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Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales

Citation

Chang, Sarah; Ward, Hillary; Russello, Michael (2022), Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales, Dryad, Dataset, https://doi.org/10.5061/dryad.dv41ns20d

Abstract

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

Methods

Genotyping-in-Thousands by sequencing (GT-seq) following Campbell et al. (2015) Molecular Ecology Resources as modified in Schmidt et al. (2020) Molecular Ecology Resources.

Usage Notes

288_baseline.vcf: vcf file of genotypic data at 288 SNPs for all baseline individuals used for panel development 

261_GTseq_BCnovelsamples_genepop.txt: genepop file of genotypic data at 261 SNPs collected with GT-seq used for panel testing

282_GTseq_WoodLake_18_19_genepop.txt: genepop file of genotypic data at 282 SNPs collected with GT-seq used for Wood Lake application.

218_GTseq_WoodLake_12_14_genepop.txt: genepop file of genotypic data at 218 SNPs collected with GT-seq used for Wood Lake application and comparison with previous genotyping methods.

Metadata.csv: text file containing individual metadata for all samples used including sample identifiers, location, geographic basin, reproductive ecotype, and migratory ecotype.