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Meek MH, Baerwald MR, Stephens MR, et al. Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon. Ecol Evol. 2016;6(21):7706-7716doi: 10.1002/ece3.2493.
Meek, M. H., Baerwald, M. R., Stephens, M. R., Goodbla, A., Miller, M. R., Tomalty, K. M. H., & May, B. (2016). Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon. Ecology and evolution, 6(21), 7706-7716. https://doi.org/10.1002/ece3.2493
Meek, Mariah H, et al. "Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon." Ecology and evolution vol. 6,21 (2016): 7706-7716. doi: https://doi.org/10.1002/ece3.2493
Meek MH, Baerwald MR, Stephens MR, Goodbla A, Miller MR, Tomalty KMH, May B. Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon. Ecol Evol. 2016 Oct 05;6(21):7706-7716. doi: 10.1002/ece3.2493. eCollection 2016 Nov. PMID: 30128122; PMCID: PMC6093154.
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Ecol Evol. 2016 Oct 05;6(21):7706-7716. doi: 10.1002/ece3.2493. eCollection 2016 Nov.

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

Ecology and evolution

Mariah H Meek, Melinda R Baerwald, Molly R Stephens, Alisha Goodbla, Michael R Miller, Katharine M H Tomalty, Bernie May

Affiliations

  1. Department of Natural Resources Cornell University Ithaca NY USA.
  2. Department of Animal Science University of California Davis Davis CA USA.
  3. School of Natural Science University of California, Merced Merced CA USA.

PMID: 30128122 PMCID: PMC6093154 DOI: 10.1002/ece3.2493

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.

Keywords: Central Valley; RAD‐sequencing; fish; genetic stock identification; linkage map; management

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