Gene flow results from movement between populations, homogenising gene pools and impacting genetic variation and evolution. Growing evidence suggests that movement of individuals among populations may be more strongly determined by ecological traits. We compared genetic and morphometric differentiation in four species of bats — Eonycteris spelaea, Cynopterus sphinx, Rhinolophus affinis and Hipposideros pomona — which differ in their flight capability and roosting requirement to understand their effects in shaping genetic structure. Hypervariable region I of the mitochondrial control region was amplified from 40 E. spelaea, 28 C. sphinx, 44 R. affinis and 57 H. pomona sampled from locations spread across the Andaman archipelago. Populations of E. spelaea were nearly panmictic; R. affinis were differentiated into two clusters, and H. pomona were differentiated into three clusters. Consistent genetic and morphometric clusters were obtained for C. sphinx and the genetic break for C. sphinx occurs between Middle and South Andaman Islands, coincided with the Jarawa Tribal Reserve. In conclusion, poorly-dispersing, caveroosting species show high population structure, but when flight capability is very well-developed, the effect of disjunct roost availability is offset. The genetic structure of C. sphinx where we expected panmixia, is possibly confounded by the colonization history of its two genetic lineages and its habitat use which may prevent significant gene flow between the two lineages.
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