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Chinese Science Bulletin

, Volume 53, Issue 10, pp 1457–1467 | Cite as

Positive Darwinian selection in human population: A review

  • DongDong Wu
  • YaPing Zhang
Review Genetics
  • 75 Downloads

Abstract

This paper reviews a large number of genes under positive Darwinian selection in modern human populations, such as brain development genes, immunity genes, reproductive related genes, perception receptors. The research on the evolutionary property of these genes will provide important insight into human evolution and disease mechanisms. With the increase of population genetics and comparative genomics data, more and more evidences indicate that positive Darwinian selection plays an indispensable role in the origin and evolution of human beings. This paper will also summarize the methods to detect positive selection, analyze the interference factors faced and make suggestions for further research on positive selection.

Keywords

natural selection positive selection population genetics comparative genomics 

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References

  1. 1.
    Darwin C, Wallace A R. On the tendency of the species to form varieties and on the perpetuation of the species by natural means of selection. J Proc Linnaean Soc London (Zoology), 1858, 3: 45–62Google Scholar
  2. 2.
    Nei M. Selectionism and neutralism in molecular evolution. Mol Biol Evol, 2005, 22: 2318–2342PubMedCrossRefGoogle Scholar
  3. 3.
    Nei M, Kumar S. Molecular Evolution and Phlogenetics. New York: Oxiford University, 2000Google Scholar
  4. 4.
    Kimura M. Evolutionary rate at the molecular level. Nature, 1968, 217: 624–626PubMedCrossRefGoogle Scholar
  5. 5.
    King J L, Jukes T H. Non-Darwinian evolution. Science, 1969, 164: 788–798PubMedCrossRefGoogle Scholar
  6. 6.
    Eyre-Walker A. The genomic rate of adaptive evolution. Trends Ecol Evol, 2006, 21(10): 569–575PubMedCrossRefGoogle Scholar
  7. 7.
    Smith N G, Eyre-Walker A. Adaptive protein evolution in Drosophila. Nature, 2002, 415: 1022–1024PubMedCrossRefGoogle Scholar
  8. 8.
    Fay J C, Wyckoff G J, Wu C I. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature, 2002, 415: 1024–1026PubMedCrossRefGoogle Scholar
  9. 9.
    Ohta T. Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci USA, 2002, 99: 16134–16137PubMedCrossRefGoogle Scholar
  10. 10.
    Ohta T. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst, 1992, 23: 263–286CrossRefGoogle Scholar
  11. 11.
    Ohta T. Population size and rate of evolution. J Mol Evol, 1972, 1: 305–314CrossRefGoogle Scholar
  12. 12.
    Wang E T, Kodama G, Baldi, P, et al. Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci USA, 2006, 103: 135–140PubMedCrossRefGoogle Scholar
  13. 13.
    Voight B F, Kudaravalli S, Wen X, et al. A map of recent positive selection in the human genome. PLoS Biol, 2006, 4(3): e72PubMedCrossRefGoogle Scholar
  14. 14.
    Sabeti P C, Schaffner S F, Fry B, et al. Positive natural selection in the human lineage. Science, 2006, 312: 1614–1620PubMedCrossRefGoogle Scholar
  15. 15.
    Nielsen R, Bustamante C, Clark A G, et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol, 2005, 3: e170PubMedCrossRefGoogle Scholar
  16. 16.
    Nielsen R. Molecular signatures of natural selection. Annu Rev Genet, 2005, 39: 197–218PubMedCrossRefGoogle Scholar
  17. 17.
