In this study, codon substitution rates of CpG to TpG mutations, TpG to CpG mutations, and non-CpG transitions and transversions were estimated by comparing the coding regions of thousands of human and chimpanzee genes from entire genome and inferring their ancestral sequences by assuming macaque genes as the outgroup.
As seen in Figure 1, a marked difference was not observed between the synonymous substitution rates of autosomes and X chromosome. This result indicates that the effect of "male-driven evolution"  is not strong. The male-driven evolution is a phenomenon in which the number of mutations is proportional to the number of germ-line cell divisions, so that the sperms have a higher rate of mutation than the eggs. There are large discrepancies among the results of previous studies with regard to the effect of male-driven evolution on mutation rates  In this study, a large variation in the rates of the substitution caused by CpG hypermutation among chromosomes and genes was observed. The mutation rate of the X chromosome was within the range of the mutation rate among autosomes, which is expected considering the variation in substitution rates among chromosomes. Thus, this finding suggests that the effect of male-driven evolution on the mutation rate was less than that of regional variation.
Vogel and Motulsky  pointed out that since the deamination of methyl-C occurs spontaneously and is independent of DNA replication, the rate of CpG mutations should be scaled with time and not with the number of cell divisions. Recently, Taylor et al.  investigated male mutation bias separately at non-CpG and CpG sites by using human-chimpanzee whole-genome alignments. They concluded that CpG hypermutation is weakly affected by the number of cell divisions. In this study, I demonstrated that the effect of male-driven evolution on CpG hypermutation is less strong than that of other chromosomal properties. Thus, although our result is similar to that of Vogel and Motulsky , I cannot exclude the findings of Taylor et al. . Variation in the mutation rates among chromosomes must be one of the causes of the discrepancies among the results of previous studies with regard to the effect of male-driven evolution on mutation rates. Therefore, further study is warranted in this area.
Table 2 indicated that the CpG to TpG substitution rates were negatively correlated to the GC content of the chromosomes. This is consistent with the recent finding that the CpG mutation rates in the non-coding regions of human genes are positively correlated to the local GC content [11–14]. On one hand, table 2 showed that other types of substitution rates were positively correlated to the GC content of the chromosomes. On the other hand, multiple regression analyses shown in table 3 indicated that other types of substitution rates were negatively correlated to the GC content but the correlation was not significant. It should be noted that GC content, gene density, and frequency of CpG islands were correlated to each other. Discrepancy of these coefficients indicates that the effects of genetic features other than GC content on TpG to CpG substitution rates might have overcome that of GC content.
The results presented in this study also suggest that codon substitution rates are positively correlated to gene density. The reason of this correlation is unclear, but it might be due to fact that DNA melting is the rate-limiting step in cytosine deamination . The difference between CpG hypermutability of the coding and non-coding regions may be due to the difference in the reason of DNA melting in the 2 regions. In the case of the coding regions, the cause of DNA melting is transcription; the DNA molecule separates into 2 single-strands before being transcribed. The frequency of transcription was positively correlated to the expression level of the gene, which in turn was positively correlated to the number of CpG islands . In contrast, the reason for DNA melting in the non-coding region is not transcription but denaturation. The base pairs open one at a time, far below the melting temperature, and the half-life of individual GC base pairs are approximately 3 times longer than those of individual AT base pairs , so that the rate of CpG hypermutability in the non-coding region is positively correlated to the local GC content. If this is the case, CpG hypermutability will depend on the expression level of the genes. Recent study on mouse genes showed that the effect of gene expression level on codon bias is weaker than both the effect of gene expression level on amino acid composition and the effect of CpG hypermutability on codon bias , so that effect of gene expression level on mutation rate would be relatively small. Further study is needed in this area.
In this study, the codon substitution rates were estimated by using the coding regions of thousands of human and chimpanzee genes and inferring their ancestral sequences by assuming macaque genes as the outgroup. All types of substitutions show a significant negative correlation to Grantham's distance. This result indicates that the properties of amino acids are one of the major factors influencing the variation among non-synonymous substitutions, as previously reported .
The reason for the specific correlation found between codon substitution rates and chromosome sizes might be the physical distance between the genes and telomeres. Tyekucheva et al.  suggested that distances from telomeres play important roles on mutation rates. However, the numbers of substitutions are not very large; thus, dividing too many bins by the distance from the telomeres may yield weak results. As more data become available, incorporating these additional predictors in the regression analyses may be beneficial. Of special interest would be data on species other than humans.
On the basis of these results, a model that incorporates these genetic features was developed. The result shown above indicates that including GC content, gene density, CpG island density to the model improves the ability of prediction of the substitution rates