Phylogenetic Analysis Reveals Rapid Evolutionary Dynamics in the Plant RNA Virus Genus Tobamovirus |
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Authors: | Israel Pagán Cadhla Firth Edward C Holmes |
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Institution: | (1) Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA;(2) Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA;(3) Present address: Center for Infection and Immunity, Columbia University, New York, NY 10032, USA |
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Abstract: | Early studies on the evolutionary dynamics of plant RNA viruses suggested that they may evolve more slowly than their animal
counterparts, sometimes dramatically so. However, these estimates were often based on an assumption of virus–host codivergence
over time-scales of many millions of years that is difficult to verify. An important example are viruses of the genus Tobamovirus, where the assumption of host–virus codivergence over 100 million years has led to rate estimates in the range of ~1 × 10−8 nucleotide substitutions per site, per year. Such a low evolutionary rate is in apparent contradiction with the ability of
some tobamoviruses to quickly overcome inbred genetic resistance. To resolve how rapidly molecular evolution proceeds in the
tobomaviruses, we estimated rates of nucleotide substitution, times to common ancestry, and the extent of congruence between
virus and host phylogenies. Using Bayesian coalescent methods applied to time-stamped sequences, we estimated mean evolutionary
rates at the nucleotide and amino acid levels of between 1 × 10−5 and 1.3 × 10−3 substitutions per site, per year, and hence similar to those seen in a broad range of animal and plant RNA viruses. Under
these rates, a conservative estimate for the time of origin of the sampled tobamoviruses is within the last 100,000 years,
and hence a far more recently than proposed assuming codivergence. This is supported by our cophylogeny analysis which revealed
significantly discordant evolutionary histories between the tobamoviruses and the plant families they infect. |
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