Fly-derived DNA and camera traps are complementary tools for assessing mammalian biodiversity

Background: Metabarcoding of vertebrate DNA found in invertebrates (iDNA) represents a potentially powerful tool for monitoring biodiversity. Preliminary evidence suggests fly iDNA biodiversity assessments compare favorably with established approaches such as camera trapping or line transects. Aims and Methods: To assess whether fly-derived iDNA is consistently useful for biodiversity monitoring across a diversity of ecosystems, we compared metabarcoding of the mitochondrial 16S gene of fly pool-derived iDNA (range = 49–105 flies/site, N = 784 flies) with camera traps (range = 198–1,654 videos of mammals identified to the species level/site) at eight sites, representing different habitat types in five countries across tropical Africa. Results: We detected a similar number of mammal species using fly-derived iDNA (range = 8–15 species/site) and camera traps (range = 8–27 species/site). However, the two approaches detected mostly different species (range = 6%–43% of species detected/site were detected with both methods), with fly-derived iDNA detecting on average smaller-bodied species than camera traps. Despite addressing different phylogenetic components of local mammalian communities, both methods resulted in similar beta-diversity estimates across sites and habitats. Conclusion: These results support a growing body of evidence that fly-derived iDNA is a cost- and time-efficient tool that complements camera trapping in assessing mammalian biodiversity. Fly-derived iDNA may facilitate biomonitoring in terrestrial ecosystems at broad spatial and temporal scales, in much the same way as water eDNA has improved biomonitoring across aquatic ecosystems.