DOI: 10.5061/dryad.dz08kps5b
title: Pacific Rim Chinook salmon genetic stock identification baseline of SNP genotypes

description: Genetic stock identification (GSI) can be an effective tool for fisheries
 management, but development of reference baselines can be challenging for
 species with broad geographic distributions. Mixed stock fisheries of
 Chinook salmon (Oncorhynchus tshawytscha) have utilized GSI analyses for
 decades with various genetic baselines, but these have largely become
 outdated with advances in technology that enable more efficient
 genotyping. In this study, we compiled a large genetic baseline of single
 nucleotide polymorphism (SNP) markers for 391 populations that encompass
 the entire geographic range of Chinook salmon. Using cross validation
 simulations, we demonstrated that a multi-tiered assignment approach can
 provide high accuracy at both tier 1 (broad scale with three coastwide
 reporting groups; 97.8% mean accuracy) and tier 2 (fine scale regional
 reporting groups; up to 97.7% mean accuracy) levels. Realistic mixture
 simulations showed that this multi-tiered approach can provide highly
 effective GSI results for several common mixed stock fisheries
 applications in the Pacific Ocean. This new SNP baseline and multi-tiered
 assignment approach provides the most comprehensive GSI range-wide
 baseline for Chinook salmon over any previous applications and enables
 highly efficient genotyping solutions for these scenarios.
description: We assembled SNP data that was provided by the genetics
 laboratories of several different agencies. The data has been tested for
 its ability to perform genetic stock identification estimates.
description: # Coastwide Chinook SNP GSI Baseline
 [https://doi.org/10.5061/dryad.dz08kps5b](https://doi.org/10.5061/dryad.dz08kps5b) This dataset contains genotypes that can be used to make genetic stock identification estimates of Chinook salmon. ## Description of the data and file structure The files are formatted for the program Ms.GSI. There is a single Tier1 baseline file, and three Tier2 baseline files containing genotypes (file names = (`*_Genotypes.csv`). These files contain the columns: sampletype - should be "reference" for all individuals indiv - Unique identifier for each individual collection - the population or sample each individual belongs to repunit - the reporting group each individual belongs to Subsequent columns contain the genotypes for each locus (2 columns per locus) Each baseline file also has an accompanying `pop_info` file (file names = "*pop_info.csv"). These files have the columns: collection - Population or sample corresponding to those in the baseline file repunit - Reporting group each collection belongs to grpvec - A unique numerical value for each reporting group The baseline files can also be used in the program Rubias. The numeric allele designations were converted from the original base designations using the commonly used translation: A = 1, C = 2, G = 3, T = 4, "-" = 5. ## Sharing/Access information Links to other publicly accessible locations of the data: * [http://fishgen.net](http://fishgen.net) Data was derived from the following sources: * Templin, W.D., Seeb, J.E., Jasper, J.R., Barclay, A.W. and Seeb, L.W. 2011. Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies. Molecular Ecology Resources, 11: 226-246. [https://doi.org/10.1111/j.1755-0998.2010.02968.x](https://doi.org/10.1111/j.1755-0998.2010.02968.x) * Clemento, A. J., E. D. Crandall, and J. C. Garza. 2014. Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (*Oncorhynchus tshawytscha*) in the California Current large marine ecosystem. Fishery Bulletin 112(2-3):112-130. * Larson, W. A., J. E. Seeb, C. E. Pascal, W. D. Templin, and L. W. Seeb. 2014. Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (*Oncorhynchus tshawytscha*) from western Alaska. Canadian Journal of Fisheries and Aquatic Sciences 71(5):698-708. * Hess, J. E., N. R. Campbell, A. P. Matala, D. J. Hasselman, and S. R. Narum. 2016. Genetic Assesment of Columbia River Stocks, 4/1/2014 - 3/31/2015, Annual Report, 2008-907-00. Bonneville Power Administration. [https://critfc.org/wp-content/uploads/2021/08/16-03.pdf](https://critfc.org/wp-content/uploads/2021/08/16-03.pdf) * Barclay, A. W., D. F. Evenson, and C. Habicht. 2019. New Genetic Baseline for Upper Cook Inlet Chinook Salmon Allows for the Identification of More Stocks in Mixed Stock Fisheries: 413 Loci and 67 Populations. Alaska Department of Fish and Game, Fishery Manuscript Series No. 19-06. [https://www.adfg.alaska.gov/FedAidPDFs/FMS19-06.pdf](https://www.adfg.alaska.gov/FedAidPDFs/FMS19-06.pdf) * McKinney, G. J., C. E. Pascal, W. D. Templin, S. E. Gilk-Baumer, T. H. Dann, L. W. Seeb, and J. E. Seeb. 2020. Dense SNP panels resolve closely related Chinook salmon populations. Canadian Journal of Fisheries and Aquatic Sciences 77(3):451-461. * Beacham, T. D., C. Wallace, K. Jonsen, B. G. Sutherland, C. Gummer, and E. B. Rondeau. 2021. Estimation of conservation unit and population contribution to Chinook salmon mixed-stock fisheries in British Columbia, Canada, using direct DNA sequencing for single nucleotide polymorphisms. Canadian Journal of Fisheries and Aquatic Sciences 78(10):1422-1434. ### CHANGE LOG **17 March 2025**: * Deleted an extra line that was in the file: "Chinook_SNP_Baseline_Tier2_Northern_pop_info.csv" * Changed some of the collection names in the file "Chinook_SNP_Baseline_Tier2_Columbia_pop_info.csv" so that they are more descriptive. **19 March 2025** * Changed collection names in the genotype file to match the pop_info file **2 May 2025** * Changed "Warm_Springs" to "WarmSprings" so that collection name in the Columbia popinfo file would match the Columbia genotypes file.