Protecting life history diversity: Using genomics to aid conservation of imperiled salmon
Populations of California’s Central Valley Chinook salmon (Oncorhynchus tshawytscha)are listed as federally threatened or endangered under the U.S. Endangered Species Act. This is due to a variety of stressors, such as harvest, habitat alteration, dam construction, and hatcheries. We have had a limited understanding of the genetic structure and diversity found in these populations, which hinders our ability to determine the appropriate management units. Additionally, we’ve lacked a method for assigning individuals back to their natal populations, impeding accurate monitoring and research programs. This is particularly problematic given the different listing statuses among the seasonal runs (Winter, Spring, Fall, and Late-fall) and the need for assessing water management impacts on population abundance. We employed newly developed genomic tools to better assess the genetic diversity of these populations by sampling across the genome and examining signatures of selection.
We used restriction site associated DNA sequencing (RAD-seq), discovering over 20,000 new Single Nucleotide Polymorphism (SNP) markers. We show fine-scale population structuring in the Central Valley and constructed a high density SNP linkage map. Additionally, we developed a panel of markers that accurately identifies unknown individuals to run. We interpret these results in the face of the current Chinook salmon conservation and restoration efforts being implemented in the Central Valley of California.