A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity

Before environmental DNA (eDNA) can establish itself as a robust tool for
biodiversity monitoring, comparison with existing approaches is necessary,
yet is lacking for terrestrial mammals. Moreover, much is unknown
regarding the nature, spread and persistence of DNA shed by animals into
terrestrial environments, or the optimal experimental design for
understanding these potential biases. To address some of these challenges,
we compared the detection of terrestrial mammals using eDNA analysis of
soil samples against confirmed species observations from a long-term
(~9-yr) camera trapping study. At the same time, we considered multiple
experimental parameters, including two sampling designs, two DNA
extraction kits and two metabarcodes of different sizes. All mammals
regularly recorded with cameras were detected in eDNA. In addition, eDNA
reported many unrecorded small mammals whose presence in the study area is
otherwise documented. A long metabarcode (≈220bp) offering a high
taxonomic resolution, achieved a similar efficiency as a shorter one
(≈70bp) and a phosphate buffer-based extraction gave similar results as a
total DNA extraction method, for a fraction of the price. Our results
support that eDNA-based monitoring should become a valuable part of
ecosystem surveys, yet mitochondrial reference databases need to be
enriched first.