Authors: Francisco M Codoñer José M Cuevas Jesús A SánchezNavarro Vicente Pallás Santiago F Elena
Publish Date: 2005/10/06
Volume: 61, Issue: 5, Pages: 697-705
Abstract
We have carried out an evolutionary study of the two proteins encoded by the RNA 3 from members of the plant virus family Bromoviridae Using maximum likelihood methods we have inferred the patterns of amino acid substitution that better explain the diversification of this viral family The results indicate that the molecular evolution of this family was rather complex with each protein evolving at different rates and according to different patterns of amino acid substitution These differences include different amino acid equilibrium frequencies heterogeneity in substitution rates among sites and covariation among sites Despite these differences the model of protein evolution that better fits both proteins is one specifically proposed for the evolution of globular proteins We also found evidence for coevolution between domains of these two proteins Finally our analyses suggest that the molecular clock hypothesis does not hold since different lineages evolved at different rates The implications of these results for the taxonomy of this important family of plant viruses are discussedWe thank John W Randles and Mario A Fares for critical reading of the manuscript We also thank two anonymous reviewers for very helpful comments FMC JMC and JASN acknowledge fellowships from the Spanish CSIC Bioinformatics I3P program the Welcome Trust and the Ramón y Cajal program MEC respectively This study was supported by Grant BIO0204099C0202 MCyTFEDER to VP and Grant BMC200300066 MECFEDER Grant GV04B280 Generalitat Valenciana and the EMBO Young Investigator Program to SFE
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