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Viewed in Chapter 1), I Used an Empirical FST-Outlier Method University of Alberta Population genomics of North American grey wolves (Canis lupus) by James Christopher Knowles A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Science in Systematics and Evolution Biological Sciences ©James Christopher Knowles Fall 2010 Edmonton, Alberta Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission. Examining Committee David Coltman, Biological Sciences Jocelyn Hall, Biological Sciences Stephen Moore, Agricultural, Food and Nutritional Science ABSTRACT Previous studies of the grey wolf (Canis lupus) using microsatellites have showed strong population structure despite the high mobility of individuals. I re-assessed the structure of North American grey wolves by genotyping 132 wolves at a genome-wide set of >26 000 single nucleotide polymorphisms (SNPs), and found less population structure, a strong pattern of isolation by distance, and determined that gene flow between subpopulations relates to prey specialization. To assess how accurately smaller data sets assign individuals, I analyzed sub-sets of SNPs and found that small marker sets varied greatly in estimates of subpopulation assignment, and showed high discordance with assignments determined when using all 26k markers. Finally, using a genome scan to detect natural selection I identified SNPs in three genes that may have undergone directional selection, contain variation with observed phenotypic consequences in other mammal species and may be related to adaptation in grey wolves. ACKNOWLEDGEMENTS I am most grateful for the support and guidance of my supervisor, David Coltman, for providing me the opportunity to study in his lab. I truly appreciated his advice and patience during my extended stay at the U of A. Thanks also to my committee advisors Jocelyn Hall and Stephen Moore. Many people at UCLA were either directly involved in or helped out with my research. Of course, none of the research would have been possible without Bob Wayne, who provided me with funding, a place in his laboratory, and much advice. John Novembre provided practical and theoretical assistance with analysis on many occasions. John Pollinger was helpful during many stages of both laboratory work and data processing. Katie Semple-Delaney instructed me in the use of ARC software, and Eunjung Han gave me access to some necessary data. Last but certainly not least Bridgett vonHoldt was an immense help to me throughout my research. She provided instruction and guidance on everything from laboratory work to data processing and analysis. I must also thank several people at the University of Alberta who provided assistance along the way. Jocelyn Poissant routinely provided guidance and encouragement, and Aaron Shafer kindly helped with editing and made useful suggestions for the manuscript. Patrick James helped me get my head around various aspects of ordination analyses. Thanks to Bill Clark who aided in tissue sub-sampling while I was away at UCLA. Charlene Nielsen was most helpful with assistance using ARC software. Tissue samples for this project were made available by Lindsey Carmichael, Marco Musiani, Link Olson, Brandy Jacobsen, Parks Canada, and the University of Alaska Museum. Lindsey and Marco both kindly allowed the use of their genetic and phenotypic data, for which I am most thankful, and Marco in particular provided advice and encouragement during the course of this research. On a more personal level, I sincerely appreciated the support of all friends, family, and lab-mates. In particular, both my parents, Judith L. Eger and James A. Knowles, provided advice and assistance from the beginning. Finally, I’d like to thank Amber Polywkan for always being there for me during the past three years, even when ‘being there’ meant moving to Edmonton for the final stage of my research. TABLE OF CONTENTS CHAPTER 1: GENERAL INTRODUCTION ................................1 Grey wolf taxonomic history............................................................................ 1 Grey wolf characteristics and life history....................................................... 2 SNP identification and genotyping.................................................................. 4 Population genomics ......................................................................................... 9 Thesis goals ...................................................................................................... 12 CHAPTER 2: POPULATION STRUCTURE OF NORTH AMERICAN GREY WOLVES.......................................................15 Introduction..................................................................................................... 15 Methods............................................................................................................ 16 Sample selection and genotyping.................................................................. 16 Population structure ...................................................................................... 18 Subpopulation structure ................................................................................ 20 Isolation by distance ..................................................................................... 20 Comparison of SNP data sets and microsatellites for determining population structure......................................................................................................... 21 Results .............................................................................................................. 25 Population structure ...................................................................................... 25 Subpopulation structure ................................................................................ 26 Isolation by distance ..................................................................................... 26 Comparison of SNP data sets and microsatellites for determining population structure......................................................................................................... 27 Discussion......................................................................................................... 28 Population structure ...................................................................................... 29 Genetic differentiation across subpopulations .............................................. 34 Subpopulation structure ................................................................................ 35 Isolation by distance ..................................................................................... 37 Comparison of SNP data sets and microsatellites for determining population structure......................................................................................................... 40 Conclusions...................................................................................................... 43 CHAPTER 3: A GENOME SCAN TO DETECT SELECTED GENES IN NORTH AMERICAN GREY WOLVES...................58 Introduction..................................................................................................... 58 Methods............................................................................................................ 60 Detection of FST outliers between subpopulations........................................ 60 Detection of directional selection on outlier loci.......................................... 60 Identification of candidate genes .................................................................. 61 Results .............................................................................................................. 62 Detection of outlier loci and directional selection ........................................ 62 Identification of candidate genes .................................................................. 62 Discussion......................................................................................................... 63 Detection of directional selection on outlier loci.......................................... 63 Identification of candidate genes .................................................................. 66 Conclusions...................................................................................................... 70 CHAPTER 4: SYNTHESIS.............................................................76 Conclusions...................................................................................................... 77 Future directions............................................................................................. 80 LITERATURE CITED ....................................................................83 LIST OF TABLES Table 2-1 Pair-wise FST values between subpopulations of 46 wolves assessed using 26k SNPs Table 3-1 Pair-wise FST values between subpopulations of 71 wolves assessed
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