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

Sales, Naiara, University of Salford, https://orcid.org/0000-0002-2922-3561

McKenzie, Maisie B., University of Salford

Drake, Joseph, University of Massachusetts-Amherst

Harper, Lynsey R., University of Hull

Browett, Samuel S., University of Salford

Coscia, Ilaria, University of Salford

Wangensteen, Owen S., University of Tromso

Baillie, Charles, University of Salford

Bryce, Emma, University of Aberdeen

Dawson, Deborah A., University of Sheffield

Ochu, Erinma, University of Salford

Hänfling, Bernd, University of Hull

Handley, Lori Lawson, University of Hull

Mariani, Stefano, University of Salford

Lambin, Xavier, University of Aberdeen

Sutherland, Christopher, University of Massachusetts-Amherst

McDevitt, Allan, University of Salford

naiarasl@gmail.com

Published Feb 05, 2020 on Dryad. https://doi.org/10.5061/dryad.d51c59zzf

Cite this dataset

Sales, Naiara et al. (2020). Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems [Dataset]. Dryad. https://doi.org/10.5061/dryad.d51c59zzf

Abstract

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.