Genetic Monitoring for Managers


Types of GEM

Category II GeM Project Example: Mixture Proportions

The application of microsatellites for stock identification of Yukon River Chinook salmon.

Beacham et al. 2008

types mixture fig 1
Locations of the 10 Canadian and 9 U.S. Yukon River populations of Chinook salmon surveyed for microsatellite variation 1987-2003, and the location of the Bio Island test fishery, where an independent sample was obtained for comparison with the baseline. [from Beacham et al. 2008]

Because the Yukon River drainage includes spawning populations of Chinook salmon (Oncorhynchus tshawytscha) in both Canada and the United States, the fishery is cooperatively managed by both countries. Their principal goal is rebuilding and conserving stocks while providing fishing opportunities to both countries. Knowledge of salmon origins and the relative abundances of stocks captured in mixed-stock fisheries are important for setting harvest limits and monitoring the effects of harvests. Mixed-stock analysis using genetic data is an efficient and effective method for determining stock origin.

Baseline samples from adult salmon were collected from 19 Yukon River Chinook salmon populations between 1985 and 2003. Genomic DNA was extracted from either liver, scales, operculum punches, or fin clips.

A single microsatellite locus or 9 single-nucleotide polymorphisms (SNPs) can provide accurate and reasonably precise estimates of stock composition to country of origin.

In this study, fish stock origin was examined using 30 microsatellite loci and compared to an existing nine-locus SNP baseline. Reliable population-specific estimation of stock composition was obtained with a minimum of five microsatellite loci.


types mixture fig 4 types mixture fig 3
Salmon play an important role in economies, traditions, and recreational opportunities throughout their distribution.


Beacham et al. (2008) examined genetic variation for 19 populations of Chinook salmon from the Yukon River using microsatellite loci and an existing single-nucleotide polymorphism (SNP) baseline. Both markers systems provided accurate and reasonably precise estimates of salmon stock composition to country of origin at a fraction of the cost traditional methods.

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Accuracy of assignment of individual Chinook salmon to country, region, and population as a function of the number of loci examined. [from Beacham et al. 2008]


Using this approach, managers can accurately and precisely allocate Chinook salmon harvest quotas to the level of region or major drainage, providing a powerful tool for assessing and regulating fisheries. This information can be used for apportionment of harvests, characterization of run timing and migratory patterns, stock run reconstruction, stock recruitment models, and risk assessment. The rapid turn around of a genetic monitoring approach allows in-season management. A combination of genetic mixed stock analysis and sonar provides a convenient and cost effective method to monitor all stocks simultaneously. More details can be found at: