Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses.
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses.
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DOI：
10.1093/molbev/msq088
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发表时间：
2010-09
影响因子：
10.7
通讯作者：
Rambaut A
中科院分区：
文献类型：
--
作者：
Firth C;Kitchen A;Shapiro B;Suchard MA;Holmes EC;Rambaut A
双链（ds）DNA病毒通常被描述为通过与其宿主的长期共趋异关系进化，这种模式预计与低核苷酸取代率有关。然而，dsDNA病毒与其宿主之间共趋异的假设很少得到严格的检验，尽管绝大多数dsDNA病毒的核苷酸取代率估计都是基于这一假设。因此，重要的是要估计的dsDNA病毒的进化速率独立的假设宿主病毒共趋异。在这里，我们探索使用贝叶斯框架内的时间结构序列数据来估计7种人类dsDNA病毒的进化速率，包括天花病毒（VARV）（天花的病原体）和单纯疱疹病毒-1。我们的分析显示，尽管VARV基因组可能以大约1 × 10−5个替换/位点/年的速度进化，因此接近许多RNA病毒的进化速度，但许多其他双链DNA病毒的进化速度仍然难以估计。合成数据集的构建，以告知我们的解释，估计这些dsDNA病毒的替代率和这些分析表明，给定一个适当的长度和采样深度的序列数据集，它是可能的使用时间结构化分析，以估计替代率的许多dsDNA病毒独立于假设的宿主-病毒共趋异。最后，一些双链DNA病毒的进化速度可能接近RNA病毒的进化速度，这一发现对我们理解这一主要病毒群的长期进化历史和出现潜力具有重要意义。
Double-stranded (ds) DNA viruses are often described as evolving through long-term codivergent associations with their hosts, a pattern that is expected to be associated with low rates of nucleotide substitution. However, the hypothesis of codivergence between dsDNA viruses and their hosts has rarely been rigorously tested, even though the vast majority of nucleotide substitution rate estimates for dsDNA viruses are based upon this assumption. It is therefore important to estimate the evolutionary rates of dsDNA viruses independent of the assumption of host-virus codivergence. Here, we explore the use of temporally structured sequence data within a Bayesian framework to estimate the evolutionary rates for seven human dsDNA viruses, including variola virus (VARV) (the causative agent of smallpox) and herpes simplex virus-1. Our analyses reveal that although the VARV genome is likely to evolve at a rate of approximately 1 × 10−5 substitutions/site/year and hence approaching that of many RNA viruses, the evolutionary rates of many other dsDNA viruses remain problematic to estimate. Synthetic data sets were constructed to inform our interpretation of the substitution rates estimated for these dsDNA viruses and the analysis of these demonstrated that given a sequence data set of appropriate length and sampling depth, it is possible to use time-structured analyses to estimate the substitution rates of many dsDNA viruses independently from the assumption of host-virus codivergence. Finally, the discovery that some dsDNA viruses may evolve at rates approaching those of RNA viruses has important implications for our understanding of the long-term evolutionary history and emergence potential of this major group of viruses.
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