Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
Nat Rev Genet. 2020 Jul;21(7):428-444. doi: 10.1038/s41576-020-0233-0. Epub 2020 May 18.
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.
了解物种之间的系统发育关系是生物学许多研究的基础。一个准确的系统发育树是我们理解进化中的主要转变的基础，例如新的身体计划或新陈代谢的出现，并且是推断新基因的起源、检测分子适应、理解形态特征进化以及重建最近分化物种的种群动态的关键。尽管数据越来越丰富，并且有可用的强大分析方法，但在可靠的树构建方面仍然存在许多挑战。在这里，我们讨论了系统发育分析的主要步骤，包括鉴定直系同源基因或蛋白质、多序列比对以及替换模型和推断方法的选择。理解不同的误差来源和减轻误差的策略对于组装准确的生命之树至关重要。
