A comprehensive dated phylogeny of China’s vascular plants reveals a hidden global biodiversity hotspot

This archive contains the phylogenetic trees of vascular plants in China, time-calibrated trees based on fossil records, geographic distribution data of species, and custom scripts used during the spatiotemporal analysis.Data sets involved:Folder: 1_phylogenetic_reconstructionThe folder contains a series of phylogenetic tree files and auxiliary files, such as the optimal tree and 100 bootstrap replicates.chn_vascular_plants_best_ML_tree_2025.trechn_vascular_plants_bootstrap_tree_2025.treFolder: 2_divergence_time_estimationThe folder contains a series of time-calibrated phylogenetic tree files and auxiliary files, such as the dated optimal tree and 100 bootstrap replicates (with fixed topology).chn_vascular_plants_dated_best_tree_2025.trechn_vascular_plants_dated_fixed_topo_100trees_2025.treFolder: 3_geographic_distribution_dataThe folder contains the geographical distribution data of vascular plants in China at the genus and species level, including genus/species names, their corresponding taxonomic attributes, and grid numbers where they occur.chn_vascular_plants_species_grid_distribution_data.csvchn_vascular_plants_genus_grid_distribution_data.csvCode files involved:Folder: ScriptsAll code files related to data analysis and required input files are in the Scripts folder. see 0_README.md for details.The scripts are listed as follows：1.1_TemporalAnaly_Extracting_node_ages_for_LAR.R1.2_TemporalAnaly_Lineage_accumulation_rate(LAR)_calculation_and_draw.jl1.3_TemporalAnaly_Divergence_time_stacked_barplot.R1.4_TemporalAnaly_Comparison_of_temporal_distribution_between_endemics_and_non-endemics.R2_Taxonomic_endemism_analysis_workflow.R3_Phylogenetic_endemism_analysis_workflow.R4_Sensitivity_test_of_diversity_in_central_China_based_on_GBIF_coordinate_data.R5_Comparison_of_divergence_times_with_other_studies.R