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Neutral Evolution

  • Naruya Saitou
Chapter
Part of the Computational Biology book series (COBO, volume 17)

Abstract

Neutral evolution is the default process of the genome changes. This is because our world is finite and the randomness is important when we consider history of a finite world. The random nature of DNA propagation is discussed using branching process, coalescent process, Markov process, and diffusion process. Expected evolutionary patterns under neutrality are then discussed on fixation probability, rate of evolution, and amount of DNA variation kept in population. We then discuss various features of neutral evolution starting from evolutionary rates, synonymous and nonsynonymous substitutions, junk DNA, and pseudogenes.

Keywords

Gene Copy Evolutionary Rate Nonsynonymous Substitution Fixation Probability Neutral Evolution 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Kimura, M. (1983). The neutral theory of molecular evolution. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
  2. 2.
    Nei, M. (1987). Molecular evolutionary genetics. New York: Columbia University Press.Google Scholar
  3. 3.
    Mouse Genome Sequencing Consortium. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520–562.CrossRefGoogle Scholar
  4. 4.
    International Chicken Genome Sequencing Consortium. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695–716.CrossRefGoogle Scholar
  5. 5.
    Kimura, M. (1968). Evolutionary rate at the molecular level. Nature, 217, 624–626.CrossRefGoogle Scholar
  6. 6.
    Bonner, J. T. (2008). The social amoebae: The biology of cellular slime molds. Princeton: Princeton University Press.Google Scholar
  7. 7.
    Cook, R. E. (1979). Asexual reproduction: A further consideration. American Naturalist, 113, 769–772.CrossRefGoogle Scholar
  8. 8.
    Ewens, W. J. (1979). Mathematical population genetics. Berlin/New York: Springer.MATHGoogle Scholar
  9. 9.
    Watson, H. W., & Galton, F. (1874). On the probability of the extinction of families. Journal of Anthropological Institute, 4, 138–144.Google Scholar
  10. 10.
    Haccou, P., Jagers, P., & Vatutin, V. A. (2005). Branching processes: Variation, growth, and extinction of populations. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
  11. 11.
    Crow, J. F. (1989). The estimation of inbreeding from isonymy. Human Biology, 61, 935–948.Google Scholar
  12. 12.
    Saitou, N. (1983). An attempt to estimate the migration pattern in Japan by surname data (in Japanese). Jinruigaku Zasshi, 91, 309–322.Google Scholar
  13. 13.
    Fisher, R. A. (1930). The distribution of gene ratios for rare mutations. Proceedings of Royal Society of Edinburgh, 50, 205–220.Google Scholar
  14. 14.
    Feller, W. (1968). Introduction to probability theory and its applications (3rd ed., Vol. 1). New York: Wiley.MATHGoogle Scholar
  15. 15.
    Crow, J. F., & Kimura, M. (1970). An introduction to population genetics theory. New York: Prentice-Hall.Google Scholar
  16. 16.
    Howell, N. (1979). Demography of the Dobe !Kung. New York: Academic.Google Scholar
  17. 17.
    Saitou, N., Shimizu, H., & Omoto, K. (1988). On the effect of the fluctuating population size on the age of a mutant gene. Journal of the Anthropological Society of Nippon, 96, 449–458.CrossRefGoogle Scholar
  18. 18.
    Kingman, J. F. C. (1982). On the genealogy of large populations. Journal of Applied Probability, 19A, 27–43.CrossRefMathSciNetGoogle Scholar
  19. 19.
    Hudson, R. R. (1983). Testing the constant rate neutral allele model with protein sequence data. Evolution, 37, 203–217.CrossRefGoogle Scholar
  20. 20.
    Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437–460.Google Scholar
  21. 21.
