Resolving Adaptive and Demographic Divergence among Chinook Salmon Populations in the Columbia River Basin

Chinook salmon Oncorhynchus tshawytscha in the Columbia River basin (CRB) comprise three lineages-lower Columbia River and sympatric interior ocean and stream types-each with distinct biological attributes. To evaluate the adaptive and neutral genetic variation of this species in the CRB, we genotyped 54 Chinook salmon populations using a panel of 96 single-nucleotide polymorphism (SNP) loci. All three lineages were represented among the collections and were widely distributed across locations, ranging from the upper Salmon River to near the Columbia River estuary. Our goal was to explore local adaptation as a process shaping the population structure and genetic variation among Chinook salmon beyond the inferences possible with neutral marker data. In our analyses with putatively neutral SNPs, the population structure of Chinook salmon throughout the CRB was generally concordant with that of previous studies using microsatellites. Regression analyses and outlier methods identified 28, 17, and 29 candidate SNP loci for positive selection among stream-type, ocean-type, and lower-river Chinook salmon, respectively. The candidate SNP markers were tested for association with seven environmental variables using multiple methods. We identified unambiguous markers, including nine candidates in the stream-type lineage and seven in the ocean-type lineage that were significantly correlated with elevation and/or temperature. The association of six candidates markers in the lower-river lineage could not be confirmed by population structure analyses and remained ambiguous. We observed a significant association of isolation by distance for the ocean-and stream-type lineages with our SNP panel; however, there was also a significant relationship between pairwise F-ST and several habitat variables. In all cases, the apparent adaptive variation complemented the results of demographic genetic structure but with higher resolution of population differentiation.