Spatial heterogeneity of extinction risk for flowering plants in China

Understanding the spatial characteristics of extinction risk and its drivers is crucial to revealing the underlying processes of biodiversity loss and sustainability. However, in megadiverse countries with high climatic and topographic heterogeneity, studies on extinction risk are often challenged by complexities associated with scale effects. Here, using two million fine-grain distribution records and a mega-phylogeny including 27,185 species, we find that the extinction risk of flowering plants in China is spatially concentrated in southwestern China. Our multiple-scale analyses suggest that spatial threatening processes of flowering plants in China are driven by multiple drivers and are scale dependent. Unstable vegetation structure (i.e., proportion of growth forms) is inferred to be the dominant extinction driver at the national scale, followed by topographic (i.e., roughness) and evolutionary drivers (i.e., average evolutionary distinctiveness rarity). On finer scale analyses indicate that the dominant extinction drivers vary across vegetation regions and zones. Despite regional heterogeneity, we detect a clear geographical continuity in extinction drivers, with West China dominated by vegetation structure drivers, East & South China topographic drivers, and Northeast China evolutionary drivers. Our findings highlight that identification of scale-dependent drivers of extinction risk is crucial for targeted conservation practice in megadiverse countries like China.Data sets involved: Folder: DataLayers_county_levelThe folder contains a number of related layers, such as topography of China, major vegetation regions and county level layers. These layers and the attribute tables can be used to draw most of the maps relevant to this article.      - county_info.shp      - vegRegions_info.shp      - china_dem1.shp Folder: Dataset_extinction risk of speciesThis folder is accompanied by a sheet table containing information on extinction risk at regional or national level for each species in this paper.      - Dataset_extinction risk of species.xlsx Folder: Dataset_extinction risks for eight vegetation regionsDue to the significant stratified heterogeneity of extinction risk for flowering plants, we divided China into eight distinct regions based on the Vegetation Regionalization Map of China (1: 6,000,000) (Fig. 2 in manuscript). Each .csv file contains a list of flowering plants and the extinction risks of this vegetation region. Moreover, these files can also be executed together with the R codes to detect the phylogenetic signal of extinction risk in each vegetation region.       -1_VegRegions_1.csv      -1_VegRegions_2.csv      -1_VegRegions_3.csv      -1_VegRegions_4.csv      -1_VegRegions_5.csv      -1_VegRegions_6.csv      -1_VegRegions_7.csv      -1_VegRegions_7.csv Folder: Dataset_extinction risks for three vegetation ZonesWe divide China into three zones, West China, Northeast China, and East & South China, according to topography and precipitation incorporating vegetation boundaries, to further test whether spatial extinction risks of flowering plants in China are scale-dependent. The folder contains extinction risk of each species distributed in three vegetation zones.      - 1_VegZone_1_East & South.csv      - 1_VegZone_2_West.csv      - 1_VegZone_3_Northeast.csv Folder: Dataset_spatial information in countiesThe folder a sheet with various types of information for each county      - Dataset_spatial information in counties.csv Folder: PhylogenyThe phylogeny used in this study was based on an existing species-level tree of life of flowering plants in China33. The original phylogeny was reconstructed by Hu et al.45, which included 13,321 species (12,160 native to China) and 2,991 genera (2,743 native to China). The phylogeny was dated by Lu et al.33 with 138 calibrations, using the penalized likelihood (PL) approach as implemented in treePL46. The complete species trees were then generated by inserting 13,864 additional species without sequence data into the randomly selected nodes below the corresponding genera of the backbone tree with the “V.PhyloMaker”47 package in R48, according to available taxonomic information. Finally, a set of complete species trees that include 27,185 species representing 2,859 genera from 252 families of flowering plants native to China were generated. In this study, we selected the first complete-species tree in 10_species_trees_27,185sp_s2.tre (available in Dryad: https://doi.org/10.5061/dryad.6m905qg2w) for downstream analyses.      - 1_chn_ang_completeTree_randomly insert .tre      - 1_chn_ang_timeTree.tre Code files involved:Folder: 0_CodeMost of code files related to data analyses and charting is in this folder.      - 0_DR_statistic_China.R      - 0_DT_divergence time.R      - 0_ED_PD_sesPD_PE_sesPE_RPE_.R      - 0_missForest_missingData.R      - 0_model_vegRegions_example.R      - 0_phylosignal_D_caper_for_VegRegions and zones_example.R      - 0_SpatialPack_ttest.R- vegRegions_histogram_for_Figure 5 .R- vegZones_histogram_for_Figure 6.R