The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston’s generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.

中文翻译：

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古细菌：多样化生命的第一个领域。


对多样化生命起源的研究一直受到技术和概念上的困难、争议和先验论的困扰。现在人们普遍认为，普遍的生命之树植根于无核生物，而古细菌和真核生物是互为姐妹的群体。然而，进化研究绝大多数集中在核酸和蛋白质序列上，它们仅部分完成了系统发育分析、现实进化模型的制定和树重建优化三个主要步骤中的两个。在缺乏性格极化的情况下，即没有识别祖先和派生性格状态的能力，任何关于生命之树的根源的陈述都应该被认为是可疑的。在这里，我们展示了大分子结构和新的系统发育分析框架，该框架侧重于生物系统的部分而不是整体，提供了深刻而可靠的系统发育信号，并使我们能够提出起源假设。我们回顾了十多年的系统发育学研究，这些研究在数百万编码蛋白质和 RNA 的基因组普查中挖掘信息。我们展示了如何使用符合韦斯顿普遍性标准的分子积累过程模型来支持一致的系统发育图景，其中多样化生命的起源可以追溯到古细菌的早期历史。