1. Department of Zoology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
2. Wildlife Genetics Unit, Division of Chemical Pathology, University of Cape Town, Observatory, 7925, South Africa
3. Present address: Laboratory of Genomic Diversity, National Cancer Institute, PO Box B, Frederick, Maryland 21702, USA.

Correspondence to: Cassandra M. Miller-Butterworth^1,2,3 Email: cbutterworth@mail.ncifcrf.gov
Microsatellite primer sequences and unique mitochondrial DNA control region haplotype sequences have been deposited in GenBank under accession numbers AY056588-AY056592 and AY228384-AY228439 respectively.

Abstract

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^{1, 2}. In general, strongly substructured mammalian populations either are separated by non-traversable barriers or belong to terrestrial species with low dispersal abilities³. 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 flow⁴. Male-biased dispersal is considered typical for mammals⁵, 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.