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

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

Our fundamental assumption is that incongruences between virus and host topologies imply the occurrence of cross-species transmission. To test the validity of this assumption, we reconciled the viruses with the phylogenetic history of their hosts. By associating 'event costs' with host-jumping, as well as with lineage duplication and extinction events, we found the range of optimal co-phylogenetic solutions for each virus family ( Fig 5A) . As with the analysis of topological distances, this revealed that cross-species transmission was the most common evolutionary event in all virus families studied here, with co-divergence consistently less frequent (with the possible exception of the Hepadnaviridae-see below), and lineage duplication and extinction playing a much more minor role. We next reconstructed the history of these evolutionary events in detail in the Hepadnaviridae (i.e. the most co-divergent virus family). This revealed that under the most likely co-phylogenetic scenario the proportion of crossspecies transmission represents 0.57 of all events (i.e. co-divergence = 9 events; duplications = 0; extinction = 1; host-jumping = 13; Fig 5B) . Since the nPH85 distance for the hepadnavirus data set was 0.6, we suggest that our method generates results consistent with the reconciliation analysis. In addition, one important disadvantage of performing full reconciliation analysis is that co-phylogenetic methods such as that implemented in Jane [15] and Tarzan [16] are not straightforward since they offer many combinations of possible events and are difficult to compare between families, especially in cases with more than~50 viruses where there are many possible co-phylogenetic scenarios. Despite these limitations, our reconciliation analysis did reveal the possible causes of the topological incongruence between the virus and host phylogenies.