The macroevolutionary dynamics of pharyngognathy in fishes fail to support the key innovation hypothesis

Key innovations, traits that provide species access to novel niches, are thought to be a major generator of biodiversity. One commonly cited example of key innovation is pharyngognathy, a set of modifications to the pharyngeal jaws found in some highly species-rich fish clades such as cichlids and wrasses. Here, using comparative phylogenomics and phylogenetic comparative methods, we investigate the genomic basis of pharyngognathy and the impact of this innovation on diversification. Whole genomes resolve the relationships of fish clades with this innovation and their close relatives, but high levels of topological discordance suggest the innovation may have evolved fewer times than previously thought. Closer examination of the topology of noncoding elements accelerated in clades with the pharyngognathy innovation reveals hidden patterns of shared ancestry across putatively independent transitions to pharyngognathy. When our updated phylogenomic relationships are used alongside large-sc..., , , # DATA DRYAD REPOSITORY README

Citation: Borstein SR, Hammer MP, O'Meara BC, and McGee MD. 2024. The macroevolutionary dynamics of pharyngognathy in fishes fail to support the key innovation hypothesis. *Nature Communications* 15:10325. 10.1038/s41467-024-53141-4

## Description of the data and file structure

### Directories

#### DietAnalysis: Data, results, and scripts related to phylogenetic comparative analysis of trophic levels

##### Files

* BBMV_Data.RData: Phylogeny and formatted data used in BBMV analysis. Used in BBMV_MCM.R and BBMV_Scripts.R
* BBMV_MCMC.R: Script to perorm MCMC BBMV analyses
* BBMV_Scripts.R: Script to run BM, OU, and BBMV model comparisons.
* BBMV_Scripts.RData: Output for models in BBMV_Scripts.R
* BBMV_Summary_Scripts.R: Scripts to calculate 95% CI for BBMV parameter estimates and make figures of macroevolutionary landscapes.
* nonpharyngognath_TL.BBMV.Dat: R data object for BBMV MCMC analysis for non-pharyngognathous fishes.
* pharyngognath_PJA.TL.LOO_...,

关键创新——即赋予物种侵入全新生态位能力的性状——被认为是生物多样性形成的核心驱动因素之一。被广泛引述的关键创新案例之一是咽颌式（pharyngognathy），即部分物种丰富度极高的鱼类支系（如慈鲷与隆头鱼）所具有的咽颌特化结构。本研究借助系统发育基因组学与系统发育比较分析方法，探究咽颌式的基因组基础及其对物种多样化的影响。全基因组数据明确了携带该创新性状的鱼类支系及其近缘类群的系统发育关系，但高水平的拓扑结构不一致性表明，该创新性状的演化次数可能少于此前的推测。对携带咽颌式创新支系中加速演化的非编码元件拓扑结构进行细致剖析后，我们发现了看似独立的咽颌式演化事件间存在的隐蔽共祖模式。当我们将更新后的系统发育基因组关系与大规模[...]，，，# 数据Dryad仓库说明文档

引用：Borstein SR、Hammer MP、O'Meara BC 与 McGee MD. 2024. 鱼类咽颌式的宏观演化动力学不支持关键创新假说. *Nature Communications* 15:10325. DOI: 10.1038/s41467-024-53141-4

## 数据与文件结构说明
### 目录
#### DietAnalysis：与营养级系统发育比较分析相关的数据、结果及脚本
##### 文件
* BBMV_Data.RData：用于BBMV分析的系统发育树与格式化数据集，供BBMV_MCM.R与BBMV_Scripts.R调用
* BBMV_MCMC.R：执行MCMC BBMV分析的脚本
* BBMV_Scripts.R：运行BM、OU及BBMV模型比较的脚本
* BBMV_Scripts.RData：BBMV_Scripts.R生成的模型输出结果
* BBMV_Summary_Scripts.R：用于计算BBMV参数估计值的95%置信区间，并绘制宏观演化景观图的脚本
* nonpharyngognath_TL.BBMV.Dat：用于非咽颌类鱼类BBMV MCMC分析的R数据对象
* pharyngognath_PJA.TL.LOO_...