The Effect of Recombination on the Reconstruction of Ancestral Sequences
The Effect of Recombination on the Reconstruction of Ancestral Sequences
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DOI：
10.1534/genetics.109.113423
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发表时间：
2010-04-01
期刊：
影响因子：
3.3
通讯作者：
Posada, David
中科院分区：
文献类型：
--
作者：
Arenas, Miguel;Posada, David
虽然存在多种方法来重建祖先序列，但所有这些方法都假设单一系统发育是比对中所有位置的基础，因此重组尚未发生。通过计算机模拟，我们发现重组可能严重影响祖先序列重建（ASR），并量化了这种影响。如果忽略重组，则恢复的祖先序列可能与样本的最近共同祖先 (GMRCA) 完全不同，并且更类似于每个重组片段处的部分最近共同祖先 (MRCA) 的串联。当为不同的重组片段假设独立的系统发育树时，片段 MRCA 的估计显着改善。重要的是，我们证明重组可以改变根据真实数据进行的 ASR 得出的生物学预测。鉴于重组在核基因上广泛存在，特别是在RNA病毒和一些细菌中，在这些情况下祖先序列的重建应考虑重组的潜在影响，并且最好使用适应重组的方法进行。
While a variety of methods exist to reconstruct ancestral sequences, all of them assume that a single phylogeny underlies all the positions in the alignment and therefore that recombination has not taken place. Using computer simulations we show that recombination can severely bias ancestral sequence reconstruction (ASR), and quantify this effect. If recombination is ignored, the ancestral sequences recovered can be quite distinct from the grand most recent common ancestor (GMRCA) of the sample and better resemble the concatenate of partial most recent common ancestors (MRCAs) at each recombination fragment. When independent phylogenetic trees are assumed for the different recombinant segments, the estimation of the fragment MRCAs improves significantly. Importantly, we show that recombination can change the biological predictions derived from ASRs carried out with real data. Given that recombination is widespread on nuclear genes and in particular in RNA viruses and some bacteria, the reconstruction of ancestral sequences in these cases should consider the potential impact of recombination and ideally be carried out using approaches that accommodate recombination.