Reference databases and taxonomic assignment
Taxonomic assignment was performed using the ecotag function of OBItools package. For both Teleo and MiFish markers, taxonomic assignments were made using a comprehensive reference database of 12S rRNA barcodes for over 90% French Guiana’s freshwater fish (Brosse et al., submitted). MG2 sequences were obtained from BOLD (Ratnasingham & Hebert, 2007) through the Gui-Bol project (Barcoding Guianese fishes, see Papa et al. 2021). To enable meaningful comparisons of fish assemblages across survey methods, we only kept assignments reaching species-level resolution and showing ≥97% sequence identity with the reference database. Sequences below this threshold were discarded, and assignments were further refined to exclude taxa never documented in the Approuague River systems, based on Le Bail (2012).