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.

迁徙物种的有效保护与管理，需要对其独特种群进行精准识别——即便这些种群在迁徙廊道中发生混合。尽管追踪遥测（telemetry）长期以来被用于研究迁徙动物的运动模式与栖息地利用规律，但基因组学工具正逐渐在诸多方面成为更具优势的替代方案，可实现低成本的规模化应用。本研究验证了基因组学资源在筛选可用于快速精准识别的单核苷酸多态性（single-nucleotide polymorphisms, SNPs）方面的应用价值，这类分子标记可实现对加利福尼亚中央大谷地濒危奇努克鲑鱼（Chinook salmon）的快速精准识别。研究证实，从基于限制性酶切位点相关DNA测序（restriction site-associated DNA sequencing）开发的11500余个SNPs集合中筛选出的80个优质基因座，可精准识别奇努克鲑鱼的洄游类群以及类群内的特定种群。目前尚无针对加利福尼亚中央谷地奇努克鲑鱼的SNP分型组合，能够达到本研究所展示的高种群归属准确率。该分型组合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，同时也证实了利用基因组学手段研究迁徙物种的巨大应用潜力。