Using genomics to quantify population structure and genetic diversity of the Arctic char (Salvelinus alpinus) in the Lower Northwest Passage, Nunavut, Canada

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Li, Peiwen
Population genomics , Arctic char , Salmon fishery , DNA sequencing , RNA sequencing , Population genetics , Fishery management , GTseq
The contemporary genetic diversity and population structure of a species reflect past and present demographic changes, and the combined effects of microevolutionary forces on its populations. Understanding the factors that shape geographical distributions and intraspecific genetic diversity is an important first step in the formulation of conservation and management plans. Because of their ecological, evolutionary, cultural, and economic significance, many efforts have been dedicated to genetic studies of wild populations of salmonid species like the Arctic char (Salvelinus alpinus). Despite this, patterns of genetic diversity remain uncharacterized in the King William Island (KWI) region of the Lower Northwest Passage (LNWP), Nunavut. Given rapid climate warming in the Arctic, food insecurity issues among Indigenous populations, and the success of a char fishery in Cambridge Bay, the Gjoa Haven community in KWI is eager to establish its own science-based, ecologically-sound, and sustainable char fishery. Key to this aspiration is the delineation of distinct char populations (stocks) to guide fisheries management. This thesis centres on quantifying and understanding the patterns of genetic diversity in char in the LNWP using two genome-wide panels of Single Nucleotide Polymorphism markers (SNPs) obtained from DNA and RNA sequencing (DNAseq and RNAseq). Using DNAseq data comprising 3,074 SNPs for 413 individuals and a series of population genetics approaches, I found deep genetic differentiation between char populations in the KWI and those on the mainland around Chantrey Inlet, ~200km to the south. I also found 22 SNPs with possible signatures of selection, and associations between genetic distance, geographic distance, and environmental variables. I then focused on the two clusters to infer their demographic histories, and found support for an isolation-with-migration demographic scenario over a strict-isolation model. The RNAseq datasets agreed on an overarching genetic division between KWI and Chantrey Inlet, and the presence of a mixed-stock site in Murchison River, but overall lower genetic differentiation (lower FST) compared to DNAseq data. Finally, I developed a new genetic tool for accurate and fast stock composition identification. Collectively, this work adds to salmonid population genetic studies, and brings new insights for the establishment of a char commercial fishery in the LNWP.
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