Data from: Evaluation of primer pairs for eDNA‐based assessment of Ephemeroptera, Plecoptera, and Trichoptera across a biogeographically diverse region

Macroinvertebrates serve as key indicators in ecological assessments of
aquatic ecosystems, where the composition and richness of their
communities is indicative of environmental and anthropogenic drivers.
Established monitoring of macroinvertebrates is expensive, time-consuming,
and relies on expert taxonomic knowledge. In contrast, biomonitoring based
on molecular tools can support faster characterization of aquatic
communities but needs validation for the target taxonomic groups and the
study region. Here, we used data from a biomonitoring program covering a
large biogeographic gradient to compare the routine kick-net method with
eDNA metabarcoding. We used two primer pairs targeting COI, one targeting
a broad metazoan spectrum (miCOIintF/jgHCO2198) and another more recently
developed primer pair optimized for the detection of freshwater
invertebrates (fwhF2/EPTDr2n). We used the data of the macroinvertebrate
monitoring with a focus on the orders of Ephemeroptera, Plecoptera, and
Trichoptera across 92 rivers in Switzerland, covering four continental
drainage basins and an elevational range from 198 to 1650 m a.s.l. Across
all sampled sites, the kick-net detected more distinct taxa than either of
the metabarcoding approaches. At a site level, however, both primer pairs
detected on average more species. Comparing both primer pairs, the
fwhF2/EPTDr2n primer pair captured more species assigned to the indicator
groups Ephemeroptera, Plecoptera, and Trichoptera, and showed a
significantly larger overlap with the kick-net method. However, the
community composition still varied significantly among the different
approaches. Fewer Trichopterans were recovered by eDNA metabarcoding,
whereas the fwhF2/EPTDr2n primer pair detected more Plecopterans than the
other two approaches. This study highlights the importance of optimization
and validation of novel molecular approaches under consideration of the
target organismal group and the study area.