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UBC Theses and Dissertations

Ecological genomics of kokanee salmon Lemay, Matthew Alexander


Divergent natural selection across a heterogeneous landscape can drive the evolution of locally adapted populations in which phenotypic variation is fine-tuned to the environment. At the molecular level, such processes can be inferred by identifying correlations between genetic variation and environmental variables. In this dissertation, I used multiple complementary approaches to investigate the genetic basis of adaptation in natural populations of kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka). In Chapter 2, I found that the frequency and length of alleles in the circadian regulation gene, OtsClock1b, displays a predictable distribution with respect to latitude among lakes sampled from British Columbia to Alaska, providing evidence that variation at this locus may be locally adapted to divergent photoperiod regimes. In Chapter 3, I tested for transcriptome-wide patterns of sequence divergence in reproductive ecotypes of kokanee within Okanagan Lake and found evidence for differential gene expression and asymmetrical pathogen load between ecotypes. In Chapter 4, I used restriction site associated DNA sequencing to identify ~6,000 single nucleotide polymorphisms (SNPs) from multiple spawning populations of kokanee within Okanagan Lake; statistical outlier tests revealed 20 SNPs that were putatively under divergent selection between ecotypes, many of which annotated to genes associated with early development. While there was no evidence for neutral genetic divergence, outlier SNPs demonstrated significant structure with respect to ecotype and had high assignment accuracy (>99%) in mixed composition simulations, suggesting the utility of these loci for genetic stock identification. These data support the hypothesis that kokanee ecotypes are in the early stages of ecological differentiation, making them an ideal system for investigating the genomic basis of adaptation. Results from this study will be used to assist conservation and management initiatives by providing molecular tools for in-season monitoring of ecotype abundance.

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