Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
School of Life Sciences, Earth and Environmental Sciences Programme, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
Methods Mol Biol. 2022;2569:95-116. doi: 10.1007/978-1-0716-2691-7_5.
Alphaproteobacteria is one of the most abundant bacterial lineages that successfully colonize diverse marine and terrestrial environments on Earth. In addition, many alphaproteobacterial lineages have established close association with eukaryotes. This makes Alphaproteobacteria a promising system to test the link between the emergence of ecologically important bacteria and related geological events and the co-evolution between symbiotic bacteria and their hosts. Understanding the timescale of evolution of Alphaproteobacteria is key to testing these hypotheses, which is limited by the scarcity of bacterial fossils, however. Based on the mitochondrial endosymbiosis which posits that the mitochondrion originated from an alphaproteobacterial lineage, we propose a new strategy to estimate the divergence times of lineages within the Alphaproteobacteria by leveraging the fossil records of eukaryotes. In this chapter, we describe the workflow of the mitochondria-based method to date Alphaproteobacteria evolution by detailing the software, methods, and commands used for each step. Visualization of data and results is also described. We also provide related notes with background information and alternative options. All codes used to build this protocol are made available to the public, and we strive to make this protocol user-friendly in particular to microbiologists with limited practical skills in bioinformatics.
α-变形菌是地球上成功定殖于多样海洋和陆地环境的最丰富的细菌谱系之一。此外，许多 α-变形菌谱系与真核生物建立了密切的联系。这使得 α-变形菌成为一个很有前途的系统，可以检验生态重要细菌的出现与相关地质事件之间的联系，以及共生细菌与其宿主之间的共同进化。了解 α-变形菌进化的时间尺度是检验这些假说的关键，然而，这受到细菌化石稀缺的限制。基于线粒体内共生假说，即线粒体起源于 α-变形菌谱系，我们提出了一种利用真核生物化石记录来估计 α-变形菌内谱系分歧时间的新策略。在本章中，我们通过详细描述每个步骤所使用的软件、方法和命令，描述了基于线粒体的方法来确定 α-变形菌进化时间的工作流程。还描述了数据和结果的可视化。我们还提供了相关注释，包括背景信息和替代选项。用于构建本方案的所有代码都可供公众使用，我们特别努力使本方案对在生物信息学方面实践技能有限的微生物学家友好易用。
