Phylogenetic trees of Indonesian H5N1 viruses were reconstructed from 12 separate gene datasets (Table S6) , using a maximum likelihood (ML) approach with bootstrapping analyses to assess clade robustness (Figures 1, S1-S3; computer files of dendrogram are available as Dataset S1). In all the phylogenies, viruses sampled from avian species during earlier years of outbreaks (predominantly 2003-2004) tended to cluster near the root as expected, but with a poorly resolved branching structure that is likely due to relatively low sequence divergence. In contrast, viruses sampled from recent infections (2005) (2006) (2007) from avian and mammalian hosts formed three well-supported lineages with bootstrap support (or posterior probabilities) over 90 (or 0.9) under neighbor-joining (NJ), ML and Bayesian Markov Chain Monte Carlo (BMCMC) methods. We denote these lineages as groups 1, 2, and 3 in the hemagglutinin (HA) and neuraminidase (NA) phylogenies ( Figures 1A and S2C ). This structure was preserved in the phylogenies of other genes for which sufficient sequence data were available (viruses from group 3 were missing sequence data for the NP, NS, NS1, NS2, and PB2 genes). The group 3 lineage in the MP, M1, M2, and PB1 phylogenies was only represented by the A/Indonesia/6/05 strain.