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

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

Another important aspect of assessing virus-host co-divergence is that the evolutionary time-scales of viruses and their hosts are consistent [30] . Although such a comparison is valuable, it is problematic for the present study because high rates of evolution lead to substitutional saturation in virus genomes at a much faster rate than in cellular organisms. Indeed, it is likely that many of the cross-species transmission events implied here have occurred on timescales of many millions of years. As a result, temporal signal is rapidly lost, precluding accurate estimates of their long-term evolutionary time-scales, even though the topology is often accurately recovered [31] . We therefore suggest that simpler topological comparisons such as those performed here may be a more informative way to proceed in family-level studies of cross-species transmission versus co-divergence.