Shaded habitats drive higher rates of fern diversification

Modern ferns diversified simultaneously with the rise of angiosperms. This pattern is arguably the consequence of ecological opportunities presented by shady and moist habitats that emerged with the advent of angiosperm dominated habitats. This hypothesis was tested by applying phylogenetic comparative methods that investigated the role of shaded habitats in fern diversification across 1397 fern species from 37 families. Our results showed a significant positive correlation between the occupancy of shaded habitats and diversification rates across the phylogeny of ferns compared to those of open habitats with high sunlight. Tests evaluating false correlations using hidden state speciation and extinction corroborated this result. Since the onset of the Angiosperm Terrestrial Revolution, the diversification rates of shade-dwelling ferns has exceeded those of sun-dwelling ferns.
Synthesis: Our findings support the hypothesis that shaded habitats created by the flourishing of angio..., , , # Shaded habitats have higher rates of fern diversification

[https://doi.org/10.5061/dryad.qz612jmr7](https://doi.org/10.5061/dryad.qz612jmr7)

# Description of the data and file structure

The data included phylogenetic trees at both the species level (*all_5582.tre*) and family level (*family_37.tre*), light habitat data (*sp_1397.csv*), epiphytic habitat data (*sp_4078.csv*), species containing both light and epiphytic information (*sp_1339.csv*), BAMM analysis output for all fern species (*event_data_2.5_5582.txt*), and the corresponding R script (*codes.txt*).

### Files and variables

#### File: data\_ferns.zip

**Description:**
All of our data and code are included in the zip file. The details are as follows:

* **all_5582.tre**: Phylogenetic tree of 5,582 fern species, constructed by Nitta et al. (2022).
* **family_37.tre**: Phylogenetic tree of 37 families used in our study for PGLS analysis.
* **family_37.csv**: Diversification rates estimated using both stem and crown ages, ...

现代蕨类的物种分化与被子植物的崛起同步发生。这一演化模式可被认为是被子植物主导生境出现后，随之形成的荫蔽湿润生境所提供的生态机遇所导致的结果。本研究通过系统发育比较分析方法验证了这一假说，该方法针对涵盖37个科的1397种蕨类植物，探究了荫蔽生境在蕨类物种分化中的作用。研究结果显示，与高光照的开阔生境类群相比，蕨类系统发育中占据荫蔽生境的类群，其物种分化速率与生境占据情况存在显著正相关关系。利用隐态物种形成与灭绝分析检验虚假关联的结果同样验证了这一结论。自被子植物陆地革命（Angiosperm Terrestrial Revolution）启动以来，荫蔽生境蕨类的分化速率始终高于喜光蕨类。

综合分析：本研究结果支持“被子植物繁盛所形成的荫蔽生境促进蕨类物种分化”的假说——# 荫蔽生境可提升蕨类分化速率

[https://doi.org/10.5061/dryad.qz612jmr7](https://doi.org/10.5061/dryad.qz612jmr7)

# 数据与文件结构说明

本数据集包含两类系统发育树：物种水平的（*all_5582.tre*）与科水平的（*family_37.tre*），另有光照生境数据（*sp_1397.csv*）、附生生境数据（*sp_4078.csv*）、同时包含光照与附生信息的物种数据集（*sp_1339.csv*）、所有蕨类物种的BAMM分析输出文件（*event_data_2.5_5582.txt*），以及对应的R脚本（*codes.txt*）。

### 文件与变量说明

#### 压缩包文件：data_ferns.zip

**文件说明：**
本压缩包包含本研究全部数据与代码，具体内容如下：
* **all_5582.tre**：包含5582种蕨类植物的系统发育树，由Nitta等人于2022年构建。
* **family_37.tre**：本研究用于系统发育广义最小二乘（PGLS）分析的37个蕨类科的系统发育树。
* **family_37.csv**：基于茎枝年龄与冠群年龄估算的分化速率数据集……