The maximum likelihood estimates for the 2009 H1N1 influenza pandemic. Left: Whole-genome data estimates based on both MAF and D
Right: Individual segments' estimates based on D
. (For the MAF-base estimates, see Supplementary Fig. S2, in Additional file 1.) PB2, PB1, and PA encode the RNA polymerase; HA and NA encode the glycoproteins hemagglutinin and neuraminidase; NP, M, and NS segments code the nucleoprotein, matrix proteins and non-structural proteins. Due to structural constraints and small size, the latter three segments accumulate the least number of mutations. Our estimates for the evolutionary rates, the starting time of the expansion, and presence of strong purifying selection (ω = 0.22) corroborated phylogenetic results. The mean evolutionary rate, , is in 10-3 substitutions/site/year and t
is in days. The standard errors are the 95% confidence intervals via bootstrapping.