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

Abstract

The analysis of waterborne environmental DNA (eDNA) is effective for detecting invasive species and conducting large-scale biodiversity assessments, making it a potentially powerful tool for documenting diversity at sites where large numbers of species aggregate. We explore the utility of eDNA from waterholes for describing local mammal communities, quantifying patterns of species co-occurrences, and monitoring of rare or threatened species. In savanna ecosystems water can be a scarce resource during dry seasons and in periods of drought, promoting the aggregation of medium to large mammals. To explore the reliability of eDNA as a biodiversity indicator in these arid and semi-arid environments, we compare eDNA metabarcoding and camera traps for documenting waterhole use by mammals in the Kruger National Park, South Africa. We find that eDNA metabarcoding can recover the majority of mammal species detected in camera traps, but the DNA signatures of mammal visitation are temporally limited. Detection rates varied across sites, sampling time, species, and choice of reference library, with the best performance for water-dependent large bodied mammals visiting within two days of sampling, and matched to a curated system-specific reference library. Our results demonstrate that eDNA-based approaches can be used to track mammals of conservation concern, and reflect patterns of recent waterhole use and co-occurrence across water-dependent species, but also highlight limitations including the lack of long-term eDNA persistence in small and highly utilized waterholes and variability in detection rates among species. Sequencing of eDNA is a valuable tool for next-generation biodiversity sampling and has many exciting applications, but it is not sufficient to capture long-term waterhole visitation patterns or reliably detect rare and small-bodied species.

Detecting bat environmental DNA from water-filled road-ruts in upland forest

“…More recently, methods for eDNA collection from aquatic environments have been developed for detection of terrestrial mammals, such as coyotes ( Canis latrans ) (Rodgers & Mock, 2015), invasive wild boar ( Sus scrofa ) (Davis et al, 2018), elusive jaguar ( Panthera onca ) (Wilcox et al, 2021), and even entire terrestrial mammal communities (Ushio et al, 2017; Harper et al, 2019). The detection of terrestrial mammals from an aquatic water source is dependent upon the frequency and duration the species spends drinking and/or wading through the body of water (Seeber et al, 2019), and the time since the species last visited (Farrell et al, 2020). Even with the limited release of terrestrial eDNA compared to aquatic fauna, some terrestrial birds (Day et al, 2019) and mammals (Sales et al, 2019) have displayed greater detection probability with eDNA compared to traditional monitoring methods.…”