Figure 4
Predicted versus actual responses for sets of codons with identical composition. Each line is the sum of eight codons with the same GC content (by position). Each solid circle is a species. Lines of open circles are the theoretical predictions based on the four-parameter model. (a) All-GC (blue) and all-AT (red) codons in prokaryotes. (b) Codons with two G or C and one A or T, the minority base being at the first (blue), second (green), or third (red) position. Note that the third-position slope is actually of opposite sign to the first- and second-position slopes. The orange line is what would be expected if there were no position dependence (that is, P(GC)2P(AT) as in [56]). (c) As in (b), but for codons with two A or T and one G or C. In this case, the orange line is P(AT)2P(GC). (d) As in (c), but for eukaryotes. (e) As in (d), but now each point is a randomly chosen gene in Drosophila.