Molecular phylogeography of European Sciurus vulgaris: refuge within refugia?

The red squirrel (Sciurus vulgaris) is a well-known forest animal distributed all over
Europe. Still, we are far from having a firm knowledge of the species’ phylogeography.
This study investigates the genetic differentiation of S. vulgaris across the species’ Eurasian
range, using sequence data from the mitochondrial DNA gene (D-loop, 252 base pairs, cytochrome
b, 359 base pairs), and eight variable autosomal microsatellite loci genotyped for 236
individuals. The results reveal the presence of two main mitochondrial phylogroups. The
first clade comprises the individuals from the region of Calabria in southern Italy, belonging
to the subspecies S. v. meridionalis, while the second clade contains the remainder of the studied
individuals. Bayesian analysis of microsatellite genotypes resulted in three main clusterings
corresponding to the three S. vulgaris subspecies: infuscatus, meridionalis and fuscoater.
Geographical distribution of mtDNA haplotypes and mismatch analysis suggest a common
refugium for the red squirrel across most of its present range from which expansion happened
rather rapidly. The genotype mixing of italicus with northern populations could be a residual
of postglacial expansion. The lack of mixing between the Calabrian lineage and the rest of
European red squirrel haplotypes can be seen as evidence for distinct histories throughout
the Pleistocene. Calabrian mtDNA probably diverged in an ice age contraction and
remained isolated from the neighbouring squirrel populations until very recent times.