Genome-wide differentiation and SNP-based identification of northeastern Atlantic Sebastes species

Sustainable fisheries require reliable species identification and understanding of the underlying genetic hierarchies within the targeted species. Three Sebastes species are commonly found in the northeastern Atlantic: Sebastes mentella (beaked redfish), Sebastes norvegicus (golden redfish), and Sebastes viviparus (Norway redfish). These species are morphologically similar and have largely overlapping distribution ranges. Besides, three cryptic species for S. norvegicus and three depth-defined ecotypes for S. mentella have been suggested. Genetic knowledge and methods are needed to identify and monitor these species and to look at their geographic distribution. Here, a total of 99 specimens of S. mentella, S. viviparus as well as S. norvegicus A and B were sequenced in pools and aligned against a reference genome from a sister species, S. fasciatus (Acadian redfish). The measured divergence between all pairs, including the cryptic species pair S. norvegicus A and B, was high (mean FST = 0.33-0.61) and encompassing throughout genomes. Several shared megabase-scale regions of elevated divergence were observed, likely representing regions of reduced recombination. Moreover, 2914 fish collected across the northeastern Atlantic were analysed with a discriminatory SNP panel of high resolution (mean FST= 0.60-0.91), revealed few possible hybrids, and supported further sub-structuring within mentella and S. norvegicus B. The latter was split into two groups, one of which was the previously recognized giant morph and confirmed here for the first time in Norway. Sebastes mentella had two to three groups, likely representing previously identified depth-related ecotypes. Our study shows high genetic distinctiveness between acknowledged northeast-Atlantic Sebastes species, and between the cryptic species S. norvegicus A and B. Previously identified, fast-growing giant seems to be closely related to S. norvegicus B. Only few SNP markers are necessary for accurate species determination, facilitating further studies and widely applicable monitoring.