We now compare the results from pairwise rate estimates across subtypes A-H3N2 and B with those from application of the MCA to the same data. These results are summarized in Table 2 and Histograms of the time of most recent common ancestor for subtypes A-H3N2, B and C, respectively, derived from molecular clock estimates on hemagglutinin (HA), matrix (MP) and nonstructural (NS) gene sequences This discrepancy between the two sets of estimates of the TMRCA likely owes to the inability of the MCA to integrate information from the period of evolution between the two subtypes, leading to a substantial underestimate of the rate of substitution, and consequent underestimation of the date of the TMRCA.