Genetic diversity and population structure of Raja clavata in the North-East Atlantic

Thornback Ray (Raja clavata) is a relatively abundant commercial skate species occurring in coastal waters of the North-East Atlantic and Mediterranean, listed by the IUCN as Near Threatened. It is the dominant skate species caught in commercial fisheries in northern European seas. Historically, regional population declines have been observed, although increased landings indicate increases in population size in several areas over recent decades. This study describes the genetic diversity and population structure of Raja clavata hierarchically among ecoregions, spanning the Greater North Sea (GNS), Celtic Sea (CS), and Bay of Biscay and Iberian coast (BB), as well as within ecoregions by ICES Divisions. Over 8000 samples were collected (2004 – 2022) and genotyped. Subsequent quality control resulted in a SNP dataset of >4000 SNPs for analyses. Estimates of genetic diversity are provided among and within ecoregions. Small yet significant genetic differentiation was evident globally (Fst,global = 0.0042) and among all ecoregions via pairwise Fst (Fst,GNS-CS = 0.003, Fst,CS-BB = 0.007, Fst,GNS-BB = 0.009; p-values < 0.01). Only ICES Divisions 4b and 4c in the GNS (Fst,4b-4c = 0.00004, p = 0.144) showed no significant genetic differentiation within ecoregions. AMOVA, discriminant component analysis, and admixture modelling provide further evidence and describe the population structure on both hierarchical population levels investigated. This is the largest known genetic study of Raja clavata, to our knowledge. This research helps to inform stock identification and thus assessment, conservation and fisheries management, by accounting for genetic population structure at different spatial scales in the North-East Atlantic.
Keywords: population structure; genetics; SNP; elasmobranch; North-East Atlantic