Genetic structure of a species is associated with historical and recent events, such as gene flow and colonization processes. Studies on terrestrial populations in the low elevation areas of Taiwan show that genetic differentiations are based on barriers provided by the Central Mountain Range. The pattern of genetic structures in bats may differ from other terrestrial mammals because of their ability to fly. I examined genetic variations of the mitochondrial D-loop segments of two hipposiderid bats, Hipposideros terasensis and Coelops frithi formosanus. These two species differ in flight ability and population size.
Extremely low genetic variation was found in H. terasensis. Two major haplotypes were widely distributed in distinct areas. This species underwent a founder effect when colonizing Taiwan, followed by rapid population expansion. This significant (chi-square test, P< 0.0001) geographical population structure may have been caused by two colonizations from mainland China. The low gene flow between the two haplotypes suggested female philopatry. In C. f. formosanus, haplotypes were highly variable and did not overlap among sampling localities. There were unique haplotypes for each colony. This suggested significant (chi-square test, P< 0.0001) geographical population structure and isolation-by-distance. This restricted gene flow was caused by discontinued distribution and the bat’s tendency for slow flight over short distances.