Data from: Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): a test with Guianese freshwater fishes

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.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.