DOI: 10.57760/sciencedb.17283
title: Spatial heterogeneity of extinction risk for flowering plants in China
title: Spatial heterogeneity of extinction risk for flowering plants in China

description: Abstract:Understanding the variability of extinction risk and its potential drivers across different spatial extents is crucial to revealing the underlying processes of biodiversity loss and sustainability. However, in countries with high climatic and topographic heterogeneity, studies on extinction risk are often challenged by complexities associated with extent effects. Here, using 2.02 million fine-grained distribution records and a phylogeny including 27,185 species, we find that the extinction risk of flowering plants in China is spatially concentrated in southwestern China. Our analyses suggest that spatial extinction risks of flowering plants in China may be caused by multiple drivers and are extent dependent. Vegetation structure based on proportion of growth forms is likely the dominant extinction driver at the national extent, followed by climatic and evolutionary drivers. Finer extent analyses indicate that the potential dominant extinction drivers vary across zones and vegetation regions. Despite regional heterogeneity, we detect a geographical continuity potential in extinction drivers, with variation in West China dominated by vegetation structure, South China by climatice, and North China by evolution. Our findings highlight that identification of potential extent-dependent drivers of extinction risk is crucial for targeted conservation practice in countries like China. Authors: Lina Zhao1,2, Jinya Li3, Russell L. Barrett4,5, Bing Liu1,2,6, Haihua Hu1,2, Limin Lu1,2*, Zhiduan Chen1,2,6* Affiliations:1State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.2China National Botanical Garden, Beijing 100093, China.3State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.4National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan 2567, New South Wales, Australia.5Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Kensington 2052, New South Wales, Australia.6Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.*Corresponding author. Email: liminlu@ibcas.ac.cn (LML); zhiduan@ibcas.ac.cn (ZDC). Funding:This work was supported by National Natural Science Foundation of China (32122009), National Key Research Development Program of China (2022YFF0802300 and 2023YFF0805800), International Partnership Program of CAS (151853KYSB20190027), the Youth Innovation Promotion Association CAS (2020080), Sino-Africa Joint Research Center, Chinese Academy of Sciences, International Research and Education Development Program (SAJC201613), and the K.C.Wong Education Foundation (GJTD-2020-05). RLB acknowledges financial support from the Chinese Academy of Sciences President's International Fellowship Initiative. 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 Floder: Dataset_extinction driversThe folder contains five types of hypothesized extinction driver acting on flowering plants in China      - ExtintionDriver_Anthropogenic.csv      - ExtintionDriver_Climatic.csv      - ExtintionDriver_Evolutionary.csv      - ExtintionDriver_Topographic.csv      - ExtintionDriver_VegetationStructure.csv 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_Zone_North.csv      - 1_Zone_South.csv      - 1_Zone_West.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_Zone_example      - 0_phylosignal_D_caper_for_VegRegions and zones_example.R      - 0_SpatialPack_ttest.R- vegRegions_histogram_for_Figure 4 .R- vegZones_histogram_for_Figure 5.R
description: Abstract:Understanding the variability of extinction risk and its potential drivers across different spatial extents is crucial to revealing the underlying processes of biodiversity loss and sustainability. However, in countries with high climatic and topographic heterogeneity, studies on extinction risk are often challenged by complexities associated with extent effects. Here, using 2.02 million fine-grained distribution records and a phylogeny including 27,185 species, we find that the extinction risk of flowering plants in China is spatially concentrated in southwestern China. Our analyses suggest that spatial extinction risks of flowering plants in China may be caused by multiple drivers and are extent dependent. Vegetation structure based on proportion of growth forms is likely the dominant extinction driver at the national extent, followed by climatic and evolutionary drivers. Finer extent analyses indicate that the potential dominant extinction drivers vary across zones and vegetation regions. Despite regional heterogeneity, we detect a geographical continuity potential in extinction drivers, with variation in West China dominated by vegetation structure, South China by climatice, and North China by evolution. Our findings highlight that identification of potential extent-dependent drivers of extinction risk is crucial for targeted conservation practice in countries like China. Authors: Lina Zhao1,2, Jinya Li3, Russell L. Barrett4,5, Bing Liu1,2,6, Haihua Hu1,2, Limin Lu1,2*, Zhiduan Chen1,2,6* Affiliations:1State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.2China National Botanical Garden, Beijing 100093, China.3State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.4National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan 2567, New South Wales, Australia.5Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Kensington 2052, New South Wales, Australia.6Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.*Corresponding author. Email: liminlu@ibcas.ac.cn (LML); zhiduan@ibcas.ac.cn (ZDC). Funding:This work was supported by National Natural Science Foundation of China (32122009), National Key Research Development Program of China (2022YFF0802300 and 2023YFF0805800), International Partnership Program of CAS (151853KYSB20190027), the Youth Innovation Promotion Association CAS (2020080), Sino-Africa Joint Research Center, Chinese Academy of Sciences, International Research and Education Development Program (SAJC201613), and the K.C.Wong Education Foundation (GJTD-2020-05). RLB acknowledges financial support from the Chinese Academy of Sciences President's International Fellowship Initiative. 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 Floder: Dataset_extinction driversThe folder contains five types of hypothesized extinction driver acting on flowering plants in China      - ExtintionDriver_Anthropogenic.csv      - ExtintionDriver_Climatic.csv      - ExtintionDriver_Evolutionary.csv      - ExtintionDriver_Topographic.csv      - ExtintionDriver_VegetationStructure.csv 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_Zone_North.csv      - 1_Zone_South.csv      - 1_Zone_West.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_Zone_example      - 0_phylosignal_D_caper_for_VegRegions and zones_example.R      - 0_SpatialPack_ttest.R- vegRegions_histogram_for_Figure 4 .R- vegZones_histogram_for_Figure 5.R