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UBC Theses and Dissertations

Genomic analysis of species identity and hybridization within a species complex of Salvelinus (Pisces: Salmonidae) in western North America Liu, Di (Amy)


Hybrid zones, where diverged lineages meet and interbreed, are often exploited to study natural mechanisms associated with varying stages of speciation. My thesis focuses on the western North American Arctic char (Salvelinus alpinus), bull trout (Salvelinus confluentus), and Dolly Varden (Salvelinus malma), described as a “species complex” due to their close inter-relationships, variable morphology, and tendency to hybridize. These aspects have caused debate over their taxonomic and physical identification. Furthermore, a recent subspecies contact zone between northern Dolly Varden (Salvelinus malma malma, NDV) and southern Dolly Varden (Salvelinus malma lordi, SDV), including an admixed population in the Chignik Lake watershed of southwestern Alaska, was recently described. Little is known about the hybrid composition, the effects of ecological selection on proportion of ancestry, and the resulting genomic landscape of this population. In my first chapter, I developed TaqMan assays for efficient, cost-effective, and accurate genotyping of sympatric char species and their hybrids for research, conservation, and management purposes. In my second chapter, I created a genotyping-by-sequencing library to investigate the Chignik Lake watershed population in the context of a NDV and SDV contact zone. My results show that the Chignik Lake watershed population is admixed between NDV and SDV, genetically diverse, and likely the result of historical introgression. I found associations between sampled habitat, distance from the estuary, compared with the proportion of the genome that was NDV (QNDV). In addition, the number of seaward migrations significantly correlated with QNDV, suggesting divergent selection on life history traits resulting from admixture, consistent with findings in other salmonids. Finally, Bayesian genomic cline analysis revealed outlier loci associated with excess ancestry for NDV, and I identified several putative biological processes associated with those outlier loci. My findings suggest that: (i) NDV and SDV show weak reproductive isolation from each other resulting in extensive admixture in the Chignik Lake watershed, and (ii) divergence seen within the watershed may be shaped by diverse habitats and historical gene flow. Future work should take advantage of replicate populations within this contact zone to assess the generality of my results.

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