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

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

Clearly, identifying the relative frequencies of co-divergence versus cross-species transmission is of central importance to understanding the basic mechanisms of virus evolution and disease emergence. In particular, it is important to determine whether some virus families have a greater propensity to jump hosts than others and, if so, what factors govern this pattern. Currently, however, there is no quantitative or comparative measure of the frequency of crossspecies transmission versus co-divergence, so that determining whether one virus family is more likely to jump species boundaries than another is difficult to assess. One simple and powerful way to estimate these key evolutionary parameters is via 'co-phylogenetic' analysis that assesses the degree of phylogenetic congruence (i.e. similarity) between hosts and their parasites [12] . In particular, a clear congruence between the host and virus phylogenies provides strong evidence for a history of co-divergence, whereas phylogenetic incongruence (i.e. discordance) is compatible with cross-species transmission.