    Fu, Y.-X. (2006). Exact coalescent for the Wright-Fisher model. Theoretical Population Biology, 69, 385–394.CrossRefMATHGoogle Scholar
  22. 22.
    Hein, J., Schierup, M. H., & Wiuf, C. (2005). Gene genealogies, variation, and evolution – a primer in coalescent theory. Oxford: Oxford University Press.MATHGoogle Scholar
  23. 23.
    Wakeley, J. (2008). Coalescent theory: An introduction. Greenwood Village: Roberts & Co.Google Scholar
  24. 24.
    Kimura, M. (1955). Solution of a process of random genetic drift with a continuous model. Proceedings of National Academy of Sciences USA, 41, 144–150.CrossRefMATHGoogle Scholar
  25. 25.
    Kimura, M. (1964). Diffusion models in population genetics. Journal of Applied Probability, 1, 177–232.CrossRefMATHMathSciNetGoogle Scholar
  26. 26.
    Kimura, M., & Ohta, T. (1971). Protein polymorphism as a phase of molecular evolution. Nature, 229, 467–469.CrossRefGoogle Scholar
  27. 27.
    Kimura, M., & Crow, J. F. (1964). The number of alleles that can be maintained in a finite population. Genetics, 49, 725–738.Google Scholar
  28. 28.
    Kimura, M. (1969). The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics, 61, 893–903.Google Scholar
  29. 29.
    Kimura, M. (1968). Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles. Genetical Research, 1, 247–269.CrossRefGoogle Scholar
  30. 30.
    Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004). Detection of large-scale variation in the human genome. Nature Genetics, 36, 949–951.CrossRefGoogle Scholar
  31. 31.
    Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Maner, S., Massa, H., Walker, M., Chi, M., et al. (2004). Large-scale copy number polymorphism in the human genome. Science, 305, 525–528.CrossRefGoogle Scholar
  32. 32.
    Zuckerkandl, E., & Pauling, L. (1965). Evolutionary divergence and convergence in proteins. In V. Bryson & H. J. Vogel (Eds.), Evolving genes and proteins (pp. 97–166). New York: Academic.Google Scholar
  33. 33.
    Kimura, M., & Ohta, T. (1973). Mutation and evolution at the molecular level. Genetics (Supplement), 73, 19–35.Google Scholar
  34. 34.
    Wu, C.-I., & Li, W.-H. (1985). Evidence for higher rates of nucleotide substitution in rodents than in man. Proceedings of the National Academy of Sciences of the United States of America, 82, 1741–1745.CrossRefGoogle Scholar
  35. 35.
    Li, W.-H., & Wu, C.-I. (1987). Rates of nucleotide substitution are evidently higher in rodents than in man. Molecular Biology and Evolution, 4, 74–82.Google Scholar
  36. 36.
    Rhesus Macaque Sequencing and Analysis Consortium. (2007). Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316, 222–234.CrossRefGoogle Scholar
  37. 37.
    Abe, K., Noguchi, H., Tagawa, K., Yuzuriha, M., Toyoda, A., Kojima, T., Ezawa, K., Saitou, N., Hattori, M., Sakaki, Y., Moriwaki, K., & Shiroishi, T. (2004). Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC end sequence-SNP analysis. Genome Research, 14, 2239–2247.CrossRefGoogle Scholar
  38. 38.
    Hendriks, W., Leunissen, J., Nevo, E., Bloemendal, H., & de Jong, W. W. (1987). The lens protein alpha A-crystallin of the blind mole rat, Spalax ehrenbergi: Evolutionary change and functional constraints. Proceedings of the National Academy of Sciences of the United States of America, 84, 5320–5324.CrossRefGoogle Scholar
  39. 39.
    Ikemura, T. (1985). Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution, 2, 13–34.Google Scholar
  40. 40.
    Ohno, S. (1972). So much “junk” DNA in our genome. Brookhaven Symposium in Biology, 23, 366–370.Google Scholar
  41. 41.
    International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature, 431, 931–945.CrossRefGoogle Scholar
  42. 42.
    Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., & Haussler, D. (2004). Ultraconserved elements in the human genome. Science, 304, 1321–1325.CrossRefGoogle Scholar
  43. 43.
    Takahashi, M., & Saitou, N. (2012). Identification and characterization of lineage-specific highly conserved noncoding sequences in mammalian genomes. Genome Biology and Evolution, 4, 641–657.CrossRefGoogle Scholar
  44. 44.
    Bejerano, G., Lowe, C. B., Ahituv, N., King, B., Siepel, A., Salama, S. R., Rubin, E. M., Kent, W. J., & Haussler, D. (2006). A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature, 441, 87–90.CrossRefGoogle Scholar
  45. 45.
    Sasaki, T., Nishihara, H., Hirakawa, M., Fujimura, K., Tanaka, M., Kokubo, N., Kimura-Yoshida, C., Matsuo, I., Sumiyama, K., Saitou, N., Shimogori, T., & Okada, N. (2008). Possible involvement of SINEs in mammalian-specific brain formation. Proceedings of the National Academy of Sciences of the United States of America, 105, 4220–4225.CrossRefGoogle Scholar
  46. 46.
    Johnson, J. M., Edwards, S., Shoemaker, D., & Schadt, E. E. (2005). Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments. Trends in Genetics, 21, 93–102.CrossRefGoogle Scholar
  47. 47.
    Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigo, R., Gingeras, T. R., et al. (2007). Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project. Nature, 447, 799–816.CrossRefGoogle Scholar
  48. 48.
    van Bakel, H., Nislow, C., Blencowe, B. J., & Hughes, T. R. (2010). Most “dark matter” transcripts are associated with known genes. PLoS Biology, 8, e1000371.CrossRefGoogle Scholar
  49. 49.
    Li, W.-H., Gojobori, T., & Nei, M. (1981). Pseudogenes as paradigm of the neutral evolution. Nature, 292, 237–239.CrossRefGoogle Scholar
  50. 50.
    King, J. L., & Jukes, T. H. (1969). Non-Darwinian evolution. Science, 164, 788–798.CrossRefGoogle Scholar
  51. 51.
    Lehninger, A. L. (1975). Biochemistry. New York: Worth Publishers.Google Scholar
  52. 52.
    Toyohara, H., Nakata, T., Touhata, K., Hashimoto, H., Kinoshita, M., Sakaguchi, M., Nishikimi, M., Yagi, K., Wakamatsu, Y., & Ozato, K. (1996). Transgenic expression of L-gulono-gamma-lactone oxidase in medaka (Oryzias latipes), a teleost fish that lacks this enzyme necessary for L-ascorbic acid biosynthesis. Biochemical and Biophysical Research Communications, 223, 650–653.CrossRefGoogle Scholar
  53. 53.
    Nishikimi, M., Fukuyama, R., Minoshima, S., Shimizu, N., & Yagi, K. (1994). Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man. Journal of Biological Chemistry, 269, 13685–13688.Google Scholar
  54. 54.
    Cole, S. T., & others. (2001). Massive gene decay in the leprosy bacillus. Nature, 409, 1007–1011.Google Scholar
  55. 55.
    Saitou, N. (2007). Genomu Shinkagaku Nyumon (written in Japanese, meaning ‘Introduction to evolutionary genomics’). Tokyo: Kyoritsu Shuppan.Google Scholar
  56. 56.
    Babarinde, I. A., & Saitou, N. (2013). Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders. Genome Biology and Evolution (advance access).Google Scholar
  57. 57.
    Ohtsuka, H., Oyanagi, M., Mafune, Y., Miyashita, N., Shiroishi, T., Moriwaki, K., Kominami, R., & Saitou, N. (1996). The presence/absence polymorphism and evolution of p53 pseudogene within the genus Mus. Molecular Phylogenetics and Evolution, 5, 548–556.CrossRefGoogle Scholar
  58. 58.
    Nei, M. (2013a). Mutation-driven evolution. Oxford: Oxford University Press.Google Scholar
  59. 59.
    Takahatan, N. (1993). Allelic genealogy and human evolution. Molecular Biology and Evolution, 10, 2–22.Google Scholar

Copyright information

© Springer-Verlag London 2013

Authors and Affiliations

  • Naruya Saitou
    • 1
  1. 1.Division of Population GeneticsNational Institute of Genetics (NIG)MishimaJapan

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