Sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene have been shown to be useful for species identification in various groups of animals. However, the DNA barcoding approach has never been tested on African fruit bats of the family Pteropodidae (Mammalia, Chiroptera). In this study, the COI gene was sequenced from 120 bats collected in the Central African Republic and belonging to either Epomophorus gambianus or Micropteropus pusillus, two species easily diagnosed on the basis of morphological characters, such as body size, skull shape and palatal ridges. Two additional molecular markers were used for comparisons: the complete mitochondrial cytochrome b gene and the intron 7 of the nuclear β-fibrinogen (FGB) gene. Our results reveal an unexpected discordance between mitochondrial and nuclear genes. The nuclear FGB signal agrees with our morphological identifications, as the three alleles detected for E. gambianus are divergent from the fourteen alleles found for M. pusillus. By contrast, this taxonomic distinction is not recovered with the analyses of mitochondrial genes, which support rather a polyphyletic pattern for both species. The conflict between molecular markers is explained by multiple mtDNA introgression events from M. pusillus into E. gambianus or, alternatively, by incomplete lineage sorting of mtDNA haplotypes associated with positive selection on FGB alleles of M. pusillus. Our work shows the failure of DNA barcoding to discriminate between two morphologically distinct fruit bat species and highlights the importance of using both mitochondrial and nuclear markers for taxonomic identification.
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