Systematic studies characterize the substitution process and substitution rate process of several classes of viral subtypes in, for example, Dengue, influenza subtype A, human immunodeficiency virus (HIV) and the virus responsible for sudden acute respiratory syndrome (SARS). For the last three viruses, a unique zoonotic transfer appears to co-occur with substantial changes in both the composition of nucleotides and amino acids as well as alterations in the rate of nucleotide substitution [15, 14, 1] . In Dengue, where a single subtype simultaneously inhabits two hosts (humans and Aedes aegypti) in a persistent zoonotic process, the introduction of the virus to new geographical environments associates with a dramatic increase in sequence diversity [25] . Unfortunately, no studies thus far analyze the rate of nucleotide substitution during either geographical invasion or zoonosis. Consequently, studies of the date of origins of viral subtypes must use strong a priori assumptions on the rate structure of nucleotide substitution.