Data from: SNPs reveal a genetic cline across the northeast Atlantic and enable powerful population assignment in the European lobster

Resolving stock structure is crucial for fisheries conservation to ensure
that the spatial implementation of management is commensurate with that of
biological population units. To address this in the economically important
European lobster (Homarus gammarus), genetic structure was explored across
the species’ range using a small panel of single nucleotide polymorphisms
(SNPs) previously isolated from restriction-site associated DNA
sequencing; these SNPs were selected to maximise differentiation at a
range of both broad- and fine-scales. After quality control and filtering,
1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The
results revealed a pronounced phylogeographic break between the Atlantic
and Mediterranean basins, while structure within the Mediterranean was
also apparent, partitioned between lobsters from the central Mediterranean
and the Aegean Sea. In addition, a genetic cline across the northeast
Atlantic was revealed using both putatively neutral and outlier SNPs, but
the precise driver(s) of this clinal pattern –isolation-by-distance,
secondary contact, selection across an environmental gradient, or a
combination of these factors– remains undetermined. Putatively neutral
markers differentiated lobsters from Oosterschelde, an estuary on the
Dutch coast, a finding likely explained by past bottlenecks and limited
gene flow with adjacent North Sea populations. Building on the findings of
our spatial genetic analysis, we were able to test the accuracy of
assigning lobsters at various spatial scales, including to basin of origin
(Atlantic or Mediterranean), region of origin and sampling location. The
predictive model assembled using 79 SNPs correctly assigned 99.7 % of
lobsters not used to build the model to their basin of origin, but
accuracy decreased to region of origin and again to sampling location.
These results are of direct relevance to managers of lobster fisheries and
hatcheries, and provide the basis for a genetic tool for tracing the
origin of European lobsters in the food supply chain.