The geographic locations of virus isolation were either obtained from the sequence databases, or obtained through personal communication with Catherine Smith (from Disease Control and Prevention, Atlanta, USA), or inferred from their strain names (Tables 1 and S6 ). The locations of isolates were indicated on the map of main island of Java in Indonesia (Figure 4 ). Due to the limit of our geographical data, the localities of the isolates shown in the map (Figure 4 ) should be regarded as arbitrary within the province which is the highest precision level shared by all viral samples. Each of the reassortant viruses was assigned with a state of either Greater Jakarta (surroundings included) or West Java depending on its place of origin ( Table 1 ). The migratory history of the reassortant viruses (n = 25) between these geographical states were inferred based on the refined ML phylogeny of HA and NA ( Figure  S4 ) independently using two parsimony optimization methods, called ACCTRAN (accelerated transformation) and DELTRAN (delayed transformation) implemented in PAUP* software. The geographical states of all ancestral nodes in the tree were estimated to achieve minimum state changes in overall, and therefore the number of state changes and state of the MRCA of the reassortant was obtained. Polytomies were randomly resolved 1,000 times, and state changes were estimated separately for each resolution. The mean number of state changes was then calculated. To test against the null hypothesis of completely unrestricted migration between geographical states (panmixis), the mean number of observed state changes was compared with the frequency distribution of the mean number of expected state changes under the null hypotheses. The null distribution and critical values were generated by randomly shuffling the states of isolates 5,000 times (the Slatkin-Maddison test [22, 24, 64] ). The migratory history of group 2 viruses was also studied using the HA gene in a similar manner, while each group 2 virus was assigned to either of four widely ranged geographical states: Greater Jakarta and surroundings, the rest of Java, Sumatra, and Sulawesi Selatan, including Papua. This assignment scheme is comparable to that of reassortant viruses, as West Java is part of Java.