Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems

1.  Environmental DNA (eDNA) metabarcoding has revolutionised
biomonitoring in both marine and freshwater ecosystems. However, for
semi-aquatic and terrestrial animals, the application of this technique
remains relatively untested. 2.  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). 3. 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.
4. 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
≥0.95 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. 5. 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.