DOI: 10.5061/dryad.s7h44j1gz
title: Cenozoic evolutionary history obscures the Mesozoic origins of acanthopterygian fishes

description: Sister lineage comparisons provide a valuable tool for understanding
 evolutionary origins of species-rich clades. Percomorpha, comprising over
 18,900 species, represents one of the most species-rich vertebrate clades.
 However, the phylogenetic resolution of its sister lineage remains
 unclear, obscuring whether contrasts in histories of diversification
 provide insights into the factors that gave rise to this clade’s
 diversity. Using 887 ultraconserved element loci and Sanger-sequenced
 nuclear genes, we resolve the phylogenetic relationships of the three
 closest relatives of Percomorpha-the roughies, flashlightfishes,
 porcupinefishes, and fangtooths (Trachichthyiformes), the squirrelfishes
 and soldierfishes (Holocentridae), and the whalefishes, bigscales, and
 alfonsinos (Berycoidei)-and the placement of percomorphs among them.
 Contrary to expectations from the fossil record, we demonstrate that
 living lineages of Berycoidei, Holocentridae, and Trachichthyiformes all
 diversified after the Cretaceous-Paleogene mass extinction. Our findings
 show that multiple clades in Trachichthyiformes and Berycoidei
 independently colonized deep ocean habitats during the climatically
 unstable Eocene and Oligocene and shallow-water reefs during the extensive
 hotspot migration and faunal turnover of the Early Miocene. Due to their
 complex evolutionary history, the closest relatives of Percomorpha are not
 ideal for understanding the origins of this exceptionally species-rich
 clade.
description: # Cenozoic evolutionary history obscures the Mesozoic origins of
 acanthopterygian fishes
 [https://doi.org/10.5061/dryad.s7h44j1gz](https://doi.org/10.5061/dryad.s7h44j1gz) ## Description of the data and file structure All data was either downloaded from Genbank or, in the case of newly-sequenced DNA, was sanger-sequenced from loaned or previously collected specimens.  ### Files and variables #### File: Whalefishes\_code.R **Description:** R code for all analyses conducted in R in this study #### File: Ancestral\_Reconstruction\_Data.zip **Description:** Input data to R for life history trait ancestral state reconstructions ##### Files * Habitat_phytools.csv: habitat states for phytools with references * Habitat_states: habitat states for phytools direct input * Reef_association: reef association states for phytools * Larval_morphology_and_sexual_dimorphism: presence/absence of the megalomycterid male stage and larval morphologies for phytools #### File: COI\_Beryciformes.zip **Description:** Sequence data and IQ-TREE output from the analysis of COI data from Berycoidea on Genbank #### File: gene\_trees\_mark\_1.zip **Description:** Sequence data and IQ-TREE output from the analysis of Sanger-sequenced nuclear gene data (newly generated + Genbank); Genbank sequences are annotated with their NCBI accession numbers #### File: IQ\_TREE.zip **Description:** IQ*TREE and ASTRAL* outputs from the analysis of the UCE data from available contigs + UCEs extracted from available whole genome sequences on Genbank. #### File: BEAST.zip **Description:** Input and output for BEAST time calibration analyses. #### Code/software R/RStudio: for analyzing the csv files IQ-TREE: all maximum likelihood analyses were conducted in IQ-TREE BEAST: Bayesian time-calibration analysis was conducted in BEAST ## Access information Other publicly accessible locations of the data: * NCBI Genbank Data was derived from the following sources: * NCBI Genbank ## Change log * Dec 2024: some formatting was modified in accordance with our revisions, including reorganization * Jan 2025: added HiSSE output directory and IQTREE output directory with re-run analyses based on revised UCE set * Feb 2025: removed diversification output directories (HiSSE) and input; these analyses were removed upon peer-review given that they are not relevant to the push of the paper and do not show any clear result; they are included in earlier versions for reference; reorganized files into Ancestral_Reconstruction_Data.zip and updated README.  * Feb 10 2025: removed gene-trees-mark1.zip, new sequences are uploaded to genbank and in Table 1 of the article.