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

• Published in: Ecology and evolution Vol. 6; no. 21; pp. 7706 - 7716
• Main Authors: Meek, Mariah H., Baerwald, Melinda R., Stephens, Molly R., Goodbla, Alisha, Miller, Michael R., Tomalty, Katharine M. H., May, Bernie
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01-11-2016; John Wiley and Sons Inc; Wiley
• Subjects: Central Valley; Corridors; Deoxyribonucleic acid; DNA; DNA sequencing; Ecological monitoring; Fish; Fish conservation; genetic stock identification; Genomics; Habitat utilization; linkage map; management; Migratory species; Oncorhynchus tshawytscha; Original Research; Population genetics; Populations; RAD‐sequencing; Salmon; Single-nucleotide polymorphism; Telemetry; Threatened species; Wildlife conservation; Central Valley; United States > US; California; INE, USA, California; USA, California, Central Valley; Central Valley; genetic stock identification; management; RAD‐sequencing; linkage map; fish
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.2493

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.
Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. Here, we demonstrate the usefulness of genomic data for identifying single‐nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled Chinook salmon in the Great Central Valley of California. This SNP 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.