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

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FIGURE 6. — The effect of ambiguous characters on the probability of incorrectly rejecting a molecular clock model of evolution in an ML framework. The proportion of 100 replicates in which the clock model was rejected in a χ² test (df = 2; y-axis) is plotted against the length of Gene B (x-axis), distribution of ambiguous characters (shade of gray), the rate of Gene A (columns), and the rate of Gene B (rows). Because rate heterogeneity was not accommodated in these analyses (see text), the model of evolution was underparameterized in analyses presented off the diagonal. Note that substantial inflation of Type I error requires both rate variation (off diagonal) and ambiguous characters (black or dark gray points).