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The combination of comparative genomics and population genetics may provide important clues regarding human evolution. We have hypothesized that the divergence between various human and chimpanzee orthologs will be reflected in the variability of single nucleotide polymorphisms (SNPs) that are localized in the vicinity of the corresponding loci in different human populations. Consistently with this notion, more diverged genes between humans and chimpanzees are more likely to be associated with human speciation and are anticipated to contain SNPs with reduced variability between different human populations. In order to test this hypothesis, we have compared the rate of non synonymous nucleotide substitutions (Ka) between 255 chimpanzee and human orthologs with the average deviation in the allelic frequencies of corresponding closely linked SNPs in two distinct human populations: The Yoruba people in Ibadan, Nigeria (YRI) and US residents with ancestry from Northern and Western Europe, collected in 1980 by the Centre d’Etude du Polymorphisme Humain (CEU). We found a significant (p

Allelic Frequency in Human SNPs Predicts the Rate of Non-Synonymous Nucleotide Substitutions between Human and Chimpanzee Genes