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.