Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates
Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates
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DOI：
10.1098/rspb.2014.0732
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发表时间：
2014-07-07
影响因子：
4.7
通讯作者：
Ho, Simon Y. W.
中科院分区：
文献类型：
--
作者：
Duchene, Sebastian;Holmes, Edward C.;Ho, Simon Y. W.
病毒进化和出现的时间尺度已被广泛研究，但往往知之甚少。病毒进化时间尺度的分子分析通常依赖于核苷酸替换速率的估计，其根据测量的时间范围而变化几个数量级。我们分析了所有主要病毒组的数据，发现核苷酸取代率的估计值与进化时间尺度之间存在强烈的负相关关系。引人注目的是，这种关系在不同的病毒群体内部和之间都得到了维护。灵长类慢病毒的详细案例研究表明，序列饱和和纯化选择的组合效应可以解释这种随时间变化的速率变化模式。因此，我们的分析表明，在病毒的进化时间尺度的研究需要重新考虑的替代率作为一个动态的，而不是作为一个静态的，分子进化的特点。改进病毒进化速率的建模有可能改变我们对病毒起源的理解。
Time-scales of viral evolution and emergence have been studied widely, but are often poorly understood. Molecular analyses of viral evolutionary time-scales generally rely on estimates of rates of nucleotide substitution, which vary by several orders of magnitude depending on the timeframe of measurement. We analysed data from all major groups of viruses and found a strong negative relationship between estimates of nucleotide substitution rate and evolutionary timescale. Strikingly, this relationship was upheld both within and among diverse groups of viruses. A detailed case study of primate lentiviruses revealed that the combined effects of sequence saturation and purifying selection can explain this time-dependent pattern of rate variation. Therefore, our analyses show that studies of evolutionary time-scales in viruses require a reconsideration of substitution rates as a dynamic, rather than as a static, feature of molecular evolution. Improved modelling of viral evolutionary rates has the potential to change our understanding of virus origins.