The Chimpanzee Genome Project

David N Cooper, Cardiff University, Cardiff, UK
Hildegard Kehrer‐Sawatzki, University of Ulm, Ulm, Germany

Published online: July 2008

DOI: 10.1002/9780470015902.a0020753

In 2005, a draft genome sequence of the common chimpanzee (Pan troglodytes) was published by the Chimpanzee Sequencing & Analysis Consortium (CSAC). This sequence has allowed us to catalogue the genetic differences which have accumulated since humans and chimpanzees diverged from their common ancestor 5–7 million years ago. These differences include approximately 35 million single-nucleotide substitutions and 5 million insertion/deletion events within the alignable regions. This catalogue of differences has been used to assess the magnitude and regional variation of the mutational forces which have shaped the two genomes, and to measure the strength of positive and negative selection acting on their genes.

Keywords: chimpanzee genome sequencing; polymorphism; nucleotide divergence; positive selection; rapid evolution; human–chimpanzee differences

Figure 1. Human–chimpanzee divergence in 1-Mb segments across all chromosomes shown in the form of a box plot. The edges of the box indicate quartiles, the notches, the standard error of the median whereas the vertical bars denote the range of divergence. The X- and Y-chromosomes are clearly outliers. However, significant local variation within each of the autosomes was noted. Reprinted by Macmillan Publishers Ltd with permission from Chimpanzee Sequencing and Analysis Consortium et al. (2005).
Figure 2. Regional variation in divergence rates comparing human and chimpanzee chromosome 1. Human–chimpanzee divergence, G+C content and human recombination rates in sliding 1-Mb windows along human and chimpanzee chromosome 1. Close to the telomere of the short arm of chromosome 1 (1p), the divergence and G+C content were clearly elevated. Within the chromosome, regions of low G+C content and high divergence frequently colocalize with dark G bands. Reprinted by Macmillan Publishers Ltd with permission from Chimpanzee Sequencing and Analysis Consortium et al. (2005).
Figure 3. Divergence rates versus G+C content for 1-Mb segments across the autosomes. Depending on the recombination rate, the relationship between divergence and G+C content varies. In those genomic regions with recombination rates less than 0.8 cM Mb–1 (blue), an inverse relationship was noted. However, there is a tendency for regions of high divergence to be (G+C)-poor and low-divergence regions to be more frequently (G+C)-rich. In regions with recombination rates greater than 2.0 cM Mb–1, whether within 10 Mb (red) or proximal (green) of chromosome ends, both divergence and G+C content appear to be uniformly high. Reprinted by Macmillan Publishers Ltd with permission from Chimpanzee Sequencing and Analysis Consortium et al. (2005).
Figure 4. Length distribution of large indel events (>15 kb) determined using paired-end sequences from chimpanzee mapped against the human genome. Both the total number of candidate human insertions/chimpanzee deletions (green) and the number of bases altered (yellow) are shown. Reprinted by Macmillan Publishers Ltd with permission from Chimpanzee Sequencing and Analysis Consortium et al. (2005).
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 References
    Ashburner M, Ball CA, Blake JA et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25: 25–29.
    Azevedo L, Suriano G, van Asch B, Harding RM and Amorim A (2006) Epistatic interactions: how strong in disease and evolution? Trends in Genetics 22: 581–585.
    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.
    Chen JM, Montier T and Férec C (2001) Molecular pathology and evolutionary and physiological implications of pancreatitis-associated cationic trypsinogen mutations. Human Genetics 109: 245–252.
    Cheng Z, Ventura M, She X et al. (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437: 88–93.
    Chimpanzee Sequencing and Analysis Consortium, Mikkelsen TS, Hillier LW et al. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87.
    Dorus S, Vallender EJ, Evans PD et al. (2004) Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 119: 1027–1040.
    Enard W and Pääbo S (2004) Comparative primate genomics. Annual Review of Genomics and Human Genetics 5: 351–378.
    Enard W, Przeworski M, Fisher SE et al. (2002) Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418: 869–872.
    Fay JC, Wyckoff GJ and Wu CI (2001) Positive and negative selection on the human genome. Genetics 158: 1227–1234.
    Ferrer-Costa C, Orozco M and de la Cruz X (2007) Characterization of compensated mutations in terms of structural and physico-chemical properties. Journal of Molecular Biology 365: 249–256.
    Galtier N and Duret L (2007) Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends in Genetics 23: 273–277.
    Gao L and Zhang J (2003) Why are some human disease-associated mutations fixed in mice? Trends in Genetics 19: 678–681.
