Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
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DOI：
10.1038/s41467-019-13443-4
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发表时间：
2019-12-02
影响因子：
16.6
通讯作者：
Knight, Rob
中科院分区：
文献类型：
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作者：
Zhu, Qiyun;Mai, Uyen;Knight, Rob
基因组数据的快速增长为微生物进化关系的更新提供了机会，但这受到单个基因不协调进化的挑战。在这里，我们使用多种策略，基于一套全面的381个标记，建立了10,575个均匀采样的细菌和古生菌基因组的参考系统发育图。我们的树表明，与先前的估计相比，古生菌和细菌之间的进化距离非常近，此前的估计仅限于较少的“核心”基因，如核糖体蛋白。结果的稳健性测试了几个变量，包括分类群和现场采样，氨基酸替代的异质性和饱和度，非垂直进化，以及排除候选门辐射(CPR)类群的影响。我们的结果提供了域级别关系的更新视图。
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.