Pisani Davide, Cotton James A, McInerney James O
Department of Biology, The National University of Ireland, Maynooth, Maynooth, County Kildare, Ireland, UK.
Mol Biol Evol. 2007 Aug;24(8):1752-60. doi: 10.1093/molbev/msm095. Epub 2007 May 15.
Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry, and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes. Using our signal-stripping method, we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria, and the Thermoplasmatales, an archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria, because up to 83% of eukaryotic genes with a prokaryotic homolog have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria.
真核生物传统上被认为是生命之树的三个自然分类之一，是古细菌的姐妹群。然而，真核生物基因组中充满了源于真细菌的基因，并且已经提出了20多种相互矛盾的假说来解释真核生物的起源。在这里，我们使用一种基于超级树的新型系统发育信号去除方法来检验这些假说的预测，并基于分布在185个基因组中的多达5741个单基因家族的系统发育关系重建生命超级树。使用我们的信号去除方法，我们表明真核生物基因组中存在三种不同的系统发育信号。按强度顺序，这些信号将真核生物与蓝细菌、变形菌和嗜热栖热菌（一种古细菌（广古菌）类群）联系起来。这些信号对应于参与真核生物进化的不同共生伙伴：质体、线粒体和难以捉摸的宿主谱系。根据我们的全基因组数据，真核生物几乎不是古细菌的姐妹群，因为高达83%的具有原核同源物的真核基因起源于真细菌，而非古细菌。结果排除了当前关于真核生物起源的所有假说，除了两个：那些假设线粒体起源于硫依赖或氢依赖互养的假说。
