Fig. 3.

Empirical mutation rates explain the spectrum of adaptive substitutions better than randomized rates. In A–C, the white bars show the distribution of log-likelihood differences for randomized vs. empirical mutation rates for (A) S. cerevisiae, (B) E. coli, and (C) M. tuberculosis. A value of 0 (dashed vertical line) means that a randomized rate performs as well as the empirical mutation rate. The fraction of randomized rates providing a better model fit than the empirical rates (i.e., right of 0) is 0.2%, 3.7%, and 4.2% for A, B and C, respectively. Data are based on 10⁶ randomized rates. Note that A–C have different limits on their horizontal axes. In D–F, the empirical mutation rate is shown in relation to the inferred mutation rate on a double-logarithmic scale for (D) S. cerevisiae, (E) E. coli, and (F) M. tuberculosis. Symbol types correspond to D, Inset. The dashed diagonal line indicates y = x.