(a) Proportion of genes rejected for 15 mammalian pairs using the disparity index test in testing the null hypothesis of homogeneity of substitution patterns in fourfold-degenerate sites at a 5% significance level (26). The total number of genes examined is shown in parentheses next to the name of the species pair; the number of genes rejected is shown next to the corresponding bar.

(b) Scatter plot showing the relationship of DGC4 (GC content difference at fourfold-degenerate sites in orthologous sequences) with p4 proportion of fourfold-degenerate sites with A/T<-->G/C difference) for genes passing (black) and failing (red) the disparity index test. Green markers show the expected relationship of DGC4 calculated from sequence length and p4 for each gene by using equation 10 in ref. 26.

(c) Overestimation of evolutionary distance caused by genes evolving with heterogeneous patterns of evolution for seven representative mammalian pairs. Open bars show the estimate of average distance from all genes passing the homogeneity test (26, 27). Dark bars show the average distance for the rejected genes (heterogeneous).

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