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

Abstract

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, four 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 relatively unbiased picture of local mammal diversity. Carrion flies therefore represent an extraordinary and thus far unexploited resource of mammal DNA, which will probably prove useful for future inventories of wild mammal communities.

The microbiome of New World vultures

“…Amplification of potentially contaminating human DNA was reduced by the addition of blocker oligos during PCR. Although these primers have been successfully used in other dietary DNA studies [6][7][8] , we detected mammalian amplicons in only four (8%) of the vulture hindgut samples (all turkey vultures). In contrast, mammalian DNA was readily amplified from most facial swabs (B90%), representing nine mammalian families (Bovidae, Canidae, Cervidae, Didelphidae, Equidae, Leporidae, Mephitidae, Procyonidae, Suidae).…”

The ecology of environmental DNA and implications for conservation genetics

“…For example, snow samples containing urine have been used for species and individual identification of French wild canids (Valiere and Taberlet 2000), and traces of saliva left on browsed twigs have been used to identify ungulate species (Nichols et al 2012). eDNA methods have been applied to bulk-collected carrion flies, not in a study of the flies themselves, but rather as a tool to assess local mammalian biodiversity (Calvignac-Spencer et al 2013). Similarly, spider web can serve as an eDNA source for both the spider and its prey (Xu et al 2014).…”

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

“…8 using gut or faecal DNA in parasites (Schnell et al, 2012), herbivores (Hibert et al, 2013) or detritivores (Calvignac-Spencer et al, 2013b), the estimation of abundance is much more difficult in these cases because many individuals often feed on the same individual prey (or host) without necessarily causing its death. This means that although presence or absence of the prey (or host) species can be accurately estimated (Calvignac-Spencer et al, 2013a), the occurrence of prey DNA in the faeces of parasites, herbivores or detritivores (i.e.…”