Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis
Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis
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DOI：
10.1007/s00239-001-0064-3
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发表时间：
2002-02-01
影响因子：
3.9
通讯作者：
Holmes, EC
中科院分区：
文献类型：
--
作者：
Jenkins, GM;Rambaut, A;Holmes, EC
研究RNA病毒中核苷酸替换的速率对于我们理解它们的进化至关重要。在这里，我们报告了一个全面的分析，在50 RNA病毒使用最近开发的最大似然系统发育方法的替代率。这项分析揭示了一个显着的关系，遗传分歧和分离时间的广泛阵列的RNA病毒，虽然更多的速率变化通常存在于谱系比预期的限制下的分子钟。尽管缺乏一个分子时钟，在统计上显着的变化范围内的整体置换率是令人惊讶的狭窄的那些病毒的遗传分化和时间之间的显着关系被发现，就像是当同义位点被认为是单独的情况下，在分子时钟被拒绝的频率较低。对可能解释这一速率变化的生态和遗传因素的分析显示，一些证据表明，媒介传播病毒的替代率显著较低，以及速率与基因组长度之间的弱相关性。最后，模拟研究表明，我们的最大似然估计的取代率是有效的，即使分子钟被拒绝，提供足够大的数据集进行分析。
The study of rates of nucleotide substitution in RNA viruses is central to our understanding of their evolution. Herein we report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method. This analysis revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Despite the lack of a molecular clock, the range of statistically significant variation in overall substitution rates was surprisingly narrow for those viruses where a significant relationship between genetic divergence and time was found, as was the case when synonymous sites were considered alone, where the molecular clock was rejected less frequently. An analysis of the ecological and genetic factors that might explain this rate variation revealed some evidence of significantly lower substitution rates in vector-borne viruses, as well as a weak correlation between rate and genome length. Finally, a simulation study revealed that our maximum likelihood estimates of substitution rates are valid, even if the molecular clock is rejected, provided that sufficiently large data sets are analyzed.