Advances in Anthropology 2014. Vol.4, No.1, 50-52 Published Online February 2014 in SciRes (http://www.scirp.org/journal/aa ) http://dx.doi.org/10.4236/aa.2014.41007 OPEN ACCESS 50 Allelic Frequency in Human SNPs Predicts the Rate of Non-Synonymous Nucleotide Substitutions between Human and Chimpanzee Genes Hippokratis Kiaris, Athanasios G. Papavassiliou Department of Biochemistry, University of Athens Medical School, Athens, Greece Email: hkiaris@med.uoa.gr Received December 5 th , 2013; revised January 3 rd , 2014; accepted February 2 nd , 2014 Copyright © 2014 Hippokratis Kiaris, Athanasios G. Papavassiliou. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In accordance of the Creative Commons Attribu- tion License all Copyrights © 2014 are reserved for SCIRP and the owner of the intellectual property Hippokra- tis Kiaris, Athanasios G. Papavassiliou. All Copyright © 2014 are guarded by law and by SCIRP as a guardian. The combination of comparative genomics and population genetics may provide important clues regard- ing 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 popula- tions. In order to test this hypothesis, we have compared the rate of non synonymous nucleotide substitu- tions (Ka) between 255 chimpanzee and human orthologs with the average deviation in the allelic fre- quencies 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 < 0.05) nega- tive association between the Ka and the degree of variation in the corresponding allelic frequencies be- tween the human populations which implies that the most significant genes for human speciation are as- sociated lower variability between the human populations examined. This observation is consistent with the strong selective advantage offered by these nucleotide substitutions during human evolution and pre- dicts that a low polymorphic rate is consistent with the presence of genes with an essential role in human speciation. Keywords: HapMap; Chimpanzee Genome; Human Speciation Introduction The genetic details of human speciation and the identification of the array of the genes with the most important role in the divergence of humans and chimpanzees from their common evolutionary ancestor, represents an intriguing problem in modern biology because of its obvious importance in the study of human evolution (Disotell, 2006; Raaum et al., 2005). In addition it possesses important implications in biomedicine since it ultimately aims to identify genes intrinsically related to human behavior, physiology and pathology (Fisher & Marcus, 2006; Premack, 2007). The recent completion of the human and the chimpanzee genome projects and the advancement of the emerging field of comparative genomics provided investigators with tremendous tools to study these processes and phenomena and offered unique opportunities to answer questions related to human speciation (The Chimpanzee Sequencing and Analysis Consortium, 2005). In example, a major question in this line of research is associated with the identification of the class of genes that played the most prominent role in the acquisition of traits that are unique and specific to humans. However, the simple comparison between genomes such as that of the human and the chimpanzee provides only limited information, given the relatively low nucleotide divergence between these species. Such analyses usually take into consideration the frequency of non synonymous nucleotide substitutions that occur between different genomes. The later refer to changes in the primary sequences of genes that result in differences in the correspond- ing amino-acids and thus, in the resulting protein products. Therefore, novel comparative genomic approaches have to be developed aiming to reduce the number genes potentially asso- ciated with “human-specific” traits and facilitate their analysis. Methods Here, we have tried to apply such a simple comparative ge- nomic-population genetics approach that takes into considera- tion both the rate of non synonymous nucleotide substitutions between chimpanzees and humans in a given gene and the de- gree of variation of single nucleotide polymorphisms (SNPs) in two remotely related human populations. Such remotely related human populations are expected to have only minimal interac- tion with each other over the course of human history and therefore, to have only restricted genetic exchanges. Our ap-