    Bustamante C D, Fledel-Alon A, Williamson S, et al. Natural selection on protein-coding genes in the human genome. Nature, 2005, 437: 1153–1157PubMedCrossRefGoogle Scholar
  18. 18.
    Mekel-Bobrov N, Gilbert S L, Evans P D, et al. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science, 2005, 309: 1720–1722PubMedCrossRefGoogle Scholar
  19. 19.
    Evans P D, Anderson J R, Vallender E J, et al. Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans. Hum Mol Genet, 2004, 13: 489–494PubMedCrossRefGoogle Scholar
  20. 20.
    Zhang J. Evolution of the human ASPM gene, a major determinant of brain size. Genetics, 2003, 165: 2063–2070PubMedGoogle Scholar
  21. 21.
    Kouprina N, Pavlicek A, Mochida G H, et al. Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PLoS Biol, 2004, 2: e126PubMedCrossRefGoogle Scholar
  22. 22.
    Wang Y, Su B. Molecular evolution of microcephalin, a gene determining human brain size. Hum Mol Genet, 2004, 13: 1131–1137PubMedCrossRefGoogle Scholar
  23. 23.
    Evans P D, Anderson J R, Vallender E J, et al. Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size. Hum Mol Genet, 2004, 13: 1139–1145PubMedCrossRefGoogle Scholar
  24. 24.
    Evans P D, Gilbert S L, Mekel-Bobrov N, et al. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science, 2005, 309: 1717–1720PubMedCrossRefGoogle Scholar
  25. 25.
    Zhang J, Webb D M, Podlaha O. Accelerated protein evolution and origins of human-specific features FOXP2 as an example. Genetics, 2002, 162: 1825–18352PubMedGoogle Scholar
  26. 26.
    Enard W, Przeworski M, Fisher SE, et al. Molecular evolution of FOXP2, a gene involved in speech and language. Nature, 2002, 418: 869–872PubMedCrossRefGoogle Scholar
  27. 27.
    Clark A G, Glanowski S, Nielsen R, et al. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science, 2003, 302: 1960–1963PubMedCrossRefGoogle Scholar
  28. 28.
    Wang Y Q, Qian Y P, Yang S, et al. Accelerated evolution of the pituitary adenylate cyclase-activating polypeptide precursor gene during human origin. Genetics, 2005, 170: 801–806PubMedCrossRefGoogle Scholar
  29. 29.
    Hughes A L, Nei M, Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature, 1988, 335: 167–170PubMedCrossRefGoogle Scholar
  30. 30.
    van Valen L. A new evolutionary law. Evol Theory, 1973, 1: 1–30Google Scholar
  31. 31.
    Zhang J, Webb D M. Rapid evolution of primate antiviral enzyme APOBEC3G. Hum Mol Genet, 2004, 13: 1785–1791PubMedCrossRefGoogle Scholar
  32. 32.
    Sawyer S L, Emerman M, Malik H S. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol, 2004, 2: e275PubMedCrossRefGoogle Scholar
  33. 33.
    Sabeti P C, Walsh E, Schaffner S F, et al. The case for selection at CCR5-Δ32. PLoS Biol, 2005, 3: e378PubMedCrossRefGoogle Scholar
  34. 34.
    Bamshad M J, Mummidi S, Gonzalez E, et al. A strong signature of balancing selection in the 5′ cis-regulatory region of CCR5. Proc Natl Acad Sci USA, 2002, 99: 10539–10544PubMedCrossRefGoogle Scholar
  35. 35.
    Maayan S, Zhang L, Shinar E, et al. Evidence for recent selection of the CCR5-Δ32 deletion from differences in its frequency between Ashkenazi and Sephardi Jews. Genes Immun, 2000, 1: 358–361PubMedCrossRefGoogle Scholar
  36. 36.
    Wooding S, Stone A C, Dunn D M, et al. Contrasting effects of natural selection on human and chimpanzee CC chemokine receptor 5. Am J Hum Genet, 2005, 76: 291–301PubMedCrossRefGoogle Scholar
  37. 37.
    Zhang Y W, Oliver A, Ryder, et al. Intra-and interspecific variation of the CCR5 gene in higher primates. Mol Biol Evol, 2003, 20(10): 1722–1729PubMedCrossRefGoogle Scholar
