Data from: A congruent phylogenomic signal places eukaryotes within the Archaea.

Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook 'three domains' tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.

阐明细胞生命主要类群间的演化关系，对理解生物多样性的演化历程具有重要意义，但由于所涉时间跨度极长，该问题颇具难度。在基于信息基因（informational genes）构建的经典教科书中的“三域系统树”中，真核生物（eukaryotes）与古菌（Archaea）共享一个不包含细菌（Bacteria）的共同祖先。然而，针对同一数据集开展的部分系统发育分析却将真核生物置于古菌域内，将其作为不同古菌演化支的最近缘类群。本研究采用先进的系统发育分析方法，并优化了古菌生物多样性的采样方案，对这两种相互对立的假说的支持强度进行了比较。此外，本研究同时使用新建与已有的系统发育一致性检验方法，探究了数据集内的不确定性与冲突程度。分析结果显示，多数观测到的系统发育不一致性要么支持度较弱，要么与适配性不佳的演化模型相关。本研究的所有系统发育分析——无论是针对小亚基核糖体RNA（small subunit ribosomal RNA）与大亚基核糖体RNA（large subunit ribosomal RNA），还是串联蛋白质编码基因（concatenated protein-coding genes）——均恢复出一个包含真核生物与TACK古菌超门（TACK archaeal superphylum）的单系群（monophyletic group），该超门涵盖奇古菌门（Thaumarchaeota）、深古菌门（Aigarchaeota）、泉古菌门（Crenarchaeota）与初古菌门（Korarchaeota）。因此，尽管本研究结果并未为标志性的三域生命树提供支持，但与扩展的胞质假说（extended eocyte hypothesis）相一致——该假说指出真核生物核演化支的关键组分起源于古菌辐射演化类群内部。