Multi-species models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams

Environmental DNA (eDNA) sampling can provide accurate, cost-effective,
landscape-level data on species distributions. Previous studies have
compared the sensitivity of eDNA sampling to traditional sampling methods
for single species, but similar comparative studies on multi-species eDNA
metabarcoding are rare. Using hierarchical species occupancy-detection
models, we examined whether key choices associated with eDNA metabarcoding
(primer selection, low-abundance read filtering, and the number of
positive water samples used to classify a species as present at a site)
affect the sensitivity of metabarcoding, relative to backpack
electrofishing for fish in freshwater streams. Under all scenarios
(teleostei and vertebrate primers; 0%, 0.1% and 1% read filtering
thresholds; 1 or 2 positive samples required to classify species as
present), we found that eDNA metabarcoding is, on average, more sensitive
than electrofishing. Combining vertebrate and teleostei markers resulted
in higher detection probabilities relative to the use of either marker in
isolation. Increasing the threshold used to filter low abundance reads
decreased species detection probabilities but did not change our overall
finding that eDNA metabarcoding was more sensitive than electrofishing.
Using a threshold of two positive water samples (out of 5) to classify a
species as present typically had negligible effects on detection
probabilities compared to using one positive water sample. Our findings
demonstrate that eDNA metabarcoding is generally more sensitive than
electrofishing for conducting fish surveys in freshwater streams, and that
this outcome is not sensitive to methodological decisions associated with
metabarcoding.