On Genome Evolution with Innovation

  • Damian Wójtowicz
  • Jerzy Tiuryn
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4162)


We introduce and analyse a simple probabilistic model of genome evolution. It is based on three fundamental evolutionary events: gene duplication, loss and innovation, and it is called DLI model. The focus of the paper is around the size distribution of gene families. The formulas for equilibrium gene family sizes are derived showing that they follow a logarithmic distribution. We consider also a disjoint union of DLI models and we present the result of this study. Some empirical results for microbial genomes are presented.


Gene Duplication Genome Evolution Paralogous Gene Bacillus Anthracis Yarrowia Lipolytica 
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.


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  1. 1.
    Dujon, B., et al.: Genome evolution in yeasts. Nature 430, 35–44 (2004)CrossRefGoogle Scholar
  2. 2.
    Enright, A.J., Van Dongen, S., Ouzounis, C.A.: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 30(7), 1575–1584 (2002)CrossRefGoogle Scholar
  3. 3.
    Feller, W.: An introduction to probability theory and its applications. John Wiley and Sons, Inc., New York (1961)Google Scholar
  4. 4.
    Fitch, W.M.: Homology, a personal view on some of the problems. Trends in Genetics 16(5), 227–321 (2000)CrossRefGoogle Scholar
  5. 5.
    Huynen, M.A., van Nimwegen, E.: The Frequency Distribution of Gene Family Size in Complete Genomes. Molecular Biology Evolution 15(5), 583–589 (1998)Google Scholar
  6. 6.
    Jordan, K., Makarova, K.S., Spouge, J.L., Wolf, Y.I., Koonin, E.V.: Lineage-Specific Gene Expansions in Bacterial and Archeal Genomes. Genome Research 11, 555–565 (2001)CrossRefGoogle Scholar
  7. 7.
    Karev, G.P., Wolf, Y.I., Rzhetsky, A.Y., Berezovskaya, F.S., Koonin, E.V.: Birth and death of protein domains: A simple model of evolution explains power law behavior. BMC Evolutionary Biology 2, 18 (2002)CrossRefGoogle Scholar
  8. 8.
    Karev, G.P., Wolf, Y.I., Koonin, E.V.: Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve? Bioinformatics 15(19), 1889–1900 (2003)CrossRefGoogle Scholar
  9. 9.
    Kimura, M.: The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge (1983)CrossRefGoogle Scholar
  10. 10.
    Li, W.-H.: Moclecular Evolution. Sinauer Associates, Inc., Publishers, Sunderland Massachusetts (1997)Google Scholar
  11. 11.
    Luz, H., Vingron, M.: Family specific rates of protein evolution. Bioinformatics 22(10), 1166–1171 (2006)CrossRefGoogle Scholar
  12. 12.
    Ohno, S.: Evolution by Gene Duplication. Springer, Berlin (1970)Google Scholar
  13. 13.
    Peterson, J.D., Umayam, L.A., Dickinson, T.M., Hickey, E.K.: O. White The Comprehensive Microbial Resource. Nucleic Acids Research 29(1), 123–125 (2001)CrossRefGoogle Scholar
  14. 14.
    Slonimski, P.P., Mosse, M.O., Golik, P., Henaût, A., Diaz, Y., Risler, J.L., Comet, J.P., Aude, J.C., Wozniak, A., Glemet, E., Codani, J.J.: The first laws of genomics. Microbial and Comparative Genomics 3(46) (1998)Google Scholar
  15. 15.
    Slonimski, P.P.: Comparision of complete genomes: Organization and evolution. In: Proceedings of the Third Annual Conference on Computational Molecular Biology, RECOMB 1999. Stanislaw Ulam Memorial Lecture, vol. 310. ACM Press, New York (1999)Google Scholar
  16. 16.
    Tiuryn, J., Rudnicki, R., Wójtowicz, D.: A case study of genome evolution: From continuous to discrete time model. In: Fiala, J., Koubek, V., Kratochvíl, J. (eds.) MFCS 2004. LNCS, vol. 3153, pp. 1–24. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  17. 17.
    Tiuryn, J., Wójtowicz, D., Rudnicki, R.: A Model of Evolution of Small Paralog Families in Genomes (2006) (submited for publication)Google Scholar
  18. 18.
    Yanai, I., Camacho, C.J., DeLisi, C.: Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification. Physical Review Letters 85(12), 2641–2644 (2000)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Damian Wójtowicz
    • 1
  • Jerzy Tiuryn
    • 1
  1. 1.Institute of InformaticsWarsaw UniversityWarsawPoland

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