Equilibrium Dynamics Shape Diversity Patterns Across Terrestrial Tetrapod Clades

This repository contains scripts and documentation organized into folders, each designated for specific analyses conducted in this study. Below is an outline of the folder structure and contents. For setup and usage details, please refer to this README.

1. Species Presence and Absence per Grid Cell (PAM folder)

Contains geographic data on species presence (1) or absence for each grid cell, separated by tetrapod group: amphibians (PAM_amphibians.rds), birds (PAM_birds.rds), mammals (PAM_mammals.rds), squamates (PAM_squamata.rds), and testudines & crocodiles (PAM_testcroc.rds).

Latitude and longitude coordinates are also provided.

2. Environmental Variables (environmental_data folder)

Includes environmental variables for each grid cell (environmental_data.rds), with data on temperature (°C), precipitation (mm), and net primary productivity (NPP).

Also contains grid cell IDs and latitude/longitude coordinates.

3. Evolutionary Rates Across Species and Grid Cells (evol_rates_merged folder)

Contains evolutionary rate data, including DR, BAMM, and MiSSE speciation estimates for each species and its corresponding grid cells.

Species tip age estimates are also provided.

4. Identified Clades Using Laplacian Spectrum Approach (laplacian_clades folder)

Includes files for 129 tetrapod clades identified via the Laplacian spectrum approach, saved in .json format.

Each file lists the clade ID and the corresponding species within that clade, separated by tetrapod group.

5. Phylogenies

This folder holds phylogenies for each tetrapod group used in the study.

6. Grid Cell Network

Contains equal-area grid cells at 1° x 1° resolution (GriMap100_clean*), used as spatial units in the analyses.

7. Path Analysis Example (path_analysis_example folder)

Contains example R code (path_analysis_clades.R) illustrating path models performed for each tetrapod clade.

Example uses mammalian clades; replace data to apply to other clades.

8. Path Analysis Outputs (path_analysis_output folder)

Provides outputs from path analyses conducted for each clade within each tetrapod group.

The file path_analysis_clades.csv consolidates all path outputs, identifying each clade’s physiology (endotherms or ectotherms), climate origin (warm or cool), and additional data such as clade richness and range size.

9. Comparing Effects by Clade Physiology and Climate Origin (clade_characteristics folder)

Contains R code (clades_characteristics.R) for replicating the analyses shown in Figures 3 and 4 of the main text.