Diversification of rice yellow mottle virus and related viruses spans the history of agriculture from the neolithic to the present

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.

Figure 1. Divergence times of RYMV and sobemoviruses.

The tree was reconstructed from the full sequences by Bayesian inference under an uncorrelated lognormal relaxed molecular clock model. The age of RYMV was used for calibration (node 1). Nodes 2–4 are associated with more internal nodes. External node “a” gathers SeMV and SBMV, the two most closely related sobemoviruses. The posterior probabilities are below the nodes (italics). The divergence times (in years) are positioned at the nodes, and the 95% HPD intervals are indicated in brackets. The species names and the sequence accession numbers are given in Table 1.

Figure 2. Divergence times of sobemoviruses and related viruses.

The tree was reconstructed from the RdRp sequences by Bayesian inference under an uncorrelated lognormal relaxed molecular clock model. The age of RYMV was used for calibration (node 1). Nodes 4–7 are associated with more internal nodes. External node “b” gathers CYDV-RPS and CYDV-RPV, the two most closely related poleroviruses. External node “c” gathers BYDV-PAS and BYDV-MAV, the two most closely related luteoviruses. The posterior probabilities are below the nodes (italics). The divergence times (in years) are positioned at the nodes, and the 95% HPD intervals are indicated in brackets. The species genus is indicated alongside the vertical line. The species names and the sequence accession numbers are given in Table 1.

Figure 3. Divergence times of RYMV, sobemoviruses, and related viruses.

The divergence times and the 95% HPD intervals are in brackets and framed. Nodes 1 to 8 encompass plant virus diversification at the intra-specific, intra- and inter-generic levels, as indicated by the vertical lines. Nodes “a,” “b,” and “c” gather closely related pairs of viruses. The time axis spreads from the beginning of the Neolithic period to the present.