Figure 1.
The figure shows the number of synonymous and nonsynonymous nucleotide differences in 13,731 human–chimpanzee orthologous gene pairs.
Table 1.
Biological Process Categories with an Excess of Putatively Positively Selected Genes (Nominal p less than 0.05; MWU) among a Total of 133 Biological Process Categories
Table 2.
Test for an Excess of Putatively Positively Selected Genes by Tissue Type
Table 3.
The Top 50 Genes Showing Evidence for Positive Selection
Figure 2.
The figure shows the frequency spectra of nonsynonymous (red) and synonymous (black) mutations among the 50 genes showing the strongest evidence for positive selection in the interspecific comparison. Also shown is the expectation from the standard neutral model, expectations from the neutral model taking the protocol used to select the 50 genes into account (see text), and from the prediction of the selection model. On the x-axis is the number of derived allele in a sample of size 30 chromosomes (Count), and on the y-axis is the proportion of sites expected in the sample with a particular frequency.
Figure 3.
Power of the Likelihood Ratio Test for Positive Selection
The power is shown as a function of the proportion of the dN/dS ratio, and for sequence lengths (n) of 150 and 500 codons. Power is defined as the proportion of tests that are significant at the 5% level. Simulation parameters, including codon frequencies, transition/transversion bias, and divergence times, are equal to the values estimated from the data. Notice the logarithmic x-axis.