Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon

Abstract

Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large‐scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single‐nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled Chinook salmon in the Great Central Valley of California. We show that 80 well‐chosen loci, drawn from a pool of over 11,500 SNPs developed from restriction site‐associated DNA sequencing, can accurately identify Chinook salmon runs and select populations within run. No other SNP panel for Central Valley Chinook salmon has been able to achieve the high accuracy of assignment we show here. This panel will greatly improve our ability to study and manage this ecologically, economically, and socially important species and demonstrates the great utility of using genomics to study migratory species.

Science Advancements Key to Increasing Management Value of Life Stage Monitoring Networks for Endangered Sacramento River Winter-Run Chinook Salmon in California

“…• A DNA-based method of determining Chinook salmon stock (geographic) or run (winter, spring, fall/ late-fall) with genetic baselines developed for Central Valley salmon stocks using microsatellites , single-nucleotide polymorphisms, or sequencing (Clemento et al 2014;Meek et al 2014Meek et al , 2016). …”

Population structure and genomic evidence for local adaptation to freshwater and marine environments in anadromous Arctic Char (Salvelinus alpinus) throughout Nunavik, Québec, Canada

“…While most pairs of sampled rivers sharing an estuary had very low genetic differentiation, we found evidence of substructure within those systems, suggesting that genomic tools could be used for stock assignment of adult fish (e.g. Meek et al, 2016; Moore et al 2017). The evidence we found for local adaptation to marine environments is in concordance with the neutral genetic structure at a broader scale, as major oceanographic basins around Nunavik are contrasted both in their environments and ancestry of their Arctic Char populations.…”

Managing for Salmon Resilience in California’s Variable and Changing Climate

“…Straying of trucked hatchery fish, especially into streams without hatcheries, reduces local adaptation in the recipient population and degrades local adaptations. Indeed, the trucking program is a likely cause of the genetic homogenization of Central Valley fallrun Chinook Salmon (Williamson and May 2005;Meek et al 2014Meek et al , 2016; this homogenization is unusual for such a large salmon stock complex. Moreover, unmarked hatchery fish on the spawning grounds mask declines in the abundance of wild fish (Johnson et al 2012).…”