Distributions of d_N, d_S, and radical and conservative amino acid changes. (A) Distribution of d_S and (B) distribution of d_N (numbers of synonymous substitutions per synonymous site and of nonsynonymous substitutions per nonsynonymous site). (C) Distribution of the ratio ω = d_N/d_S for the melanogaster–pseudoobscura comparison of 9184 inferred orthologous protein-coding genes. (D–F) Distributions of α, the ratio of rates of substitution that are radical to those that are conservative, based on 9184 alignments of orthologous protein-coding genes in D. pseudoobscura and D. melanogaster. Radical changes influence charge (D), polarity (E), or polarity and volume (F) to a greater degree than do conservative changes. A substitution model was fitted by maximum likelihood to estimate these rate parameters.