Ancestral Inference and the Study of Codon Bias Evolution: Implications for Molecular Evolutionary Analyses of the Drosophila melanogaster Subgroup
Figure 1
Silent divergence under departures from equilibrium major codon usage.
The x-axis shows MCU values prior to a change in Ne. A: expected instantaneous per locus rates of pu and up fixations when Ne decreases to 1/3 its original value across genes. B: expected dup,pu = (#up−#pu)/(#up+#pu) for the 1/3Ne scenario (decreasing codon bias). C and D: expected instantaneous silent rates and dup,pu after a doubling of Ne (increasing codon bias). Legends and X-axis scales apply to graphs in the same column. See text for details of the model. The curves assume that variation in selection coefficients underlies MCU variation among genes (u/v = 1 across genes).