DOI: 10.5281/zenodo.14008084
title: Equilibrium Dynamics Shape Diversity Patterns Across Terrestrial Tetrapod Clades

description: This repository contains all scripts, data, and documentation supporting the analyses in our study. The materials are organized into folders corresponding to specific steps of the workflow. This README provides a detailed guide to the structure, contents, and usage of each folder.



Folder Structure and Contents

1. Environmental Variables (Grid_level_environment)





Contains grid-cell level environmental variables in environmental_data.rds.





Includes temperature (°C), precipitation (mm), and net primary productivity (NPP).




Includes grid cell IDs and latitude/longitude coordinates.







2. Evolutionary Rates Across Species and Grid Cells (Grid_level_speciation)





Contains present-day speciation rate estimates for each species.





Includes DR, BAMM, and ClaDS estimates.




Maps each species’ speciation rate to its corresponding grid cells.







3. Evolutionary Time Across Grid Cells (Grid_level_assemblage_age)





Contains files used for BioGeoBEARS DEC model integration at the grid-cell level for each tetrapod clade (amphibians, reptiles, birds, mammals).




Each clade is organized in a separate folder with the following files:





Assemblage age: arrival_time_clade*.csv




Most likely biogeographic areas per grid cell: clade*_biogeo_area.csv




Presence/absence matrix: clade*_PAM.csv




Clade phylogenetic tree: clade*_tree.tre




DEC area file: geo_area_clade*.data




DEC outputs: results_DEC_clade*.Rdata




Estimated geographic area plots across the phylogeny: DEC_plot_clade*.pdf







4. Path Analysis Example (Path_model)





Contains an example R script: path_analysis_clades.R.





Illustrates path models applied to tetrapod clades.




Example uses mammalian clades; replace the dataset to run on other clades.







5. Path Analysis Outputs (Path_outputs_&_clade_traits)





Contains outputs from path analyses for each tetrapod clade.





Path_all_effects.csv consolidates all path outputs and includes clade-level traits (see Methods in the main paper).




Other files include:





Path_direct_effects.csv – direct effects across clades




Path_indirect_via_productivity.csv – indirect effects via productivity




Path_indirect_via_speciation.csv – indirect effects via speciation




Path_indirect_via_time.csv – indirect effects via evolutionary time









6. Path Output Figures (Path_outputs_figures)





Contains R scripts to visualize path model outputs across tetrapod clades:





Direct effects: Path_direct_effects.R




Indirect effects: Path_indirect_via_productivity.R, Path_indirect_via_speciation.R, Path_indirect_via_time.R




Total effects: Path_total_effects.R







7. Clade-Level Trait Effects on Richness (Clade_level_effects.R)





Contains the R script Clade_level_effects.R.




Explores whether the effects of the tested predictors on species richness depend on clade-level traits, including:





Physiological traits: endothermy vs ectothermy




Spatial–historical traits: climate origin, range size, centroid displacement, displacement rate




Temporal/size-related traits: clade age, species richness