DOI: 10.5281/zenodo.17591794
title: Divergent pathways shape climatic niches and body size evolution across terrestrial vertebrates

description: About this repository

Motivation

This repository contains the data and code used in the manuscript "Divergent pathways shape climatic niches and body size evolution across terrestrial vertebrates". In this study, we investigated the relationship between the evolution of climatic niche, body size, and microhabitat use among terrestrial vertebrates. Our goal was to identify the direction and strength of evolutionary associations among these traits and to test whether these relationships follow common or lineage-specific pathways. By combining large-scale climatic and trait datasets, we revealed how distinct evolutionary mechanisms have shaped the evolutionary pathways of amphibians, reptiles, birds, and mammals through time.

How to use

File structure

The GitHub repository contains three scripts:





01_extraction.qmd – Generates the priors for BAMM, checks the convergence of the runs, calculates the median evolutionary rates, and extracts the rate-through-time matrix. It uses trait data from TetrapodTraits, and the phylogenies used are available on Zenodo




02_metrics/02_metrics.qmd – Builds the community matrix for each terrestrial vertebrate group, loads the bioclimatic variables per grid, and calculates the niche position and breadth for each species. The results feed into 01_extraction.qmd, but they can also be downloaded directly from Zenodo




03_analysis/03_analysis.qmd – Performs structural equation modeling analyses incorporating phylogenetic autocorrelation, runs sensitivity tests, and generates the main figures of the manuscript, which were later refined in InkScape.



The Zenodo (vertebrates_evolution.zip) deposit contains the following folders:





BAMM/ – Contains all files generated by BAMM. Inside, there are three subfolders:





body_size/ – Evolutionary rates for body size for each vertebrate group.




niche_position/ – Evolutionary rates for climatic niche position.




niche_breadth/ – Evolutionary rates for climatic niche breadth.






traits/ – Species-level data, including niche metrics and trait data from TetrapodTraits.




spatial_data/ – Shapefiles and species distribution data for each vertebrate group derived from TetrapodTraits.



Description

The workflow follows three main steps: (1) obtaining evolutionary metrics (01_extraction.qmd), (2) calculating climatic niche metrics (02_metrics.qmd), and (3) testing causal relationships through structural equation modeling (03_analysis.qmd). Climatic niche metrics are generated in the 02_metrics.qmd script, and the resulting values serve as input for 01_extraction.qmd, which is executed twice: first to extract evolutionary rates of body size, and later to obtain evolutionary rates of the climatic niche.

To reproduce the full analytical workflow:





Run 01_extraction.qmd to extract evolutionary rates of body size;




Run 02_metrics.qmd to calculate climatic niche metrics;




Run 01_extraction.qmd again to extract evolutionary rates of the climatic niche;




Run 03_analysis.qmd to perform structural equation modeling and generate the main figures of the manuscript.



Usage notes

R 4.4.1 software is required to open and ensure reproducibility of all scripts. All analyses were performed in R and are fully reproducible using the materials provided here.

License

The code and data in this repository are provided for peer review and collaboration purposes only. They are not licensed for public use or redistribution until the associated manuscript is formally published. If you are interested in using this material before publication, don't hesitate to get in touch with the author at mmoroti@gmail.com.