Environmental DNA from soil reveals the presence of a “lost” Afrotherian species

Abstract

Environmental DNA (eDNA) sampling has attracted worldwide attention over the past few years as an emerging approach to characterising and monitoring biodiversity, and has become particularly important for species that are rare, elusive or endangered. Most animal studies to date have focused on aquatic taxa; studies on other metazoan taxa, particularly wildlife in terrestrial environments, are scarce, with only a handful utilizing soil sources. We aimed to investigate the use of DNA barcoding from soil eDNA in (1) detecting rare/elusive/threatened species and (2) as a tool to investigate and potentially monitor range distributions. Through extensive eDNA sampling along the west coast of South Africa, we aimed to refine the distributions of four golden mole species thought to occur there, and specifically to determine whether De Winton’s golden mole, Cryptochloris wintoni (IUCN Critically Endangered; Possibly Extinct), is in fact extant or extinct. Sequences were generated for three barcode markers (mtDNA cyt b, 12S and nuclear GHR) using next-generation amplicon sequencing. Tissue samples from four specimens were used to generate reference sequences for species identification, along with available GenBank sequences. We were able to (1) successfully detect all four species in our data, and (2) improve records of the distributions of these species. Furthermore, we uncovered cryptic diversity in Eremitalpa granti. Our data conclusively reveal the presence of the elusive Cryptochloris wintoni and suggest that this species may in fact be widespread, but not necessarily abundant, and certainly less so in areas subjected to mining activities, which continue to pose a threat to the species.