Highly accurate species identification of Eastern Pacific rockfishes (Sebastes spp.) with high-throughput DNA sequencing

Genetic species identification is often necessary for species flocks, such as rockfishes in the genus Sebastes (Teleostei, Scorpaenidae). Traditional visual identification methods are challenged by the presence of many sympatric rockfish species with morphologically similar juveniles. Here we present a straightforward approach for species identification in rockfishes using 96 nuclear microhaplotype loci that can be efficiently genotyped using high-throughput DNA sequencing. Self-assignment of nearly 1 000 samples from 54 species resulted in > 99% accurate species identification at a 95% confidence threshold. Phylogenetic relationships of Sebastes uncovered with these same loci were highly concordant with relationships previously derived primarily with mitochondrial DNA. We also assessed ascertainment bias and consequent reduced nucleotide diversity and heterozygosity in non-ascertainment species to understand the potential utility of these markers for those species. The data and protocol presented here will be useful for research and management of rockfishes in the Northeastern Pacific Ocean.