Historical biogeography and population genetic structure of the giant gilded catfish ( Brachyplatystoma rousseauxii ): expanding Humboldtian connectivity routes between the Orinoco and Amazon River basins

Understanding the evolutionary history of species within a geographic context is key to historical biogeography, as it reveals how geological and climatic changes shaped biodiversity. This is especially important in ecologically significant regions like the Amazon and Orinoco basins. Together, they host the world’s greatest freshwater fish diversity (∼3,500 species), sharing a common but not yet fully understood evolutionary history. The gilded catfish ( Brachyplatystoma rousseauxii ), an ancient species widely distributed as a metapopulation in Neotropics, is an important model for studying past connectivity, divergence, and historical processes shaping fish diversity between these basins. This study analyzed the genetic structure, connectivity routes, and demographic history of B. rousseauxii using nuclear (microsatellite and ddRADseq) and mitochondrial DNA. Population structure analyses and coalescent models indicate that B. rousseauxii populations from the Orinoco and Amazon basins are genetically distinct, with no evidence of current gene flow. However, our results support the occurrence of a possible secondary contact event after the divergence, with the Boa Vista population retaining the genetic signal of this process. The ancestral population split occurred at the Rupununi Portal around 2.54 Ma (ddRAD) or 1.31 Ma (mtDNA). Then, the species colonized the Branco and Orinoco Rivers ∼1.90 Ma (ddRAD) or 0.6 Ma (mtDNA), rapidly expanding in the Orinoco (>1.3 or >0.29 Ma), while colonization of the Amazon from the Branco River was more recent (≤1.0 or ≤0.15 Ma). Population expansion signal was detected in the Orinoco (∼0.20 Ma), whereas the Amazon remained stable. Our findings suggest that the rise of the Vaupés Arch in the Late Miocene does not explain the observed genetic divergence. Likewise, the Casiquiare Canal and Japurá-Guaviare headwaters are not connectivity routes between basins. Instead, the Rupununi Portal, including the recent capture of the Branco River by the Negro River, was the last point of connection and played a key role in shaping B. rousseauxii ’s distribution. These findings provide insights into Neotropical fish biogeography and the historical configuration of the Orinoco and Amazon basins.