Population and Landscape Genetics of Arctic Grayling (Thymallus arcticus) by Jessica Rae Reilly A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Ecology Department of Biological Sciences University of Alberta © Jessica Rae Reilly, 2014 Abstract I investigated the population and landscape genetics of Arctic Grayling (Thymallus arcticus) distributed throughout several connected river systems in Alberta, Canada. Broad- and fine-scale population structure was examined by genotyping nine microsatellite loci in 1,116 Arctic Grayling captured from 40 sites in the Hay River, Peace River, and Athabasca River basins. Genetic diversity tended to decline from north to south (allele richness-latitude: Spearman’s rank correlation rs = 0.793, P < 0.05), with the lowest level detected in a stocked population. Significant genetic divergence between and within major river basins was found (overall FST (θ) = 0.13) as well as strong isolation by distance patterns in the Peace River basin (Mantel r = 0.97, P < 0.001) and Athabasca River basin (Mantel r = 0.95, P < 0.001). Evidence for gene flow among sites in neighbouring rivers (i.e., 25–100 km apart) was common; significant genetic differentiation tended to occur at the sub-basin level. Allelic richness (Ar) was associated with variables describing post-glacial colonization route, spatial position in the stream network, and density of anthropogenic disturbance. These findings have important implications for species management and conservation, particularly in regards to management unit delineation, supplementation procedures, conservation priorities (i.e., protecting small and/or isolated stocks), and land-use planning. ii Preface This thesis is an original work by Jessica Rae Reilly. Fish collection by University of Alberta staff was conducted in accordance to guidelines approved by the University of Alberta Animal Care and Use Committee (Protocol No. 758/09/13) and was permitted under provincial Fish Research Licences (Licence No. 12-2003 FRL, 12-0437 FRL, and 12-1201 FRL). Chapter 2 of this thesis has been published as Jessica R. Reilly, Cynthia A. Paszkowski, and David W. Coltman, 2014, “Population Genetics of Arctic Grayling Distributed Across Large, Unobstructed River Systems”, Transactions of the American Fisheries Society, vol. 143, issue 3, 802-816. I was responsible for the data collection and analysis as well as the manuscript composition. Cynthia A. Paszkowski and David W. Coltman were involved with concept formation and manuscript composition. iii Acknowledgments I would like to thank my co-supervisors, Dr. Cindy Pazskowski and Dr. David Coltman for taking a chance on a project outside of their usual research focus and a graduate student with little laboratory and academic experience. I sincerely appreciate all the encouragement, guidance, and trust I experienced during my research – particularly when pursuing fishy side-jobs in my “free time”. I wish to acknowledge my past and present committee members, Dr.Fangliang He and Dr. Michael Sullivan, for their time and input on the project. A big thank you to Michael, who put me on the path to graduate studies (and Arctic Grayling!). This thesis would not have been possible without the help of many fellow graduate students, post-docs, academic staff and friends. Thank you Joshua Miller, Corey Davis, Fred Noddin, Cathy Cullingham, Jill Hamilton, Rene Malenfant, Dana Seidal, Jess Haines, Jamie Gorrell, Jim O’Neil and Emma Wolfe. I think I owe everyone a beer or ten… Support for this research was provided by the Alberta Conservation Association, NSERC, Canadian Wildlife Federation, Alberta Sport, Recreation, Parks and Wildlife Foundation, Golder Associates Ltd., Northern Lights Fly Tyers/Trout Unlimited Edmonton Chapter, Edmonton Old Timers Fishing Club, and the Canadian Circumpolar Institute of the University of Alberta. Tissues samples were provided by Alberta Environment and Sustainable Resource Development and Northern Lights Fly Tyers/Trout Unlimited Edmonton Chapter. Finally, I would like to thank my family for their continued support. In particular, thank you, Blair, for standing beside me through all the stress, field work, long hours in front of a computer, and grayling-saturated conversations… I promise I’ll talk about something else now! iv Table of Contents Chapter 1: Population and Landscape Genetics of Arctic Grayling ...................... 1 Species description ............................................................................................... 1 Conservation and management ............................................................................ 3 Population and landscape genetics ..................................................................... 3 Thesis goals and overview .................................................................................... 5 Chapter 2: Population Genetics of Arctic Grayling Distributed Across Large, Unobstructed River Systems ....................................................................................... 7 Introduction .......................................................................................................... 7 Methods ................................................................................................................ 9 Results................................................................................................................. 13 Discussion........................................................................................................... 17 Conservation implications .................................................................................. 20 Chapter 2 Tables and Figures ........................................................................... 22 Chapter 3: Predictors of Intra-population Genetic Diversity of a Stream-Dwelling Salmonid, the Arctic Grayling .................................................................................. 35 Introduction ........................................................................................................ 35 Methods .............................................................................................................. 38 Results................................................................................................................. 42 Discussion........................................................................................................... 44 Conservation implications .................................................................................. 47 Chapter 3 Tables and Figures ........................................................................... 49 Chapter 4: Summary of Major Findings ................................................................ 56 Chapter 2 result summary: Population structure and genetic diversity ............ 56 Chapter 3 result summary: Predictors of genetic diversity ................................ 57 Conservation and management implications ..................................................... 58 Future directions ................................................................................................ 60 Conclusion ......................................................................................................... 61 References ................................................................................................................... 63 v List of Tables Table 2-1. Site location and genetic diversity of Arctic Grayling captured in the Hay River, Peace River, and Athabasca River basins in Alberta, Canada. Shown are the number of individuals genotyped (N), expected heterozygosity (Hexp), and rarefied estimates of allele richness (Ar) and private allele richness (Pa). ...................... 22 Table 2-2. Polymerase chain reaction (PCR) conditions and diversity of nine microsatellite loci used to genotype Arctic Grayling. The number of alleles (N) and size range (in base pairs, bp), are given for each locus. Average expected heterozygosity (Hexp) per locus is an average value from all 40 sample sites. ... 23 Table 2-3. Pairwise FST estimates (θST, Weir and Cockerham 1984) among sample sites (see Table 2-1 for site code definitions). Bold and underlined values are not significantly different from panmixia following Bonferroni correction (P < 0.00006). ............................................................................................................ 24 Table 2-4. P values associated with pairwise FST estimates (θST, Weir and Cockerham 1984; Table 3) among sample sites (see Table 2-1 for site code definitions). Asterisks indicate significant FST estimates following Bonferroni correction (P < 0.00006). ............................................................................................................. 26 Table 2-5. Genetic variance among regions (VAR), among groups (VAG), and within groups (VWG) partitioned by analysis of molecular variance (AMOVA; Excoffier et al. 2005). All values were significant (P < 0.001). See Table 2-1 for site code and sub-basin definitions. .......................................................................................... 28 Table 3-1. Site location and genetic diversity of Arctic Grayling captured in the Athabasca River basin in Alberta, Canada. Sites are grouped based on the general location of sub-populations identified using individual clustering analysis (see Chapter 2). Shown are the number of individuals genotyped (N), rarefied estimates of allele richness (Ar), expected