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

Naiara Sales, Maisie McKenzie, Joe Drake, Lynsey Harper, Samuel Browett, Ilaria Coscia, Owen Wangensteen, Charles Baillie, Emma Bryce, Deborah Dawson, Erinma Ochu, Bernd Hänfling, Lori Lawson-Handley, Stefano Mariani, Xavier Lambin, Chris Sutherland, Allan D. McDevitt*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)707-716
Number of pages10
JournalJournal of Applied Ecology
Volume57
Issue number4
Early online date10 Mar 2020
DOIs
Publication statusPublished - Apr 2020

Keywords

  • biomonitoring
  • camera trapping
  • eDNA metabarcoding
  • latrine surveys
  • mammals
  • occupancy modelling
  • rivers
  • ENVIRONMENTAL DNA
  • DYNAMICS
  • OCCUPANCY

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