Figure 3
Example of processes spurring MM events in virus populations. Examples include (a) intrahost adaptation (a selective process) and (b) interhost transmission (a demographic process). The tree in (a) characterizes, for example, neuraminidase (NA) or hemagglutinin (HA) evolution in the influenza A virus, driven by positive selection; selection by host immunity is ongoing, whereas that from drug treatment may be intermittent. The tree in (b) represents interhost transmission and its associated bottleneck; for viruses that compartmentalize (such as human cytomegalovirus and HIV), similar patterns follow transmission to new compartments. The colored squares below the trees roughly indicate the diversity of the population through time. Intrahost adaptation may temporally decrease diversity owing to genetic hitchhiking, though single snapshots may not reflect varying temporal levels of diversity. During interhost transmission, diversity decreases owing to the associated bottleneck but then may quickly recover in the new host.
