The Effect of Gene Conversion on the Divergence Between Duplicated Genes

Corresponding author: Hideki Innan, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030., hideki.innan{at}uth.tmc.edu (E-mail)

Communicating editor: J. B. WALSH

Nonindependent evolution of duplicated genes is called concerted evolution. In this article, we study the evolutionary process of duplicated regions that involves concerted evolution. The model incorporates mutation and gene conversion: the former increases d, the divergence between two duplicated regions, while the latter decreases d. It is demonstrated that the process consists of three phases. Phase I is the time until d reaches its equilibrium value, d₀. In phase II d fluctuates around d₀, and d increases again in phase III. Our simulation results demonstrate that the length of concerted evolution (i.e., phase II) is highly variable, while the lengths of the other two phases are relatively constant. It is also demonstrated that the length of phase II approximately follows an exponential distribution with mean , which is a function of many parameters including gene conversion rate and the length of gene conversion tract. On the basis of these findings, we obtain the probability distribution of the level of divergence between a pair of duplicated regions as a function of time, mutation rate, and . Finally, we discuss potential problems in genomic data analysis of duplicated genes when it is based on the molecular clock but concerted evolution is common.

This article has been cited by other articles:

				B. Frajman, F. Eggens, and B. Oxelman Hybrid Origins and Homoploid Reticulate Evolution within Heliosperma (Sileneae, Caryophyllaceae)--A Multigene Phylogenetic Approach with Relative Dating Syst Biol, July 3, 2009; (2009) syp030v1. [Abstract] [Full Text] [PDF]

				K. S. Caldwell and R. W. Michelmore Arabidopsis thaliana Genes Encoding Defense Signaling and Recognition Proteins Exhibit Contrasting Evolutionary Dynamics Genetics, February 1, 2009; 181(2): 671 - 684. [Abstract] [Full Text] [PDF]

				P. Guillon, N. Ruvoen-Clouet, B. Le Moullac-Vaidye, S. Marchandeau, and J. Le Pendu Association between expression of the H histo-blood group antigen, {alpha}1,2fucosyltransferases polymorphism of wild rabbits, and sensitivity to rabbit hemorrhagic disease virus Glycobiology, January 1, 2009; 19(1): 21 - 28. [Abstract] [Full Text] [PDF]

				M. Aguade Nucleotide and Copy-Number Polymorphism at the Odorant Receptor Genes Or22a and Or22b in Drosophila melanogaster Mol. Biol. Evol., January 1, 2009; 26(1): 61 - 70. [Abstract] [Full Text] [PDF]

				S. Mano and H. Innan The Evolutionary Rate of Duplicated Genes Under Concerted Evolution Genetics, September 1, 2008; 180(1): 493 - 505. [Abstract] [Full Text] [PDF]

				S. Takuno, T. Nishio, Y. Satta, and H. Innan Preservation of a Pseudogene by Gene Conversion and Diversifying Selection Genetics, September 1, 2008; 180(1): 517 - 531. [Abstract] [Full Text] [PDF]

				K. M. Teshima and H. Innan Neofunctionalization of Duplicated Genes Under the Pressure of Gene Conversion Genetics, March 1, 2008; 178(3): 1385 - 1398. [Abstract] [Full Text] [PDF]

				K. Zhang and N. A. Rosenberg On the Genealogy of a Duplicated Microsatellite Genetics, December 1, 2007; 177(4): 2109 - 2122. [Abstract] [Full Text] [PDF]

				K. R. Thornton The Neutral Coalescent Process for Recent Gene Duplications and Copy-Number Variants Genetics, October 1, 2007; 177(2): 987 - 1000. [Abstract] [Full Text] [PDF]

				P. Labbe, A. Berthomieu, C. Berticat, H. Alout, M. Raymond, T. Lenormand, and M. Weill Independent Duplications of the Acetylcholinesterase Gene Conferring Insecticide Resistance in the Mosquito Culex pipiens Mol. Biol. Evol., April 1, 2007; 24(4): 1056 - 1067. [Abstract] [Full Text] [PDF]

				F. Zhang and T. Peterson Gene Conversion Between Direct Noncoding Repeats Promotes Genetic and Phenotypic Diversity at a Regulatory Locus of Zea mays (L.) Genetics, October 1, 2006; 174(2): 753 - 762. [Abstract] [Full Text] [PDF]

				Y.-S. Lin, J. K. Byrnes, J.-K. Hwang, and W.-H. Li Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes PNAS, September 26, 2006; 103(39): 14412 - 14416. [Abstract] [Full Text] [PDF]

				A. Kubota, H. Iwata, H. M. H. Goldstone, E.-Y. Kim, J. J. Stegeman, and S. Tanabe Cytochrome P450 1A4 and 1A5 in Common Cormorant (Phalacrocorax carbo): Evolutionary Relationships and Functional Implications Associated with Dioxin and Related Compounds Toxicol. Sci., August 1, 2006; 92(2): 394 - 408. [Abstract] [Full Text] [PDF]

				A. D Peel, M. J Telford, and M. Akam The evolution of hexapod engrailed-family genes: evidence for conservation and concerted evolution Proc R Soc B, July 22, 2006; 273(1595): 1733 - 1742. [Abstract] [Full Text] [PDF]

				J. H. Thomas Concerted Evolution of Two Novel Protein Families in Caenorhabditis Species Genetics, April 1, 2006; 172(4): 2269 - 2281. [Abstract] [Full Text] [PDF]

				N. Backstrom, H. Ceplitis, S. Berlin, and H. Ellegren Gene Conversion Drives the Evolution of HINTW, an Ampliconic Gene on the Female-Specific Avian W Chromosome Mol. Biol. Evol., October 1, 2005; 22(10): 1992 - 1999. [Abstract] [Full Text] [PDF]

				R. P. Sugino and H. Innan Estimating the Time to the Whole-Genome Duplication and the Duration of Concerted Evolution via Gene Conversion in Yeast Genetics, September 1, 2005; 171(1): 63 - 69. [Abstract] [Full Text] [PDF]

				N. L. Prigoda, A. Nassuth, and B. K. Mable Phenotypic and Genotypic Expression of Self-incompatibility Haplotypes in Arabidopsis lyrata Suggests Unique Origin of Alleles in Different Dominance Classes Mol. Biol. Evol., July 1, 2005; 22(7): 1609 - 1620. [Abstract] [Full Text] [PDF]

				D. Schmidt and R. Durrett Adaptive Evolution Drives the Diversification of Zinc-Finger Binding Domains Mol. Biol. Evol., December 1, 2004; 21(12): 2326 - 2339. [Abstract] [Full Text] [PDF]

				L.-z. Gao and H. Innan Very Low Gene Duplication Rate in the Yeast Genome Science, November 19, 2004; 306(5700): 1367 - 1370. [Abstract] [Full Text] [PDF]