Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada.
Elife. 2019 Feb 25;8:e42535. doi: 10.7554/eLife.42535.
The is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the and (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the has a derived position within the . A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the . Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the .
是一组非常多样化和古老的细菌。以前推断其深层系统发育的尝试一直受到方法学人为因素的困扰。为了克服这一问题，我们分析了一组 200 个单拷贝和保守基因的数据集，并采用了多种策略来减少组成人为因素的影响。这些策略包括使用新的数据集特定的混合模型和编码方案，以及去除组成上有偏差的位置、基因和分类群。我们表明，和（真核生物的两种内寄生菌）彼此之间不是姐妹关系，而是在 中具有衍生地位。我们的综合结果也为更高层次的分类学提出了一个更新的建议。我们稳健的共识系统发育将作为一个框架，用于未来的研究，旨在将线粒体和新的环境多样性置于 中。
