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. 2009 May 21;58(1):130–145. doi: 10.1093/sysbio/syp017

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FIGURE 4. — The effect of ambiguous characters on Bayesian posterior probabilities when rates differ between unambiguous (A) and ambiguous (B) genes. In each graph, the average posterior probability of the true tree (y-axis) is plotted as a function of the length of Gene B (x-axis), pattern of ambiguous characters (shade of gray), rate of Gene A (column), and rate of Gene B (row). Graphs show results from analyses in which rate variation was modeled in a partitioned analysis (partitioned by gene) with a dirichlet(1,1) rate prior. Therefore, the model of evolution is overparameterized along the diagonal (equal rates; analogous to Figure 3b) and correctly parameterized off the diagonal. Note that the magnitude and direction of bias are a function of the relative rates of the ambiguous and unambiguous genes. Also note that in some cases, the bias is strongest when the number of ambiguous sites is low.