The Influence of Basin Fragmentation on the Genetic Structure of Neotropical Fishes

ABSTRACT Aim Basin fragmentation during dry climatic periods can divide drainage systems into isolated endorheic units, profoundly affecting the genetic structure of freshwater organisms. This study aims to perform a comparative phylogeographic analysis incorporating different freshwater fish species where we assessed the roles of isolation by distance (IBD), barriers (IBB) and environment (IBE) in shaping the genetic diversity of seven neotropical fish species using mitochondrial DNA. Location Argentina, Brazil and Uruguay endorheic and exorheic basins. Taxon Hypostomus cordovae , Rineloricaria catamarcensis , Oligosarcus jenynsii and Hoplisoma longipinne . Methods Samples were collected across multiple localities for each species and grouped based on basin type (endorheic vs. exorheic), hydrographic system and environmental criteria. Mitochondrial DNA (COI or D‐loop) was sequenced, and phylogenetic reconstructions, haplotype networks, genetic diversity indices and population structure analyses were performed. Distance‐based Redundancy Analysis (db‐RDA) was used to evaluate the influence of isolation by distance (IBD), barriers (IBB) and environment (IBE) on genetic structuring. Environmental variables such as altitude, latitude and turbidity, vegetation cover, and land surface temperature were derived from remote sensing data. Results Basin fragmentation (IBB) is the main driver of genetic divergence in Hypostomus cordovae and Hoplisoma longipinne . Geographic distance (IBD) significantly influenced H. cordovae , Rineloricaria catamarcensis and Oligosarcus jenynsii (Continental Group), while environmental factors such as altitude (IBE) contributed to the structure of H. longipinne and O. jenynsii . Main Conclusions These findings emphasise the importance of adopting an integrative approach to understanding genetic diversification in freshwater organisms. They highlight the complex interplay of historical, geographical and ecological processes in fragmented river systems. Furthermore, they underscore the conservation significance of isolated endorheic basins as reservoirs of unique genetic lineages.