Rate of nucleotide substitution

Range >1E-04 substitution/site/year
Organism Rice yellow mottle virus (RYMV)
Reference Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet. 2008 Apr9(4):267-76 p.272 left column top paragraphPubMed ID18319742
Primary Source [56] Fargette, D. et al. Rice yellow mottle virus, an RNA plant virus, evolves as rapidly as most RNA animal viruses. J. Virol. 16 Jan 2008 (doi: 10.1128/JVI.02506-07).PubMed ID18199644
Method Primary source abstract: "The rate of evolution of an RNA plant virus has never been estimated using temporally spaced sequence data, by contrast to the information available on an increasing range of animal viruses. Accordingly, the evolution rate of Rice yellow mottle virus (RYMV) was calculated from sequences of the coat protein gene of isolates collected from rice over a 40-year period in different parts of Africa. The evolution rate of RYMV was estimated by pairwise distance linear regression on five phylogeographically defined groups comprising a total of 135 isolates. It was further assessed from 253 isolates collected all over Africa by Bayesian coalescent methods under strict and relaxed molecular clock models and under constant size and skyline population genetic models."
Comments P.271 right column bottom paragraph to p.272 left column top paragraph: "There have been numerous suggestions that plant RNA viruses evolve more slowly than RNA viruses that infect animals. Both tobamoviruses and closteroviruses have shown few genetic changes between isolates that are separated in space (ref 51) and time (ref 52), even after decades (ref 53) or centuries (ref 54). It has been proposed that these low rates are due to severe population bottlenecks (ref 55), although changes in population size will not affect the rate of neutral substitution. Similarly, it has also been suggested that rates of non-synonymous substitution are reduced in plant viruses compared with their animal counterparts because of weaker immune-mediated positive selection (ref 47). However, the first estimate of the substitution rate of a plant RNA virus that was made using serially sampled data was recently calculated at >10−4 subs/site/year, which is firmly within the distribution of substitution rates of RNA viruses observed in animal RNA viruses (primary source)."
Entered by Uri M
ID 112776