Genetic variation among South African hares (Lepus spec.) as inferred from mitochondrial DNA and microsatellites

The inter- and intraspecific taxonomy of the genus Lepus is highly controversial. Since these animals play an important ecological role as prey species, their conservation is of high priority. A prerequisite for adequate management strategies is the precise knowledge of taxonomic borders and geographic distributions of the taxa in question. Especially in African hares the clear delimitations of the species and subspecies are still unresolved. In an attempt to obtain a clearer understanding of the evolutionary history, the phylogenetic relationships and the detection of conservation relevant units in African hares, a molecular investigation using mitochondrial DNA sequence data and information from six microsatellite loci was initiated. In this study, the phylogenetic analyses of DNA sequence data of the mitochondrial control region and the cytochrome b gene identified 2 major maternal lineages within South African hares that were further subdivided into two clusters each. The nuclear genetic structure revealed by six dedicated microsatellite loci confirmed this subdivision. While the mitochondrial diversity was characterized by high sequence divergences and haplotype diversities, the nuclear variation seemed more moderate with relatively low FST and RST values. Using the information content of the six microsatellite loci developed for this project, the results of assignment tests strongly supported the validity of the four genetic lineages. The levels of of cytochrome b sequence divergences among the four clusters suggested that they may warrant distinct species status (applying the phylogenetic species concept). The data are suggestive of two species groups consisting of two sister species each: A "saxatilis" group with Lepus saxatilis sensu stricto and another species (possibly L. victoriae), and a "capensis" group with L. capensis s. str. and another, yet to be described species. Applying a molecular clock for cytochrome b, the historical dates for the separation of the South African hares from European outgroup species and the split between the two South African species groups were calculated as 4.84 and 3.45 million years ago, respectively. The divergence dates between the sister species was 1.09-1.45 million years ago. Following the biological species concept, the two major clades represent two species: L. saxatilis sensu lata and L. capensis s. I. , that are both subdivided into two geographically separated phylogroups, one in the southern parts of the country and one in the northern. These intraspecific lineages meet the criteria of evolutionarily significant units and should be considered separately in conservation actions. The evolutionary history of scrub and Cape hares in South Africa has been influenced mainly by contiguous range expansions and sudden population size expansions during the Pleistocene climate changes.