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.
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References
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.
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.
Conery, J. S., and M. Lynch. 2001. Nucleotide substitutions and the evolution of duplicate genes. Pacific Symp. Biocomput. 6: 167-178.
Cormen, T. H., C. E. Leiserson, and R. L. Rivest. 1990. Introduction to Algorithms. McGraw-Hill.
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.
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.
Li, W.-H. 1999. Molecular Evolution. Sinauer Assocs., Sunderland, MA.
Lynch, M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes. Mol. Biol. Evol. 114: 914-925.
Lynch, M. 2003. Gene duplication and evolution. In A. Moya (ed.), Evolution: From Molecules to Ecosystems. Oxford University Press. (in press).
Lynch, M., and J. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1154.
Lynch, M., and A. Force. 2000. The origin of interspecific genomic incompatibility via gene duplication. Amer. Natur. 156: 590-605.
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.
Ohno, S. 1970. Evolution by Gene Duplication. Springer-Verlag, Berlin.
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.
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.
Sokal, R. R., and F. J. Rohlf. 1995. Biometry. 3rd Ed. Freeman, Yew York.
Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
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Lynch, M., Conery, J.S. The evolutionary demography of duplicate genes. J Struct Func Genom 3, 35–44 (2003). https://doi.org/10.1023/A:1022696612931
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DOI: https://doi.org/10.1023/A:1022696612931