fcassemiro/South-American-freshwater-fish: Freshwater Fishes of the South America

We compiled 306,425 occurrence records of 4,967 freshwater bony fish species in South America through an extensive search of the literature, museums, FishBase (http://www.fishbase.org/), FishNet (http://www.fishnet2.net), Global Biodiversity Information Facility (GBIF) (http://www.gbif.org/), SpeciesLink (http://splink.cria.org.br), and Datos de Peces de Aguas Continentales de Argentina (http:// http://www.pecesargentina.com.ar/base_peces/inicio_busq.html). We automated the process of data filtering by writing and implementing code that considered all possible errors in those databases (e.g., georeferencing errors, synonymies, collection year, typographic errors, exotic species). We removed all records of species that are exotic to South America, based on Gubiani et al. (2018). Species names were validated following the Catalog of Fishes of the California Academy of Sciences (http://www.calacademy.org/scientists/projects/catalog-of-fishes) and carefully revised by taxonomic specialists in Neotropical fishes. 

We used a newly-compiled, comprehensive, time-calibrated tree of Neotropical freshwater fish taxa based on DNA sequence studies, generated by dozens of published papers over three decades by the ichthyological research community, and all available at GenBank. We assembled a supermatrix comprising 43,850 bp from 51 independently aligned and trimmed markers, including 5,984 terminal taxa representing 3,169 species (51%), and 861 genera (99%) for the entire Neotropical freshwater fish fauna. We performed tree searches in RAxML assuming independent GTR + G models for partitions and a start tree with a few justifiable node constraints. After randomly sampling one specimen per species, we estimated divergence times using “Congruification,” a tool for time-scaling large trees using secondary calibrations from a reference time-calibrated tree, including 31 fossil calibrations from time-calibrated phylogenies of Actinopterygii (Hughes et al. 2018) and Potamotrygonidae (Fontenelle et al. 2021).