Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems

Abstract

Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring in both marine and freshwater ecosystems. However, for semi‐aquatic and terrestrial animals, the application of this technique remains relatively untested. We first assess the efficiency of eDNA metabarcoding in detecting semi‐aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, using occupancy modelling we compared the detection efficiency of eDNA metabarcoding to multiple conventional non‐invasive survey methods (latrine surveys and camera trapping). eDNA metabarcoding detected a large proportion of the expected mammalian community within each area. Common species in the areas were detected at the majority of sites. Several key species of conservation concern in the UK were detected by eDNA sampling in areas where authenticated records do not currently exist, but potential false positives were also identified. Water‐based eDNA metabarcoding provided comparable results to conventional survey methods in per unit of survey effort for three species (water vole, field vole and red deer) using occupancy models. The comparison between survey ‘effort’ to reach a detection probability of ≥.95 revealed that 3–6 water replicates would be equivalent to 3–5 latrine surveys and 5–30 weeks of single camera deployment, depending on the species. Synthesis and applications. eDNA metabarcoding can be used to generate an initial ‘distribution map’ of mammalian diversity at the landscape level. If conducted during times of peak abundance, carefully chosen sampling points along multiple river courses provide a reliable snapshot of the species that are present in a catchment area. In order to fully capture solitary, rare and invasive species, we would currently recommend the use of eDNA metabarcoding alongside other non‐invasive surveying methods (i.e. camera traps) to maximize monitoring efforts.

Genetic tools in the management of invasive mammals: recent trends and future perspectives

“…The early and rapid detection of newly introduced mammals is vital to prevent further spread that could subsequently result in a more costly eradication programme. Given the elusive nature of many mammalian species, detection and monitoring often require indirect observations such as searching for latrines, faeces, hair, or tracks, or direct observations such as live‐trapping or camera‐trapping surveys (Sales et al ). These can require differing levels of expertise and resources, but despite high levels of expertise it is not always possible to assign indirect field signs correctly to a species without further confirmation via DNA analysis (Harrington et al ).…”

Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals?

“…In 2019, a pilot study on European mink detection and population monitoring using the environmental DNA (eDNA) metabarcoding method was performed in Northeastern Spain (La Roja and Basque Country) [ 62 , 63 ]. Due to its semiaquatic lifestyle, European mink DNA has a high detection potential from environmental (freshwater) samples, as is the case with other species living in aquatic environments [ 104 , 105 ].…”

How to design optimal eDNA sampling strategies for biomonitoring in river networks

“…While initial studies on biodiversity assessments in riverine ecosystems sampled at one or few locations within a single watershed, without the goal of a catchment-level perspective (e.g. Mächler et al [2014]; Thomsen et al [2012]), more recent works with a biodiversity focus aimed at resolving diversity across the whole catchment [Deiner et al, 2016;Mächler et al, 2019;Sales et al, 2020]. This immediately brings up the question of where to sample, and how many samples to take, to effectively assess biodiversity across a catchment.…”