Journal of Molecular Evolution

, Volume 54, Issue 2, pp 156–165

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

Authors

  • Gareth M.  Jenkins
    • Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
  • Andrew  Rambaut
    • Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
  • Oliver G.  Pybus
    • Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
  • Edward C.  Holmes
    • Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Article

DOI: 10.1007/s00239-001-0064-3

Abstract

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.

Key words: RNA viruses — Substitution rate — Molecular clock — Maximum likelihood — Codon bias

Copyright information

© Springer-Verlag New York Inc. 2002