Genome-wide differentiation and SNP-based identification of northeastern Atlantic <i>Sebastes</i> species

Abstract Sustainable fisheries require reliable specimen identification and understanding of underlying genetic hierarchies within target species. Three Sebastes species are commonly found in the northeastern Atlantic: Sebastes mentella (beaked redfish), S. norvegicus (golden redfish), and S. viviparus (Norway redfish). These species are morphologically similar and have largely overlapping distribution ranges. Furthermore, 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 survey their geographic distribution. Here, a total of 99 specimens of S. mentella, S. viviparus, and cryptic S. norvegicus type A and B were used for pooled sequencing 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 and analysed with a discriminatory single nucleotide polymorphism (SNP) panel of high resolution (mean FST = 0.60–0.91), revealed few possible hybrids, and supported further substructuring within S. mentella and S. norvegicus B. The latter was split into two groups, one of which was the previously recognized ‘giant’ morph, confirmed here for the first time in Norway. In S. mentella, two to three genetic groups were found, 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’ morphs seem closely related to S. norvegicus B. Only few SNP markers are necessary for accurate species determination, facilitating further studies and widely applicable monitoring.