Genome-wide markers reveal differentiation between and within the cryptic sister species, sunset and vermilion rockfish

Abstract The vermilion rockfish complex, which consists of the cryptic sister species and sunset rockfish, is one most valuable recreational fisheries on U.S. West Coast. These are currently managed as a single because uncertainty surrounding relative contribution each within existing data sources, stock status not fully known. A reliable cost-effective method needed to disentangle these that will allow for development abundance indices, life history profiles, catch histories may potentially support species-specific assessments. Using restriction-site associated DNA sequence (RADseq) markers we generated 10,003 polymorphic loci characterize complex. PCA Bayesian clustering approaches based clearly distinguished between rockfishes identified hybrid individuals. included 203 highly differentiated (F ST ? 0.99) nucleotide polymorphisms, consider candidates in planned diagnostic assay capable distinguishing species. In addition delineating species, subsets interspecific allowed insight into intraspecific differentiation both Population genetic analyses two weakly divergent groups with similar levels diversity. Vermilion however, were characterized by three distinct much stronger signals significantly different diversities. Collectively, contribute well-informed, management strategies protect this