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

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

To date, co-phylogenetic studies of viruses have largely focused on the evolution of a subset of viruses within a particular virus family, and have not been performed in a comparative manner. For example, although there has been much work dedicated toward describing co-divergence in herpesviruses, these studies generally only encompass one particular host type (e.g. primates [13] ) and so may fail to capture the broader picture of potential host jumps among more distantly related species. Hence, there has been no attempt to use analyses of this kind to provide a broad-scale comparative and quantitative measure of the frequency of co-divergence and cross-species transmission in virus evolution. Herein, we provide such an analysis. Specifically, using a normalized tree topology distance metric based on the Penny and Hendy distance metric that enables comparisons between pairs of virus and host trees with different numbers of tips [14] , which we now term the 'nPH85' distance (where n = normalized), we compare phylogenies of virus families and their hosts. While this method does not explicitly model host-switching events, it does provide a simple means to compare multiple topologies of virus-host pairs, and accounts for differences in sample size and the fact that several viruses from a specific family can infect a single host species.