The ancestral nucleotide sequences of all internal nodes were reconstructed using joint ML method [68] implemented in HYPHY. Amino acid changes along the pre-emergence lineage were determined, and were then mapped onto the three-dimensional structure of the N-terminal domain of M1 matrix protein molecule [30] available (PDB-ID: 1EA3) in RCSB Protein Data Bank. Figure S6 Substitution rates of HA and NA genes from reassortant and group 2 parental strains. 95% higher probability densities (HPDs) are indicated by the error bars. 1st, 2nd, 3rd, and C denote the rate for the 1st codon position, 2nd codon position, 3rd codon position, and whole sequence (non-partitioned), respectively. Substitution rate units for codon partitioned and non-partitioned sequences are substitution/codon/year and substitution/site/year, respectively. Table S5 Estimations of dN/dS using 1-ratio and 2-ratio lineage-specific selection models. These estimations were performed in HYPHY software. Gene datasets other than PB1, HA, NA, M1, and M2 were not analyzed because group 3 is represented by the single virus IDN/6/05. Found at: doi:10.1371/journal.ppat.1000130.s014 (0.03 MB DOC)