Early biogeography of Otophysi points to the Neotropics as the cradle of Characiphysan fishes

Freshwaters represent less than 1% of Earth's surface and 0.02% of available aquatic habitable volume, but host nearly half of the 35,500 known species of bony fishes. Ostariophysan fishes represent 70% of all freshwater fishes with ca. 12,000 species distributed in five speciose orders. They constitute a large radiation whose internal phylogenetic relationships are still intensively debated. To better understand their early evolutionary history and origin, we reconstructed their phylogenetic relationships through a dense taxonomic sampling and the combined use of complete mitochondrial genomes and sequences of four nuclear genes. Maximum Likelihood of phylogenetic reconstructions and time tree estimates were applied to a data set consisting of 687 ostariophysan species for a total of 21,701 aligned positions, including 15,707 variable sites, and a Maximum Likelihood of model-based estimation of ancestral areas was used to reconstruct the early evolution of Otophysi. We produced a highl..., Two data sets were assembled and subsequently combined, including a set of complete mitochondrial genomes and four nuclear data sets, including myh6, rag1, rag2, and sh3px. The nuclear genes come from the study by Rabosky et al. (2018) and were already filtered for rogue sequences corresponding to misidentification and/or paralogs. Only four nuclear genes were selected out of 21, which corresponds to those with a taxonomic coverage above 20% for ostariophysan fishes (Rabosky et al., 2018). The mitogenomes analyzed here come from different sources. First, previously published mitogenomes already assembled and annotated were downloaded from NCBI GenBank. Second, we inspected libraries of raw Illumina sequencing reads from previous studies using Ultra Conserved Element (UCE) to extract mitogenomes whenever enough reads were present to assemble a scaffold of at least 12,000 base pairs. For this, SRA files were downloaded from NCBI GenBank or ENA. Third, new mitogenomes were produced for Cha..., , # Early biogeography of Otophysi points to the Neotropics as the cradle of Characiphysan fishes

[https://doi.org/10.5061/dryad.crjdfn3fj](https://doi.org/10.5061/dryad.crjdfn3fj)

## Description of the data and file structure

Combined use of mitogenome and nuclear genes to reconstruct phylogenetic relationships among Characyphisan fishes

### Files and variables

#### File: TreeS1_mitochondrial.treefile

**Description:** Phylogenetic reconstruction based on mitochondrial genomes with bootstrap scores derived from 5,000 replicates in Newick format

#### File: TreeS2_nuclear.treefile

**Description:** Phylogenetic reconstruction based on four nuclear genes with bootstrap scores derived from 5,000 replicates in Newick format

#### File: TreeS3_concatenate.treefile

**Description:** Phylogenetic reconstruction based on the concatenated mitochondrial genomes and four nuclear genes with bootstrap scores derived from 5,000 replicates in Newick format

#### File: TreeS4_chronos_discrete_10.tr...,