Journal of Molecular Evolution

, Volume 71, Issue 4, pp 298–307 | Cite as

Phylogenetic Analysis Reveals Rapid Evolutionary Dynamics in the Plant RNA Virus Genus Tobamovirus



Early studies on the evolutionary dynamics of plant RNA viruses suggested that they may evolve more slowly than their animal counterparts, sometimes dramatically so. However, these estimates were often based on an assumption of virus–host codivergence over time-scales of many millions of years that is difficult to verify. An important example are viruses of the genus Tobamovirus, where the assumption of host–virus codivergence over 100 million years has led to rate estimates in the range of ~1 × 10−8 nucleotide substitutions per site, per year. Such a low evolutionary rate is in apparent contradiction with the ability of some tobamoviruses to quickly overcome inbred genetic resistance. To resolve how rapidly molecular evolution proceeds in the tobomaviruses, we estimated rates of nucleotide substitution, times to common ancestry, and the extent of congruence between virus and host phylogenies. Using Bayesian coalescent methods applied to time-stamped sequences, we estimated mean evolutionary rates at the nucleotide and amino acid levels of between 1 × 10−5 and 1.3 × 10−3 substitutions per site, per year, and hence similar to those seen in a broad range of animal and plant RNA viruses. Under these rates, a conservative estimate for the time of origin of the sampled tobamoviruses is within the last 100,000 years, and hence a far more recently than proposed assuming codivergence. This is supported by our cophylogeny analysis which revealed significantly discordant evolutionary histories between the tobamoviruses and the plant families they infect.


Tobamoviruses Evolutionary dynamics Virus–host codivergence 

Supplementary material

239_2010_9385_MOESM1_ESM.pdf (361 kb)
Supplementary material 1 (PDF 360 kb)


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Israel Pagán
    • 1
  • Cadhla Firth
    • 1
    • 3
  • Edward C. Holmes
    • 1
    • 2
  1. 1.Department of Biology, Center for Infectious Disease DynamicsThe Pennsylvania State UniversityUniversity ParkUSA
  2. 2.Fogarty International CenterNational Institutes of HealthBethesdaUSA
  3. 3.Center for Infection and ImmunityColumbia UniversityNew YorkUSA

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