Genomics of maturation age in Yukon Chinook

Selective fishing may cause evolutionary changes in harvested fish stocks, but widespread genomic evidence for ‘Fishing Induced Evolution’ remains lacking. Rapid declines in size and age at maturation in AYK Chinook salmon is a potential harbinger of evolutionary change linked to selective fishing. Here we seek to test the overarching hypothesis that variation in age, and therefore size, of adult Chinook salmon in the Yukon River watershed has an underlying genomic basis associated with specific loci. Testing of this hypothesis is the first step towards addressing whether changes in escapement quality are the result of evolutionary change consistent with selective gill net fishing. Our overarching objective is to characterize the genomic architecture of maturation age in Yukon Chinook using low coverage whole genome sequencing of 454 Chinook spanning age ranges from three to seven years. To accomplish this goal, we had to identify the sex determination region in the Chinook from this study to confirm genomic sex. We identified that ~30% of Chinook being aged and sexed at Pilot station were being misidentified as the incorrect sex. Once we had sexes genetically distinguished, we searched for candidate regions and candidate genes associated with maturation age in male and female fish collected at Pilot Station (Kusilvak, Yukon River) between 2007 and 2020. We identified strikingly different patterns between male and female Chinook salmon. The results show that maturation has a different genomic basis in males versus females. We found a strong association with maturation age in males on Chromosome 17 (the sex determining region or SDY), but several potential candidate regions associated with maturation age in females, non with the same association as in males. This result means that selection against the late-maturation in males is decoupled from selection against late-maturation in females, and fisheries selection is more likely to cause an evolutionary response in males than in females. Since external sex determination at Pilot Station was found to be unreliable, testing this hypothesis in the future will require combining genetic sex determination with age and size data.

Identification of specific genomic markers associated with escapement quality is necessary to understand how maturation age and size are likely to respond to management options (e.g. changes in gill net mesh size restrictions) and will inform our understanding of adaptive potential in depressed Yukon Chinook salmon.