Data from: The macroevolutionary singularity of snakes
Cite this dataset
Title, Pascal et al. (2024). Data from: The macroevolutionary singularity of snakes [Dataset]. Dryad. https://doi.org/10.5061/dryad.p5hqbzkvb
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this dramatic radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5,400 loci) from 1,018 species. Through concerted changes in the dynamics of phenotypic evolution and speciation, snakes have transformed the macroecological landscape through their impact on the trophic architecture of animal communities. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the profound impact of historical contingency on vertebrate biodiversity.
README: The macroevolutionary singularity of snakes
This repository contains all data and code used to infer the squamate phylogeny, prepare trait and other datasets, run comparative analyses, and generate all main and supplemental figures. README files with additional information are provided within repository subfolders.
Description of the data and file structure
Data files are provided via Data Dryad and R/Python scripts are provided in the associated Zenodo repository, but the data folder and scripts folder are intended to be placed in a common directory so that file paths in the scripts can point to the appropriate data files.
Data are organized into several subfolders that are aligned with the different stages of analysis. Scripts generally mirror this structure.
Code for comparative analyses and main or supplemental figures should be runnable by the user. Code for other stages of analysis are shared for the sake of transparency, but are not runnable as provided.
Phylogenies can be found in the data repository, in 1.tree_inference > mainTrees
Diversification and trait data can be found in alldat.csv (see associated readme).
Funding
National Science Foundation, Award: 1754398, Division of Environmental Biology
David and Lucile Packard Foundation
Coordenação de Aperfeicoamento de Pessoal de Nível Superior
National Council for Scientific and Technological Development
Foundation for Research Support of the Federal District
California State University, Dominguez Hills, RSCA
National Science Foundation, Award: 1754425, Division of Environmental Biology
National Science Foundation, Award: 0905765, Division of Biological Infrastructure
National Science Foundation, Award: 1441719, Division of Environmental Biology
Australian Research Council
National Council for Scientific and Technological Development, Award: 304715/2021-2
Fundação de Apoio à Pesquisa do Estado da Paraíba
Coordenação de Aperfeicoamento de Pessoal de Nível Superior, Award: AUXPE 88881.312082/2018-01, PRINT UFPB
National Science Foundation, Award: 0415430, Division of Environmental Biology
National Science Foundation, Award: 9200779, Division of Environmental Biology
National Science Foundation, Award: 9505518, Division of Environmental Biology