Time-calibrated phylogeny of Neotropical Freshwater Fishes

The Neotropical Freshwater Fish (NFF) fauna exhibits the greatest phenotypic disparity and species richness among all continental aquatic vertebrate faunas, with more than 6,345 species distributed across the mostly tropical regions of Central and South America. The two several decades have seen a proliferation of molecular phylogenies, often at the species level, covering almost all 875 valid NFF genera. This study presents the most comprehensive genome-wide, time-calibrated phylogenetic hypothesis of NFF species to date, based on DNA sequences generated over decades through collaborative efforts of the multinational ichthyological research community. Our purpose is to compile an extensive dataset and organize it systematically, allowing for continuous refinement and expansion, thereby enabling researchers to evaluate macroevolutionary hypotheses in the NFF. Using thousands of DNA sequences from dozens of studies, we compiled a supermatrix of 51 markers across 5,984 taxa, comprising 3,167 species representing 50% of NFF species, and estimating divergence times based on a fossil-calibrated phylogenomic tree of fishes. We used this dataset to infer the most species-rich time-calibrated phylogeny of the NFF taxa to date, summarizing the collective efforts of the ichthyological research community since the midpoint of the last century. We hope this dataset provides a framework for forthcoming evolutionary studies of the NFF fauna, documenting macro-scale patterns in the world's most diverse continental vertebrate fauna.