Lopez P, Forterre P, Philippe H
Phylogénie et Evolution Moléculaires (UPRESA Q8080), Bâtiment 444, Université Paris-Sud, 91405 Orsay-Cedex, France.
J Mol Evol. 1999 Oct;49(4):496-508. doi: 10.1007/pl00006572.
A few duplicated genes have been found useful to root the universal tree of life. Despite controversial results, the consensus led to locate the root in the eubacterial branch. However, we demonstrated (Philippe and Forterre 1999) that all these markers were in fact unsuitable for any firm conclusion, mainly because of their high level of mutational saturation, which masks a major part of the phylogenetic signal. But then, the very persistence of signal for events as early as the separation of the three domains becomes puzzling. This paradox was studied here for translation elongation factor proteins, EF-1alpha and EF-2, which appeared to be one of the least confusing markers. We showed that these proteins do not conform to a classical rate-across-sites pattern, as those modeled by a gamma law, but rather to a covarion-based model, because the evolutionary rate of a given position often changes between taxonomic groups. Conservation of the very ancient signal can thus be better explained by the covarion model: a substitution can occur in deep branches, and the position remains constant afterward, as "fossilized" by a change of covation. As no reconstruction method has up to now taken into account this complex model, we devised a simple method for extracting the phylogenetic signal, by considering the variability of sequence positions within predefined phylogenetic groups. We showed that noise quantitatively prevailed upon signal. Parsimony will produce erroneous topologies, because it has to minimize primarily the number of steps of the noise. In contrast, our method effectively concentrated the signal and was more suitable for inferring ancient events. We consequently found the eubacterial rooting to be presumably due to a long branch attraction artifact, because of the higher evolutionary rate of Eubacteria for these proteins. Among the two other rooting possibilities, the eukaryotic rooting appeared to be more supported, although not enough to be conclusive.
已发现一些重复基因有助于确定生命的通用树的根。尽管结果存在争议，但共识是将根定位在真细菌分支中。然而，我们证明（菲利普和福泰尔，1999年），所有这些标记实际上都不适用于得出任何确凿结论，主要是因为它们的突变饱和度很高，掩盖了系统发育信号的很大一部分。但是，对于早在三个域分离时就发生的事件，信号的持续存在却令人费解。本文针对翻译延伸因子蛋白EF-1α和EF-2研究了这一悖论，这两种蛋白似乎是最不容易混淆的标记之一。我们表明，这些蛋白不符合伽马法则所模拟的经典的位点间速率模式，而是符合基于共变模型，因为给定位置的进化速率在分类群之间经常变化。因此，共变模型可以更好地解释非常古老信号的保守性：一个替换可以发生在深层分支中，并且该位置随后保持不变，就像被共变变化“固定”一样。由于目前还没有重建方法考虑到这个复杂模型，我们设计了一种简单的方法来提取系统发育信号，即考虑预定义系统发育组内序列位置的变异性。我们表明，噪声在数量上超过了信号。简约法会产生错误的拓扑结构，因为它必须主要最小化噪声的步数。相比之下，我们的方法有效地集中了信号，更适合推断古老事件。因此，我们发现真细菌的生根可能是由于长枝吸引假象，因为这些蛋白在真细菌中的进化速率更高。在另外两种生根可能性中，真核生物生根似乎得到了更多支持，尽管还不足以得出确凿结论。
