Equilibrium Dynamics Shape Diversity Patterns Across Terrestrial Tetrapod Clades

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