The sequences from dataset 2 (see Methods) and the ancient sequences were aligned in MAFFT59. The tree was constructed in PhyML60, optimizing for topology, branch lengths and rates, with 100 bootstraps (see Methods). Internal nodes with < 70% bootstrap support are shown as polytomies. Ancient genotype A sequences are shown in red, ancient genotype B sequences in orange, ancient genotype D sequences in blue and novel genotype sequences in green. Taxon names indicate: genotype or subgenotype, GenBank accession number, age, abbreviation of country of sequence origin, region of sequence origin, host species and optional additional remarks. Note that the maximum likelihood tree shows topological uncertainty (polytomies) in areas where the BEAST225 tree (Fig. 2) is well resolved. This is the case for two reasons. First, BEAST2 always produces a fully resolved binary topology without polytomies. Second, and more important, BEAST2 creates a time tree and uses tip dates to constrain the possible topologies under consideration. Thus, BEAST2 can know that certain topologies are unlikely or impossible, whereas maximum likelihood cannot and thus inherently has greater uncertainty regarding tree topology.