The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods
The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods
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DOI：
10.1098/rstb.2009.0034
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发表时间：
2009-08-12
影响因子：
6.3
通讯作者：
Embley, T. Martin
中科院分区：
文献类型：
--
作者：
Foster, Peter G.;Cox, Cymon J.;Embley, T. Martin
三域树将真核生物和古细菌描绘为单系姐妹群，是早期真核进化的主导模型。相比之下，“卵母细胞假说”（即真核生物被认为起源于古细菌内部，是泉古菌门（也称为卵母细胞）的姐妹）在文献中基本上被忽视了。我们使用试图适应这些数据的明显特征的跨位点组成异质性和跨树组成和速率矩阵异质性的方法，研究了分子序列数据对这两个竞争假设的支持。当使用不能充分模拟此类异质性的标准方法分析核糖体 RNA 基因时，三域树得到了支持。然而，当使用成分异质模型时，这种支持被削弱或丧失，同时对真核起源的卵母细胞树的支持也随之增加。无论是否使用组成异质模型，对 41 个蛋白质编码基因的组合氨基酸序列的分析都支持了双核细胞树。使用模拟检查了我们数据的替代饱和可能产生的影响；这些结果表明，序列中的位点间速率变化延迟了饱和，并且这些数据中似乎存在古代关系的系统发育信号。
The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the 'eocyte hypothesis', where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.