Development and Validation of an eDNA Primer Set for Rockfishes in the Alaska Current Provides a New Tool for Fisheries Management Environmental DNA

Environmental DNA (eDNA) metabarcoding primers that target specific taxonomic groups can alleviate the common shortcoming of metabarcoding studies in differentiating closely related taxa of interest. Here, we describe the development and validation of an eDNA metabarcoding primer set for the diverse genus of rockfishes (Sebastes sp.), with a focus on species found in the Alaska Current—many of which are commercially and recreationally important or of conservation concern. Our results demonstrate that the Sebastes D‐loop primer set improves upon existing fish eDNA metabarcoding primer sets by providing accurate species identification for nearly all of the 42 species of rockfishes tested. Using this primer set with mock community samples resulted in substantial amplification bias across 18 rockfishes, suggesting that a quantitative metabarcoding model would be appropriate for correcting bias in future datasets. Testing the Sebastes D‐loop primers with aquarium eDNA samples containing 11 species of rockfishes (high eDNA concentration) and eDNA samples collected on a trawl survey in the Aleutian Islands (low eDNA concentration) confirmed that the primer set is robust to varying rockfish species compositions and concentrations. These findings highlight the potential of the Sebastes D‐loop primer set as a valuable tool for enhancing species identification and characterization of species assemblages in eDNA studies, and as a reliable method for rockfish population monitoring and assessment.