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 next determined whether there was any association between the relative frequency of codivergence and larger scale biological properties, such as the number of viruses per family and whether the viruses in question possess RNA or DNA genomes. To better display this analysis branches on the co-phylogenetic trees were colored according to host type, which comprised mammals, fish, birds, reptiles, amphibians, invertebrates, and plants (Fig 4) , such that each cophylogeny incorporated between one (i.e. Potyviridae) and five (i.e. Togoviridae) host types. Notably, we found a significant association between the number of viruses per virus family and the nPH85 (p<0.005) (Fig 6A) . Importantly, because we expect no association between [15] . Boxplots illustrate the range of the proportion of possible events. The 'event costs' associated with incongruences between trees were conservative towards co-divergence and defined here as: 0 for co-divergence, 1 for duplication, 1 for host-jumping and 1 for extinction. Virus families are ranked in order of highest mean co-divergence to lowest mean co-divergence. Abbreviations on the x-axis are as follows: 'Co-div' = co-divergence, 'Dup' = duplication, 'HJ' = host-jumping, 'Ext' = extinction. (B) Reconciliation of the Hepadnaviridae phylogeny with that of their vertebrate hosts, again utilizing the co-phylogenetic method implemented in Jane [15] . The figure illustrates all possible codivergence, extinction and host-jumping events (no lineage duplication events were reconstructed in this case). the number of viruses and hosts per family and the nPH85 under our tree distance metric, this result implies that sampling more viruses increases the likelihood of detecting host jumping events. In addition, we found that DNA viral families had, on average, a shorter nPH85 distance than families of RNA viruses (p<0.05) (Fig 6B) . Note that there is no significant difference (p = 0.5) between the number of viruses in families of DNA viruses compared to those in RNA virus families. In this context it is striking that the five families with the shortest topological distances all possessed DNA genomes. This analysis also revealed that segmented viruses had a significantly larger nPH85 distance than non-segmented viruses (p<0.05), and that negative-sense RNA viruses had a larger nPH85 distance than positive-sense RNA viruses (p<0.005); however, the sample sizes within all these categories were small so that these results should be treated with caution. Finally, we note that although the duration of infection (for example, the division between acute versus chronic infections) is clearly a parameter that would likely affect the frequency of host jumping [3, 5] , we were unfortunately unable to perform any analyses of this variable on the data available here as it tends to be host-specific rather than a general characteristic of individual virus families.