San Francisco Estuary and Watershed Science

Genetic diversity is the fundamental building block of biodiversity and the necessary ingredient for adaptation. Specifically, the intra-specific diversity (biocomplexity) comprised of phenotypic and genetic variation partitioned within and among populations can determine the ability of a species to respond to changing environmental conditions. Here, we explore the biocomplexity of California’s Central Valley Chinook salmon (Oncorhynchus tshawytscha) population complex at the genomic level by quantifying population genomic diversity among and within migration life-history phenotypes. Notably, despite apparent gene flow among populations with the same migration (life history) phenotypes inhabiting different tributaries, each group is characterized by a distinct component of unique genomic diversity. While enumerating biodiversity contained within individual hierarchical levels is informative, it is important to consider inter- and intra-specific diversity simultaneously as there may be emergent properties at higher levels due to presence of diversity at lower ones. Our results emphasize the importance of formulating conservation goals focused to maintain biocomplexity at both the phenotypic and genotypic level. Doing so will preserve the species’ adaptive potential and increase the probability of persistence of the population complex despite changing environmental pressures.