Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots

TL;DR

Environmental DNA metabarcoding helps discover rare and threatened species in tropical regions, aiding conservation efforts.

Contribution

The study demonstrates how eDNA metabarcoding can detect elusive and threatened species in the Tropical Andes.

Findings

eDNA metabarcoding identified elusive, threatened, or presumed extinct amphibian species in the Tropical Andes.

Bycatch data revealed invasive species and pathogens, highlighting environmental threats.

The method is effective despite incomplete reference data and high biodiversity.

Abstract

Environmental DNA (eDNA) metabarcoding is an emerging and versatile tool in biodiversity research. With recent advances in field sampling techniques, this approach becomes increasingly suited for application in tropical ecosystems where biodiversity monitoring gaps remain significant and species detection is particularly challenging. Using amphibians as a model, we harness eDNA metabarcoding in 52 localities in the Tropical Andean biodiversity hotspot to rapidly trace elusive, threatened, or presumed extinct species as a baseline for conservation action. Metabarcoding ‘bycatch’ of non-target species further revealed specific environmental threats through the detection of invasive species and pathogens, thus facilitating integrative conservation assessments despite the incompleteness of reference data and the vast species richness hampering biodiversity assessments in complex tropical communities. Consequently, we call for more intense employment of eDNA metabarcoding in conservation to rapidly bridge critical knowledge gaps on elusive species or declining populations in tropical biodiversity hotspots.

The online version contains supplementary material available at 10.1038/s41598-026-41937-x.

Figures