Abstract
Recent research has revealed that some plant viruses, like many animal viruses, have measurably evolving populations. Most of these viruses have single-stranded positive-sense RNA genomes, but a few have single-stranded DNA genomes. The studies show that extant populations of these viral species are only decades to centuries old. The genera in which they are placed have diverged since agriculture was invented and spread around the world during the Holocene period. We suggest that this is not mere coincidence but evidence that the conditions generated by agriculture during this era have favoured particular viruses. There is also evidence, albeit less certain, that some plant viruses, including a few shown to have measurably evolving populations, have much more ancient origins. We discuss the possible reasons for this clear discordance between short- and long-term evolutionary rate estimates and how it might result from a large timescale dependence of the evolutionary rates. We also discuss briefly why it is useful to know the rates of evolution of plant viruses.
Highlights
Recent research has revealed that some plant viruses, like many animal viruses, have measurably evolving populations
We discuss the possible reasons for this clear discordance between short- and long-term evolutionary rate estimates and how it might result from a large timescale dependence of the evolutionary rates
In 2002, Stenger et al (2002) reported that differences that appeared during passaging of wheat streak mosaic virus (WSMV), taken together with differences within its population in North America, indicated that this virus had been diverging at about 1.161024 nucleotide substitutions per site per year (Stenger et al, 2002) since it first invaded those wheat crops in the early 20th century (McKinney, 1937)
Summary
In 2002, Stenger et al (2002) reported that differences that appeared during passaging of wheat streak mosaic virus (WSMV), taken together with differences within its population in North America, indicated that this virus had been diverging at about 1.161024 nucleotide substitutions (ns) per site per year (Stenger et al, 2002) since it first invaded those wheat crops in the early 20th century (McKinney, 1937). The evolutionary rate estimates obtained from serial or heterochronous sampling, or from node dating, suggest that extant species all arose in recent times and at least three of the most damaging plant virus genera radiated within the last few thousand years: luteovirids (i.e. species of the Luteoviridae), 9000 years ago; potyviruses, 6600 years ago; sobemoviruses, 3000 years ago; and the TYLCVs, which are probably representative of the begomoviruses, 10 000 years ago These major taxa of crop-infecting viruses all diversified in the period since humankind invented agriculture (Fargette et al, 2008b; Gibbs et al, 2008c) they may have originated even earlier and survived as small founder populations. This, and the birth–death topology, suggest that despite large populations within individual infected plants, only small numbers survive the hazards of being transmitted to new hosts; there is probably strong selection for survival of the ecologically fittest
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