Regional genetic in situ differentiation despite phylogenetic heterogeneity in Alpine mountain hares

We analysed 128 mountain hares Lepus timidus varronis from eastern Switzerland with respect to genetic variability, differentiation and phylogeography. The molecular markers chosen were 443 bp of the mitochondrial control region and 13 microsatellite loci (12 of which were polymorphic). Among the 113 successfully sequenced hares, five yielded introgressed brown hare Lepus europaeus haplotypes, making our study one of few to show introgression of mitochondrial brown hare alleles into mountain hare gene pools rather than the other way around. Overall haplotype and nucleotide diversities were 0.91 and 0.0081, and observed and expected heterozygosities were 0.40 and 0.54. Our Swiss sample did not show unequivocal signals of substructuring and probably represents a (nearly) pan-mictic population. We also analysed the 20 haplotypes we found phylogeographically in a global framework by adding 143 published sequences from throughout the species' distribution range. The resulting haplotype network lacked an overall geographical structure, but instead consisted of many geographically meaningful subclusters that were scattered throughout the network, including different groups of Russian, Scandinavian or Alpine sequences. This pattern is in line with earlier findings and expectations for arctic species and is indicative of a continuous population across the European continent during the last ice age. Unexpectedly, our Swiss haplotypes all clustered together, suggesting that most of them originated in situ after the isolation of the Alpine population in the late Pleistocene.