Environmental Adaptation in Chinook Salmon (Oncorhynchus tshawytscha) throughout their Native Geographic Range

Chinook salmon (Oncorhynhcus tschawytcha) are anadromous members of the salmonid family of fishes (salmon, trout, and char), and have a vast geographic distribution in North America that spans a diversity of habitats from Central California to Northern Alaska.  Throughout this range, Chinook salmon display notable neutral genetic structure with support for at least three major genetic lineages.  In part, this broad genetic structure is attributed to geological and glacial events that created refugia and historic barriers to gene flow, but natural selection is also likely to have influenced this genetic variation due to the heterogeneity observed in landscape features throughout the range.  Here we utilize a multivariate landscape genomics approach to identify associations between genome-wide variation at 19,703 SNPs and a suite of environmental and climate variables in 46 populations of Chinook salmon from California to Alaska.  We identify adaptive loci associated with climate variation that sheds light on how natural selection has shaped genetic divergence throughout this species natural range.  Our results support the conclusion that range-wide genetic divergence is a result of ecological adaptation to local selective forces in addition to genetic drift as a result of isolation by distance and/or geological barriers to gene flow.