    Gilad Y, Man O and Glusman G (2005) A comparison of the human and chimpanzee olfactory receptor gene repertoires. Genome Research 15: 224–230.
    Gilad Y, Oshlack A, Smyth GK, Speed TP and White KP (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242–245.
    Han K, Lee J, Meyer TJ et al. (2007) Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genetics 3: 1939–1949.
    Harris RA, Rogers J and Milosavljevic A (2007) Human-specific changes of genome structure detected by genomic triangulation. Science 316: 235–237.
    Hedges DJ, Callinan PA, Cordaux R et al. (2004) Differential alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Research 14: 1068–1075.
    Hellmann I, Ebersberger I, Ptak SE, Pääbo S and Przeworski M (2003) A neutral explanation for the correlation of diversity with recombination rates in humans. American Journal of Human Genetics 72: 1527–1535.
    International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931–945.
    International Human Genome Sequencing Consortium, Lander ES, Linton LM et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–920.
    Jensen-Seaman MI, Furey TS, Payseur BA et al. (2004) Comparative recombination rates in the rat, mouse, and human genomes. Genome Research 14: 528–538.
    Kvikstad EM, Tyekucheva S, Chiaromonte F and Makova KD (2007) A macaque's-eye view of human insertions and deletions: differences in mechanisms. PLoS Computational Biology 3: 1772–1782.
    Lercher MJ and Hurst LD (2002) Human SNP variability and mutation rate are higher in regions of high recombination. Trends in Genetics 18: 337–340.
    Li WH, Yi S and Makova K (2002) Male-driven evolution. Current Opinion in Genetics & Development 12: 650–656.
    Marais G (2003) Biased gene conversion: implications for genome and sex evolution. Trends in Genetics 19: 330–338.
    Messer PW and Arndt PF (2007) The majority of recent short DNA insertions in the human genome are tandem duplications. Molecular Biology and Evolution 24: 1190–1197.
    Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520–562.
    Newman TL, Tuzun E, Morrison VA et al. (2005) A genome-wide survey of structural variation between human and chimpanzee. Genome Research 15: 1344–1356.
    Nielsen R, Bustamante C, Clark AG et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology 3: e170.
    Noonan JP, Coop G, Kudaravalli S et al. (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314: 1113–1118.
    Rat Genome Sequencing Project Consortium, Gibbs RA, Weinstock GM et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493–521.
    Reich DE, Schaffner SF, Daly MJ et al. (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nature Genetics 32: 135–142.
    Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222–234.
    Schroeder SA, Gaughan DM and Swift M (1995) Protection against bronchial asthma by CFTR F508 mutation: a heterozygote advantage in cystic fibrosis. Nature Medicine 1: 703–705.
    Taudien S, Ebersberger I, Glöckner G and Platzer M (2006) Should the draft chimpanzee sequence be finished? Trends in Genetics 22: 122–125.
    Taylor J, Tyekucheva S, Zody M, Ciaromonte F and Makova KD (2006) Strong and weak male mutation bias at different sites in the primate genomes: insights from the human–chimpanzee comparison. Molecular Biology and Evolution 23: 565–573.
    Vanhamme L, Paturiaux-Hanocq F, Poelvoorde P et al. (2003) Apolipoprotein L-I is the trypanosome lytic factor of human serum. Nature 422: 83–87.
    Wall JD (2003) Estimating ancestral population sizes and divergence times. Genetics 163: 395–404.
    Watanabe H, Fujiyama A, Hattori M et al. (2004) DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429: 382–388.
    Yohn CT, Jiang Z, McGrath SD et al. (2005) Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biology 3: e110.
 Further Reading
    Disotell TR (2006) ‘Chumanzee’ evolution: the urge to diverge and merge. Genome Biology 7: 240.
    Kelkar YD, Tyekucheva S, Chiaromonte F and Makova KD (2008) The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Research 18: 30–38.
    Pollard KS, Salama SR, King B et al. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genetics 2: e168.
    Prabhakar S, Noonan JP, Pääbo S and Rubin EM (2006) Accelerated evolution of conserved noncoding sequences in humans. Science 314: 786.
    Xing J, Witherspoon DJ, Ray DA, Batzer MA and Jorde LB (2007) Mobile DNA elements in primate and human evolution. American Journal of Physical Anthropology Supplement 45: 2–19.

Related Sub-Topics:

Evolutionary Genomics | Molecular Evolution | Human Evolution | Evolution of Species | Evolution of Coding and Functional Modules
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Article Title: The Chimpanzee Genome Project
 
How to Cite close
Cooper, David N, and Kehrer‐Sawatzki, Hildegard(Jul 2008) The Chimpanzee Genome Project. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020753]