Data from: Remnant salmon life history diversity rediscovered in a highly compressed habitat

Chinook salmon (Oncorhynchus tshawytscha) display remarkable life history
diversity underpinning their ability to adapt to environmental change.
Maintaining life history diversity is vital to the resilience and
stability of Chinook salmon metapopulations, particularly under rapidly
changing climates. However, the conditions that promote life history
diversity are rapidly disappearing, as anthropogenic forces promote
homogenization of habitats and genetic lineages. In this study, we use the
highly modified Yuba River in California to understand if distinct genetic
lineages and life history still exist, despite reductions in spawning
habitat and hatchery practices that have promoted introgression. There
currently is a concerted effort to protect federally listed spring run
populations, given that few wild populations still exist. Despite this, we
lack a comprehensive understanding of the genetic and life history
diversity of Chinook salmon present in the Yuba River system. To
understand this diversity, we collected migration timing data and GREB1L
genotypes from hook-and-line, acoustic tagging, and carcass surveys of
Chinook salmon in the Yuba River between 2009-2011. Variation in the
GREB1L region of the genome is tightly linked with run timing in Chinook
salmon throughout the range, but the relationship between this variation
and entry on spawning grounds is little explored in the Central Valley. We
found that the date Chinook salmon crossed the lowest barrier to Yuba
River spawning habitat (Daguerre Point Dam) was tightly correlated with
their GREB1L genotype. Importantly, our study confirms that ESA-listed
spring run Chinook salmon are spawning in the Yuba River, promoting a
portfolio of life history and genetic diversity, despite spawning in a
compressed habitat. This work highlights the need to identify and protect
this life history diversity in heavily impacted systems to maintain
healthy Chinook salmon metapopulations in those systems. Without this, we
run the risk of losing the last vestiges of important variation.