Cenozoic evolutionary history obscures the Mesozoic origins of acanthopterygian fishes

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 ..., , , # 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
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