Phylogeography of roe deer (Capreolus capreolus) populations: the effects of historical genetic subdivisions and recent nonequilibrium dynamics

Abstract

We sequenced 704 mitochondrial DNA (mtDNA) control-region nucleotides and genotyped 11 autosomal microsatellites (STR) in 617 European roe deer (Capreolus capreolus) samples, aiming to infer the species' phylogeographical structure. The mtDNA sequences were split in three distinct haplogroups, respectively, named: Clade West, sampled mainly in Iberia; Clade East, sampled mainly in Greece and in the Balkans; and Clade Central, which was widespread throughout Europe, including the eastern countries and Iberia, but not Greece. These clades might have originated in distinct Iberian and Balkanic refuges during the penultimate or the last glaciations. Clades East and West contributed little to the current postglacial mtDNA diversity in central Europe, which apparently was recolonized mainly by haplotypes belonging to Clade Central. A unique subclade within Clade Central grouped all the haplotypes sampled from populations of the Italian subspecies C. c. italicus. In contrast, haplotypes sampled in central and southern Spain joined both Clade Central and Clade West, suggesting that subspecies C. c. garganta has admixed origin. STR data support a genetic distinction of peripheral populations in north Iberia and southern Italy, and show the effects of anthropogenic disturbance in fragmented populations, which were recently reintroduced or restocked and not may be in mutation-drift equilibrium. Roe deer in central Europe are mainly admixed, while peripheral populations in north Portugal, the southern Italian Apennines and Greece represent the remains of refugial populations and should be managed accordingly.

Influence of Holocene environmental change and anthropogenic impact on the diversity and distribution of roe deer

“…In addition to these divisions, significant internal structuring has been detected in roe sampled from the Italian and Iberian peninsulas. This supports the existence of a subspecies in central-southern Italy (C. c. italicus) (Lorenzini et al, 2002;Randi et al, 2004) and an additional Celtic-Iberian group in centralsouthern Spain (Royo et al, 2007). Taken together, these data likely reflect the existence of several glacial refugia .…”

“…Genetic variation of the European roe deer divides into central, eastern and western lineages. The central lineage is widespread throughout Europe, whereas the eastern lineage is found mainly in Greece and Serbia and the western lineage is mainly in Spain and Portugal (see Lorenzini et al, 2003;Randi et al, 2004;Lorenzini and Lovari, 2006). In addition to these divisions, significant internal structuring has been detected in roe sampled from the Italian and Iberian peninsulas.…”

“…Our aDNA sequence data were compared against three published modern data sets (Randi et al, 2004;Royo et al, 2007;Baker and Hoelzel, 2013). Details of the exact data used and corresponding accession numbers are provided in Supplementary Table S4.…”

“…A 388-bp region of the consensus mitochondrial DNA (mtDNA) control region was used for subsequent analyses. The European data set was divided into the lineages eastern, western and central as well as the subspecies C. c. italicus (as previously described by Randi et al, 2004) and the Celtic-Iberian group (as previously described by Royo et al, 2007). Summary statistics were calculated in DnaSP10.4.9 (Rozas et al, 2003) for each of the lineages individually and combined, as well as for the ancient and modern UK samples individually and combined.…”

“…Tau (t; calculated using ARLEQUIN 3.5) was used to estimate expansion time (T) using the equation: T ¼ t/2 m where m is the mutation rate in units of substitutions per locus per generation (Rogers and Harpending, 1992). The roe deer generation time was taken to be 3 years (after Randi et al, 1998Randi et al, , 2004.…”