The maximum clade credibility phylogenetic tree recovered under one of the best-fit models (exponential growth strict-clock) identified using BEAST Almost identical results were obtained under the constant population size strict-clock model (available from the authors on request). The best fit model indicates that: (1) the sugarcane-to-Coix SSRV transmission event that initiated the experiment, which actually occurred in 1976, was estimated to have occurred in 1971 (95% highest clade credibility interval = 1962–1979, indicated by the red posterior probability distribution beneath the tree) and (2) the date of the three-way 1984 sugarcane virus population split was estimated to have occurred in 1985 (95% highest probability density = 1980 – 1989 indicated by the blue posterior probability distribution for the tMRCA situated beneath the tree). Thus, applying the estimated SSRV substitution rate quite accurately recovers the dates of two important events in the 32-year long SSRV evolution experiment.
Harkins et al. Virology Journal 2009 6:104 doi:10.1186/1743-422X-6-104