Synonymous and nonsynonymous distances help untangle convergent evolution and recombination.
Synonymous and nonsynonymous distances help untangle convergent evolution and recombination.
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DOI：
10.1515/sagmb-2014-0078
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发表时间：
2015-08
影响因子：
0.9
通讯作者：
Minin VN
中科院分区：
文献类型：
--
作者：
Chi PB;Chattopadhyay S;Lemey P;Sokurenko EV;Minin VN
当从多序列比对中估计系统发育时，研究人员通常假设没有重组。然而，如果存在重组，那么树估计和所有下游分析将受到影响，因为序列比对的不同片段支持不同的系统发育。同样，分子水平上的趋同选择压力也可能导致序列比对中系统发育树的不一致。目前检测系统发育不一致的方法无法区分这两种不同的机制，并假设不一致是重组或其他水平遗传信息转移的结果。我们提出了一种新的基于同义密码子替换距离的重组检测方法，可以进行这种区分。尽管丢弃非同义替换中包含的信息会损失一些能力，但当系统发育不一致信号是由收敛进化引起的时，我们的新方法比可比较的重组检测方法具有更低的假阳性概率。我们将我们的方法应用于三个实证例子，其中我们分析了：1)来自人类免疫缺陷病毒传播网络的序列，2)来自38个不同地理位置的幽门螺杆菌菌株的tlpB基因序列，以及3)从一位患者纵向取样的丙型肝炎病毒序列。
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because different segments of the sequence alignment support different phylogenies. Similarly, convergent selective pressures at the molecular level can also lead to phylogenetic tree incongruence across the sequence alignment. Current methods for detection of phylogenetic incongruence are not equipped to distinguish between these two different mechanisms and assume that the incongruence is a result of recombination or other horizontal transfer of genetic information. We propose a new recombination detection method that can make this distinction, based on synonymous codon substitution distances. Although some power is lost by discarding the information contained in the nonsynonymous substitutions, our new method has lower false positive probabilities than the comparable recombination detection method when the phylogenetic incongruence signal is due to convergent evolution. We apply our method to three empirical examples, where we analyze: 1) sequences from a transmission network of the human immunodeficiency virus, 2) tlpB gene sequences from a geographically diverse set of 38 Helicobacter pylori strains, and 3) Hepatitis C virus sequences sampled longitudinally from one patient.