Cryptic Diversity and Patterns of Structure in Nine Species of North Pacific Rockfishes ( Sebastes spp. and Sebastolobus spp.)

ABSTRACT

Understanding how habitat and life history traits contribute to population genetic structure is critical for evaluating conservation risks and identifying optimal management of wild populations. Species derived from adaptive radiations can provide a useful model for studying such patterns because the presence of some consistent traits allows for closer examination of attributes which differ. Here, we examine population structure in rockfishes (genera Sebastes and Sebastolobus ), a group of speciose, recently diverged marine fishes that exhibit a continuum of genetic structure, from cryptic species to putative genetic panmixia. In this study, we analyse low‐coverage whole genome resequencing data from nine rockfish species and identify four major types of genetic differentiation: cryptic diversity, isolation‐by‐distance (IBD), no detectable structure (putative panmixia) and no detectable structure with a single genomic region putatively underlying local adaptation. Two species, Dark ( Sebastes ciliatus ) and Northern ( S. polyspinis ) rockfishes, each exhibited cryptic diversity consisting of two sympatric groups differentiated at every chromosome throughout the genome. Black rockfish in Southeast Alaska also had two genetic groups, despite an overall signal of IBD from the West Coast of North America through the Gulf of Alaska (GOA). Five species showed evidence of genetic panmixia throughout the sampled range, while Yelloweye Rockfish exhibited high gene flow across ~4000 km, from southern California to the GOA, but had strong differentiation between the Salish Sea and the outer coast. Of the species in which no structure was detected, only Blackspotted Rockfish had one outlier region exhibiting signatures of potential local adaptation. Our results highlight how multiple mechanisms likely promote genetic structure in rockfishes, hinting at tentative links to depth distributions and offshore habitats that might influence patterns of differentiation in rockfishes more broadly. Further, this study provides genetic data for some of the most abundant rockfishes in commercial fisheries in the Northeast Pacific, enhancing the scientific information available for informing fisheries management.