Genomic changes associated with reproductive and migratory ecotypes in sockeye salmon (oncorhynchus nerka)

Abstract

Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating thegenomic changes associatedwith specific lifehistory traits.Here,weused pairedmigratory [anadromousvs. resident (kokanee)] and reproductive [shore-vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associatedDNA sequencingwas used to genotype this sampling at 7,347singlenucleotide polymorphisms,334ofwhichwere identifiedasoutlier loci andcandidates for divergent selectionwithin at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments.Of particular note, one locuswas detected as themost significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake).We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms andgenomic regions identifiedinour study offer a rangeofmechanistichypotheses associatedwiththegenetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.