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

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

Cladograms were constructed for all host species from which the viruses of interest were isolated. In each case the host tree topologies used were the most up-to-date available in the literature [40] [41] [42] [43] [44] . For the vector-borne viruses studied here, in which viruses pass between arthropods and vertebrates, the appropriate vertebrate species were assigned as the hosts. In contrast, for insect-specific viruses, where there is no evidence for vertebrate involvement, the relevant invertebrate species were assigned as the hosts. Since there were often multiple viruses that infected the same host species, multiple lineages within a single host (i.e. polytomies) were added to the host phylogenetic tree to ensure the number of hosts equaled that of the virus tree. The addition of these polytomies does not influence the nPH85 distance metric (described in detail below) because the distance between a polytomous clade and one that is fully resolved is zero [14] .