Scatter plot of CAI versus ENC values for each of the 12 genomes. The reference set for CAI is relative to each genome (see text for details). The red dots are the genes that are localized in the fourth chromosomes (element F) in D. melanogaster. The dashed line indicates the CAI index value that a gene with equal codon usage (no CUB) would have, which occurs when mutation bias to A/T is exactly balanced by selection to G/C. One interpretation of these graphs is that genes to the right of the dashed lines are dominated by selection for codon usage, whereas genes to the left are dominated by mutation bias.