Genome phylogenies indicate a meaningful α-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales
Genome phylogenies indicate a meaningful α-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales
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DOI：
10.1093/molbev/msj009
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发表时间：
2006-01-01
影响因子：
10.7
通讯作者：
McInerney, JO
中科院分区：
文献类型：
--
作者：
Fitzpatrick, DA;Creevey, CJ;McInerney, JO
线粒体分支在生命之树上的位置一直是个问题。稀疏采样，横向基因转移如何可能覆盖系统发育信号的不确定性，以及系统发育推断的不确定性都导致了这个问题。在这里，我们使用超树方法和完整的基因组序列来解决这个问题。我们首先确定，一个明智的α-变形菌系统发育树的存在，它可以自信地推断使用orthopathic基因。我们发现，这些正交基因树的一致性显着优于随机机会可能预期。有一些证据表明α-变形菌内存在水平基因转移，但似乎仅限于少数基因（类似于23%），其中大多数（类似于74%）可以归类为可操作的。这意味着，跨物种的基因转移不应过度阻碍该基因的定位。然后，我们表明，有一个一贯的强烈信号，放置在这棵树上，这种放置是相对不敏感的方法或数据集的pathon。创建了由15种线粒体编码的蛋白质组成的串联比对，这些蛋白质在所考虑的时间轴中不太可能经历任何横向基因转移。这种排列推断，线粒体的姐妹群，对于已经采样的分类群来说，是立克次体目。
Placement of the mitochondrial branch on the tree of life has been problematic. Sparse sampling, the uncertainty of how lateral gene transfer might overwrite phylogenetic signals, and the uncertainty of phylogenetic inference have all contributed to the issue. Here we address this issue using a supertree approach and completed genomic sequences. We first determine that a sensible alpha-proteobacterial phylogenetic tree exists and that it can confidently be inferred using orthologous genes. We show that congruence across these orthologous gene trees is significantly better than might be expected by random chance. There is some evidence of horizontal gene transfer within the alpha-proteobacteria, but it appears to be restricted to a minority of genes (similar to 23%) most of whom (similar to 74%) can be categorized as operational. This means that placement of the mitochondrion should not be excessively hampered by interspecies gene transfer. We then show that there is a consistently strong signal for placement of the mitochondrion on this tree and that this placement is relatively insensitive to methodological approach or data set. A concatenated alignment was created consisting of 15 mitochondrion-encoded proteins that are unlikely to have undergone any lateral gene transfer in the timeline under consideration. This alignment infers that the sister group of the mitochondria, for the taxa that have been sampled, is the order Rickettsiales.