Phylogeny and geospatial data on the native woody trees and shrubs of southern Africa

Reconstructed phylogeny of woody trees and shrubs including over 1300 species (some non-native species are included) from 115 families and 541 genera. We sequenced the core plant barcodes (rbcLa and matK) from sampled material, and merged these data with matching barcode sequence data in GenBank from tree species native to the region. We then used the merged sequence matrix to reconstruct a comprehensive phylogeny of south African woody trees and shrubs, following protocols detailed in Maurin et al. (2014). Branch lengths were calibrated in millions of years using Bayesian MCMC implemented in BEAST v.1.4.8 and 28 fossil calibrations from Bell et al. (2010) as minimum age constrains, except for the root of the Eudicots, which was set at 124 myr. Voucher specimen information and GenBank accession numbers are listed on the BOLD DataSystem (www.boldsystems.org). Geospatial data for southern Africa at a resolution of 0.5º × 0.5º grid cells, listing latitude and longitude centroids for each cell, and matching data on woody plant phylogenetic diversity, total species richness, richness of threatened woody plants, AET, elevation, human population density, Nitrogen addition as fertilzer, cropland and per capita GDP.本数据集包含来自115个科、541个属的1300余种木本乔木与灌木（其中包含部分非本土物种）的重建系统发育树。研究人员对采样材料的植物核心条形码（core plant barcodes，rbcLa与matK）进行测序，并将所得数据与基因序列数据库（GenBank）中该区域本土乔木物种的匹配条形码序列数据进行合并。随后，研究人员遵循Maurin等人（2014年）详述的实验流程，利用合并后的序列矩阵重建了南非木本乔木与灌木的综合系统发育树。借助BEAST v.1.4.8中实现的贝叶斯马尔可夫链蒙特卡洛（Bayesian MCMC）方法，以28组来自Bell等人（2010年）的化石校准数据作为最小年龄约束，对分支长度进行了百万年尺度的校准；仅真双子叶植物（Eudicots）的根节点年龄被设定为124百万年。凭证标本信息以及GenBank登录号可在BOLD数据系统（BOLD DataSystem，www.boldsystems.org）中查询获取。本数据集还包含分辨率为0.5º×0.5º的南非地理空间数据，具体涵盖各网格单元的纬度、经度质心，以及与之匹配的木本植物系统发育多样性、物种总丰富度、受威胁木本植物丰富度、实际蒸散量（AET）、海拔、人口密度、氮肥施入、耕地面积与人均国内生产总值（per capita GDP）等相关数据。