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

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 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 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.

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

“…In this study, the assignments of simulated purebreds and hybrids reclassified all but 47 individuals (7%) to their originating classes which highlight the performance of the 77 species‐specific SNP to discriminate first‐, second‐, and third‐generation hybrids (Nussberger, Greminger, Grossen, Keller, & Wandeler, ; Pujolar et al, ). The combination of powerful markers, simulations to assess their power, and the use of an appropriate molecular statistical approach as implemented in NewHybrids can be helpful in identifying precisely advanced hybrid classes (Boecklen & Howard, ; Pritchard et al, ; Pujolar et al, ). We emphasis that, with the increase availability of abundant genome‐wide markers in closely related species, identification of species diagnostic markers and their genotyping across many individuals using low density genotyping assay is an accessible way to refine our understanding on hybridization dynamics in many biological systems (Benjamin et al, ; Nussberger et al, ; Pujolar et al, ).…”

“…We used HybridLab (Nielsen, Bach, & Kotlicki, 2006) to simulate first- NewHybrids v 1.1 beta3 (Anderson & Thompson, 2002) was used to assign the simulated genotypes into the different hybrid classes. Among the 21 possible purebred or hybrid classes up to 3 generations, only 15 have different genotype frequency classes (defined as the expected proportion of the loci within an individual harboring zero, one or two alleles from one of the species) and can thus in principle be differentiated using NewHybrids (Anderson & Thompson, 2002;Pritchard et al, 2016). Theoretical genotypic frequencies of all hybrid classes are detailed in Table S2.…”

Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence‐related genes

“…For quality control and analyses, we also used two pre‐existing 220K SNP data sets: a data set of known aquaculture escapees ( n = 192, Pritchard et al., ), and a data set of adults collected from the Teno mainstem ( n = 463) and the neighbouring river Borselva ( n = 17; Barson et al., ). The adult Teno mainstem sample included the individuals genotyped with a 7K SNP array by Johnston et al.…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…Hatchery released and native extirpated salmon populations were identified in Poland using an Atlantic salmon array (Pocwierz-Kotus et al, 2015;Bernas et al, 2016). Understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes (Pritchard et al, 2016). Using the Atlantic salmon array, a set of 200 SNPs differentiating an Atlantic salmon stock from Teno River, Norway and escapees was identified.…”