Through the Prism of eDNA: Exploring Cryptic Freshwater Bivalves Diversity in a Mega‐Diverse Tropical Environment

ABSTRACT

Environmental DNA (eDNA) has transformed biodiversity monitoring by enabling sensitive, non‐invasive species detection. However, its potential to resolve taxonomic uncertainties and uncover biogeographic patterns in tropical freshwater ecosystems remains underused. This study addresses an apparent discrepancy: while the Guiana Shield is recognized as a hotspot of aquatic biodiversity, the recorded diversity of freshwater bivalves in Guiana has been notably low, and their distribution patterns remain poorly understood. To address this paradox, we conducted the first large‐scale eDNA survey of freshwater bivalves in South America. Between 2019 and 2023, we collected water samples from 115 sites across the Maroni and Oyapock river basins in French Guiana. Cryptic species initially detected through eDNA were subsequently confirmed through targeted malacological sampling and molecular barcoding (COI, 16S) of collected specimens. These data were used to build a regionally calibrated reference database for taxonomic assignment of eDNA sequences. This integrative approach led to substantial taxonomic revisions, including the description of two new genera and two cryptic species. In addition, eDNA analysis revealed six additional Molecular Operational Taxonomic Units (MOTUs), likely corresponding to undescribed species. Overall, this study increases the number of known Unionid species in French Guiana from five to eighteen, more than tripling current species richness estimates. Beyond taxonomic discoveries, eDNA further revealed consistent basin‐scale patterns, with both species richness and intraspecific genetic diversity (as measured by Amplicon Sequence Variants) peaking in upstream areas with limited human disturbance and declining downstream in regions affected by gold mining and deforestation. These findings demonstrate the value of eDNA as a tool not only for monitoring but also for advancing taxonomy and biogeography in understudied tropical ecosystems. By revealing hidden diversity and expanding spatial coverage at minimal cost, eDNA enables more accurate assessments of freshwater biodiversity and informs conservation strategies at landscape scales.