pEX Codebase: Anthropocene Imperilment of Ancient Diversity and Evolutionary Potential in Terrestrial Vertebrates
Year: 2025
Type: other
Abstract: Pyron et al. pEX Codebase — Version 3 This archive contains the revised R workflow, required inputs, retained analytical outputs, and publication figures for estimating extinction probability (pEX) and examining its phylogenetic, ecological, and spatial consequences across terrestrial vertebrates. The analyses draw on the TetrapodTraits attribute dataset and TetrapodTrees phylogenetic dataset, including 100 sampled tree replicates. Earlier iterations accompanied the preprint. Changes in version 3 This version consolidates and revises the earlier releases into a numbered workflow covering observed-trait model training, imputed-trait projections, model validation, trait importance, temporal calibration, ED/DR analyses, future land-use scenarios, alternate-tree sensitivity analyses, and spatial analyses. It includes the inputs and cached results needed to use this release without combining files from previous versions. Archive contents Input ZIP: traits, tree replicates, assessment histories, spatial data, and future land-use inputs. Output ZIP: predictor matrices, fitted models, cached analyses, summary tables, and generated figures. Individual R scripts and publication figures: available separately for direct access. README.md: archive layout, extraction instructions, script sequence, and cache/recomputation controls. DATA_DICTIONARY.md: definitions, units, and missing-value conventions for the compact summary tables. environment_versions.txt: R, CmdStan, and package versions recorded during archive preparation. Direct-download summary tables TetrapodTrees_species_summary.csv: taxonomy, status and imputation information, current and future pEX, and ED/DR for 33,281 species. TetrapodTrees_family_summary.csv: species counts, expected extinction and survival totals, and median pEX, ED, and DR for 519 families. These standalone CSVs are identical to the copies included in the output ZIP. Using the archive Begin with README.md. Extract _inputs/ and _outputs/ beside the numbered R scripts, and place figure assembly scripts in Figures/. Expensive stages default to reusing retained results where available and compatible; missing results may trigger computation. For reproducibility, cite the DOI specific to this version when using these files. We used OpenAI Codex with the gpt-6-astra model (accessed September 2026) to assist in refactoring the existing R workflow, updating file-path and cache handling, and preparing archive documentation under author direction. The authors retain responsibility for the code, analyses, and scientific conclusions.
Authors: Pyron, Robert, Moura, Mario, Bowie, Rauri, Freire de Brito, Selma, Ceron, Karoline, Colston, Timothy, Esselstyn, Jacob, Magalhães Guedes, Jhonny José, Guralnick, Robert, Valentim, Hidalgo, Mooers, Arne, de Toledo Moroti, Matheus, Paiva e Paiva, Maria Fernanda, Pennell, Matthew, Pirani, Renata, Shamekhi, Reza, Sales Souza, José Alan, Riva Tonini, João Filipe, Upham, Nathan, de Oliveira Xavier, João Paulo, Jetz, Walter
Institutions: George Washington University, Universidade Federal da Paraíba, Universidade Estadual do Ceará, Universidade Estadual de Campinas (UNICAMP), Universidade Federal do Ceará, University of Puerto Rico-Mayaguez, Universidade Federal de Goiás, University of Florida, Simon Fraser University, University of Richmond, Arizona State University, Yale University
Language: English
Subfield: Nature and Landscape Conservation
Field: Environmental Science
Domain: Physical Sciences
SDG: Life on land
Open Access status: green
Funder: National Science Foundation
Awards: Collaborative Research: VertLife Terrestrial: A complete, global assembly of phylogenetic, trait, spatial and environment characteristics for a model clade, Postdoctoral Research Fellowships in Biology for FY 2009, BRC-BIO: Community Assembly and Transmission of Puerto Rican Reptile Microbiomes: Evolutionary, Ecological, and Pathogen Implications, Collaborative Research: VertLife Terrestrial: A complete, global assembly of phylogenetic, trait, spatial and environment characteristics for a model clade, RAPID: Population Assessment and Sampling of an Invasive Species Wave in Puerto Rico: Apex-Predator Hypercompetition, Collaborative Research: VertLife Terrestrial: A complete, global assembly of phylogenetic, trait, spatial and environment characteristics for a model clade, Collaborative Research: Are Bornean Areas of Endemism the Evolutionary Source of Southeast Asias Remarkable Terrestrial Biodiversity?, Collaborative Research: VertLife Terrestrial: A Complete, Global Assembly of Phylogenetic, Trait, Spatial, and Environment Characteristics for a Model Clade, Collaborative Research: VertLife Terrestrial: A complete, global assembly of phylogenetic, trait, spatial and environment characteristics for a model clade
OpenAlex ID: W7080221646