Inferring ancient divergences requires genes with strong phylogenetic signals
Inferring ancient divergences requires genes with strong phylogenetic signals
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DOI：
10.1038/nature12130
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发表时间：
2013-05-16
期刊：
影响因子：
64.8
通讯作者：
Rokas, Antonis
中科院分区：
文献类型：
--
作者：
Salichos, Leonidas;Rokas, Antonis
为了解决不同基因树之间的不一致性，即拓扑冲突，基因组学研究将串联与诸如去除流氓分类单元或使用缓慢进化的基因等做法结合起来。对来自23个酵母基因组的1，070个直系同源物的系统基因组学分析确定了1，070个不同的基因树，它们都与从串联推断的同源性不一致。不一致的严重程度增加了较短的节间位于更深的生育期。值得注意的是，尽管大多数实践对酵母的染色体发生几乎没有影响或产生负面影响，但使用具有高平均节间支持的基因或节间显著提高了推断的鲁棒性。我们在脊椎动物和后生动物基因组数据集的分析中获得了类似的结果。这些结果质疑的唯一依赖串联和相关的做法，并认为，选择基因与强大的系统发育信号，并证明没有显着的不一致是必不可少的，准确重建古代分歧。
To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences.