Positively selected sites were detected using random effect likelihood (REL) and fixed effect likelihood (FEL) methods [26] via the Datamonkey website [63] . Bayes factors larger than 50 and pvalues smaller than 0.1 were used as thresholds for strong evidence of selection in REL and FEL, respectively. To test lineage-specific positive selection, the two-ratio branch model was used, which pre-specifies a single rate of synonymous substitution (dS) for the whole phylogeny and two rates of non-synonymous substitution (dN 1 and dN 2 ). The dN 1 was specified for the pre-emergence lineage (indicated as the ancestral branch connecting the group 3 MRCA; see Figure 1B ) for the group 3 viruses (including the reassortant viruses for M1, M2, and PB1 genes). The dN 2 was specified for other lineages across the phylogenies. The ML estimates of these rate parameters were performed in HYPHY version 0.99 [67] . The resulting likelihood score of the two-ratio model was then compared with that of the one-ratio model, which assumes the same dN and dS across the phylogeny, using the likelihood ratio test (LRT, with degree of freedom = 1). The substitution model MG94XGTR+C 4 was used.