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: CO...

姊妹支系比较是解析物种丰富类群演化起源的重要研究工具。包含超过18900个物种的鲈形类（Percomorpha），是物种多样性最高的脊椎动物类群之一。然而其姊妹支系的系统发育分辨率仍未明确，这使得我们难以通过多样化历史的差异，解析推动该类群物种多样性形成的关键因素。本研究利用887个超保守元件位点（ultraconserved element loci）与经桑格测序（Sanger-sequenced）的核基因序列，解析了鲈形类（Percomorpha）的三个最近缘类群的系统发育关系——即燧鲷目（Trachichthyiformes，包含燧鲷、电筒鱼、豪猪鱼与尖牙鱼）、金鳞鱼科（Holocentridae，包含金鳞鱼与士兵鱼）以及金眼鲷亚目（Berycoidei，包含鲸口鱼、大鳞鱼与红金眼鲷）——并明确了鲈形类在上述类群中的系统发育位置。与化石记录的预期相悖，本研究证实金眼鲷亚目（Berycoidei）、金鳞鱼科（Holocentridae）与燧鲷目（Trachichthyiformes）的现生支系均在……之后发生了多样化演化。# 新生代演化历史掩盖了棘鳍鱼类（acanthopterygian fishes）的中生代起源

[https://doi.org/10.5061/dryad.s7h44j1gz](https://doi.org/10.5061/dryad.s7h44j1gz)

## 数据与文件结构说明

所有数据均从基因银行（GenBank）下载获取；对于新测序的DNA样本，则通过对借阅或既往采集的标本进行桑格测序获得。

### 文件与变量说明

#### 文件：Whalefishes_code.R
**描述：** 本研究中所有基于R语言开展的分析代码

#### 文件：Ancestral_Reconstruction_Data.zip
**描述：** 用于R语言开展生活史性状祖先状态重建的输入数据

##### 附属文件
* Habitat_phytools.csv：附带参考文献的phytools软件生境状态数据
* Habitat_states：phytools软件直接输入所需的生境状态数据
* Reef_association：phytools软件所需的珊瑚礁关联状态数据
* Larval_morphology_and_sexual_dimorphism：phytools软件所需的巨口鱼科雄性阶段有无数据及幼体形态学数据

#### 文件：CO...