Population genomics reveals fine-scale three-dimensional structure within two sympatric Sebastes species in the Northwest Atlantic

An ideal fishery stock assessment requires a comprehensive understanding of population structure across landscapes. In the Gulf of St. Lawrence and the Laurentian Channel (GSL-LC), massive Sebastes recruitments occurred in early 2010s, nearly 30 years after the last strong cohort. This recruitment had resulted in abundant Sebastes mentella, but also involved the morphologically nearly indistinguishable S. fasciatus. Both species show multiple populations, but spatially explicit information at a management- relevant scale is lacking to support robust scientific advices for sustainable fisheries. Temporal variation in the Sebastes recruitment also remains poorly characterized, and it is unknown if the recruitment is synchronized at the species or population level. This study aimed to 1) characterize the current fine- scale genomic structure of S. mentella and S. fasciatus in the GSL-LC, 2) compare the genetic composition of different cohorts, and 3) evaluate relationship between genomic structure and two key factors in redfish management, depth, and management units. Our genomic datasets (> 16,000 SNPs, N = 2,248 redfish) revealed substructure within the previously identified S. mentella GSL ecotype and five S. fasciatus populations within the GSL-LC. While all genetic groups were represented in the recent cohort samples, our results suggested unequal contributions of S. fasciatus populations to massive recruitment events. The spatial distribution of genetic groups within both species revealed a three- dimensional structure tied to management units and depth. Our findings underscore the importance of revising management measures to incorporate population structure thereby reducing the risk of overexploiting smaller populations, particularly S. fasciatus, and promoting sustainable fisheries.