DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishes

To address this gap, we used DNA barcoding of 94 taxa from six orders, 32 families, and 73 genera, sourced from the BOLD Systems platform and samples in the middle and lower SFR regions. Analyses revealed distinct patterns of genetic divergence. The BOLD platform identified 111 bins, 75 as MATCH, 32 as SPLIT, two as MERGE and two MIXTURE.

We detected taxonomic confusions in the genera Astyanax and Psalidodon. Fourteen taxa exhibited high cryptic diversity, corroborated by lineage delimitation methods (BINs, ASAP, and GMYC). A significant portion of this cryptic diversity (eight lineages) is concentrated in the upper SFR, a region with tectonic faults, geomorphological reactivations, and the transposition of another basin, which likely contributed to genetically divergent lineages.

Our data fill shortfalls in Linnaean and Darwinian knowledge about the SFR ichthyofauna, considering its hydrogeological formation. We hope this information will serve as a foundation for future management and conservation plans for this important ichthyofauna.