Discordance between mitochondrial and nuclear genetic structure in the bat Chaerephon pumilus (Chiroptera: Molossidae) from southern Africa

The aim of this study was to investigate the evolutionary determinants of genetic structure in a molossid bat, Chaerephon pumilus, from South Africa based on 306 nucleotides of the mitochondrial control region and six microsatellite markers. We recovered strong mitochondrial genetic structure, with 90% of the molecular variance occurring among four phylogenetically-defined groups. Mismatch distributions and Bayesian skyline analyses of mitochondrial data indicated that the sample comprised subgroups, which were at demographic equilibrium over the Late Pleistocene era. Analyses based on microsatellite data contrasted strongly with the mitochondrial data. Three admixed populations were recovered; only 3% of the nuclear variance occurred among populations, which was low and not significant. This is indicative of little nuclear genetic structure among the groups of C. pumilus, which appear to comprise a single interbreeding population. Consistent with this, global Fis was not significant. Such high levels of mitochondrial genetic structure in the absence of significant nuclear structure are consistent with female philopatry, secondary contact between diverged genetic lineages and introgression.