A major advantage of the current phylogeography implementation is the ability to infer the migration process in natural time scales. The panels in Figure 5 summarize the temporal dynamics of A-H5N1 spatial diffusion inferred using the shared rate matrix (KML files, Dataset S1 and S2 for HA and NA respectively, which enable visualizing the spread over time in Google Earth are available as supporting information). The lines connecting different locations represent branches in the MCC tree on which state exchanges occur and circle areas reflect the number of branches maintaining a particular state at that time point. By May 1997, Avian influenza lineages have accumulated in Guangdong, where the virus was originally isolated from a farmed goose [33] , and to a large extent in Hong Kong Southeast Asia resulting in severe A-H5N1 outbreaks in 2003. Finally, A-H5N1 virus also spreads to the west in a second major transmission wave. Since this occurs after a major outbreak in migratory waterfowl at Qinghai Lake in Northern China, migratory birds could play a prominent role in this dissemination pathway [37] .