Data from: Genome-wide SNP assessment of contemporary European red deer genetic structure highlights the distinction between peripheral populations and the main admixture zones in Europe

Genome-wide technologies open up new possibilities to clarify questions on
genetic structure and phylogeographic history of taxa previously studied
with microsatellite loci and mitochondrial sequences. Here, we used 736
individual red deer (Cervus elaphus) samples genotyped at 35,701 single
nucleotide polymorphism loci (SNPs) to assess the population structure of
the species throughout Europe. The results identified 28 populations, with
higher degrees of genetic distinction in peripheral compared to mainland
populations. Iberian red deer show high genetic differentiation, with
lineages in Western and Central Iberia maintaining their distinctiveness,
which supports separate refugial ranges within Iberia along with little
recent connection between Iberian and the remaining Western European
populations. The Norwegian population exhibited the lowest variability and
the largest allele frequency differences from mainland European
populations, compatible with a history of bottlenecks and drift during
postglacial colonization from southern refugia. Scottish populations
showed a high genetic distance from the mainland but high levels of
diversity. Hybrid zones were found between Eastern and Western European
lineages in Central Europe as well as in the Pyrenees, where red deer from
France are in close contact with Iberian red deer. Anthropogenic
restocking has promoted the Pyrenean contact zone, admixture events in
populations on the Isle of Rum and the Netherlands, and at least partly
the admixture of the two main lineages in central-eastern Europe. Our
analysis enabled detailed resolution of the population structure of a
large mammal widely distributed throughout Europe and contributes to
resolving the evolutionary history, which can also inform conservation and
management policies.