Fig. 2.

Maximum likelihood model of mutation rate dynamics fit to synonymous mutations. (A) Point mutation rate estimates, expressed on a genome-wide basis. The ancestral rate was derived from a previous analysis of nonmutator clones from eight experimental populations (31). Error bars are 95% confidence intervals. (B) Relative mutation rates for two mutY compensatory mutations inferred from the maximum likelihood model and expressed relative to the mutT-only rate. Box plots show the probability distribution of this parameter, where the box shows the upper and lower quartiles, the black line the median, and the whiskers the 95% confidence interval. (C) Timing of changes in mutation rates and phylogenetic branch points. Each box plot shows the probability distribution, in time, for a branch point or change in mutation rate (with quartiles, median, and confidence limits as above). The phylogeny is overlaid on the box plots.