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

DATA AVAILABILITY : The data generated and analysed in the current study are available on GenBank (accession numbers: OP279338-OP279343). Additional data generated but not analysed in the current study may be found in the supplementary information, and/or upon reasonable request from the authors.SUPPLEMENTARY INFORMATION : FIGURE S1. Maximum likelihood bootstrap consensus trees of sampled specimens and eDNA contigs for cyt b (a) 12S (b). TABLE S1. Bioinformatic filtering of environmental DNA (eDNA) NGS data using the BBDuk function in geneious prime. TABLE S2. Comprehensive list of hits from the preliminary BLAST searches conducted in geneious prime.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.In part by Re:wild and in part by the National Research Foundation (NRF) Foundational Biodiversity Information Programme and supported by Rand Merchant Bank. Open access funding provided by Stellenbosch University.http://link.springer.com/journal/10531hj2024BiochemistryGeneticsMicrobiology and Plant PathologyZoology and EntomologySDG-15:Life on lan

Optimising observing strategies for monitoring animals using drone-mounted thermal infrared cameras

The proliferation of relatively affordable off-the-shelf drones offers great opportunities for wildlife monitoring and conservation. Similarly the recent reduction in cost of thermal infrared cameras also offers new promise in this field, as they have the advantage over conventional RGB cameras of being able to distinguish animals based on their body heat and being able to detect animals at night. However, the use of drone-mounted thermal infrared cameras comes with several technical challenges. In this paper we address some of these issues, namely thermal contrast problems due to heat from the ground, absorption and emission of thermal infrared radiation by the atmosphere, obscuration by vegetation, and optimizing the flying height of drones for a best balance between covering a large area and being able to accurately image and identify animals of interest. We demonstrate the application of these methods with a case study using field data, and make the first ever detection of the critically endangered riverine rabbit (Bunolagus monticularis) in thermal infrared data. We provide a web-tool so that the community can easily apply these techniques to other studies (http://www.astro.ljmu.ac.uk/~aricburk/uav_calc/)

Diamond mine or gold mine? Using eDNA to identify golden moles along the west coast of South Africa

Golden moles (Chrysochloridae) represent one of the most threatened mammal groups in southern Africa. The west coast of South Africa is an important but under-surveyed part of their range. Vast stretches of the coastal dune habitats have been severely impacted by alluvial diamond mining over the past century, and rapidly developing residential areas and agriculture have continued to transform large sections of these habitats, particularly over the past two decades. This has created concern among conservationists for the conservation status and continued survival of golden mole species in these dune ecosystems. In spite of the prevailing diamond mining activities, we are interested in finding a shimmer of the “living gold” of the Chrysochloridae that potentially still exists here, and when we do, devising plans to protect it.http://afrotheria.net/ASG.htmlam2022BiochemistryGeneticsMicrobiology and Plant Patholog