Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present Denis Fargette 1 *, Agne ` s Pinel-Galzi 1 , Drissa Se ´re ´me ´ 2 , Se ´ verine Lacombe 3 , Euge ´nie He ´ brard 1 , Oumar Traore ´ 2 , Gnissa Konate ´ 2 1 Institut de Recherche pour le De ´veloppement (IRD), UMR RPB, Montpellier, France, 2 Institut de l’Environnement et de Recherches Agricoles (INERA), Laboratoire de Biotechnologie et de Virologie Ve ´ge ´ tale, Kamboinse ´, Ouagadougou, Burkina Faso, 3 Institut de Recherche pour le De ´veloppement (IRD), UMR GDP, Montpellier, France 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. Citation: Fargette D, Pinel-Galzi A, Se ´re ´me ´ D, Lacombe S, He ´brard E, et al. (2008) Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present. PLoS Pathog 4(8): e1000125. doi:10.1371/journal.ppat.1000125 Editor: Edward C. Holmes, The Pennsylvania State University, United States of America Received March 31, 2008; Accepted July 14, 2008; Published August 15, 2008 Copyright: ß 2008 Fargette et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was funded by the ECOGER action of the French National Program ANR ‘‘Ecosphe `re continentale: processus, mode ´ lisation et risques environnementaux.’’ Support by INRA is also acknowledged. Competing Interests: The authors have declared that no competing interests exist. * E-mail: Denis.Fargette@mpl.ird.fr Introduction The mechanisms of evolution of plant viruses are being progressively unraveled [1–3], yet the timescale of their evolution remains an enigma. Even the order of magnitude is unknown [4]. Several viruses showed few genetic changes between isolates separated in space and time, sometimes for centuries [5–8]. In contrast, 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. The paradox is addressed here by calculating the divergence time of plant viruses at the intra- and inter-specific levels using RYMV and related 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 accumu- lation of genetic changes over time. Recently, new methods enable the incorporation of variable rates into molecular dating [13]. Here, 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]. RYMV causes an emergent disease that was first observed in 1966 in Kenya. Since then, it has been reported in nearly all rice- growing countries of sub-Saharan Africa. RYMV is transmitted by coleopterous insects and is also disseminated abiotically. It has a narrow host range limited to wild and cultivated rices and a few related grasses [15]. There is no evidence of recombination between RYMV isolates [16,17]. The rate of evolution of RYMV was recently evaluated using the coat protein (CP) sequences of 253 isolates collected between 1966 and 2006 from all over Africa [10]. The same group of sequences is analyzed here to assess the time of their most recent common ancestor (TMRCA), which is a measure of the divergence time of RYMV. The TMRCA was calculated by a Bayesian coalescent analysis of the sequences using several molecular clock and population genetic models [14]. Sobemoviruses infect both monocotyledonous and dicotyle- donous plants, but the host range of each virus species is narrow and confined to a few plant species of the Poaceae or Fabaceae. Sobemoviruses are transmitted by beetle vectors, seeds and direct contact [18]. They share a common genomic organization, as found after re-sequencing some of the virus species [19,20]. Ten sobemovirus species have been fully sequenced, nine of them are currently registered by ICTV [18] and a tentative one, Imperata yellow mottle virus (IYMV), was recently isolated from Imperata cylindrica in Africa [56]. Their genomes contain four open reading PLoS Pathogens | www.plospathogens.org 1 August 2008 | Volume 4 | Issue 8 | e1000125