Figure 5.

Shifts in site frequency spectra among codon pairs. (A) Difference in average frequency of derived states/polymorphic site for C/T codon pairs relative to codon usage (i.e., proportion of C-ending codons). (B) Difference in average frequency of derived states/site for C/T codon pairs relative to Δpref for T→C changes. (C, D) Corresponding figures for G/A codon pairs. Letters in legend correspond to single-letter amino acid codes; blue, fourfold degenerate amino acids; light blue, codon pair from fourfold degenerate subclass of sixfold degenerate amino acids; red, codon pair from isoleucine or twofold degenerate subclass of sixfold degenerate amino acids; gold, twofold degenerate amino acids. Dashed lines correspond to linear regression through all points.