Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Geoghegan, Jemma L.; Duchêne, Sebastián; Holmes, Edward C.

To provide a quantitative measure of host switching we compared 19 virus families, incorporating viruses infecting a diverse sample of eukaryotic hosts including mammals, birds, reptiles, amphibians, fish, plants and insects. Under the measure we utilize here, when nPH85 = 0 between the virus and host trees it implies that their topologies are identical such that there is very strong evidence for co-divergence ( Fig 1A) . Conversely, if nPH85 = 1, there are no clades in common such that co-divergence is implausible ( Fig 1B) . Crucially, this metric does not depend on where the mismatched clades are located in the tree. For example, for a pair of virus and host trees that differ in one clade, the nPH85 is the same whether species jumping events were recent (i.e. shallow nodes Fig 1C) or ancient (i.e. deep nodes Fig 1D) . Importantly, the nPH85 distance increases as the number of incongruent nodes (i.e. nodes that differ) between the virus and host trees increases ( Fig 1E) .