Shaded habitats drive higher rates of fern diversification
Data files
Mar 04, 2025 version files 29.98 MB
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data_ferns.zip
29.98 MB
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README.md
1.60 KB
Abstract
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 angiosperms resulted in the acceleration of fern diversification as a consequence of the successful colonization of shaded moist habitats in angiosperm dominated forests.
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, as well as the shade proportion of the 37 families.
- sp_4078.csv: Dataset indicating epiphytic (1) and terrestrial (0) habitats, representing shade- and sun-dwelling species, respectively.
- sp_1397.csv: Dataset indicating sun (1) and shade (0) habitats
- sp_1339.csv: Dataset categorizing species by epiphytic, terrestrial, sun, and shade habitats.
- event_data_2.5_5582.txt: BAMM analysis data for all the 5582 species.
- codes.txt: Code for running the models.
Code/software
All R codes are provided in the file codes.txt. Annotations are provided throughout the script.