基于分子数据的系统发生树构建  

Phylogenetic Tree Reconstruction Based on Molecular Data

作　　者：彭焕文 王伟[1,2,3] Huanwen Peng;Wei Wang(State Key Laboratory of Systematic and Evolutionary Botany,Institute of Botany,Chinese Academy of Sciences,Beijing 100093,China;China National Botanical Garden,Beijing 100093,China;University of Chinese Academy of Sciences,Beijing 100049,China)

机构地区：[1]中国科学院植物研究所,系统与进化植物学国家重点实验室,北京100093 [2]国家植物园,北京100093 [3]中国科学院大学,北京100049

出　　处：《植物学报》2023年第2期261-273,共13页Chinese Bulletin of Botany

基　　金：中国科学院战略性科技先导专项(B类)(No.XDB31030000);国家自然科学基金(No.32170210,No.32011530072,No.31770233,No.31770231)。

摘　　要：系统发生学是研究生物类群间进化关系的学科。随着测序技术、分析方法和计算能力的改进,分子数据被广泛应用,促进了系统发生学的快速发展。系统发生树已成为生态学和比较生物学等研究领域的有力工具。然而,许多研究在进行系统发生树构建时更侧重各种软件的使用,一些基本原则或注意事项有时会被弱化甚至忽视。该文详细介绍了基于分子数据进行系统发生树构建的工作流程和基本方法,包括类群取样、分子标记选择、序列比对、分区及模型选择、序列联合分析以及拓扑结构检验等关键步骤。此外,该文还为系统发生树构建常用的3种方法(最大简约法、最大似然法和贝叶斯法)提供了相应的软件操作流程和运行命令,以期为相关研究提供参考。Phylogenetics is a discipline reconstructing evolutionary relationships of organisms.With improvements in sequencing technique,analytic methods,and computation power,the molecular data have been used widely and have promoted greatly the rapid development of molecular phylogenetics.The phylogenetic tree has become a powerful tool in many areas of biology,such as ecology and comparative biology.Currently,phylogenetic studies mainly focus on phy-logenetic tree reconstructions by using various software,however,some fundamental principles or matters that should be paid attention when performing phylogenetic analyses are sometimes weakened or even ignored.Here,we present the workflow and methods in details for phylogenetic tree reconstruction based on molecular data,including taxon sampling,molecular marker selection,sequence alignment,partitioning and model selection,combined analysis of multiple markers,and topological test.Currently,the widely used methods of phylogenetic reconstructions are maximum parsimony,maximum likelihood,and Bayesian inference.We thereby provide the detailed operating flows and corresponding com-mands for these three methods,respectively.We expect this paper will provide a reference for relevant researches.

关 键 词：系统发生树构建 分子系统学 联合分析 核苷酸替换模型 

分 类 号：Q811.4[生物学—生物工程]