Concems for Wild Ungulates The muskox - a Unique Opportunity Genetic Variability and Sarnples Muskox Hierarchical Genetic Structure From Populations to Individuals The Effect of Waterways on Genetic Exchange in Muskoxen A Genetic Evaluation of Muskoxen Conservation and Management Molecular Evolution and Genetic Distance Thesis Organisation Chapter 2 MICROSATELLITE VARIABILITY IN TEE MUSKOX OVIBOS MOSCHATUS ABSTRACT INTRODUCTION Variable Muskox Microsatellite Loci Objectives METHODS Optimizing Microsateilite Primers for Ovibos moschatus Estimating Microsatellite Polyrnorphism in Muskoxen RESULTS AND DISCUSSION Factors Affecting Variability at Microsatellite Loci in Ovibos moscha~ General Implications ACKNOWLEDGEMENTS FiGWLEGENDS Chapter 3 MICROSATELLITE VARIATION IN THE MUSKOX OWBOS MOSCtlATUS: EVIDENCE OF ISOLATION IN A LATE WISCONSIN ICE FREE GLACIAL REFUGE ABSTRACT INTRODUCTION Late Wisconsin Ice - Free Refuges in Arctic North America Genetic differentiation in muskoxen Expectations fiom Models of Recent Muskox Diversification METHODS Sampling and DNA Extraction Microsatellite Typing Microsatellite Variability at the Sample Location Level Genealogical Relationships among Sample Locations Analysis of Muskox Lineages RESULTS Sample Location Microsatellite Diversity DISCUSSION Genetic Structure in Muskox Recent Muskox Diversification Evidence for the Diversibing Role of North American Arctic Refuges ACKNOWLEDGEMENTS FIGURE LEGENDS Chapter 4. THE ROLE OF THE ARCTIC OCEAN IN GENETIC EXCHANGE AMONG ISLAND MUSKOXEN OVIBOS MOSCHATUS: EVIDENCE FROM MICROSATELLITES ABSTRACT INTRODUCTION Genetic Exchange and Geographic Distance Different Genetic and Geographic Distance Relationships for Different Landscapes MEXHODS Samples And Their Geography Microsatellite Loci Analyses RESULTS Simple Linear Regression Multiple Regression Generalized Mantel Analysis Accounting for Genealogical Structure in Arctic Island Muskoxen DISCUSSION Summary of Findings 94 Interindividual Genetic Distance and Varying Geographic Scale 95 Two concems: Geographic Distance and Genetic polyrnorphism 96 The Varied role of The Arctic Ocean 97 Conclusions and Implications 100 ACKNOWLEDGEMENTS 102 FIGURE LEGENDS 103 Chapter 5 USING GENETICS TO EVALUATE CONSERVATION PRACTICES FOR MUSKOXEN OVIBOS MOSCHATUS: EVIDENCE FROM MICROSATELLlTES ABSTRACT INTRODUCTION Muskox Conservation: A Unique Large Ungulate Opportunity Cumnt Conservation and Management of Endernic Muskoxen Defining the Critena for Evaluation of Conservation and Management of Muskoxen A Genetic Evaluation of Current Conservation and Management METHODS Sarnples and their Geography Molecular Methods Analyses RESULTS Comparative Variability across AI1 Muskox Relative Contribution to Diversity Spatial Autocorrelation DISCUSSION The Recent History of Muskoxen Departures from QuasiStationarity - a Measure of Short Tem Equilibrium Genetic Evaluation of Current Conservation and Management of Muskoxen ACKNOWLEDGEMENTS FIGURE LEGENDS Chapter 6 GENERAL DISCUSSION AND SIJMMARY A Test of the Banks Island Refuge A Better Test for Arctic Ocean Watergaps The Relative Contribution of Males and Femdes to Dispersal Estimates Greatest Perceived Threats to Muskoxen Populations s-ary Literature Cited Appendices Appendix 1: 14 Locus genotypes for 172 muskoxen. Appendix 2: Two pairwise distance matrices. Appendix 3: Individuai Assignment probabilities for 172 muskoxen Appendix 4: Assignment Matrix of 172 rnuskoxen to three major rnuskox lineages. Appendix 5: Likelihood distances between three muskox lineages. Vita List of Figures Figure 2-1. Map showing location of 16 of the 18 samples used in this study. Figure 2-2. Distribution of repeat unit size for perfect repeats. Figure 3- 1. Geographic limits of muskoxen. Figure 3-2. Alternative muskoxen genealogies. Figure 3-3 Consensus trees of 10 000 resampled replicates for Dm and Ds. Figurr 3-4. Evolutionary relationships among the three muskox lineages. Figure 4-1. Geographic limits and genealogical relationship within the muskox. Figure 4-2. Al1 directions