基于分子数据的系统发生树构建

doi:10.11983/CBB22224

摘要/Abstract

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。

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

Abstract: 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 phylogenetic 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 commands for these three methods, respectively. We expect this paper will provide a reference for relevant researches.

Key words: phylogenetic tree reconstruction, molecular systematics, combined analysis, nucleotide substitution model

彭焕文, 王伟. 基于分子数据的系统发生树构建. 植物学报, 2023, 58(2): 261-273.

Huanwen Peng, Wei Wang. Phylogenetic Tree Reconstruction Based on Molecular Data. Chinese Bulletin of Botany, 2023, 58(2): 261-273.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB22224

https://www.chinbullbotany.com/CN/Y2023/V58/I2/261

图/表 3

图1 基于分子数据构建系统发生树的流程 MP: 最大简约法; ML: 最大似然法; BI: 贝叶斯法

Figure 1 The pipeline of phylogenetic tree reconstruction based on molecular data MP: Maximum parsimony; ML: Maximum likelihood; BI: Bayesian inference

图2 Sanger测序获得的双向引物DNA序列色谱图橙色方框示序列两端不明确碱基, 红色箭头示2个色谱图中相互冲突的碱基。

Figure 2 DNA sequence chromatograms obtained through Sanger sequencing using both forward and reverse primers Orange boxes show the ambiguous bases in both ends of the sequences, and red arrows show the conflicting base calls between two chromatograms.

图3 序列比对示例 (A) 编码蛋白的序列比对; (B) 含有难排区域(黑色方框)的非编码序列比对; (C) 含有多聚碱基区域(橙色方框)的非编码序列比对

Figure 3 Examples for sequence alignment (A) Alignment for protein-coding sequences; (B) Alignment for non-coding sequences with a difficult-to-align region (indicated by black box); (C) Alignment for non-coding sequences with a poly-base region (indicated by orange box)

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