Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity

Large-scale monitoring schemes are essential in assessing global mammalian biodiversity, and in this framework leeches have recently been promoted as an indirect source of DNA from terrestrial mammal species. Carrion feeding flies are ubiquitous and can be expected to feed on many vertebrate carcasses. Hence, we tested whether fly-derived DNA analysis may also serve as a novel tool for mammalian diversity surveys. We screened DNA extracted from 201 carrion flies collected in tropical habitats of Côte d’Ivoire and Madagascar for mammal DNA using multiple PCR systems and retrieved DNA sequences from a diverse set of species (22 in Côte d’Ivoire, 4 in Madagascar) exploiting distinct forest strata and displaying a broad range of body sizes. Deep-sequencing of amplicons generated from pools of flies performed equally well as individual sequencing approaches. We conclude that the analysis of fly-derived DNA can be implemented in a very rapid and cost-effective manner and will give a relativel...