Wild Pacific salmon in British Columbia (BC) is an important food source supporting commercial and recreational fisheries, and for First Nations they play a significant cultural, social and economic role. Since the 1990s, the total value of the commercial catch in BC has decreased from $263M to $24M reflecting the declines in Pacific salmon populations. With climate change, stocks are becoming mismatched to new environments, and fisheries management and industry must respond to sustain yields. We expect that the productive fish of the future will not be those most prevalent in BC today. As a result, there is a pressing need to identify adaptive genetic variation that may withstand climate change.
This project evaluated a cost-effective strategy to identify an atlas of adaptive genetic variants in a species of extraordinary economic and cultural significance – the Chinook salmon. Using a two-pronged approach, they first identified genes associated with latitude and correlated climate variables in a larger sample of a model species (three-spine stickleback). They then tested for parallel variation between the model species and Chinook salmon. By the end of the project, 1021 stickleback and 121 Chinook whole genomes from populations spanning from California to Alaska were sequenced. In Chinook salmon, they found a total of 183 candidate adaptive genes and 29 of those were also found to be adaptive in stickleback. This provides evidence that the principle of deep-sequencing of a model species could be a cost-effective method to identify adaptive genetic variants that can withstand climate change in a focal species where direct deep-sequencing is cost-prohibitive.