DOI: 10.5061/dryad.k6djh9w71
title: Data from: Fine-tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches

description: Accurate quantification of biodiversity can be demanding and expensive.
 Although environmental DNA (eDNA) metabarcoding can facilitate
 biodiversity assessments through non-invasive, cost-efficient, and rapid
 surveys, the approach struggles to outperform traditional morphological
 approaches in providing reliable quantitative estimates for surveyed
 species (e.g., abundance and biomass). We present an integrated
 methodology for improving biodiversity surveys that pairs eDNA
 metabarcoding with morphological data, following a series of taxonomic and
 geographic filters. We demonstrate its power by applying it to a new
 spatiotemporal dataset generated on an Iberian-wide distributed aquatic
 mesocosm infrastructure that spans a wide biogeographic gradient. By
 building upon the strengths that these two approaches offer, our framework
 improved taxonomic resolution for 30% of the taxa and enabled species’
 traits (e.g., body-size) and abundance to be assigned to 85% of the taxa
 in hybrid datasets. These results indicate that eDNA-based assessments can
 complement, but not always replace, conventional approaches. Integrating
 conventional and modern eDNA metabarcoding approaches, already available
 in the ecologist’s toolbox, will greatly enhance biodiversity assessments.
description: Fieldwork was conducted in the Iberian Ponds Network (IPN), a
 multi-region experimental facility using 192 freshwater pond mesocosms
 (hereafter ponds) distributed across six locations in the Iberian
 Peninsula, ranging from southern semi-arid (Murcia, Toledo), temperate
 (Évora, Porto) and alpine environments (Jaca and Madrid; Fig. S1), varying
 in annual average temperature and total precipitation (more details on the
 IPN and climate of each region in Supporting Information). Fieldwork was
 carried out in the six locations once a year every Spring from 2016 to
 2018. Three different trophic groups (phytoplankton, zooplankton, and
 macroinvertebrates) were surveyed using standard sampling procedures for
 both eDNA metabarcoding and morphology. For details on sample collection
 and processing see Supporting Information. Raw
 sequences resulted from eDNA metabarcoding approach were then analysed
 using DADA2 (Callahan et al., 2016). Taxonomic assignment was performed
 using BLASTn and the NCBI nt database (Benson et al., 2005) at 97%
 similarity, and classification was attributed using the software MEGAN
 Community Edition (Huson et al., 2016). Taxonomic assignments, and their
 associated amplicon sequence variants (ASVs), that returned incomplete
 taxonomy or unknown identifiers were excluded from further analysis. An
 additive strategy was used regarding the number of PCR replicates (Alberdi
 et al., 2017), i.e., through combining the sequences of all PCR replicates
 from one sample to maximize diversity detection (e.g., Leray &
 Knowlton, 2015). Morphological identification was done
 to the lowest taxonomic level possible for all three trophic groups.
 Individuals’ enumeration was done using a light microscope (phytoplankton
 and rotifers) and a stereomicroscope (cladocerans, copepods and
 macroinvertebrates) using standard methods for each trophic group.
 Species’ biomasses were calculated by their dry weights, which was
 estimated from published allometric relationships using individual
 measurements.<br> Further details in paper and Supporting
 Information.