  38. 38.
    Li H P, Zhang Y W, Zhang Y P, et al. Neutrality tests using DNA polymorphism from multiple samples. Genetics, 2003, 163: 1147–1151PubMedGoogle Scholar
  39. 39.
    Swanson W J, Yang Z, Wolfner M F, et al. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc Natl Acad Sci USA, 2001, 98: 2509–2514PubMedCrossRefGoogle Scholar
  40. 40.
    Swanson W J, Vacquier V D. The rapid evolution of reproductive proteins. Nat Rev Genet, 2002, 3: 137–144PubMedCrossRefGoogle Scholar
  41. 41.
    Wyckoff G J, Wang W, Wu C I. Rapid evolution of male reproductive genes in the descent of man. Nature, 2000, 403: 261–263CrossRefGoogle Scholar
  42. 42.
    Shi P, Zhang J, Yang H, et al. Adaptive diversification of bitter taste receptor genes in mammalian evolution. Mol Biol Evol, 2003, 20: 805–814PubMedCrossRefGoogle Scholar
  43. 43.
    Soranzo N, Bufe B, Sabeti P C, et al. Positive selection on a high-sensitivity allele of the human bitter-taste receptor TAS2R16. Curr Biol, 2005, 15: 1257–1265PubMedCrossRefGoogle Scholar
  44. 44.
    Wooding S, Kim U K, Bamshad M J, et al. Natural selection and molecular evolution in PTC, a bitter-taste receptor gene. Am J Hum Genet, 2004, 74: 637–646PubMedCrossRefGoogle Scholar
  45. 45.
    Gilad Y, Bustamante C D, Lancet D, et al. Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am J Hum Genet, 2003, 73: 489–501PubMedCrossRefGoogle Scholar
  46. 46.
    Yu F, Sabeti PC, Hardenbol P, et al. Positive selection of a pre-expansion CAG repeat of the human SCA2 gene. PLoS Genet, 2005, 1(3): e41PubMedCrossRefGoogle Scholar
  47. 47.
    Nachman M W, Crowell S L. Contrasting evolutionary histories of two introns of the duchenne muscular dystrophy gene, Dmd, in Humans. Genetics, 2000, 155: 1855–1864PubMedGoogle Scholar
  48. 48.
    Huttley G A, Easteal S, Southey M C, et al. Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Nat Genet, 2000, 25: 410–413PubMedCrossRefGoogle Scholar
  49. 49.
    Fleming M A, Potter J D, Ramirez C J, et al. Understanding missense mutations in the BRCA1 gene: An evolutionary approach. Proc Natl Acad Sci USA, 2003, 100: 1151–1156PubMedCrossRefGoogle Scholar
  50. 50.
    Wang X, Zhang J, Zhang Y P. Erratic evolution of SRY in higher primates. Mol Biol Evol, 2002, 19: 582–584PubMedGoogle Scholar
  51. 51.
    Kwiatkowski D P. How malaria has affected the human genome and what human genetics can teach us about malaria. Am J Hum Genet, 2005, 77: 171–192PubMedCrossRefGoogle Scholar
  52. 52.
    Ruwende C, Hill A. Glucose-6-phosphate dehydrogenase deficiency and malaria. J Mol Med, 1998, 76: 581–588PubMedCrossRefGoogle Scholar
  53. 53.
    Sabeti P C, Usen S, Farhadian S, et al. CD40L association with protection from severe malaria. Genes Immun, 2002, 3: 286–291PubMedCrossRefGoogle Scholar
  54. 54.
    Baum J, Ward R H, Conway D J. Natural selection on the erythrocyte surface. Mol Biol Evol, 2002, 19: 223–229PubMedGoogle Scholar
  55. 55.
    Zimmerman P A, Woolley I, Masinde G L, et al. Emergence of FY*A null in a plasmodium vivax-endemic region of Papua New Guinea. Proc Natl Acad Sci USA, 1999, 96: 13973–13977PubMedCrossRefGoogle Scholar
  56. 56.
    Hamblin M T, Thompson E E, Rienzo A D. Complex signatures of natural selection at the duffy blood group locus. Am J Hum Genet, 2002, 70: 369–383PubMedCrossRefGoogle Scholar
  57. 57.
