Linking community structure and climate vulnerability in desert plant assemblages of southern California

Title Linking community structure and climate vulnerability in desert plant assemblages of southern California Authors and Affiliations Hector Zumbado-Ulate¹ ²Luis E. Barrios²Danelle A. Baronia²G. Darrel Jenerette²Lynn C. Sweet² ¹ Escuela de Ciencias Biológicas, Universidad Nacional, Heredia, Costa Rica² Center for Conservation Biology, University of California, Riverside, CA 92521, USA Associated Publication American Journal of BotanyStatus: accepted This Zenodo archive supports the manuscript: Linking community structure and climate vulnerability in desert plant assemblages of southern California Overview This Zenodo repository contains the data, metadata, and supporting materials used to generate the results presented in the associated manuscript. The archive is intended to ensure long-term preservation, transparency, and reproducibility of all analyses. All analyses were conducted in R and include species distribution modeling (JSDMs and SDMs), spatial analyses, phylogenetic regionalization, and projections of future range shifts for angiosperm species in desert ecosystems of southern California. Contents of This Archive This Zenodo deposit includes: Raw datasets used in the analyses Processed datasets derived from raw inputs Metadata files describing variables, units, and data sources Supplementary materials required to reproduce the analyses File names and formats are documented within the metadata files. Code Availability The R scripts used for data processing, analyses, and figure generation are publicly available on GitHub: 🔗 https://github.com/hzumbado/desert_angiosperms_repository The code is organized as a self-contained R Project and the computational environment is administered using the renv package. This ensures that package dependencies and versions are recorded and can be restored consistently across systems. The GitHub repository includes: An R Project file (.Rproj) A renv.lock file specifying exact package versions Structured scripts following the analytical workflow The Zenodo archive is designed to be used in conjunction with the GitHub repository. Computational Environment All analyses were conducted using: R version: 4.5.2 Key R Packages Core packages used in the analyses include: ENMeval — evaluation and tuning of species distribution models ecospat — niche dynamics and spatial ecology analyses phyloregion — phylogenetic regionalization and diversity metrics Hmsc — Hierarchical Modelling of Species Communities tidyverse — data manipulation and visualization terra — spatial raster processing sf — vector-based spatial analysis ggplot2 — figure generation Exact package versions are recorded in the renv.lock file and can be restored automatically. Present and Future Climate Scenarios All present and future climate datasets (19 bioclimatic variables) were obtained from WorldClim version 2.1, at a spatial resolution of 30 arc-seconds (~1 km at the equator): present: https://www.worldclim.org/data/worldclim21.html future: https://www.worldclim.org/data/cmip6/cmip6_clim30s.html Future climate projections were derived from CMIP6 downscaled climate datasets and were used to model potential future shifts in angiosperm species distributions. Specifically: Shared Socio-economic Pathways (SSPs): SSP1–2.6 (SSP126) SSP2–4.5 (SSP245) SSP5–8.5 (SSP585) Time period: 2081–2100 Global Circulation Models (GCMs): ACCESS-CM2 EC-Earth3-Veg HadGEM3-GC31-LL For each SSP, climatic variables were averaged across the three GCMs to reduce uncertainty associated with individual model projections. Details on variable selection, processing, and aggregation are provided within the metadata files and associated R scripts. Reproducibility To reproduce the analyses: Download and extract this Zenodo archive. Clone or download the GitHub repository linked above. Open the R Project file (.Rproj) in R (version 4.5.2). Restore the package environment using: renv::restore() Update file paths in the scripts if necessary. Run scripts sequentially following their numeric prefixes. Data Usage Notes Data are provided for research and academic use. Users should consult metadata files for data sources, preprocessing steps, and known limitations. Derived products should be cited appropriately. License Data: Creative Commons Attribution 4.0 International Code: GNU General Public License 3.0 License details are provided within the Zenodo record and the associated GitHub repository. Citation If you use these data or materials, please cite both the Zenodo archive and the associated manuscript: Zumbado-Ulate, H., Barrios, L. E., Baronia, D. A., Jenerette, G. D., & Sweet, L. C.Linking community structure and climate vulnerability in desert plant assemblages of southern CaliforniaAmerican Journal of Botany.Zenodo DOI: 10.5281/zenodo.18167096 Contact Corresponding author: Hector Zumbado-UlateAffiliation: Escuela de Ciencias Biológicas, Universidad Nacional, Costa RicaEmail: [e-mail]