nach oben

Erschienen in:

2013 | OriginalPaper | Buchkapitel

4. Neutral Evolution

verfasst von : Naruya Saitou

Erschienen in: Introduction to Evolutionary Genomics

Verlag: Springer London

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config

KI-gestützte Suche

Aus

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.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Vorheriges Kapitel Phylogeny

Nächstes Kapitel Natural Selection

Kimura, M. (1983). The neutral theory of molecular evolution. Cambridge: Cambridge University Press.CrossRef

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

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

International Chicken Genome Sequencing Consortium. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695–716.CrossRef

Kimura, M. (1968). Evolutionary rate at the molecular level. Nature, 217, 624–626.CrossRef

Bonner, J. T. (2008). The social amoebae: The biology of cellular slime molds. Princeton: Princeton University Press.

Cook, R. E. (1979). Asexual reproduction: A further consideration. American Naturalist, 113, 769–772.CrossRef

Ewens, W. J. (1979). Mathematical population genetics. Berlin/New York: Springer.MATH

Watson, H. W., & Galton, F. (1874). On the probability of the extinction of families. Journal of Anthropological Institute, 4, 138–144.

10.

Haccou, P., Jagers, P., & Vatutin, V. A. (2005). Branching processes: Variation, growth, and extinction of populations. Cambridge: Cambridge University Press.CrossRef

11.

Crow, J. F. (1989). The estimation of inbreeding from isonymy. Human Biology, 61, 935–948.

12.

Saitou, N. (1983). An attempt to estimate the migration pattern in Japan by surname data (in Japanese). Jinruigaku Zasshi, 91, 309–322.

13.

Fisher, R. A. (1930). The distribution of gene ratios for rare mutations. Proceedings of Royal Society of Edinburgh, 50, 205–220.

14.

Feller, W. (1968). Introduction to probability theory and its applications (3rd ed., Vol. 1). New York: Wiley.MATH

15.

Crow, J. F., & Kimura, M. (1970). An introduction to population genetics theory. New York: Prentice-Hall.

16.

Howell, N. (1979). Demography of the Dobe !Kung. New York: Academic.

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.CrossRef

18.

Kingman, J. F. C. (1982). On the genealogy of large populations. Journal of Applied Probability, 19A, 27–43.CrossRefMathSciNet

19.

Hudson, R. R. (1983). Testing the constant rate neutral allele model with protein sequence data. Evolution, 37, 203–217.CrossRef

20.

Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437–460.

21.

Fu, Y.-X. (2006). Exact coalescent for the Wright-Fisher model. Theoretical Population Biology, 69, 385–394.CrossRefMATH

22.

Hein, J., Schierup, M. H., & Wiuf, C. (2005). Gene genealogies, variation, and evolution – a primer in coalescent theory. Oxford: Oxford University Press.MATH

23.

Wakeley, J. (2008). Coalescent theory: An introduction. Greenwood Village: Roberts & Co.

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.CrossRefMATH

25.

Kimura, M. (1964). Diffusion models in population genetics. Journal of Applied Probability, 1, 177–232.CrossRefMATHMathSciNet

26.

Kimura, M., & Ohta, T. (1971). Protein polymorphism as a phase of molecular evolution. Nature, 229, 467–469.CrossRef

27.

Kimura, M., & Crow, J. F. (1964). The number of alleles that can be maintained in a finite population. Genetics, 49, 725–738.

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.

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.CrossRef

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.CrossRef

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.CrossRef

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.

33.

Kimura, M., & Ohta, T. (1973). Mutation and evolution at the molecular level. Genetics (Supplement), 73, 19–35.

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.CrossRef

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.

36.

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

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.CrossRef

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.CrossRef

39.

Ikemura, T. (1985). Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution, 2, 13–34.

40.

Ohno, S. (1972). So much “junk” DNA in our genome. Brookhaven Symposium in Biology, 23, 366–370.

41.

International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature, 431, 931–945.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

49.

Li, W.-H., Gojobori, T., & Nei, M. (1981). Pseudogenes as paradigm of the neutral evolution. Nature, 292, 237–239.CrossRef

50.

King, J. L., & Jukes, T. H. (1969). Non-Darwinian evolution. Science, 164, 788–798.CrossRef

51.

Lehninger, A. L. (1975). Biochemistry. New York: Worth Publishers.

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.CrossRef

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.

54.

Cole, S. T., & others. (2001). Massive gene decay in the leprosy bacillus. Nature, 409, 1007–1011.

55.

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

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).

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.CrossRef

58.

Nei, M. (2013a). Mutation-driven evolution. Oxford: Oxford University Press.

59.

Takahatan, N. (1993). Allelic genealogy and human evolution. Molecular Biology and Evolution, 10, 2–22.

Titel: Neutral Evolution
verfasst von: Naruya Saitou
Verlag: Springer London
Buch: Introduction to Evolutionary Genomics
Print ISBN: 978-1-4471-5303-0

Electronic ISBN: 978-1-4471-5304-7

Copyright-Jahr: 2013
DOI: https://doi.org/10.1007/978-1-4471-5304-7_4

Springer Professional

Abstract

Bitte loggen Sie sich ein, um Zugang zu Ihrer Lizenz zu erhalten.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"