Identifying hidden biocomplexity and genomic diversity in Chinook salmon, an imperiled species with a history of anthropogenic influence

Abstract

Biocomplexity is an important mechanism for population resilience in changing environments. However, we are just beginning to understand how to identify biocomplexity so that species management efforts promote resilience and stability. Genomic techniques are emerging as an important method for identifying biocomplexity. Central Valley (CV) Chinook salmon are an example of a species at risk of extinction if better methods for identifying and protecting biocomplexity are not employed. To address this knowledge gap, we employed restriction site associated DNA sequencing to conduct the first genomic study of all major populations of CV Chinook salmon. We found greater population structure across the Central Valley than previously documented. Additionally, we show evidence for differentiation and adaptation within migratory phenotypes despite high levels of gene flow. We also determined that genomic data can vastly improve our ability to assign individuals to their natal populations, even as they mix during migration, a finding that will assist management practices. These results demonstrate how genomic study can greatly improve our ability to identify and conserve biocomplexity.