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

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

Understanding how viruses and their hosts co-evolve is central to revealing the nature of virus evolution and the determinants of disease emergence. In particular, we lack a quantitative understanding of whether some types of virus, such as those classified into different families or that possess genomes of different nucleic acid types, are better able to jump species boundaries compared to others. To investigate the comparative prevalence of cross-species transmission among viruses we measured the congruence between virus and host phylogenetic trees using a normalized tree topological distance-based approach (nPH85, [14] ). If taxonomically related viruses have an evolutionary history of co-divergence with their hosts the virus and host phylogenetic trees should be similar in topology, whereas phylogenetic incongruence is the signature of species jumping. Overall, our analysis revealed absolute departure from co-divergence among all the virus families studied here (nPH85 ! 0.6 and supported by the reconciliation analysis) suggesting that cross-species transmission occurs frequently, at least at the level of virus family. Particularly striking was that even the most slowly evolving DNA viruses, which have previously been suggested to represent exemplars of virus-host co-divergence [1] , exhibit relatively common cross-species transmission. Hence, at their most basic, these results indicate that viruses are often exposed to a variety of susceptible host species that provide opportunities for cross-species transmission.