Environmental Filtering, Trait Differentiation, and Evolutionary Conservatism Shape Bryophyte Community Assembly on the Tibetan Plateau

Tibet_bryophyte_community_data_JSDM_input.RDataProcessed RData file containing the input data for the hierarchical joint species distribution modelling analyses. The file includes bryophyte community data, environmental predictors, functional trait data, phylogenetic information, spatial coordinates, and model-design objects used to construct the HMSC models. 1. Load RData and build HMSC models.RR script for loading the processed input data, performing basic consistency checks, defining the spatial random-effect structure, constructing the HMSC models, and exporting initialization objects for subsequent Hmsc-HPC posterior sampling. This script represents the first step of the modelling workflow. 2. Run Hmsc-HPC posterior sampling for all models in the Ubuntu environment.pyPython script for running posterior sampling of the initialized HMSC models using Hmsc-HPC in an Ubuntu environment. The script executes multiple MCMC chains for each model, manages temporary and final output files, and saves posterior samples for downstream import and summarization. This script represents the second step of the modelling workflow. 3. Import Hmsc-HPC posterior output and summarize results.RR script for importing posterior samples generated by Hmsc-HPC, reconstructing fitted HMSC models, and summarizing model outputs. The script includes variance partitioning, MCMC diagnostics, estimation of phylogenetic signal, visualization of species–environment relationships, trait–environment associations, environmental response gradients, and residual species association matrices. This script represents the final step of the modelling workflow.