Abstract
Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1939 coho salmon to the correct population was 100%, and to correct brood year within population was also 100%. Inclusion of individuals requiring only a single parental genotype for identification resulted in assignments of 2101 individuals, with an accuracy of 99.95% (2000–2001) to population and 100.0% to age. With 23 regions defined by the coded-wire tag (CWT) program, and individuals displaying an assignment probability <0.85 excluded from the analysis, mean regional assignment accuracy of individuals via GSI was 98.4% over all 23 regions. A PBT–GSI or PBT system of identification will provide an alternate method of identification in the assessment and management of Canadian-origin coho salmon relative to the existing CWT program.
Highlights
Coho Salmon (Oncorhynchus kisutch) are produced in hatcheries in British Columbia, Canada, with approximately seven million juveniles released annually
We evaluated whether a combined Parentage-based tagging (PBT)/genetic stock identification (GSI) approach can emulate and perhaps improve upon the results available from the current CWT program for Coho Salmon in British Columbia production hatcheries, with a geographically expansive baseline employed for potential population assignment
15 populations, and 92.0% (1,471/1,599) of the individuals were subsequently assigned via parentage analysis with SNPPIT
Summary
Coho Salmon (Oncorhynchus kisutch) are produced in hatcheries in British Columbia, Canada, with approximately seven million juveniles released annually. Salmon marked with CWTs upon hatchery release received an adipose fin clip, with this externally-visible mark allowing CWT-marked fish to be identified visually and sampled in a fishery. Draft fisheries that exploited Coho Salmon produced only in hatcheries, most Coho Salmon released from many hatcheries in southern British Columbia, Washington, and Oregon received an adipose fin clip, but no corresponding CWT. This approach enabled mark-selective fisheries to be conducted, in which only adipose fin-clipped hatchery fish were harvested, but it impaired the recovery of CWTs, as many adipose fin-clipped individuals did not carry a CWT. The importance of CWT recovery data for salmon management is exemplified by an annex in the Pacific Salmon Treaty (PST) between Canada and the United States that obligates both countries to maintain the CWT system in support of management of fisheries relevant to the PST
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