Table 1.
Context-dependent properties of the MC2020 model.
Fig 1.
Simulation results for the ML_AA ancestral sequence of psbA under 5 models; MC with synonymous substitutions only, MC with nonsynonymous substitutions, MC2020 with synonymous substitutions only, MC2020 with nonsynonymous substitutions, and K2P with synonymous substitutions only.
The four MC and MC2020 models are shown in black and the K2P model in red.
Fig 2.
Simulation results for the MC2020 model with synonymous substitutions only for the four reconstructed ancestral sequences of psbA; MP-High (red), MP-Low (green) and ML-AA and ML-DNA (both black).
Fig 3.
Simulation results for the ML-AA ancestor of each gene under the MC2020 model with synonymous substitutions only (black) and with nonsynonymous substitutions included (red). Standard deviations are not shown for clarity of presentation.
Fig 4.
Comparisons of simulation results for each gene using the MC2020 model, with synonymous substitutions only, applied to each of the four ancestral sequences, with the extant sequence CAI values (blue). The ancestral sequences that yielded the highest and lowest simulation lines, determined by the CAI value of the ancestral sequences, are indicated and colored red and green respectively. For each gene the two plots are for the minimum (A) and maximum (B) number of mutations estimated from one of the reconstructed ancestral sequences (see text).