Data from: RAD-genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species; the American lobster (Homarus americanus).

Deciphering genetic structure in marine species has been challenging due to very weak genetic differentiation and relatively low resolution offered by limited numbers of genetic markers. Here, we genotyped 10,156 filtered SNPs using RAD-sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in ¬¬17 locations distributed across a large portion of the species’ natural distribution range. Our results first revealed the existence of a hierarchical genetic structure separating lobsters from the Gulf of Maine and the Gulf of St. Lawrence (FCT = 0.0011; P-value = 0.0002), and then identifying 11 genetically distinct populations (mean FST = 0.00185; CI: 0.0007-0.0021, P-value < 0.0002), which provided strong evidence for weak, albeit fine-scale population structuring within each region. We showed that assignment success increased with the number of most differentiated SNPs until reaching a maximum with 3000 SNPs used and then decreased to a minimum when using 10,156 SNPs. By selecting the 3000 most differentiated SNPs and applying Anderson’s (2010) method to avoid “high-grading bias”, 94.2% of the individuals were correctly assigned to their region of origin and 80.8% (range: 55.5% to 95.5%) of all individual lobsters to their local population of origin. Overall, these results demonstrate the increased accuracy of using a large number of SNPs in determining fine scale population structure and assigning individuals to population in highly connected marine species. We discuss the implications of these findings for conservation and management, in particular pertaining to the geographic scale of demographic independence.