DNA Barcoding Reveals High Diversity of Bats from the Family Phyllostomidae (Mammalia, Chiroptera) from Brazilian Biomes

The family Phyllostomidae is notable for its remarkable species richness and wide array of unique traits and behaviors, which contribute to ongoing uncertainty about the relationships within the group. Moreover, morphological similarities among some species may result in overlooked diversity. DNA barcoding has proven to be useful in the identification and delimitation of these species. Consequently, the diversity of phyllostomid bats in fragments of the Amazon, Cerrado, and Caatinga biomes was investigated using five species delimitation methods: ABGD, ASAP, mPTP, bPTP, and sGMYC. Our dataset included COI gene sequences from specimens collected in Maranhão's Amazon and Cerrado fragments and the Caatinga in Piauí, supplemented with GenBank sequences. Morphological identification revealed 30 nominal Phyllostomidae species across these biomes, whereas molecular data resolved 29 species, with Carollia represented as a single taxonomic unit at the species level. Delimitation tests identified 32–39 Molecular Operational Taxonomic Units (MOTUs), with at least two MOTUs for eight nominal species: Desmodus rotundus, Diphylla ecaudata, Gardnerycteris crenulatum, Phylloderma stenops, Micronycteris minuta, Hsunycteris thomasi, Trachops cirrhosus, and Trinycteris nicefori. Our results further indicate a relationship between the average intraspecific genetic distance and the presence of different lineages, suggesting that observed diversity patterns likely reflect undocumented species diversity. This reveals that phyllostomid bat diversity in Brazilian biomes is underestimated, with evidence of underscribed or not yet fully understood taxa, evolutionary distinct lineages, and cryptic species.