This paper is rather specific to HIV-1 with its very large population size within each infected individual, and rapid evolution rate. It would be interesting to see similar work with other organisms. Human Influenza A virus, for example, has an evolution rate very similar to HIV-1 but a very different transmission rate between infected individuals.
This is an archived static version of the original phylobabble.org discussion site.
[Paper] Timing and order of transmission events is not directly reflected in a pathogen phylogeny