DOI: 10.5061/dryad.jsxksn0cq
title: Data from: Evaluation of primer pairs for eDNA‐based assessment of Ephemeroptera, Plecoptera, and Trichoptera across a biogeographically diverse region

description: 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.
description: In the federal water quality
 assessment in Switzerland, rivers are routinely surveyed and in spring
 2019, 92 sites were sampled for eDNA. The eDNA was then extracted in a
 cleanroom. From these extracts, we generated 2 MiSeq libraries targeting
 the CO1 barcode focused on the detection of macroinvertebrates. One of the
 libraries, using the primer jgHCO2198/miCOIintF (Leray et al., 2013,
 Geller et al., 2013) was already analyzed and published in the context of
 biotic indices based on eDNA data: (https://doi.org/10.1371/journal.pone.0257510). The second library that used the primer EPTDr2n/fwhF2 (Leese et al., 2021, Vamos et al., 2017) was targeted more specifically at aquatic invertebrates. The libraries were prepared in-house and at the GDC at ETH Zurich, then bioinformatically processed by J.C.W.
description: The folder contains two eDNA metabarcoding amplicon paired-end
 sequenced raw data sets (one using the jgHCO2198/miCOIintF primers (Leray
 et al., 2013, Geller et al., 2013), the other using the EPTDr2n/fwhF2
 primers (Leese et al., 2021, Vamos et al., 2017) in two separate zip
 folders. Once unzipped, all raw sequencing files are available as fasta
 files and can be opened with a text editor.