Rapid evolutionary dynamics of pepper mild mottle virus

Pepper mild mottle virus (PMMoV) is one of the most destructive pathogens of pepper crops and has major impacts on global crop yields. Some aspects of the molecular biology of PMMoV have been studied intensively, but estimates of its evolutionary rate have shown considerable variation. We investigated the phylodynamics of PMMoV by analysing 171 nucleotide sequences of the coat protein gene, sampled between 1980 and 2016. Our Bayesian phylogenetic analyses, using the structured coalescent, dated the crown group to 1949 (95% credibility interval 1935–1962). We reveal that PMMoV has been evolving at a rate of 9.363 × 10−4 substitutions/site/year (95% credibility interval 7.362 × 10−4–1.138 × 10−3). This is similar to evolutionary rates estimated for animal RNA viruses, indicating that PMMoV has been undergoing rapid evolutionary dynamics.