植物区系组成变化除了受现代环境影响，历史过程中可能发生的隔离、分化、扩散和灭绝等进化事件也发挥着很大作用。系统发育分析提供了评价历史、进化过程对于现代分布格局影响的重要工具。系统发育多样性指数将系统发育树从图形转变为可量化的数值，促进了系统发育多样性与生态学、生物地理学的结合。DNA条形码可以重建高分辨率的宏系统发育树，提高系统发育分析精度。运用系统发育多样性的分析方法研究区系的起源（即系统发育区系学）已成为植物区系地理学新的生长点。中国-日本森林植物亚区亚热带地区是全球植物区系最复杂的地区之一。本项目拟以我国亚热带四个地区的木本植物区系为研究对象，通过DNA条形码测序，重建高分辨率宏系统发育树，开展系统发育区系学研究，揭示其区系形成原因和演化历史。本项目是国际上首次使用DNA条形码重建的宏系统发育树进行系统发育区系分析，将产生大量新DNA条形码，促进我国植物区系地理学发展。

Biogeographical patterns can be thought of as the net outcome of evolutionary, historical and ecological processes. Phylogenetic analysis provides an important tool for assessing the influence of historical and evolutionary processes on the structure of contemporary ecological systems. With the advent of DNA barcoding technique and the quick accumulation of DNA barcoding data, it made the reconstruction of mega-phylogeny with high-resolution possible. The measure of Phylogenetic Diversity, PD, defined by Faith DP (1992), is the summed branch lengths that connect species on the tree-of-life. By using PD and other related parameters, phylogenetic analysis was widely applied in community ecology, conservation biology and biogeography. Recently, the term phylofloristics was coined to describe the integration of phylogenetics and floristics, which provides one new approach to study the mechanism of variation in species composition and diversity among floras. In this study, we focus on woody plants of four subtropical regions in Sino-Japan floristic sub-kingdom, which is one of global hot-spots of plant diversity. We aim to produce more DNA barcoding, and to establish one DNA barcoding database for the woody plants in sub-tropical China. Through reconstructing the mega-phylogeny with high resolution, and relevant regression analysis between phylogenetic diversity and different environmental factors, we hope to analyze the factors that shape the species composition at different floras. This study will improve our understanding of assembly processes in sub-tropical China.