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

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.

对洄游物种开展有效保护与管理，需精准识别其独特种群——即便这些种群在洄游通道中发生混合。尽管长期以来遥测技术一直被用于研究洄游动物的活动与栖息地利用模式，但基因组工具正从多方面成为更优替代方案，可在降低成本的前提下实现大规模应用。本研究验证了基因组资源在识别单核苷酸多态性（single-nucleotide polymorphisms, SNPs）方面的应用价值，这些SNP位点可快速且精准地识别加利福尼亚州大中央谷中的濒危奇努克鲑（Chinook salmon）。研究表明，从基于限制性位点相关DNA测序开发的11500余个SNP位点池中筛选出的80个优选位点，可精准识别奇努克鲑的洄游群及其内部的选定种群。目前尚无针对中央谷奇努克鲑的SNP检测面板，能够达到本研究展示的高种群归属鉴定准确率。该检测面板将大幅提升我们对这一兼具生态、经济与社会价值的物种开展研究与管理的能力，同时也验证了利用基因组学研究洄游物种的巨大应用潜力。