Ajawatanawong Pravech
Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama VI, Rachathewi, Bangkok, 10400, Thailand.
Adv Biochem Eng Biotechnol. 2017;160:185-196. doi: 10.1007/10_2016_49.
Molecular phylogenetics is the study of evolutionary relationships among organisms using molecular sequence data. The aim of this review is to introduce the important terminology and general concepts of tree reconstruction to biologists who lack a strong background in the field of molecular evolution. Some modern phylogenetic programs are easy to use because of their user-friendly interfaces, but understanding the phylogenetic algorithms and substitution models, which are based on advanced statistics, is still important for the analysis and interpretation without a guide. Briefly, there are five general steps in carrying out a phylogenetic analysis: (1) sequence data preparation, (2) sequence alignment, (3) choosing a phylogenetic reconstruction method, (4) identification of the best tree, and (5) evaluating the tree. Concepts in this review enable biologists to grasp the basic ideas behind phylogenetic analysis and also help provide a sound basis for discussions with expert phylogeneticists.
分子系统发育学是利用分子序列数据研究生物体之间进化关系的学科。本综述的目的是向在分子进化领域缺乏坚实背景的生物学家介绍系统发育树重建的重要术语和一般概念。一些现代系统发育程序因其用户友好的界面而易于使用，但理解基于高级统计学的系统发育算法和替代模型对于在没有指导的情况下进行分析和解释仍然很重要。简要地说，进行系统发育分析通常有五个步骤：（1）序列数据准备，（2）序列比对，（3）选择系统发育重建方法，（4）识别最佳树，以及（5）评估树。本综述中的概念使生物学家能够掌握系统发育分析背后的基本思想，并有助于为与专业系统发育学家的讨论提供坚实的基础。
