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

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

An important assumption of the current study is that incongruence between virus and host topologies is a result of cross-species transmission. In some instances, however, it might be possible to explain the lack of virus-host co-evolutionary history through multiple instances of lineage duplication and extinction, without such host-switching events. To address this issue, we reconciled the co-phylogenetic relationship between viruses and their hosts. In particular, we determined the optimal solutions for co-phylogenetic reconstruction for all families, including the possibility of lineage duplication and extinction, using the Jane co-phylogenetic software package [15] . This uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find optimal solutions to reconcile cophylogenies. Although this is a simple heuristic method, it is able to generate results on relatively large data sets (although it is most effective for trees with less that~40-50 tips). Importantly, we used 'event costs' associated with incongruences between trees that were conservative towards co-divergence and defined here as: 0 for co-divergence, 1 for duplication, 1 for host-jumping and 1 for extinction. Utilizing this reconciliation, we also examined the evolution of the Hepadnaviridae in more detail as this family contains the best evidence for co-divergence (see Results).