Establishment of a national park protection system in China, including the latest target proposed to protect at least 30% of the land area, calls for a comprehensive exploration of conservation priorities incorporating multiple diversity facets. We herein evaluate the spatial distribution of Chinese flowering plants from the perspectives of richness, uniqueness, vulnerability, and evolutionary history, by integrating three mega-phylogenies and comprehensive distribution data. We detect significantly high consistency among hotspots of different diversity measures for Chinese flowering plants, suggesting that multiple facets of evolutionary diversity are concentrically distributed in China. Affording legal protection to these areas is expected to maximize positive conservation outcomes. We propose two integrative diversity indices by incorporating three richness-based and three phylogeny-based measures, respectively. Both methods identify areas with high species richness, but the integrative phylogeny-based index also locates key areas with ancient and unique evolutionary histories (e.g., Ailao-Wuliang Mts, Dabie Mts, Hainan rainforest, Karst area of Yunnan-Guizhou-Guangxi, Nanling Mts, and southeast coastal regions). Of all the diversity indices explored, phylogenetic endemism maximizes the incidental protection of other indices in most cases, emphasizing its significance for conservation planning. Finally, 42 priority areas are identified by combining the 5%-criterion hotspots of two integrative indices and the minimum area to protect all threatened species analyzed. These priorities cover only 13.3% of China’s land area but host 97.1% of species richness (23,394/24,095), 96.5% of endemic species (11,841/12,274), 100% of threatened species (2,613/2,613), and 99.3% of phylogenetic diversity for flowering plants involved in this study. These frameworks provide a solid scientific basis for national park planning in China.

The dataset contains:

(1) The time tree of 13,663 species estimated using treePL (Tactual);

time_tree_13663sp.tre

(2) The complete-species tree of 27,185 species generated by inserting species without sequence data into the basal node of its corresponding genus or family using “scenario 1” in “V.PhyloMaker” package of R (Tbasal);

species_tree_27,185sp_s1.tre

(3) Ten complete-species trees of 27,185 species generated by randomly inserting species without sequence data at or below the basal node of its corresponding genus or family using “scenario 2” in “V.PhyloMaker” package of R (Trandom).

10_species_trees_27,185sp_s2.tre