A major effect locus involved in migration timing is shared by pink and sockeye salmon

Migration is an important component of the life cycles of many organisms and differences in migration timing can greatly influence fitness. Variation in migration timing (hereafter referred to as run timing) is found in many salmon species and contributes to the portfolio of life history diversity that is vital for maintaining healthy populations. Pink salmon ( Oncorhynchus gorbuscha ) are composed of temporally isolated lineages that spawn in even and odd years. Here, we focus on early and late runs of pink salmon in Auke Creek, Alaska, which spawn a few weeks apart in the same ≈50m stretch of stream. We conducted low coverage, whole genome sequencing on pink salmon from the early and late runs of both even and odd lineages to investigate the genetic basis of run timing in this system. Within the even lineage we detected a major effect locus displaying high genetic divergence between early and late run individuals on chromosome 10 of the pink salmon genome. This same locus showed a lower - but still elevated - amount of genetic divergence in the odd lineage. The region of high divergence includes the Leucine Rich Repeat Containing 9 gene ( lrrc9 ), and genetic divergence was substantially reduced outside of this gene. The lrrc9 gene also shows high divergence between two ecotypes of sockeye salmon ( Oncorhynchus nerka ) that differ in both run timing and spawning habitat. Comparison of the lrrc9 gene region in pink and sockeye salmon shows that variation within this gene is associated with run timing in both species. However, the polymorphic sites (i.e, SNPs) and run timing alleles are unique to each species and arose from independent mutations following divergence from a common ancestor. These results demonstrate that adaptation in pink salmon can occur at small temporal scales and that complex traits can be controlled by similar genetic mechanisms in multiple species.