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Table S1 Accession numbers of the sequences used in this study.

Table S2 ML estimations of parametric demographic models (logistic growth) best-fitting to the HA and NA coding sequences of Indonesian H5N1 HPAIV.

Fig. S1 Molecular phylogeny of H5N1 HPAIV in Indonesia inferred from the NA gene.

Fig. S2 Logistic population growth of H5N1 HPAIV in Indonesia.

Fig. S3 The frequency of pairwise geographic distances.

Fig. S4 Mantel test of the spatio-genetic correlations.

Fig. S5 Parsimony reconstruction of migration history.

Fig. S6 Time-scaled phylogeny of Indonesian H5N1 HPAIV.

Fig. S7 Dispersal rate of H5N1 HPAIV in Java and Bali islands over time.

Data S1. Nucleotide sequence alignment of HA gene.

Data S2. Nucleotide sequence alignment of NA gene.

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