Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Abstract

Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA‐based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water‐limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus‐specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non‐African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over‐representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100‐fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.

Non-invasive surveys of mammalian viruses using environmental DNA

“…Fig. 12), consistent with the detection of Plains zebra's (Equus quagga) DNA from this water source [3]. Given that both captive and wild zebras have been known to contract bovine papillomaviruses [10,11] it is likely that they are susceptible to different equine papillomaviruses.…”

“…Environmental DNA (eDNA) and its subdiscipline, invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively [1,2]. Water is ubiquitous in most ecosystems, and, among invertebrates, terrestrial haematophagous leeches are abundant and can be easily collected in many tropical rainforests [3,4]. Such non-invasive nucleic acid sources can mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species.…”

Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples

“…Target capture is well known from ancient DNA (aDNA) research, for enriching endogenous components of DNA from samples of, for example, bone or hair (Carpenter et al., 2013; Cruz‐Dávalos et al., 2017; Paijmans et al., 2016). Recently, the approach has also been implemented on ancient (Slon et al., 2017) and contemporary (e.g., Seeber et al., 2019) eDNA samples. Seeber et al.…”

Environmental DNA as a management tool for tracking artificial waterhole use in savanna ecosystems

“…Waterholes are thus prime targets for biodiversity monitoring and eDNA sampling. Sequencing of eDNA present in waterholes and ponds has been successfully used for surveying terrestrial mammals in sub-Saharan Africa (Seeber et al, 2019) and Japan (Ushio et al, 2017), multiple vertebrates in Australian arid zones (Furlan et al, 2020) including the endangered Gouldian finch (Erythrura gouldiae) (Day et al, 2019), and both semi-aquatic and terrestrial mammals in the United Kingdom (Harper et al, 2019). Despite the promise of this approach, there remain many questions about its limitations, including the physical properties of eDNA that influence transport and decay (Harrison et al, 2019), best practices for limiting species identification errors due to molecular and bioinformatic workflows (Furlan et al, 2020), choice of molecular reference library for metabarcoding approaches (Porter and Hajibabaei, 2018b), and how eDNA biomonitoring compares to other emerging methods for biodiversity surveys (Schnell et al, 2015;Sales et al, 2020;Leempoel et al, 2020;Gogarten et al, 2020).…”

“…Screening of species via conserved marker genes, known as “metabarcoding” (Taberlet et al, 2012), is used for monitoring organisms from freshwater, marine, and terrestrial environments (Deiner et al, 2017), and allows for the detection of multiple species with a single sample. eDNA metabarcoding may be useful for describing local communities, quantifying patterns of species co-occurrence, and monitoring of endangered species, but its efficacy can be highly context dependent (Ushio et al, 2017; Seeber et al, 2019; Harrison et al, 2019; Sales et al, 2020; Leempoel et al, 2020). Here, we evaluate the performance of eDNA sampled from waterholes relative to species visitations documented by camera traps, and consider its application as a biodiversity survey tool to both track individual mammal species presence as well as their co-occurrences in a savanna ecosystem of high conservation value.…”