Detecting past recombination events in Potato virus Y genomic sequences using statistical methods

Molecular evolution of RNA viruses: Plant RNA viruses evolve more rapidly than the DNA of their plant hosts due to a higher mutation rate. Mutational processes include nucleotide substitution that replaces one nucleotide by another, and insertions and/or deletions that result in sequence length changes. In addition to mutation, inter-strain recombination can produce new mosaic strains9. It is important to detect recombination events because, firstly, phylogenetic studies of inter-strain relationships that assume no recombination are very likely to be incorrect, and secondly, because recombination may have important consequences for virus control strategies. We will illustrate methods to detect evidence of past recombination events in four strains of Potato virus Y (PVY). As we shall see, detecting recombination in this data set is not simple.