    Hamblin M T, Rienzo A D. Detection of the signature of natural selection in humans: Evidence from the Duffy blood group Locus. Am J Hum Genet, 2000, 66: 1669–1679PubMedCrossRefGoogle Scholar
  58. 58.
    Clark N L, Swanson W J. Pervasive adaptive evolution in primate seminal proteins. PLoS Genet, 2005 1(3): e35PubMedCrossRefGoogle Scholar
  59. 59.
    Ding Y C, Chi H C, Grady D L, et al. Evidence of positive selection acting at the human dopamine receptor D4 gene locus. Proc Natl Acad Sci USA, 2002, 99(1): 309–314PubMedCrossRefGoogle Scholar
  60. 60.
    Harpending H, Gregory C. In our genes. Proc Natl Acad Sci USA, 2002, 99(1): 10–12PubMedCrossRefGoogle Scholar
  61. 61.
    Hughes A L. Strength in numbers. Nature, 2002, 417: 795PubMedCrossRefGoogle Scholar
  62. 62.
    Bamshad M, Wooding S. Signature of natural selection in the human genome. Nat Rev Genet, 2003, 4: 99–111PubMedCrossRefGoogle Scholar
  63. 63.
    Ewens W J. The sampling theory of selectively neutral alleles. Theor Popul Biol, 1972, 3: 87–112PubMedCrossRefGoogle Scholar
  64. 64.
    Watterson G A. Heterosis or neutrality? Genetics, 1977, 85: 789–814PubMedGoogle Scholar
  65. 65.
    Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 1989, 123: 585–595PubMedGoogle Scholar
  66. 66.
    Nielsen R, Williamson S, Kim Y, et al. Genomic scans for selective sweeps using SNP data. Genome Res, 2005, 15: 1566–1575PubMedCrossRefGoogle Scholar
  67. 67.
    Fu Y X, Li W H. Statistical tests of neutrality of mutations. Genetics, 1993, 133: 693–709PubMedGoogle Scholar
  68. 68.
    Fu Y X. New statistical tests of neutrality for DNA samples from a population. Genetics, 1996, 143: 557–570PubMedGoogle Scholar
  69. 69.
    Fu Y X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 1997, 147: 915–925PubMedGoogle Scholar
  70. 70.
    Fay J C, Wu C I. Hitchhiking under positive darwinian selection. Genetics, 2000, 155: 1405–1413PubMedGoogle Scholar
  71. 71.
    Lewontin R C, Krakauer J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphism. Genetics, 1973, 74: 175–195PubMedGoogle Scholar
  72. 72.
    Akey J M, Zhang G, Zhang K, et al. Interrogating a high-density SNP Map for signatures of natural selection. Genome Res, 2002, 12: 1805–1814PubMedCrossRefGoogle Scholar
  73. 73.
    Rockman M V, Hahn M W, Soranzo N, et al. Positive selection on a human-specific transcription factor binding site regulating IL4 expression. Curr Biol, 2003, 13: 2118–2123PubMedCrossRefGoogle Scholar
  74. 74.
    Sabeti P C, Reich D E, Higgins J M, et al. Detecting recent positive selection in the human genome from haplotype structure. Nature, 2002, 419: 832–837PubMedCrossRefGoogle Scholar
  75. 75.
    Hanchard N A, Rockett K A, Spencer C, et al. Screening for recently selected alleles by analysis of human haplotype similarity. Am J Hum Genet, 2006, 78: 153–159PubMedCrossRefGoogle Scholar
  76. 76.
    Nielsen R, Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 1998, 148: 929–936PubMedGoogle Scholar
  77. 77.
    Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J Mol Evol, 2000, 51: 423–432PubMedGoogle Scholar
  78. 78.
    Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol, 1998, 15: 568–573PubMedGoogle Scholar
  79. 79.
    Yang Z. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol, 1998, 46: 409–418PubMedCrossRefGoogle Scholar
  80. 80.
    Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol, 2002, 19: 908–917PubMedGoogle Scholar
  81. 81.
