生物
系统发育树
进化生物学
计算系统发育学
鉴定(生物学)
系统发育网络
生命之树(生物学)
推论
树(集合论)
系统发育学
系统发育比较方法
树重组
适应(眼睛)
计算生物学
基因
遗传学
生态学
计算机科学
人工智能
数学分析
神经科学
数学
作者
Paschalia Kapli,Ziheng Yang,Maximilian J. Telford
标识
DOI:10.1038/s41576-020-0233-0
摘要
Knowing phylogenetic relationships among species is fundamental for many studies in biology. An accurate phylogenetic tree underpins our understanding of the major transitions in evolution, such as the emergence of new body plans or metabolism, and is key to inferring the origin of new genes, detecting molecular adaptation, understanding morphological character evolution and reconstructing demographic changes in recently diverged species. Although data are ever more plentiful and powerful analysis methods are available, there remain many challenges to reliable tree building. Here, we discuss the major steps of phylogenetic analysis, including identification of orthologous genes or proteins, multiple sequence alignment, and choice of substitution models and inference methodologies. Understanding the different sources of errors and the strategies to mitigate them is essential for assembling an accurate tree of life. Understanding evolutionary relationships between species requires the generation of accurate phylogenetic trees. In this Review, Kapli, Yang and Telford discuss the principles, steps and computational tools for phylogenetic tree building. They describe the impact of burgeoning genomic datasets as well as the diverse sources of errors and how they can be mitigated.
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