Abstract
The mechanisms of evolution of plant viruses are being unraveled, yet the timescale of their evolution remains an enigma. To address this critical issue, the divergence time of plant viruses at the intra- and inter-specific levels was assessed. The time of the most recent common ancestor (TMRCA) of Rice yellow mottle virus (RYMV; genus Sobemovirus) was calculated by a Bayesian coalescent analysis of the coat protein sequences of 253 isolates collected between 1966 and 2006 from all over Africa. It is inferred that RYMV diversified approximately 200 years ago in Africa, i.e., centuries after rice was domesticated or introduced, and decades before epidemics were reported. The divergence time of sobemoviruses and viruses of related genera was subsequently assessed using the age of RYMV under a relaxed molecular clock for calibration. The divergence time between sobemoviruses and related viruses was estimated to be approximately 9,000 years, that between sobemoviruses and poleroviruses approximately 5,000 years, and that among sobemoviruses approximately 3,000 years. The TMRCA of closely related pairs of sobemoviruses, poleroviruses, and luteoviruses was approximately 500 years, which is a measure of the time associated with plant virus speciation. It is concluded that the diversification of RYMV and related viruses has spanned the history of agriculture, from the Neolithic age to the present.
Highlights
The mechanisms of evolution of plant viruses are being progressively unraveled [1,2,3], yet the timescale of their evolution remains an enigma
The age of Rice yellow mottle virus (RYMV) provides a reliable calibration of related viruses, applying recently developed relaxed molecular clock models
It was found that RYMV diversified approximately 200 years ago, and that inter-specific diversification ranged from 500 years to 9,000 years
Summary
The mechanisms of evolution of plant viruses are being progressively unraveled [1,2,3], yet the timescale of their evolution remains an enigma. Several viruses showed few genetic changes between isolates separated in space and time, sometimes for centuries [5,6,7,8]. Recent evidence from statistical analyses of sequences of dated isolates of Tomato yellow leaf curl virus (genus Geminivirus) [9], Rice yellow mottle virus (genus Sobemovirus) (RYMV) [10] and Zucchini yellow mosaic virus (genus Potyvirus) [11] indicated rapid evolution, similar to that of most animal viruses. Molecular-dating techniques provide insights into the history of lineages that have a poor or non-existent fossil record, such as viruses [12,13]. These techniques were originally based on the assumption of a strict molecular clock reflecting steady accumulation of genetic changes over time. We applied a Bayesian Markov Chain Monte-Carlo method for performing relaxed phylogenies that is able to co-estimate phylogeny and divergence times under uncorrelated relaxed-clock models [14]
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