Comparing the Human and Chimpanzee Genomes


The idea that chimpanzees share a close relationship with humans extends as far back as the early nineteenth century. However, only during the last 50 years has mounting genetic evidence demonstrated that chimpanzees are more closely related to humans than to gorillas or other apes. Whole‐genome sequences now available for both human and common chimpanzee confirm their close genetic relationship, whereas also identifying differences that may have contributed to the emergence of species‐specific phenotypes. To better understand the potential phenotypic significance of these differences, additional comparative genomic data from other primate, mammalian and vertebrate taxa are required.

Keywords: phylogeny; Pongidae; Hominidae; phenotype; Homo (Pan)

Figure 1.

(a) Estimated pairwise genomic identity between humans and rhesus macaques, humans and chimpanzees and between two chromosomes from a single human individual. Data are from whole genome comparisons as reported in Consortium , Gibbs et al. and Levy et al. . (b) Estimated pairwise identity between humans and chimpanzees, humans and gorillas and humans and orangutans based on comparisons of the approximately 95 kb BRCA1‐encoding region as reported in Pavlicek et al. .



Bakewell MA, Shi P and Zhang J (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences of the USA 104: 7489–7494.

Britten RJ (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proceedings of the National Academy of Sciences of the USA 99: 13633–13635.

Consortium CSaA (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87.

Desmond A (1989) The Politics of Evolution. Chicago: University of Chicago Press.

Elango N, Thomas JW and Yi SV (2006) Variable molecular clocks in hominoids. Proceedings of the National Academy of Sciences of the USA 103: 1370–1375.

Gibbs RA, Rogers J, Katze MG et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222–234.

Goodman M (1962) Immunochemistry of the primates and primate evolution. Annals of the New York Academy of Sciences 102: 219–234.

Goodman M (1963) Man's place in the phylogeny of the primates as reflected in serum proteins. In: Washburn SL (ed.) Classification and Human Evolution, pp. 204–234. Chicago: Aldine.

Goodman M, Barnabas J, Matsuda G and Moore GW (1971) Molecular evolution in the descent of man. Nature 233: 604–613.

Goodman M, Grossman LI and Wildman DE (2005) Moving primate genomics beyond the chimpanzee genome. Trends in Genetics 21: 511–517.

Hahn MW, Demuth JP and Han SG (2007) Accelerated rate of gene gain and loss in primates. Genetics 177: 1941–1949.

Haygood R, Fedrigo O, Hanson B, Yokoyama KD and Wray GA (2007) Promoter regions of many neural‐ and nutrition‐related genes have experienced positive selection during human evolution. Nature Genetics 39: 1140–1144.

Hoyer BH, van de Velde NW, Goodman M and Roberts RB (1972) Examination of hominid evolution by DNA sequence homology. Journal of Human Evolution 1: 645–648.

Kouprina N, Pavlicek A, Mochida GH et al. (2004) Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PLoS Biology 2: E126.

Levy S, Sutton G, Ng PC et al. (2007) The diploid genome sequence of an individual human. PLoS Biology 5: e254.

McConkey EH and Goodman M (1997) A Human Genome Evolution Project is needed. Trends in Genetics 13: 350–351.

Mills RE, Bennett EA, Iskow RC et al. (2006) Recently mobilized transposons in the human and chimpanzee genomes. American Journal of Human Genetics 78: 671–679.

Miyamoto MM, Slightom JL and Goodman M (1987) Phylogenetic relations of humans and African apes from DNA sequences in the psi eta‐globin region. Science 238: 369–373.

Nuttall GHF (1904) Blood Immunity and Blood Relationship. Cambridge: Cambridge University Press.

Patterson N, Richter DJ, Gnerre S, Lander ES and Reich D (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441: 1103–1108.

Pavlicek A, Noskov VN, Kouprina N et al. (2004) Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition. Human Molecular Genetics 13: 2737–2751.

Polavarapu N, Bowen NJ and McDonald JF (2006) Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biology 7: R51.

Prabhakar S, Noonan JP, Paabo S and Rubin EM (2006) Accelerated evolution of conserved noncoding sequences in humans. Science 314: 786.

Sibley CG and Ahlquist JE (1984) The phylogeny of the hominoid primates, as indicated by DNA–DNA hybridization. Journal of Molecular Evolution 20: 2–15.

Wildman DE and Goodman M (2004) Humankind's place in phylogenetic classification of living primates. In: Wasser SP (ed.) Evolutionary Theory and Processes: Modern Horizons, pp. 293–311. Dordrecht: Kluwer Academic Publishers.

Wildman DE, Uddin M, Liu G, Grossman LI and Goodman M (2003) Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo. Proceedings of the National Academy of Sciences of the USA 100: 7181–7188.

Further Reading

Caccone A and Powell JR (1989) DNA divergence among hominoids. Evolution 43: 925–942.

Gazave E, Marqués‐Bonet T, Fernando O, Charlesworth B and Navarro A (2007) Patterns and rates of intron divergence between humans and chimpanzees. Genome Biology 8: R21.

Goodman M (1961) The role of immunochemical differences in the phyletic development of human behavior. Human Biology 33: 131–162.

Goodman M (1962) Evolution of the immunologic species specificity of human serum proteins. Human Biology 34: 104–150.

Goodman M (1963) Serological analysis of the systematics of recent hominoids. Human Biology 35: 377–436.

Kehrer‐Sawatzki H and Cooper DN (2007) Structural divergence between the human and chimpanzee genomes. Human Genetics 120: 759–778.

Kehrer‐Sawatzki H and Cooper DN (2007) Understanding the recent evolution of the human genome: insights from human‐chimpanzee genome comparisons. Human Mutation 28: 99–130.

Sakate R, Suto Y, Imanishi T et al. (2007) Mapping of chimpanzee full‐length cDNAs onto the human genome unveils large potential divergence of the transcriptome. Gene 399: 1–10.

Sibley CG and Ahlquist JE (1987) DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. Journal of Molecular Evolution 26: 99–121.

Wetterbom A, Sevov M, Cavelier L and Bergström TF (2006) Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution. Journal of Molecular Evolution 63: 682–690.

Wildman DE, Uddin M, Opazo JC et al. (2007) Genomics, biogeography, and the diversification of placental mammals. Proceedings of the National Academy of Sciences of the USA 104: 14395–14400.

Zuckerkandl E, Jones RT and Pauling L (1960) A comparison of animal hemoglobins by tryptic peptide pattern analysis. Proceedings of the National Academy of Sciences of the USA 46: 1349–1360.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Uddin, Monica, Wildman, Derek E, and Goodman, Morris(Jul 2008) Comparing the Human and Chimpanzee Genomes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020743]