Ancestral codon configurations in simulations of codon bias evolution.

Trees representing extant codon configurations consistent with single silent changes in the m lineage, ECC_uppppp (A) and ECC_puuuuu (E), are shown. The three most common ancestral codon configurations underlying these extant codon configurations are shown in B, C, and D for ECC_uppppp and in E, F, and G for ECC_puuuuu. Trees C and G reflect child/ancestor reverse changes and trees D and H show child/sib-ancestor parallel changes. The relative frequencies of ancestral codon configurations underlying ECC_uppppp and ECC_puuuuu in the codon bias simulations are shown as bubble plots beneath the trees. The sizes of the bubbles reflect the relative numbers of ancestral codon configurations in each class for three different MCU values. For the non-equilibrium scenarios (1/3N_e and 2N_e), the proportion of each ancestral codon configuration among the extant configurations relative to the proportion under equilibrium codon bias evolution are given. The data are from Table 1.