English: For each amino acid, we list the codons and, in parentheses, the number of 4D sites from each codon used in the bootstrap analysis – representing, in relative terms, the abundance of each codon in the genome. P-codons are all 4D sites from optimal codons grouped together, while U-codons are all 4D sites from non-optimal codons. 4D sites were binned into codons either by their ancestral allele as determined by parsimony to D. sechellia or by major allele if there is a substitution at that site between D. sechellia and D. melanogaster. Gold bars are the optimal codons for each amino acid, while dark grey bars are the non-optimal codons. 10 bootstraps determine the fraction of sites under constraint for each codon-type. Error bars represent the s.e. of the estimates. A negative value indicates an excess of polymorphism at 4D sites compared to short introns and is likely due to mispolarization assigning SNPs to the wrong codon.