Population genomics of Salish Sea chum salmon: The legacy of the salmonid whole genome duplication

The common ancestor of salmonids underwent a whole genome duplication approximately 88 million years ago. This duplication event still has a lasting impact on the form and structure of salmon genomes today and is evident in many duplicated genes and ongoing residual tetrasomic inheritance. This duplication also serves to complicate genetic analyses, as paralogous genes and sequences are difficult to distinguish, and often fully excluded prior to study. The goal of this thesis is to demonstrate how to incorporate duplicated loci into genetic studies of salmonids using high-throughput sequencing of chum salmon from the Salish Sea. In the first chapter, I develop a method to resolve paralogous loci within a pedigree and include them on a high-density linkage map. I show that paralogous loci are concentrated in 16 regions near the ends of linkage groups. These regions are inferred to have ongoing residual tetrasomic inheritance and we find that they have a lower incidence of transposable elements than the rest of the genome, a possible explanation for their stability since the whole genome duplication. In the second chapter, I use the discovered paralogous loci in a population genetic study of 10 collections of chum salmon from the Salish Sea. I compare genetic diversity and population structure at paralogous and non-paralogous loci and conduct a genome scan for association with run timing. I demonstrate that it is possible to characterize paralogous loci in wild populations and that they show similar patterns of population structure as the rest of the genome. The genome scan reveals genomic regions of elevated association with run timing, highlighting the potential downside of excluding paralogous loci in studies looking for genetic signals of adaptation.