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

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

We also investigated when the species jumping events occurred in the evolutionary history of the virus families. To do this, we determined whether phylogenetic incongruences tended to Cross-species transmission among viral families occur in deeper sections of the phylogeny or to more shallow nodes in the tree. Accordingly, we considered the number of nodes subtending clades in the host tree that are not present in the virus tree, a metric known as 'node depth'. Nodes that are deep correspond to clades that are more diverse, and often older, than those clades subtended by shallower nodes. For each pair of virus-host trees we calculated the depth of every node that differed within each virushost pair and divide each depth by the maximum node depth (Fig 3) . This normalized metric, which we term 'relative node depth', ranges between near 0 for phylogenetic incongruences at shallow nodes, and 1 for incongruences at deeper nodes. Most incongruences corresponded to shallow nodes, which is expected because there are naturally more shallow nodes than deep nodes in phylogenetic trees. However, that incongruences were found in both shallow and deep nodes suggests that co-divergence is relatively rare in these virus families, even over long evolutionary time-scales. Tanglegrams depicting pairs of rooted phylogenetic trees display the evolutionary relationship between each virus family and their host species (Fig 4; phylogenies with the individual tip labels visible are shown in S1 Fig) . Despite the obvious widespread occurrence of host jumping, a number of co-phylogenies reveal the occurrence of at least some co-divergence, as expected from the nPH85 distances. For example, the tanglegrams for the Hepadnaviridae and Poxviridae exhibit some clear matches with the evolutionary histories of their respective hosts. Most notably, their co-phylogenies show a clear segregation between distinct clades that are associated with a specific host type (mammals, birds, etc.). Conversely, the phylogenies of most RNA viruses appear to largely mismatch those of their hosts.