Contemporary population genetic structure and phylogeography of pink salmon

Thesis (Master's)--University of Washington, 2016-06

Pink salmon Oncorhynchus gorbuscha are the most abundant Pacific salmon, ranging widely across drainages of the North Pacific Ocean and Bering Sea from Japan in Asia to Washington State in North America. The species are unique in that they have an obligate two-year life cycle which leads to reproductively isolated even- and odd-year lineages. Abundance of each lineage varies by location, and relative abundance can shift from one lineage to the other through time, as has been shown in the Asian portion of the range. The existence of distinct lineages of pink salmon provides a unique opportunity to address population and evolutionary genetics questions, as the lineages can serve as replicates across the entire range of the species. For instance, population structure repeated in parallel within the lineages could help identify historical patterns of isolation due to glacial cover in the region. We used genotyping by sequencing to describe the contemporary population genetic structure of even- and odd-year lineages of pink salmon throughout their range. Our goals are twofold: to conduct a population genetic characterization of the lineages to better understand their relationship, and to describe any structure within the lineages with the intent of examining the evolution of any parallel population structure identified. We genotyped 245 individuals and incorporated genotypes from 138 previously studied individuals for 16,681 SNPs; individuals originated from seven pairs of even- and odd-year populations of pink salmon spread across their range from Japan in Asia to the Pacific Northwest of North America. It has been shown that pink salmon exhibit a complex hierarchical population structure: they possess geographic structure due to their broad species range and temporal structure due to the even- and odd-year lineages. Here, hierarchical AMOVAs reveal that a significant amount of the variation in the data was explained by differences between the lineages. The lineages show differences in the distribution of diversity with the even-year lineage populations exhibiting significantly lower observed heterozygosity than those of the odd-year lineage. Within both lineages, the pattern of population structure was consistent. The Asian and northern Alaska populations show little differentiation but differ significantly from populations in southcentral Alaska and the Pacific Northwest. We tested the partitioning of variation between Asian/northern Alaska and the southcentral Alaska/Pacific Northwest within each lineage; the proportion of variation attributed to the difference between these groups was significant in both lineages, but greater in the odd-year lineage than in the even-year. Using the contemporary population structure and known paleoecological information, we inferred patterns of shared historical refugial habitat. Our data suggest that during the last glacial maximum both lineages likely occupied a northern Beringial refugium as well as a southern North American refugium. These results highlight the influence that historical patterns of habitat availability can have on contemporary population structure, and support the hypothesis of a pre-glacial origin of the lineages.