The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise
The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise
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DOI：
10.1007/s00239-003-2575-6
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发表时间：
2004-05-01
影响因子：
3.9
通讯作者：
Snel, B
中科院分区：
文献类型：
--
作者：
Dutilh, BE;Huynen, MA;Snel, B
基于基因库的系统发育树与当前生活史的共识非常相似。然而，有人认为，由于水平基因转移和平行基因丧失，共享基因含量对系统发育重建不可靠。在这里，我们通过使用两种独立的方法将那些直系同源分布的噪声滤除作为噪声来测试这一参数。最终的系统发育确实包含很小但显着的改进。更重要的是，我们发现大多数直系同源组都包含一些系统发育信号，并且所得的系统发育是基因组跨基因分布中唯一可检测到的信号。水平基因转移或平行基因丧失不会引起基因含量树的系统偏见。
Phylogenetic trees based on gene repertoires are remarkably similar to the current consensus of life history. Yet it has been argued that shared gene content is unreliable for phylogenetic reconstruction because of convergence in gene content due to horizontal gene transfer and parallel gene loss. Here we test this argument, by filtering out as noise those orthologous groups that have an inconsistent phylogenetic distribution, using two independent methods. The resulting phylogenies do indeed contain small but significant improvements. More importantly, we find that the majority of orthologous groups contain some phylogenetic signal and that the resulting phylogeny is the only detectable signal present in the gene distribution across genomes. Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree.