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Mutation

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Introduction to Evolutionary Genomics

Part of the book series: Computational Biology ((COBO,volume 17))

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Abstract

Mutations, the fundamental sources of evolution, are described in detail. They include nucleotide substitutions, insertions/deletions of unique and repeat sequences, recombinations, gene conversions, gene duplications, and mutations affecting phenotypes. Mutation rate estimates and methods to estimate mutation rates are also discussed.

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References

  1. Kato, L., Stanlie, A., Begum, N. A., Kobayashi, M., Aida, M., & Honjo, T. (2012). An evolutionary view of the mechanism for immune and genome diversity. Journal of Immunology, 188, 3559–3566.

    Article  Google Scholar 

  2. Haldane, J. B. S. (1947). The mutation rate of the gene for haemophilia, and its segregation ratios in males and females. Annals of Eugenics 13, 262–271. (cited by Ref. [3])

    Google Scholar 

  3. Crow, J. F. (1997). The high spontaneous mutation rate: Is it a health risk? Proceedings of the National Academy of Sciences of the United States of America, 94, 8380–8386.

    Article  Google Scholar 

  4. Miyata, T., Hayashida, H., Kuma, K., Mitsuyasu, K., & Yasunaga, T. (1987). Male-driven molecular evolution: A model and nucleotide sequence analysis. Cold Spring Harbor Symposia on Quantitative Biology, 52, 863–867.

    Article  Google Scholar 

  5. Topal, M. D., & Fresco, J. R. (1976). Complementary base pairing and the origin of substitution mutations. Nature, 263, 285–289.

    Article  Google Scholar 

  6. The International Chimpanzee Chromosome 22 Consortium. (2004). DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature, 429, 382–388.

    Article  Google Scholar 

  7. Gojobori, T., Li, W.-H., & Graur, D. (1982). Patterns of nucleotide substitution in pseudogenes and functional genes. Journal of Molecular Evolution, 18, 360–369.

    Article  Google Scholar 

  8. Gojobori, T. (1983). Codon substitution in evolution and the “saturation” of synonymous changes. Genetics, 105, 1011–1027.

    Google Scholar 

  9. Saitou, N., & Ueda, S. (1994). Evolutionary rate of insertions and deletions in non-coding nucleotide sequences of primates. Molecular Biology and Evolution, 11, 504–512.

    Google Scholar 

  10. Ophir, R., & Graur, D. (1997). Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene, 205, 191–202.

    Article  Google Scholar 

  11. Winkler, H. (1930). Die Konversion der Gene. Jena: Verlag von Gustav Fischer (written in German).

    Google Scholar 

  12. Lindegren, C. C. (1953). Gene conversion in Saccharomyces. Journal of Genetics, 51, 625–637.

    Article  Google Scholar 

  13. Michell, L. B. (1955). Aberrant recombination of pyridoxine mutants of Neurospora. Proceedings of the National Academy of Sciences of the United States of America, 41, 215–220.

    Article  Google Scholar 

  14. Holliday, R. A. (1964). Mechanism for gene conversion in fungi. Genetic Research Cambridge, 5, 282–304.

    Article  Google Scholar 

  15. Brown, D. D., Wensink, P. C., & Jordan, E. (1972). A comparison of the ribosomal DNA’s of Xenopus laevis and Xenopus mulleri: The evolution of tandem genes. Journal of Molecular Biology, 63, 57–73.

    Article  Google Scholar 

  16. Eickbush, T. H., & Eickbush, D. G. (2007). Finely orchestrated movements: Evolution of ribosomal RNA genes. Genetics, 175, 477–485.

    Article  Google Scholar 

  17. Stephens, C. (1985). Statistical methods of DNA sequence analysis: Detection of intragenic recombination or gene conversion. Molecular Biology and Evolution, 2, 539–556.

    Google Scholar 

  18. Sawyer, S. A. (1989). Statistical tests for detecting gene conversion. Molecular Biology and Evolution, 6, 526–538.

    Google Scholar 

  19. Sawyer, S. A. (1999). GENECONV: A computer package for the statistical detection of gene conversion. Available at http://www.math.wustl.edu/~sawyer

  20. Kawamura, S., Saitou, N., & Ueda, S. (1992). Concerted evolution of the primate immunoglobulin a-gene through gene conversion. Journal of Biological Chemistry, 267, 7359–7367.

    Google Scholar 

  21. International Human Genome Sequencing Consortium. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921.

    Article  Google Scholar 

  22. Mouse Genome Sequencing Consortium. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520–562.

    Article  Google Scholar 

  23. Rat Genome Sequencing Project Consortium. (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428, 493–521.

    Article  Google Scholar 

  24. Rhesus Macaque Genome Sequencing and Analysis Consortium. (2007). Evolutionary and biological insights from the rhesus macaque genome. Science, 316, 222–234.

