Diversity Under Pressure: Long‐Term Genetic Decline in California's Central Valley Chinook Salmon ESA Listed Runs

ABSTRACT

Intraspecific diversity enables populations to persist under stochastic and extreme environmental conditions. One system that is representative of notable intraspecific diversity is Chinook salmon ( Oncorhynchus tshawytscha ) in the Central Valley of California, USA. It is the only place in the species range where four distinct migration timings (Winter, Spring, Fall, Late‐fall) co‐occur. These populations are declining, with Winter run listed as Endangered and Spring run as Threatened under the Endangered Species Act (ESA). To quantify temporal changes in genetic diversity of the different runs, we genotyped outmigrating juveniles using RAD‐sequencing across 20+ years of annual sampling. Tajima's D revealed significant shifts in neutral genetic variation over time in Spring and Winter runs. Effective population size ( Ne ) declined in all listed populations, and the historical Ne estimates indicate severe plummets in genetic diversity 25–50 generations ago. Our results demonstrate how anthropogenic forces have eroded the genetic diversity of ESA listed Chinook salmon populations over the past century. Moreover, this study demonstrates how an organism with genetically based life history variation (migration timing), traditionally advantageous under natural environmental variability, struggles to persist when faced with anthropogenically altered habitat and changing climate.