Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

• Main Authors: Pritchard, Victoria L., Erkinaro, Jaakko, Kent, Matthew P., Niemelä, Eero, Orell, Panu, Lien, Sigbjørn, Primmer, Craig R.
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2016
• Subjects: allelotyping; Salmo salar; introgressive hybridization; SNP array; aquaculture escapee; Holocene; Atlantic salmon
• Online Access: https://doi.org/10.5061/dryad.dg8f3

Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes, however markers currently available to discriminate the two types of parental genome have limited power to do this. Using a high-density Atlantic salmon SNP array in combination with pooled-sample allelotyping and an Fst outlier approach, we identified 200 SNPs that differentiated an important Atlantic salmon stock from the escapees potentially hybridizing with it. By simulating multiple generations of wild-escapee hybridization involving wild populations in two major phylogeographic lineages, and a genetically diverse set of escapees, we showed that both the complete set of SNPs and smaller sub-sets could reliably assign individuals to different hybrid classes up to the third hybrid (F3) generation. This set of markers will be a useful tool for investigating the genetic interactions between native wild fish and aquaculture escapes in many Atlantic salmon populations. Bayescan_Fdist2.tar.gz This archive contains files used by Pritchard et al. (2016) for Fst outlier analyses: Index.txt - index of SNPs. Bayescan*.in - Bayescan input files, SNPs in index order. Fdist*.in -Fdist2 input files, SNPs in index order. datacal.c; fdist2.c; Original_README_fdist2 - Fdist2 source code & information. R_code_for_analysing_Fdist2_output.txt - modified R code from Lotterhos & Whitlock (2014). See README file in archive for further information. Genotyping_allelotyping.tar.gz This archive contains the following data files for Pritchard et al. (2016): B_allele_freq_Naatamo_pools.csv: Uncorrected B allele frequencies for the Naatamo pools. B_allele_freq_New_Teno_pools.csv: Uncorrected B allele frequencies for the New Teno mainstem pools. B_allele_freq_Teno_Finnmark_pools.csv: Uncorrected B allele ...