Spatial heterogeneity of extinction risk for flowering plants in China

Abstract: 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 highly spatially selective and scale dependent. Our results show that unstable vegetation structure (i.e., proportion of growth forms) is the dominant driver of extinction risk at the national scale, while the dominant drivers vary across vegetation regions and zones. Three geographically adjacent and contiguous zones face distinct dominant drivers, i.e. drivers related to evolutionary history in Northeast China, drivers caused by unstable vegetation structure in West China, and topographical drivers (topographic roughness) in East & South China. 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 China. The original phylogeny was reconstructed by Hu et al. (2020), which included 13,321 species (12,160 native to China) and 2,991 genera (2,743 native to China). The phylogeny was then dated by Lu et al. (2022) with 138 calibrations, using the penalized likelihood (PL) approach as implemented in treePL. The complete species trees were generated by inserting 13,864 additional species without sequence data into the randomly selected nodes or base nodes below the corresponding genra of the backbone tree with the “V.PhyloMaker” package in R48, according to available taxonomic information.      - 1_chn_ang_completeTree_randomly insert .tre      - 1_chn_ang_timeTree.tre