The mean numbers of observed geographical state changes (GSC) of the reassortant and of the group 2 parental strains were estimated independently and compared with the null distribution of GSC values under the null hypothesis of completely unrestricted migration (i.e. panmixis; Figure S5 ) [22] . For the reassortant strain, the observed GSC value was not significantly lower than the GSC value expected under panmixis (Slatkin-Maddison test: p.0.2). Therefore the observed geographic structure is not significantly different to that expected by chance alone. For group 2 viruses, the observed GSC value for all geographical state pairs is significantly (p,0.0002) lower than the null value. However, the observed value of GSC within Java (i.e., migrations between Greater Jakarta and the rest of Java) and between the three islands (i.e. migrations between mainland Java, Sumatera and Sulawesi Selatan including Papua) are insignificantly (p.0.2) and significantly (p,0.0002) lower than the corresponding null values respectively, suggesting that the phylogeny of group 2 viruses is not geographically structured within Java, but is subdivided by island-to-island migrations. However, we could not address whether the viral migrations inside Sumatera and Sulawesi Selatan including Papua are panmictic or structured due to limited operative localities in our dataset to distinguish between different regions inside these islands. We also found that the migration of group 2 viruses from Greater Jakarta and surroundings to Sumatera and Sulawesi Selatan including Papua was more frequent than expected under the null hypothesis, and there is relatively little viral migration from the rest of Java to Sumatera and Sulawesi Selatan including Papua (Table S3 ). This observation suggests Greater Jakarta played a more salient role in dispersing group 2 viruses to other Indonesian islands than other parts of Java did. There is another family member (brother) who was confirmed with H5N1 infection (index #45, fatal); however, virus sequences are not available. f Numbers in parentheses are the unique references to the localities shown in Figure 4 . Numbers 1-6 were assigned to Greater Jakarta and surroundings; numbers 7-12 were assigned to West Java. n/a = Information not available. doi:10.1371/journal.ppat.1000130.t001