    Article  Google Scholar 

  25. Benovoy, D., & Drouin, G. (2009). Ectopic gene conversions in the human genome. Genomics, 93, 27–32.

    Article  Google Scholar 

  26. McGrath, C. L., Casola, C., & Hahn, M. W. (2009). Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. Genetics, 182, 615–622.

    Article  Google Scholar 

  27. Ezawa, K., Ikeo, K., Gojobori, T., & Saitou, N. (2010). Evolutionary pattern of gene homogenization between primate-specific paralogs after human and macaque speciation using the 4-2-4 method. Molecular Biology and Evolution, 27, 2152–2171.

    Article  Google Scholar 

  28. Nei, M., Niimura, Y., & Nozawa, M. (2008). The evolution of animal chemosensory receptor gene repertoires: Roles of chance and necessity. Nature Reviews Genetics, 9, 951–963.

    Article  Google Scholar 

  29. Ezawa, K., OOta, S., & Saitou, N. (2006). Genome-wide search of gene conversions in duplicated genes of mouse and rat. Molecular Biology and Evolution, 23, 927–940.

    Article  Google Scholar 

  30. Liu, Y., & West, S. C. (2004). Happy Hollidays: 40th anniversary of the Holliday junction. Nature Reviews Molecular Cell Biology, 5, 937–944.

    Article  Google Scholar 

  31. Ezawa, K., Ikeo, K., Gojobori, T., & Saitou, N. (2011). Evolutionary patterns of recently emerged animal duplogs. Genome Biology and Evolution, 3, 1119–1135.

    Article  Google Scholar 

  32. Winkler, H. (1920). Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. Jena: Fischer (written in German).

    Google Scholar 

  33. Watanabe, Y., et al. (2009). Molecular spectrum of spontaneous de novo mutations in male and female germline cells of Drosophila melanogaster. Genetics, 181, 1035–1043.

    Article  Google Scholar 

  34. Nei, M. (1987). Molecular evolutionary genetics. New York: Columbia University Press.

    Google Scholar 

  35. Haldane, J. B. S. (1949). The rate of mutation of human genes. Hereditas, 35, 267–273.

    Article  Google Scholar 

  36. Gardner, R. J. (1977). A new estimate of the achondroplasia mutation rate. Clinical Genetics, 11, 31–38.

    Article  Google Scholar 

  37. Smithies, O. (1995). Early days of gel electrophoresis. Genetics, 139, 1–4.

    Google Scholar 

  38. Neel, J. V., Satoh, C., Goriki, K., Fujita, M., Takahashi, N., Asakawa, J., & Hazama, R. (1986). The rate with which spontaneous mutation alters the electrophoretic mobility of polypeptides. Proceedings of the National Academy of Sciences of the United States of America, 83, 389–393.

    Article  Google Scholar 

  39. Kondrashov, A. S. (2002). Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutation, 21, 12–27.

    Article  Google Scholar 

  40. Roach, J. C., Glusman, G., Smit, A. F., Huff, C. D., Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L. B., Hood, L., & Galas, D. J. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science, 328, 636–639.

    Article  Google Scholar 

  41. Conrad, D. F., et al. (2011). Variation in genome-wide mutation rates within and between human families. Nature Genetics, 43, 712–715.

    Article  Google Scholar 

  42. Denver, D. R., Morris, K., Lynch, M., & Thomas, W. K. (2004). High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature, 430, 679–682.

    Article  Google Scholar 

  43. Denver, D. R., Dolan, P. C., Wilhelm, L. J., Sung, W., Lucas-Lledó, J. I., Howe, D. K., Lewis, S. C., Okamoto, K., Thomas, W. K., Lynch, M., & Baer, C. F. (2009). A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. Proceedings of the National Academy of Sciences of the United States of America, 106, 16310–16314.

    Article  Google Scholar 

  44. Lynch, M., et al. (2008). A genome-wide view of the spectrum of spontaneous mutations in yeast. Proceedings of the National Academy of Sciences of the United States of America, 105, 9272–9277.

    Article  Google Scholar 

  45. Haag-Liautard, C., Dorris, M., Maside, X., Macaskill, S., Halligan, D. L., Charlesworth, B., & Keightley, P. D. (2007). Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature, 445, 82–85.

    Article  Google Scholar 

  46. Keightley, P. D., Trivedi, U., Thomson, M., Oliver, F., Kumar, S., & Blaxter, M. L. (2009). Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Research, 19, 1195–1201.

    Article  Google Scholar 

  47. Fujiyama, A., Watanabe, H., Toyoda, A., Taylor, T. D., Itoh, T., Tsai, S.-F., Park, H.-S., Yaspo, M.-L., Lehrach, H., Chen, Z., Fu, G., Saitou, N., Osoegawa, K., de Jong, P. J., Suto, Y., Hattori, M., & Sakaki, Y. (2002). Construction and analysis of a human-chimpanzee comparative clone map. Science, 295, 131–134.

