The genetic architecture of ecotypic differentiation in Chinook salmon of the California Central Valley

Understanding the genomic details underlying complex behavioral traits is a foundational pursuit in biology. We use genomic and genetic techniques to dissect the heritable underpinnings of adult migration timing of Chinook salmon in the California Central Valley (CCV), home to several ecotypes not found elsewhere. We find that a previously described genomic region contributes to the seasonal shift in adult freshwater migration in the CCV, as in other river basins, but we further identify two functional domains in this locus that separately and additively influence the trait, with each allele copy affecting timing by ∼two weeks. We show how the evolution of a unique ecotype in the CCV is partially due to an allele derived from the more widespread early-migrating haplotype. However, the genomic background of the evolutionarily differentiated ecotypes contributes a similar amount to trait variation. We show how a relatively simple five-allele genetic system, in concert with genomic backgrounds, can create a remarkable diversity of phenotypes and ecotypes for this iconic species.