Code and Data for "Biogeographical Variation of Angiosperm Taxonomic Traits Exhibits a Globally Consistent Structure"

Code and Data for "Biogeographical Variation of Angiosperm Taxonomic Traits Exhibits a Globally Consistent Structure" Description This repository contains the R code and processed data for the analyses presented in: Zhang, C., Zhang, Q., Sun, X., Wang, R., Wang, H. & Zheng, P. Biogeographical Variation of Angiosperm Taxonomic Traits Exhibits a Globally Consistent Structure. The code implements principal component analysis (PCA), phylogenetic generalized linear mixed models (PGLMM), phylogenetic signal and conservation analyses (Fritz's D, consenTRAIT), evolutionary model fitting, stochastic character mapping, beta regression, null model simulations for diversity metrics, Generalized Additive Models (GAM), and spatial piecewise structural equation modeling (pSEM). All analyses were performed in R (version 4.4.3–4.5.1) across 323,681 angiosperm species and 652 terrestrial ecoregions. Contents Code01–Code23: R scripts for main analyses, one per figure/result section.Supplementary Code1: Ecoregion trait proportion calculation and Logit transformation.Data/: Processed datasets including ecoregion-level trait proportions, environmental variables, phylogenetic similarity matrices, and biome classifications.Data/Supplementary_Data/: Metadata of trait data sources. Data Sources Species occurrences: GBIF (https://doi.org/10.15468/dl.dj8zxb)Taxonomy: World Flora Online (WFO), Version 2025.02Ecoregion boundaries: WWF Terrestrial EcoregionsClimate: CHELSA V1.2, Paleoclim V1.2b, WorldClim v2.1, Global AI-PET v3Soil: Harmonized World Soil Database v2.0Phylogeny: Smith & Brown GBOTB tree via Open Tree of Life; V.PhyloMaker2 Software Requirements R (version 4.4.3 or higher) with packages: ape, betareg, caper, castor, corHMM, data.table, dplyr, factoextra, ggplot2, mgcv, nlme, patchwork, phyr, phytools, piecewiseSEM, scales, tidyr, and others (see full list in the GitHub repository). Usage 1. Download and unzip the archive.2. Set the working directory to the repository root in R/RStudio.3. Run scripts sequentially (Code01 through Code23) or individually for specific figures.4. Outputs (PDF figures and CSV data) are saved to the working directory. Related Resources GitHub repository: https://github.com/ZhangChunyu-BioGeo/Angiosperm-Biogeographical-Spectrum License MIT License. Note that some input data (e.g., GBIF occurrences) may be subject to the licensing terms of their original providers. Contact Corresponding authors: Hui Wang ([e-mail]) & Peiming Zheng ([e-mail])School of Life Sciences, Shandong University, Qingdao, China