    Article  Google Scholar 

  48. 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.

    Article  Google Scholar 

  49. Ochman, H. (2003). Neutral mutations and neutral substitutions in bacterial genomes. Molecular Biology and Evolution, 20, 2091–2096.

    Article  Google Scholar 

  50. Hanada, K., Suzuki, Y., & Gojobori, T. (2004). A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Molecular Biology and Evolution, 21, 1074–1080.

    Article  Google Scholar 

  51. Mendel, G. (1866). Versuche uber Pflanzenhybriden (written in German). Verhandlungen des Naturforschenden Verenines, Abhandlungen, Brunn, 4, 3–47.

    Google Scholar 

  52. Yoshiura, K., et al. (2006). A SNP in the ABCC11 gene is the determinant of human earwax type. Nature Genetics, 38, 324–330.

    Article  Google Scholar 

  53. Branden, C., & Tooze, J. (1991). Introduction to protein structure (p. 40). New York: Garland.

    Google Scholar 

  54. Yamamoto, F., Clausen, H., White, T., Marken, J., & Hakomori, S. (1990). Molecular genetic basis of the histo-blood group ABO system. Nature, 345, 229–233.

    Article  Google Scholar 

  55. Bhattacharyya, M. K., Smith, A. M., Ellis, T. H., Hedley, C., & Martin, C. (1990). The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell, 60, 115–122.

    Article  Google Scholar 

  56. Wray, G. A. (2007). The evolutionary significance of cis-regulatory mutations. Nature Reviews Genetics, 8, 206–216.

    Article  Google Scholar 

  57. Enattah, N. S., et al. (2002). Identification of a variant associated with adult-type hypolactasia. Nature Genetics, 30, 233–237.

    Article  Google Scholar 

Additional Citations Not Ordered According to Text Locations

  1. Kong, A., et al. (2012). Rate of de novo mutations and the importance of father’s age to disease risk. Nature, 488, 471–475.

    Article  Google Scholar 

  2. Campbel, C. D. (2012). Estimating the human mutation rate using autozygosity in a founder population. Nature Genetics, 44, 1277–1283.

    Article  Google Scholar 

  3. Ellegren, H. (2004). Microsatellites: Simple sequence with complex evolution. Genetics, 5, 435–445.

    Google Scholar 

  4. Bhargava, A., & Fuentes, F. F. (2010). Mutational dynamics of microsatellites. Molecular Biotechnology, 44(3), 250–266.

    Article  Google Scholar 

  5. Kelkar, Y. D., Tyekucheva, S., Chiaromonte, F., & Makova, K. D. (2008). The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Research, 18, 30–38.

    Article  Google Scholar 

  6. Oliveira, E. J., Padua, J. G., Zucchi, M. I., Vencovsky, R., & Vieira, M. L. (2006). Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology, 29(2), 294–307.

    Article  Google Scholar 

  7. Leclercq, S., Rivals, E., & Jarne, P. (2007). Detecting microsatellites within genomes: Significant variation among algorithms. BMC Bioinformatics, 8, 125.

    Article  Google Scholar 

  8. Boyer, J. C., Hawk, J. D., Stefanovic, L., & Farber, R. A. (2008). Sequence-dependent effect of interruptions on microsatellite mutation rate in mismatch repair-deficient human cells. Mutation Research, 640, 89–96.

    Article  Google Scholar 

  9. Ngai, M. Y., & Saitou, N. (2012). The effect of perfection status on mutation rates of microsatellites in primates (Unpublished).

    Google Scholar 

  10. Sun, J. X., et al. (2012). A direct characterization of human mutation based on microsatellites. Nature Genetics, 44, 1161–1165.

    Article  Google Scholar 

  11. Burridge, C. P., et al. (2008). Geological dates and molecular rates: Fish DNA sheds light on time dependency. Molecular Biology and Evolution, 25, 624–633.

    Article  Google Scholar 

  12. Millar, C. D., et al. (2008). Mutation and evolutionary rates in Adélie Penguins from the Antarctic. PLoS Genetics, 4, e1000209.

    Article  Google Scholar 

  13. Saitou, N. (2007). Genomu Shinkagaku Nyumon (written in Japanese, meaning ‘Introduction to evolutionary genomics’). Tokyo: Kyoritsu Shuppan.

    Google Scholar 

  14. 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.

    Article  Google Scholar 

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Authors and Affiliations

  1. Division of Population Genetics, National Institute of Genetics (NIG), Mishima, Shizuoka, Japan

    Naruya Saitou

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  1. Naruya Saitou
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Saitou, N. (2013). Mutation. In: Introduction to Evolutionary Genomics. Computational Biology, vol 17. Springer, London. https://doi.org/10.1007/978-1-4471-5304-7_2

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  • DOI: https://doi.org/10.1007/978-1-4471-5304-7_2

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  • Online ISBN: 978-1-4471-5304-7

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