    Yang Z, Nielsen R, Goldman N, et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 2000, 155: 431–449PubMedGoogle Scholar
  82. 82.
    Yang Z, Wong W, Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol, 2005, 22: 1107–1118PubMedCrossRefGoogle Scholar
  83. 83.
    Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol, 2005, 22: 2472–2479PubMedCrossRefGoogle Scholar
  84. 84.
    Anisimova M, Bielawski J P, Yang Z. Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol, 2002, 19: 950–958PubMedGoogle Scholar
  85. 85.
    Anisimova M, Bielawski J P, Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol, 2001, 18: 1585–1592PubMedGoogle Scholar
  86. 86.
    Wang H Y, Chien H C, Osada N, et al. Rate of evolution in brain-expressed genes in humans and other primates. PLoS Biol, 2007, 5(2): e13PubMedCrossRefGoogle Scholar
  87. 87.
    Xia X. What amino acid properties affect protein evolution? J Mol Evol, 1998, 47: 557–564PubMedCrossRefGoogle Scholar
  88. 88.
    McClellan D A, McCracken K G. Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains. Mol Biol Evol, 2001, 18: 917–925PubMedGoogle Scholar
  89. 89.
    Woolley S, Johnson J, Smith M J, et al. TreeSAAP: Selection on amino acid properties using phylogenetic trees. Bioinformatics, 2003, 19: 671–672PubMedCrossRefGoogle Scholar
  90. 90.
    McDonald J, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature, 1991, 351: 652–654PubMedCrossRefGoogle Scholar
  91. 91.
    Hudson R, Kreitman M, Aguade M. A Test of neutral molecular evolution based on nucleotide data. Genetics, 1987, 116: 153–159PubMedGoogle Scholar
  92. 92.
    Currat M, Excoffier L, Maddison W, et al. Comment on “ongoing adaptive evolution of ASPM, a brain size determinant in homo sapiens” and “Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans”. Science, 2006, 313: 172aCrossRefGoogle Scholar
  93. 93.
    Mekel-Bobrov N, Posthuma D, Gilbert S L, et al. Response to comment on “Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens” and “Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans”. Science, 2006, 313: 172bCrossRefGoogle Scholar
  94. 94.
    McVean G A, Myers S R, Hunt S, et al. The fine-scale structure of recombination rate variation in the human genome. Science, 2004, 304: 581–584PubMedCrossRefGoogle Scholar
  95. 95.
    Crawford D C, Bhangale T, Li N, et al. Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet, 2004, 36: 700–706PubMedCrossRefGoogle Scholar
  96. 96.
    Reed F A, Tishkoff S A. Positive selection can create false hotspots of recombination. Genetics, 2006, 172: 2011–2014PubMedCrossRefGoogle Scholar
  97. 97.
    Nielsen R. Population genetic analysis of ascertained SNP data. Hum Genomics, 2004, 1: 218–224PubMedGoogle Scholar
  98. 98.
    Haygood R, Fedrigo O, Hanson B, et al. Promoter regions of many neural-and nutrition-related genes have experienced positive selection during human evolution. Nat Genet, 2007, 39(9): 1140–1144PubMedCrossRefGoogle Scholar
  99. 99.
    Chen K, Rajewsky N. Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet, 2006, 38: 1452–1456PubMedCrossRefGoogle Scholar

Copyright information

© Science in China Press and Springer-Verlag GmbH 2008

Authors and Affiliations

  1. 1.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
  2. 2.Laboratory for Conservation and Utilization of Bio-resourceYunnan UniversityKunmingChina
  3. 3.Graduate University of Chinese Academy of SciencesBeijingChina

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