To estimate the times of the reassortment events that generated the putative reassortant viruses, the times of the MRCA (tMRCA) of the three reassortant subgroups were estimated using BMCMC methods [18, 19] . Bayes Factors (BF) [20] were used to select Author Summary H5N1 highly pathogenic avian influenza (HPAI) virus emerged in China in 1996, and has spread beyond Asia since 2003. Following the first outbreak reported in Indonesian poultry farms in December 2003, the virus spilled over to 27 Indonesian provinces by June 2006, and became endemic in the country. In the following years, repeated sporadic human infections in Indonesia had been attributed to H5N1 HPAI viruses. Nonetheless, the viral evolution and transmission have not been fully understood. Here, we report phylogenetic evidence of a group of interlineage reassortant viruses isolated from human and cats in Java. Our comparative study of the reassortant viruses and one group of genetic parents found that although their rates of evolution were similar and both of their phylogenies were not geographically structured within mainland Java, the growths of genetic diversity were different. We also detected significant positive selection on the viral matrix and polymerase genes preceding and subsequent to the emergence of the reassortant viruses, which might correspond to viral adaptation. Based on our findings, we discuss the possibility of host switching in facilitating the emergence of the reassortant strain, and call for more extensive viral surveillances in the non-avian population in Indonesia. among strict and relaxed clock models of evolution [21] . The uncorrelated exponentially-distributed clock model (UCED) significantly outperformed the other models (lnBF.3) for most datasets, except for the NA gene of the reassortant viruses, for which the strict clock model was not rejected (lnBF,1; Table S4 ).