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.
Highlights
Animal migration is one of nature’s most widespread occurrences, with migratory behavior present across all major branches of the animal kingdom (Alerstam, Hedenstrom, & Akesson, 2003; Dingle, 1996)
Based on the allele frequency difference rankings and the linkage map, we developed a suite of 114 Fluidigm single-nucleotide polymorphisms (SNPs) Type assays for the ancestry- informative markers (AIMs) panel
Conservation and management of threatened migratory species has been greatly limited by an inability to distinguish individuals from distinct populations as they mix along the migratory corridor
Summary
Animal migration is one of nature’s most widespread occurrences, with migratory behavior present across all major branches of the animal kingdom (Alerstam, Hedenstrom, & Akesson, 2003; Dingle, 1996). New advances in genome sequencing provide an opportunity to scan thousands of markers to identify a select subset needed for accurate population assignment (Amish et al, 2012; Hess et al, 2014; Lao, Duijn, Kersbergen, de Knijff, & Kayser, 2006) This approach expands our ability to track the movements, population structure, habitat use, and impacts on a large numbers of individuals from migratory populations, while minimizing handling and sampling stress (Davey et al, 2011). Genetic resources that rapidly and reliably distinguish runs and populations of Central Valley Chinook will be immensely valuable for genetic management and monitoring, as well as studies of life-history trait evolution, genomewide association, habitat use, and other questions of ecological or evolutionary interest in this threatened migratory species
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