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 species diversity may remain undetected. In zoological research, DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) has become a useful heuristic tool for aiding species resolution and informing species discovery. 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 native breeding Afrotropical bat and bird species. Using Bayesian phylogenetic modelling, we assessed DNA barcode performance at species identification, and sought to detect notable intraspecific clade partitioning hinting at 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 geographically spread records. DNA barcodes afforded greater taxonomic resolution of Afrotropical bird species than of bats (96.8% vs. 84.0%), with bats having a higher proportion of species non-monophyly (25.5% vs. 4.8%). Well-supported (≥ 95% posterior probability) clade partitioning was inferable from twenty-one bat species and fifteen bird species, and a further single under-sampled bat species and fifteen such bird species showed deep (> 2.0%) intraspecific divergences. These phylogenetic signatures allude to cryptic speciation within these volant taxa, and serve to prompt more comprehensive assessments of Afrotropical fauna. These findings also indirectly affirm the importance of paleoclimatic refugia to endemic vertebrate diversity. The current taxonomic status of birds is better supported by this molecular evidence than that of bats.