Examining patterns of inter-population genetic diversity can provide valuable information about both historical and current evolutionary processes affecting a species. Population genetic studies of flying and migratory species such as bats and birds have traditionally shown minimal population substructure, characterized by high levels of gene flow between populations. In general, strongly substructured mammalian populations either are separated by non-traversable barriers or belong to terrestrial species with low dispersal abilities. Species with female philopatry (the tendency to remain in or consistently return to the natal territory) might show strong substructure when examined with maternally inherited mitochondrial DNA, but this substructure generally disappears when biparentally inherited markers are used, owing to male-mediated gene flow. Male-biased dispersal is considered typical for mammals, and philopatry in both sexes is rare. Here we show strong population substructure in a migratory bat species, and philopatry in both sexes, as indicated by concordance of nuclear and mtDNA findings. Furthermore, the genetic structure correlates with local biomes and differentiation in wing morphology. There is therefore a close correlation of genetic and morphological differentiation in sympatric subspecific populations of this mammalian species.
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