Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

• Published in: Evolutionary Applications
• Main Authors: Pritchard, Victoria L., Erkinaro, Jaakko, Kent, Matthew P., Niemelä, Eero, Orell, Panu, Lien, Sigbjørn, Primmer, Craig R.
• Other Authors: Suomen Akatemia, Suomen Kulttuurirahasto
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2016
• Subjects: Atlantic salmon; Salmo salar
• Online Access: http://dx.doi.org/10.1111/eva.12407; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Feva.12407; https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12407

Abstract 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 single nucleotide polymorphism ( SNP ) array, in combination with pooled‐sample allelotyping and an F st outlier approach, we identified 200 SNP s 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 SNP s and smaller subsets 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 escapees in many Atlantic salmon populations.