Twenty six full length genome sequences for which year of isolation was available were used to infer evolutionary rate and dates using BEAST version 1.4.8 [41] . Demographic history of a population/species using multi-locus data, even from a small number of individuals, can precisely recover past bottlenecks in population size that cannot be characterized by analysis of a single locus [78] . Given this fact, estimates based on the whole genome sequence data are expected to be more reliable. To determine the population history of individual genotypes, 149 complete F gene sequences, which had dates of collection, were retrieved from GenBank. Phylogenetic analyses were done as described previously (Table S2 ). From the ML tree, a total of 97 isolates from genotype I, II, VI, and VII were selected to infer evolutionary rates and population dynamics. These included all available dated full length sequences from Genotypes I (24 sequences), II (28 sequences), and VI (23 sequences). The majority (95%) of genotype VII sequences were of Chinese origin. Thus, we included the seven non-Chinese sequences and picked an additional 15 sequences based on phylogenetic diversity to represent genotype VII in our analyses. The evolutionary rate (nucleotide substitutions per site per year) of each gene and concatenated genome was estimated using the Bayesian Markov chain Monte Carlo analyses (independent assumption of codivergence). Substitution models of both HKY + G 4 and GTR + G 6 with estimated base frequencies, gamma and invariable site portion were used, with uncertainty in the data reflected in the 95% high-probability density (HPD) intervals. Strict clock and uncorrelated exponential (UCED) relaxed clock models were attempted independently, and the best-fit clock model was determined to be UCED based on the Bayes Factor calculated from their posterior distributions (Table S3 ). The Coalescent Bayesian skyline plot (BSP) was used to infer the past population dynamics. The BSP was constructed using the growth rate and demographic parameters from the selected best-fit models. Bayesian Markov Chain Monte Carlo (BMCMC) analyses were run for 5-10610 8 generations depending on each dataset. Convergence of trees was checked using Tracer v1.4.1 (http://beast.bio.ed.ac.uk/Tracer).