Positive Selection on Genes in Humans as Compared to Chimpanzees

Margaret A Bakewell, University of Michigan, Ann Arbor, Michigan, USA
Jianzhi Zhang, University of Michigan, Ann Arbor, Michigan, USA

Published online: July 2008

DOI: 10.1002/9780470015902.a0020856

Positive selection has been identified and extensively studied in many human genes. In contrast, positive selection in the closest human relative, chimpanzee, has been largely unstudied until recently. With the complete sequencing of the human and chimpanzee genomes, a comparison of the types and numbers of genes that underwent positive selection in the two species is possible. The types of genes under positive selection in human and chimpanzee are different with regard to gene function, but no particular type accounts for a large part of this difference. However, significantly more genes experienced positive selection in the chimpanzee lineage than in the human lineage.

Keywords: positive selection; human; chimpanzee; molecular evolution; population size

Figure 1. Functional differences between human and chimp unshared positively selected genes (PSGs). Human and chimp PSGs show a significantly larger difference in distribution across (a) biological process groups and (b) molecular function groups than by chance (P=0.84% and 0.26%, respectively; one-tail randomization test). The 373 unshared human and chimp PSGs were randomly divided into 147 human PSGs and 226 chimp PSGs and 2 was computed. This procedure was repeated 10 000 times to obtain the null distribution of 2. The bars show the frequency distribution of the 2 values in the random divisions and the arrows show the observed 2 values. Here the randomization test is superior to the standard 2 test because the functional groups are not independent from one another and a single gene may belong to more than one group. Similar results are obtained when the seven shared PSGs are included. (c) Biological process and molecular function groups show the greatest differences between human and chimp unshared PSGs, as ranked by individual 2 values. Shown here are the groups that each contributes at least 2% of the total 2 of all groups. Groups with a higher frequency of human PSGs than chimp PSGs are in red, whereas those with a higher frequency of chimp PSGs than human PSGs are in blue. Reproduced from Bakewell et al. (2007).
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 References
    Arbiza L, Dopazo J and Dopazo H (2006) Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLOS Computational Biology 2: e38.
    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.
    Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87.
    Clark AG, Glanowski S, Nielsen R et al. (2003) Inferring nonneutral evolution from human–chimp–mouse orthologous gene trios. Science 302: 1960–1963.
    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.
    International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851–861.
    International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931–945.
    King MC and Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107–116.
    Rhesus Macaque Genome Sequencing and Analysis Consortium (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222–234.
    Rooney AP and Zhang J (1999) Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive Darwinian selection? Molecular Biology and Evolution 16: 706–710.
    Sabeti PC, Schaffner SF, Fry B et al. (2006) Positive natural selection in the human lineage. Science 312: 1614–1620.
    Sabeti PC, Walsh E, Schaffner SF et al. (2005) The case for selection at CCR5-Delta32. PLoS Biology 3: e378.
    Stephens JC, Reich DE, Goldstein DB et al. (1998) Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes. American Journal of Human Genetics 62: 1507–1515.
    Torgerson DG, Kulathinal RJ and Singh RS (2002) Mammalian sperm proteins are rapidly evolving: evidence of positive selection in functionally diverse genes. Molecular Biology and Evolution 19: 1973–1980.
    Varki A and Altheide TK (2005) Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome Research 15: 1746–1758.
    Zhang J (2004) Frequent false detection of positive selection by the likelihood method with branch-site models. Molecular Biology and Evolution 21: 1332–1339.
    Zhang J, Nielsen R and Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution 22: 2472–2479.
    Zhang J and Webb DM (2004) Rapid evolution of primate antiviral enzyme APOBEC3G. Human Molecular Genetics 13: 1785–1791.
 Further Reading
    Chen FC and Li WH (2001) Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics 68: 444–456.
    Goodman M, Porter CA, Czelusniak J et al. (1998) Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Molecular Phylogenetics and Evolution 9: 585–598.
    book Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
    book Nei M and Kumar S (2000) Molecular Evolution and Phylogenetics. New York: Oxford University Press.
    Nielsen R (2005) Molecular signatures of natural selection. Annual Review of Genetics 39: 197–218.
    Olson MV and Varki A (2003) Sequencing the chimpanzee genome: insights into human evolution and disease. Nature Reviews. Genetics 4: 20–28.
    Shi P, Bakewell MA and Zhang J (2006) Did brain-specific genes evolve faster in humans than in chimpanzees? Trends in Genetics 22: 608–613.
    Takahata N, Satta Y and Klein J (1995) Divergence time and population size in the lineage leading to modern humans. Theoretical Population Biology 48: 198–221.
    Taudien S, Ebersberger I, Glockner G and Platzer M (2006) Should the draft chimpanzee sequence be finished? Trends in Genetics 22: 122–125.
    Wall JD (2003) Estimating ancestral population sizes and divergence times. Genetics 163: 395–404.

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Adaptive Evolution | Selection and Variation | Human Evolution
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Article Title: Positive Selection on Genes in Humans as Compared to Chimpanzees
 
How to Cite close
Bakewell, Margaret A, and Zhang, Jianzhi(Jul 2008) Positive Selection on Genes in Humans as Compared to Chimpanzees. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020856]