Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Neotropical tetras of the family Characidae form the largest and most taxonomically complex clade within the order Characiformes. Previous phylogenetic relationships concur on the recognition of four major subclades, whereas knowledge on intergeneric and interspecific relationships remains largely incomplete or nonexistent. We sampled 575 specimens of 494 species and 123 genera classified in Characidae, generated new molecular data of 1.75 ultraconserved elements (UCEs), and used likelihood and Bayesian analyses. The phylogeny (1348 UCE loci: 538 472 bp) yielded clades with unprecedented resolution at species- and genus-levels, allowing us to propose a new classification of former Characidae into four families: Spintherobolidae, Stevardiidae, Characidae, and Acestrorhamphidae. The family Stevardiidae includes nine subfamilies: Landoninae, Xenurobryconinae, Glandulocaudinae, Argopleurinae, Hemibryconinae, Stevardiinae, Planaltininae, Creagrutinae, and Diapominae. The family Characidae...,

We sampled 575 specimens of 494 species and 123 genera of Characidae s.l. and outgroups representing 39.4% of the 1,255 species and 86.7% of the genera currently classified in Characidae. Staff from Arbor Biosciences quantified and enriched genomic libraries utilizing the MYbaits Target Enrichment system (MYcroarray) with the Ostariophysans-UCE-2.7Kv1 probe-set containing 6,737 baits to capture 2,708 nuclear ultraconserved element (UCE) loci. Sequencing was performed on the Illumina platform at Arbor Biosciences with additional details about laboratory procedures available in previous publications for Characiformes. We used the PHYLUCE v1.5.0 pipeline for analyses of UCE data that included the assembly of raw read sequences to contigs, the identification and separation of UCI loci from contigs, and the building of trimmed alignments of the individual UCE loci. We removed adapter contamination and low-quality bases using Illumiprocessor and Trimmomatic, and used Velvet v1.5.0 to assem..., , # Data from: Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

[https://doi.org/10.5061/dryad.bzkh189jw](https://doi.org/10.5061/dryad.bzkh189jw)

## Description of the data and file structure

Data was collected from museum specimens. Sequences were obtained from captures of ultraconserved elements of 575 taxa using Illumina approaches. Data was processed by Phyluce and analyses ran through RAxML and ExaBayes. 

### Files and variables

#### File: mafft-nexus-edge-trimmed-clean-75p.phylip

**Description:**  Data matrix 75% complete of ultraconserved elements.

#### File: mafft-nexus-edge-trimmed-clean-90p.phylip

**Description:** Data matrix 90% complete of ultraconserved elements.

## Code/software

PHYLUCE v1.5.0

RAxML v8.2.11

ExaBayes v1.5