DOI: 10.5061/dryad.1g1jwsv15
title: General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

description: Metabarcoding of environmental DNA (eDNA) is a powerful tool for
 describing biodiversity, such as finding keystone species or detecting
 invasive species in environmental samples. Continuous improvements in the
 method and the advances in sequencing platforms over the last
 decade have meant this approach is now widely used in
 biodiversity sciences and biomonitoring. For its general use, the method
 hinges on a correct identification of taxa. However, past studies have
 shown how this crucially depends on important decisions during sampling,
 sample processing, and subsequent handling of sequencing data.
 With no clear consensus as to the best practice, particularly the latter
 has led to varied bioinformatic approaches and recommendations for data
 preparation and taxonomic identification. In this study, using a
 large freshwater fish eDNA sequence dataset, we compared the frequently
 used zero-radius Operational Taxonomic Unit (zOTUs) approach of our raw
 reads and assigned it taxonomically i) in combination with publicly
 available reference sequences (open databases) or ii) with an OSU
 (Operational Sequence Units) database approach, using a curated database
 of reference sequences generated from specimen barcoding (closed
 database). We show both approaches gave comparable results for
 common species. However, the commonalities between the approaches
 decreased with read abundance and were thus less reliable and not
 comparable for rare species. The success of the zOTU approach
 depended on the suitability, rather than the size, of a reference
 database. Contrastingly, the OSU approach used reliable DNA sequences and
 thus often enabled species-level identifications, yet this resolution
 decreased with the recent phylogenetic age of the
 species. We show the need to include target group coverage, outgroups and
 full taxonomic annotation in reference databases to avoid misleading
 annotations that can occur when using short amplicon sizes as
 commonly used in eDNA metabarcoding studies. Finally, we make general
 suggestions to improve the construction and use of reference databases for
 metabarcoding studies in the future.
description: The data was collected under the framework of the federal water
 quality assessment in Switzerland. The data is generated from eDNA samples
 in Swiss rivers that are routinely surveyed. In spring 2019, 92 sites were
 sampled for eDNA with 4 replicates for each site. The eDNA filters were
 then extracted in a clean room. From these extracts, we used a nested PCR
 using the 12S Mifish primers to create an amplicon library, that was
 paired end sequenced. The 12S barcode is focused on the detection of fish
 communities. The libraries were prepared in-house and at the Genetic
 Diversity Center (user labs) at ETH Zurich.
description: The folder contains the eDNA metabarcoded amplicon paired-end
 sequences as raw data set from the Miseq sequencer. Once unzipped, all raw
 sequencing files are available as fasta files and can be opened with a
 text editor or used for further downstream bioinformatic
 workflow.