The European roe deer (Capreolus capreolus) is one of the most numerous and widespread ungulate species in Europe, which has complicated the assessment of its genetic diversity on a range-wide scale. In this study, we present the mitochondrial DNA control region (mtDNA CR) genetic diversity and population structure of roe deer in Europe based on the analyses of 3010 samples, which were described as European roe deer individuals. Our analyses revealed two main diversity hotspots, namely Eastern and Central Europe. We proposed that these hotspots result from the Siberian roe deer (C. pygargus) mtDNA introgression and the secondary contact of mtDNA clades, respectively. Significantly lower values of genetic diversity (nucleotide and haplotype diversity) were recorded in the peripheral areas of the species’ range, including the southernmost parts of the Last Glacial Maximum (LGM) refugial areas. Roe deer population in Europe consists of 2–3 genetic groups according to SAMOVA, and 15–16 clusters identified by GENELAND. The main driver of roe deer population structure in the eastern parts of the continent has been introgression of mtDNA of C. pygargus. Spatial genetic analyses revealed a complex structure of roe deer on a pan-European scale, which presumably results from post-glacial recolonization of the continent from various parts of a large LGM refugial area by different roe deer mtDNA clades and haplogroups.
