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MBE Advance Access originally published online on March 10, 2004
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Mol. Biol. Evol. 21(5):936-944. 2004
DOI: 10.1093/molbev/msh100
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Human-Specific Amino Acid Changes Found in 103 Protein-Coding Genes

Takashi Kitano*, Yu-Hua Liu*,1, Shintaroh Ueda{dagger} and Naruya Saitou*

* Division of Population Genetics, National Institute of Genetics, Mishima, Japan
{dagger} Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan

E-mail: nsaitou{at}genes.nig.ac.jp.

We humans have many characteristics that are different from those of the great apes. These human-specific characters must have arisen through mutations accumulated in the genome of our direct ancestor after the divergence of the last common ancestor with chimpanzee. Gene trees of human and great apes are necessary for extracting these human-specific genetic changes. We conducted a systematic analysis of 103 protein-coding genes for human, chimpanzee, gorilla, and orangutan. Nucleotide sequences for 18 genes were newly determined for this study, and those for the remaining genes were retrieved from the DDBJ/EMBL/GenBank database. The total number of amino acid changes in the human lineage was 147 for 26,199 codons (0.56%). The total number of amino acid changes in the human genome was, thus, estimated to be about 80,000. We applied the acceleration index test and Fisher's synonymous/nonsynonymous exact test for each gene tree to detect any human-specific enhancement of amino acid changes compared with ape branches. Six and two genes were shown to have significantly higher nonsynonymous changes at the human lineage from the acceleration index and exact tests, respectively. We also compared the distribution of the differences of the nonsynonymous substitutions on the human lineage and those on the great ape lineage. Two genes were more conserved in the ape lineage, whereas one gene was more conserved in the human lineage. These results suggest that a small proportion of protein-coding genes started to evolve differently in the human lineage after it diverged from the ape lineage.

Key Words: humanness • positive selection • hominoids • gene tree


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