DOI: 10.5061/dryad.bzkh189jw
title: Data from: Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

description: 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 includes five subfamilies: Aphyocharacinae,
 Cheirodontinae, Exodontinae, Tetragonopterinae, and Characinae. The family
 Acestrorhamphidae congregates 15 subfamilies: Oxybryconinae,
 Trochilocharacinae, Stygichthyinae, Megalamphodinae, Stichonodontinae,
 unnamed subfamily, Stethaprioninae, Pristellinae, Jupiabinae,
 Tyttobryconinae, Hyphessobryconinae, Thayeriinae, Rhoadsiinae,
 Grundulinae, and Acestrorhamphinae. The phylogeny resolves intergeneric
 relationships and supports revalidation of Myxiops, Megalamphodus,
 Ramirezella, Holopristis, and Astyanacinus, synonymy of Aphyodite,
 Genycharax, and Psellogrammus, and expansion of Cyanogaster, Makunaima,
 Deuterodon, Hasemania, Hemigrammus, Bario, Ctenobrycon, and
 Psalidodon. The phylogeny opens avenues for new systematic reviews and
 redefinitions of included genera.
description: 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 assemble fastq reads into fasta contigs. We then
 searched for the UCE loci using the Ostariophysans-UCE-2.7Kv1 probe-set
 and the “phyluce_assembly_match_contigs_to_probes” to remove duplicated or
 paralog regions. After extracting the UCE loci, we aligned them using the
 edge trimming method implemented in MUSCLE. We used the 75% complete
 matrix with loci present in at least 75% of taxa
 (<em>i.e.</em>,<em> </em>loci present in at least
 432 terminals), and the 90% complete matrix with loci present in at least
 90% of taxa (<em>i.e.</em>,<em> </em>loci present
 in at least 518 terminals).
description: # 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