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 determine the prevalence of host switching between different viruses, we inferred family-level viral phylogenies and compared these to phylogenies of their hosts. Importantly, our analytical approach-which utilizes the nPH85 distance-provides a relative measure of phylogenetic congruence that is directly comparable between data sets that differ in size (i.e. different number of viruses and host species). Our method assumes that viruses that have codiverged with their hosts will share the same tree topology. In contrast, an increasing number of host jumping events should lead to greater phylogenetic incongruence. The reasoning behind this assumption is that there exists a very large number of possible phylogenetic tree topologies even for data sets with a few samples, such that similarities between a pair of virushost trees (i.e. congruence) are highly unlikely to arise by chance. Of course, phylogenetic events other than cross-species transmission might also lead to phylogenetic incongruence and we test the validity of this assumption later in the manuscript.