Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny
Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny
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DOI：
10.1093/mlbev/msm229
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发表时间：
2008-01-01
影响因子：
10.7
通讯作者：
Doolittle, W. F.
中科院分区：
文献类型：
--
作者：
Bapteste, E.;Susko, E.;Doolittle, W. F.
最近有人提出，一个很好的解决生命之树可以通过连接共享的基因来实现。然而，这种方法有几个困难，特别是在这棵树的原核部分。我们使用一种新的基于最大似然的方法组合来解决其中的一些问题，开发这种方法是为了尽可能安全和谨慎地进行串联。首先，我们在仔细比对的核心基因上使用了应用程序concatrator。本申请使用分层似然比测试框架来评估基因同源性之间的拓扑一致性（即，不同基因是否共享相同的进化历史）和分枝长度一致性（即，具有相同历史的基因是否具有相同的相对进化速率模式）。因此，我们测试了这些核心基因是否可以串联，或者是否应该归类为不同的不一致集合。其次，我们开发了一个热图的方法研究进化的系统发育支持不同的bipartisons，当不同的系统发育质量的网站在串联增加。这些热图使我们能够跟踪哪些系统发育信号随着连接的进展而增加或减少，并检测新兴的人为分组，即当越来越多的同源位点被投入分析时，越来越多的支持组。我们发现，就7个主要的原核谱系而言，只有22个核心基因可以说是一致的，可以安全地连接起来。这个数字甚至比重建一棵“百分之一的树”所保留的基因数量还要少。“此外，这22个标记的连接导致了一个未解决的树，因为连接树中唯一的分组似乎反映了新出现的伪影。因此，使用串联的核心基因作为一个有效的框架来分类未表征的环境序列可能会产生误导。
It has recently been proposed that a well-resolved Tree of Life can be achieved through concatenation of shared genes. There are, however, several difficulties with such an approach, especially in the prokaryotic part of this tree. We tackled some of them using a new combination of maximum likelihood-based methods, developed in order to practice as safe and careful concatenations as possible. First, we used the application concaterpillar on carefully aligned core genes. This application uses a hierarchical likelihood-ratio test framework to assess both the topological congruence between gene phylogenies (i.e., whether different genes share the same evolutionary history) and branch-length congruence (i.e., whether genes that share the same history share the same pattern of relative evolutionary rates). We thus tested if these core genes can be concatenated or should be instead categorized into different incongruent sets. Second, we developed a heat map approach studying the evolution of the phylogenetic support for different bipartitions, when the number of sites of different phylogenetic quality in the concatenation increases. These heatmaps allow us to follow which phylogenetic signals increase or decrease as the concatenation progresses and to detect emerging artifactual groupings, that is, groups that are more and more supported when more and more homoplasic sites are thrown in the analysis. We showed that, as far as 7 major prokaryotic lineages are concerned, only 22 core genes can be said to be congruent and can be safely concatenated. This number is even smaller than the number of genes retained to reconstruct a "Tree of One Per Cent." Furthermore, the concatenation of these 22 markers leads to an unresolved tree as the only groupings in the concatenation tree seem to reflect emerging artifacts. Using concatenated core genes as a valid framework to classify uncharacterized environmental sequences can thus be misleading.