DNA barcoding reveals cryptic diversification and taxonomic discordance among bats and birds within sub-Saharan Africa

Abstract Cryptic species present a challenge for conservation, as undetected diversity may be lost. DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) has become a useful heuristic tool for delimiting species boundaries and detecting cryptic speciation across different animal taxa. Despite concerted efforts to genetically barcode bats and birds, comprehensive assessments have yet to be undertaken across the Afrotropics. We retrieved available DNA barcodes of bat and bird species naturally breeding within the Afrotropics. Using Bayesian phylogenetic modelling, we assessed DNA barcode performance at species identification, and to detect instances of non-monophyly (indicating potential cryptic speciation). Available DNA barcodes represent only 42.3 % and 23.6 % of the relevant bat and bird species diversity, respectively, with only 18.7 % of bat species and 7.2 % of bird species having geographic coverage. DNA barcodes afforded greater taxonomic resolution of Afrotropical bird species than of bats (96.8 % vs 84.0 %), with the bats reporting a higher species non-monophyly (25.5 % vs 4.8 %). Twenty-one bat species and fifteen bird species exhibited well-supported phylogenetic complexity. Additionally, deep intraspecific divergences (>2.0 %) were observed in one bat species and fifteen bird species. These instances of non-monophyly and deep intraspecific divergences may represent cryptic speciation within these volant taxa, suggesting greater hidden diversity of more sedentary African fauna. They also highlight the importance of areas such as the Congo-Guinean lowland forests to endemic vertebrate diversity. The current taxonomic status of birds is better supported by this molecular evidence than that of bats.