The Journal of Heredity 2001:92(6)
© 2001 The American Genetic Association 92:481-489
Genomic Divergence Between Human and Chimpanzee Estimated from Large-Scale Alignments of Genomic Sequences
From the Department of Life Science, National Tsing Hua University, Taiwan (Chen and Tzeng), and Department of Ecology and Evolution (Chen, Wang, and Li) and Committee on Genetics (Vallender), University of Chicago, Chicago, Illinois.
Address correspondence to Wen-Hsiung Li, Department of Ecology and Evolution, University of Chicago, 1101 East 57th St., Chicago, IL 60637, or e-mail: whli{at}uchicago.edu.
To study the genomic divergence between human and chimpanzee, large-scale genomic sequence alignments were performed. The genomic sequences of human and chimpanzee were first masked with the RepeatMasker and the repeats were excluded before alignments. The repeats were then reinserted into the alignments of nonrepetitive segments and entire sequences were aligned again. A total of 2.3 million base pairs (Mb) of genomic sequences, including repeats, were aligned and the average nucleotide divergence was estimated to be 1.22%. The Jukes–Cantor (JC) distances (nucleotide divergences) in nonrepetitive (1.44 Mb) and repetitive sequences (0.86 Mb) are 1.14% and 1.34%, respectively, suggesting a slightly higher average rate in repetitive sequences. Annotated coding and noncoding regions of homologous chimpanzee genes were also retrieved from GenBank and compared. The average synonymous and nonsynonymous divergences in 88 coding genes are 1.48% and 0.55%, respectively. The JC distances in intron, 5' flanking, 3' flanking, promoter, and pseudogene regions are 1.47%, 1.41%, 1.68%, 0.75%, and 1.39%, respectively. It is not clear why the genetic distances in most of these regions are somewhat higher than those in genomic sequences. One possible explanation is that some of the genes may be located in regions with higher mutation rates.
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