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Data from: Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population

Willmes, Malte1; Sturrock, Anna M.2

Published Jul 30, 2024 on Dryad. https://doi.org/10.5061/dryad.0vt4b8h5c

Data files

Jul 30, 2024 version files 92.77 MB

Abstract

Chinook salmon (Oncorhynchus tshawytscha) are ecologically, culturally and economically important across their native range. The once-abundant spring-run Chinook salmon in California have declined due to habitat loss and water diversions. Understanding the genetic composition and life history types being expressed in the few remaining populations is essential for their effective management and conservation.

In this study we combined genetics and otolith (fish ear stone) biochronologies to describe the genotypic and phenotypic diversity of Chinook Salmon in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring-run salmon. Our study found that Yuba River origin fish represented on average, 42% of spawners across six return years with large interannual variability. The remaining spawners were primarily strays from the nearby Feather River hatchery, and since 2018, also from the Mokelumne River hatchery. Among the Yuba-origin spawners, on average, 30% exhibited the spring-run genotype. The Yuba-origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the natal river. Early-migrating fry dominated the returns and their contribution rates were negatively correlated with flow. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately poor survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non-natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in-river growing conditions. Together, these findings show that the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration and reintroduction plans.