Development of <scp>SNP</scp> for <i>Sebastes</i> Species Identification With Special Focus on the Cryptic Species Complex of <i>Sebastes norvegicus</i>

The genus <i>Sebastes</i> in the North Atlantic comprises of long lived deep-waters species that have been extensively fished upon, and many stocks are severely depleted across the Atlantic. This is particularly evident for the species <i>Sebastes norvegicus</i>. In recent papers, cryptic species have been indicated within this genus and molecular markers are therefore needed to provide identification for the <i>Sebastes</i> species, including the cryptic species as a basis for advice regarding management and rebuilding of the stocks. A suite of 2800 Single Nucleotide Polymorphism (SNP) markers were identified from ddRAD sequencing data, of which 56 SNPs were organized in two multiplex reactions and tested on 191 <i>Sebastes</i> spp. from different sampling locations from Norway and Greenland. Good-quality amplification products were successfully obtained from 49 SNP markers for <i>Sebastes</i> species ID, and 3 TaqMan probes were designed to successfully assign <i>S. mentella</i>, <i>S. viviparus</i>, and the two cryptic species <i>S. norvegicus</i> types A and B. A total 47 SNPs were biallelic, with averaged <i>H</i> _E per locus ranging between 0.053 and 0.50. This SNP-based method establishes a foundation for genetically identifying the Northeast Atlantic <i>Sebastes</i> species. The findings presented should be followed by an effort to look for morphological characters to recognize the <i>S. norvegicus</i> cryptic species on site. In general, the SNP markers are a proper tool for monitoring the distribution of the species from a management perspective.