DOI: 10.5061/dryad.dc25730
title: Data from: Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): a test with Guianese freshwater fishes

description: Determining the species compositions of local assemblages is a
 prerequisite to understanding how anthropogenic disturbances affect
 biodiversity. However, biodiversity measurements often remain incomplete
 due to the limited efficiency of sampling methods. This is particularly
 true in freshwater tropical environments that host rich fish assemblages,
 for which assessments are uncertain and often rely on destructive methods.
 Developing an efficient and non-destructive method to assess biodiversity
 in tropical freshwaters is highly important. In this study, we tested the
 efficiency of environmental DNA (eDNA) metabarcoding to assess the fish
 diversity of 39 Guianese sites. We compared the diversity and composition
 of assemblages obtained using traditional and metabarcoding methods. More
 than 7,000 individual fish belonging to 203 Guianese fish species were
 collected by traditional sampling methods, and ~17 million reads were
 produced by metabarcoding, among which ~8 million reads were assigned to
 148 fish taxonomic units, including 132 fish species. The two methods
 detected a similar number of species at each site, but the species
 identities partially matched. The assemblage compositions from the
 different drainage basins were better discriminated using metabarcoding,
 revealing that while traditional methods provide a more complete but
 spatially limited inventory of fish assemblages, metabarcoding provides a
 more partial but spatially extensive inventory. eDNA metabarcoding can
 therefore be used for rapid and large-scale biodiversity assessments,
 while at a local scale, the two approaches are complementary and enable an
 understanding of realistic fish biodiversity.
description: Results of taxonomic
 assignmentsA taxon by site matrix,
 made after MOTU assignment to the reference database. For taxa described
 at the genus level or higher, the number of included species is indicated
 within parentheses.assignment_result.txtMOTUs tableA MOTU by PCR replicate matrix.MOTU_data.txtSequence reference databaseFile containing the sequence reference database for Guianese freshwater fish species.Reference_sequence.fastaRun1Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file; 3) File with experiment name, sample name and the tags, the forward primer and the reverse primer sequence associated.Run2Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file; 3) File with experiment name, sample name and the tags, the forward primer and the reverse primer sequence associated.Run3Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file; 3) File with experiment name, sample name and the tags, the forward primer and the reverse primer sequence associatedRun4Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file; 3) File with experiment name, sample name and the tags, the forward primer and the reverse primer sequence associatedSampling site dataA table with 1) site name, 2) drainage basin belonging, 3) coordinates, 4) dates of traditional and eDNA sampling, 5) sample PCR code and 6) site map number.site_data.txtResults of traditional samplingA species by site occurence matrix, obtained from traditional sampling on each site.traditional_result.txtAnalyse R scriptA R script of the analyses conducted in the manuscrit.script_analyse.R