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The evolutionary demography of duplicate genes

  • Michael Lynch
  • John S. Conery
Article

Abstract

Although gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, the rates of origin, loss, and preservation of gene duplicates are not well understood. Applying steady-state demographic techniques to the age distributions of duplicate genes censused in seven completely sequenced genomes, we estimate the average rate of duplication of a eukaryotic gene to be on the order of 0.01/gene/million years, which is of the same order of magnitude as the mutation rate per nucleotide site. However, the average half-life of duplicate genes is relatively small, on the order of 4.0 million years. Significant interspecific variation in these rates appears to be responsible for differences in species-specific genome sizes that arise as a consequence of a quasi-equilibrium birth-death process. Most duplicated genes experience a brief period of relaxed selection early in their history and a minority exhibit the signature of directional selection, but those that survive more than a few million years eventually experience strong purifying selection. Thus, although most theoretical work on the gene-duplication process has focused on issues related to adaptive evolution, the origin of a new function appears to be a very rare fate for a duplicate gene. A more significant role of the duplication process may be the generation of microchromosomal rearrangements through reciprocal silencing of alternative copies, which can lead to the passive origin of post-zygotic reproductive barriers in descendant lineages of incipient species.

gene duplication genome evolution genome size 

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References

  1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.Google Scholar
  2. Bevan, M., K. Mayer, O. White, J. A. Eisen, D. Preuss, T. Bureau, S.L. Salzberg, H. W. Mewes. 2001. Sequence and analysis of the Arabidopsis genome. Curr. Opin. Plant Biol. 4: 105-110.Google Scholar
  3. Conery, J. S., and M. Lynch. 2001. Nucleotide substitutions and the evolution of duplicate genes. Pacific Symp. Biocomput. 6: 167-178.Google Scholar
  4. Cormen, T. H., C. E. Leiserson, and R. L. Rivest. 1990. Introduction to Algorithms. McGraw-Hill.Google Scholar
  5. Grant, D., P. Cregan, and R. C. Shoemaker. 2000. Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc. Natl. Sci. USA 97: 4168-4173.Google Scholar
  6. Gu, Z., A. Cavalcanti, F.-C. Chen, P. Bouman, and W.-H. Li. 2002. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19: 256-262.Google Scholar
  7. Li, W.-H. 1999. Molecular Evolution. Sinauer Assocs., Sunderland, MA.Google Scholar
  8. Lynch, M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes. Mol. Biol. Evol. 114: 914-925.Google Scholar
  9. Lynch, M. 2003. Gene duplication and evolution. In A. Moya (ed.), Evolution: From Molecules to Ecosystems. Oxford University Press. (in press).Google Scholar
  10. Lynch, M., and J. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1154.Google Scholar
  11. Lynch, M., and A. Force. 2000. The origin of interspecific genomic incompatibility via gene duplication. Amer. Natur. 156: 590-605.Google Scholar
  12. Lynch, M., M. O'Hely, B. Walsh, and A. Force. 2001. The probability of fixation of a newly arisen gene duplicate. Genetics 159: 1789-1804.Google Scholar
  13. Ohno, S. 1970. Evolution by Gene Duplication. Springer-Verlag, Berlin.Google Scholar
  14. Shapira, S. K., and V. G. Finnerty. 1986. The use of genetic complementation in the study of eukaryotic macromolecular evolution: rate of spontaneous gene duplication at two loci of Drosophila melanogaster. Mol. Biol. Evol. 23: 159-167.Google Scholar
  15. Shioura, A., A. Tamura, and T. Uno. 1997. An optimal algorithm for scanning all spanning trees of undirected graphs. SIAM J. Comput. 26: 678-692.Google Scholar
  16. Sokal, R. R., and F. J. Rohlf. 1995. Biometry. 3rd Ed. Freeman, Yew York.Google Scholar
  17. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.Google Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Michael Lynch
    • 1
  • John S. Conery
    • 2
  1. 1.Dept. of BiologyIndiana UniversityBloomington
  2. 2.Dept. of Computer and Information ScienceUniversity of OregonEugene

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