Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis

  title={Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis},
  author={Gareth M. Jenkins and Andrew Rambaut and Oliver G. Pybus and Edward C. Holmes},
  journal={Journal of Molecular Evolution},
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… 
A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes
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Inference of viral evolutionary rates from molecular sequences.
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Genetic constraints and the adaptive evolution of rabies virus in nature.
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From Molecular Genetics to Phylodynamics: Evolutionary Relevance of Mutation Rates Across Viruses
Evidence is provided that the mutation rate determines molecular evolution across all types of viruses and a model is proposed in which deleterious mutations impose an evolutionary speed limit and set an extinction threshold in nature.
Rates of Viral Evolution Are Linked to Host Geography in Bat Rabies
A key role for host ecology in shaping the tempo of evolution in multi-host viruses is demonstrated and the power of comparative phylogenetic methods to identify the host and environmental features that influence transmission dynamics is highlighted.
Cell Tropism Predicts Long-term Nucleotide Substitution Rates of Mammalian RNA Viruses
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Evolutionary dynamics of human retroviruses investigated through full-genome scanning.
A remarkable difference in genetic stability and selective pressure at the interhost level between HIV-1 and PTLV cannot be explained by selective forces only.
A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution.
This analysis revealed widespread evidence for positive epistatic interactions at both synonymous and nonsynonymous nucleotide sites and in both clonal and recombining viruses, with the majority of these interactions spanning very short sequence regions.
Viral Mutation Rates
There appears to be a negative correlation between mutation rate and genome size among RNA viruses, and nucleotide substitutions are on average four times more common than insertions/deletions (indels) in retroviruses.


Molecular clock of viral evolution, and the neutral theory.
The results show that the evolutionary process of these viral genes can readily be explained by the neutral theory of molecular evolution, supported by the observation that synonymous substitutions always much predominate over nonsynonymous substitutions, even though the substitution rate varies considerably among the viruses.
The molecular clock of HIV-1 unveiled through analysis of a known transmission history.
  • T. Leitner, J. Albert
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1999
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Structural Constraints on RNA Virus Evolution
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Evolution of the haemagglutinin-esterase gene of influenza C virus.
The nucleotide sequences of the haemagglutinin-esterase (HE) genes of 18 influenza C virus strains isolated in Japan during the period from 1964 to 1988 were analysed to examine their evolutionary relationships, raising the possibility that immune selection may not have played a significant role in the evolution of the glycoprotein, at least not after separation into lineages occurred.
Slow Evolutionary Rate of GB Virus C/Hepatitis G Virus
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Rates and dates of divergence between AIDS virus nucleotide sequences.
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Punctuated equilibrium and positive Darwinian evolution in vesicular stomatitis virus.
Molecular phylogenetic analysis of the P gene for a larger number of diverse natural isolates of vesicular stomatitis virus reveals no evidence for a molecular clock but instead shows a stepwise evolutionary pattern unlike that ever seen before.