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Background  Population-level studies of parasites have the potential to elucidate patterns of host movement and cross-species interactions that are not evident from host genealogy alone. Bat flies are obligate and generally host-specific blood-feeding parasites of bats. Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date.    Methods  We collected a total of 125 bat flies from three  Pteropus  species ( Pteropus vampyrus, P. hypomelanus , and  P. lylei ) from eight localities in Malaysia, Cambodia, and Vietnam. We identified specimens morphologically and then sequenced three mitochondrial DNA gene fragments (CoI, CoII, cytB; 1744 basepairs total) from a subset of 45 bat flies. We measured genetic diversity, molecular variance, and population genetic subdivision (F ST ), and used phylogenetic and haplotype network analyses to quantify parasite genetic structure across host species and localities.    Results  All flies were identified as  Cyclopodia horsfieldi  with the exception of two individuals of  Eucampsipoda sundaica . Low levels of population genetic structure were detected between populations of  Cyclopodia horsfieldi  from across a wide geographic range (~1000 km), and tests for isolation by distance were rejected. AMOVA results support a lack of geographic and host-specific population structure, with molecular variance primarily partitioned within populations. Pairwise F ST  values from flies collected from island populations of  Pteropus hypomelanus  in East and West Peninsular Malaysia supported predictions based on previous studies of host genetic structure.    Conclusions  The lack of population genetic structure and morphological variation observed in  Cyclopodia horsfieldi  is most likely due to frequent contact between flying fox species and subsequent high levels of parasite gene flow. Specifically, we suggest that  Pteropus vampyrus  may facilitate movement of bat flies between the three  Pteropus  species in the region. We demonstrate the utility of parasite genetics as an additional layer of information to measure host movement and interspecific host contact. These approaches may have wide implications for understanding zoonotic, epizootic, and enzootic disease dynamics. Bat flies may play a role as vectors of disease in bats, and their competence as vectors of bacterial and/or viral pathogens is in need of further investigation.

Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia