This discrepancy between the rates and corresponding TMCRA estimates has important biological consequence. The phylogenetic divergence between subtype A-H3N2 and B corresponds to a subspeciation event for the virus. The results in this study indicate that the process of speciation is not neutral but instead a period of rapid and intense genetic change. The three genes studied here consistently show large acceleration in the rate of nucleotide substitution for the divergence period relative to the rates observed within a stable subtype. This study gives strong evidence that, at least for influenza viral subtype divergence, the process of subspeciation is associated not just with large genomic changes but also with an accelerated, finite process of adaption.