基因树冲突与系统发育基因组学研究精选.pdf

植物分类学报 46 (6): 795–807 (2008) doi: 10.3724/SP.J.1002.2008.08081 Journal of Systematics and Evolution (formerly Acta Phytotaxonomica Sinica) 基因树冲突与系统发育基因组学研究 邹新慧 葛 颂* (系统与进化植物学国家重点实验室, 中国科学院植物研究所 北京 100093) Conflicting gene trees and phylogenomics * Xin-Hui ZOU Song GE (State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China) Abstract With more and more sequence data available, it has been a widespread practice to apply multiple genes to reconstruct phylogenies at different hierarchical levels. The phenomenon of conflicting gene trees has accordingly become a remarkable and difficult problem. It is increasingly understood that the difference between gene tree and species tree and the causes behind should be fully appreciated in molecular phylogenetic studies. In this paper, we have explored the major causes resulting in conflicting gene trees, including stochastic errors, systematic errors and biological factors. We also introduced a newly developed discipline, phylogenomics, and demonstrated its power and great potential in resolving difficult phylogenetic problems using our recent phyloge- nomic study of Oryza as an example. Furthermore, we discussed some strategies and approaches in elucidating conflicting gene trees and provided some suggestions and recommendations for molecular phylogenetic studies using multiple genes. Key words conflicting gene trees, gene tree, molecular phylogenetics, phylogenomics, species tree. 摘要 随着越来越多的基因序列被运用于系统发育重建中, 随之产生的基因树冲突已成为分子系统发育研究中日益突出的 问题。因此, 在分子系统发育研究中, 应正确理解基因树和物种树之间的差异,