Fig 3. Some challenges equating phylogeny with transmission history.

The solid lines represent the phylogenetic relationship between infections that have been sampled from two or three different hosts. Shaded regions correspond to the location of virus lineages in different hosts, as indicated by colour. The transmission of a lineage from one host to another is represented by a gap between shaded regions and highlighted with a red arrow. (A) Although hosts 1 and 2 are closely related, the phylogeny does not indicate whether the infection was transmitted from host 2 to 1 (as shown), or vice versa. The transmission event may be located anywhere along the two branches connecting the hosts. (B) An infection may have been transmitted through any number of unsampled hosts before reaching the host that was sampled. (C) An unsampled host may be the source of infections transmitted to both hosts 1 and 2. (D) If pathogens establish a large diverse population within each host, the branches of the phylogeny may occur in a different order than the transmission history; as shown, hosts 1 and 3 are more closely related in the transmission history, but not in the phylogeny.