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

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

It is also possible that successful cross-species transmission occurs more frequently among phylogenetically related hosts, likely because it is easier to infect and replicate in genetically similar hosts that share less divergent cell receptors [26] . In addition, related hosts may sometimes inhabit the same geographic region, increasing the probability of cross-species transmission through more frequent exposure [13] . Indeed, a useful generality in studies of disease emergence is that the closer the phylogenetic relationship between hosts, then, given appropriate exposure, the more likely that a pathogen will be able to jump between them, in turn leading to preferential host switching [27] . If true, so that cross-species transmission results in a viral phylogeny that mirrors that of their hosts, then any phylogeny-based approach such as that utilized here will underestimate the true frequency of host jumping. As a case in point, although there is a general concordance between the phylogenies of simian immunodeficiency virus (SIV) and their primate hosts, in which four species of African green monkey harbor distinct forms of SIV that is clearly suggestive of co-divergence [19] , it has been argued that the evolutionary history of SIV may also have been shaped by preferential host switching [28] , although these mechanisms are not mutually exclusive. In contrast, incomplete lineage sorting among closely related viruses may produce a false signal for cross-species transmission when co-divergence has in fact occurred [19] . In addition, because there is growing evidence that viruses can have complex evolutionary histories with genes derived from multiple sources [29] , it is important to note that our virus phylogenies are necessarily gene trees rather than species trees. It is therefore possible that other virus gene trees will exhibit a stronger topological match with host phylogenies than those presented here, and hence provide more evidence for co-divergence. Finally, while our analysis was only based on robust phylogenetic patterns, because nodes that were topologically uncertain were excluded from the analysis, it is possible that our virus trees contain topological errors reflecting the use of sometimes small numbers of highly divergent sequences.