DOI: 10.5061/dryad.crjdfn3fj
title: Early biogeography of Otophysi points to the Neotropics as the cradle of Characiphysan fishes

description: 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 highly
 supported hypothesis of phylogenetic relationships among Otophysi, which
 points to the importance of plate tectonics in triggering several
 divergence events jointly with several subsequent range rearrangements,
 further consistent with the contraction of the tropical belt that started
 at the end of the Cretaceous and lasted throughout the Paleogene. The
 divergence of Cypriniformes and Characiphysi results from the joint
 influence of the separation of Laurasia and Gondwana, while the origin of
 Characiphysi is located in West Gondwana, and the subsequent expansion of
 the group cannot be explained without considering transcontinental
 dispersal.
description: 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
 <em>et al.</em>, 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 Characiform lineages, which are poorly
 covered in available mitochondrial genomes in international repositories,
 to complement mitogenomes coming from the two previous sources.
description: # 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.treefile **Description:** Time tree reconstructed with the discrete model and λ = 10 in Newick format #### File: AlignmentS1_mtDNA_partitions.nex **Description:** Nexus file containing the 453 aligned sequences of the mitochondrial genes (13 protein-coding, 2 ribosomal, and ITS) for 453 taxa and their associated partitions #### File: AlignmentS2_nDNA_partitions.nex **Description:** Nexus file containing the 424 aligned sequences of the four nuclear genes (MYH6, RAG1, RAG2, SH3PX3) for 414 taxa and their associated partitions #### File: AlignmentS3_concatenation_partitions.nex **Description:** Nexus file containing the 687 aligned sequences of the 16 mitochondrial and four nuclear genes (MYH6, RAG1, RAG2, SH3PX3) for 687 taxa and their associated partitions ## Access information Other publicly accessible locations of the data: * GenBank