This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Conant, G. C. Articles by Wagner, A. Search for Related Content PubMed PubMed Citation Articles by Conant, G. C. Articles by Wagner, A. Social Bookmarking                   What's this?

Letter

Asymmetric Sequence Divergence of Duplicate Genes

Department of Biology, The University of New Mexico, Albuquerque, New Mexico 87131, USA

Much like humans, gene duplicates may be created equal, but they do not stay that way for long. For four completely sequenced genomes we show that 20%–30% of duplicate gene pairs show asymmetric evolution in the amino acid sequence of their protein products. That is, one of the duplicates evolves much faster than the other. The greater this asymmetry, the greater the ratio K_a/K_s of amino acid substitutions (K_a) to silent substitutions (K_s) in a gene pair. This indicates that most asymmetric divergence may be caused by relaxed selective constraints on one of the duplicates. However, we also find some candidate duplicates where positive (directional) selection of beneficial mutations (K_a/K_s > 1) may play a role in asymmetric divergence. Our analysis rests on a codon-based model of molecular evolution that allows a test for asymmetric divergence in K_a. The method is also more sensitive in detecting positive selection (K_a/K_s > 1) than models relying only on pairwise gene comparisons.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1252603.

¹ Corresponding author.
E-MAIL gconant{at}unm.edu; FAX: (505) 277-0304.

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				A. Prachumwat and W.-H. Li Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes Genome Res., February 1, 2008; 18(2): 221 - 232. [Abstract] [Full Text] [PDF]

				D. R. Scannell and K. H. Wolfe A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast Genome Res., January 1, 2008; 18(1): 137 - 147. [Abstract] [Full Text] [PDF]

				A. Wagner, C. Lewis, and M. Bichsel A survey of bacterial insertion sequences using IScan Nucleic Acids Res., August 13, 2007; 35(16): 5284 - 5293. [Abstract] [Full Text] [PDF]

				K. P. Byrne and K. H. Wolfe Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication Genetics, March 1, 2007; 175(3): 1341 - 1350. [Abstract] [Full Text] [PDF]

				B. P. Cusack and K. H. Wolfe Not Born Equal: Increased Rate Asymmetry in Relocated and Retrotransposed Rodent Gene Duplicates Mol. Biol. Evol., March 1, 2007; 24(3): 679 - 686. [Abstract] [Full Text] [PDF]

				C. R. Johnston, C. O'Dushlaine, D. A. Fitzpatrick, R. J. Edwards, and D. C. Shields Evaluation of Whether Accelerated Protein Evolution in Chordates Has Occurred before, after, or Simultaneously with Gene Duplication Mol. Biol. Evol., January 1, 2007; 24(1): 315 - 323. [Abstract] [Full Text] [PDF]

				F. G. Brunet, H. R. Crollius, M. Paris, J.-M. Aury, P. Gibert, O. Jaillon, V. Laudet, and M. Robinson-Rechavi Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes Mol. Biol. Evol., September 1, 2006; 23(9): 1808 - 1816. [Abstract] [Full Text] [PDF]

				R. Wang, K. Chong, and T. Wang Divergence in spatial expression patterns and in response to stimuli of tandem-repeat paralogues encoding a novel class of proline-rich proteins in Oryza sativa J. Exp. Bot., August 1, 2006; 57(11): 2887 - 2897. [Abstract] [Full Text] [PDF]

				I. Braasch, W. Salzburger, and A. Meyer Asymmetric Evolution in Two Fish-Specifically Duplicated Receptor Tyrosine Kinase Paralogons Involved in Teleost Coloration Mol. Biol. Evol., June 1, 2006; 23(6): 1192 - 1202. [Abstract] [Full Text] [PDF]

				K. D. Crow and G. P. Wagner What Is the Role of Genome Duplication in the Evolution of Complexity and Diversity? Mol. Biol. Evol., May 1, 2006; 23(5): 887 - 892. [Abstract] [Full Text] [PDF]

				S.-H. Kim and S. V. Yi Correlated Asymmetry of Sequence and Functional Divergence Between Duplicate Proteins of Saccharomyces cerevisiae Mol. Biol. Evol., May 1, 2006; 23(5): 1068 - 1075. [Abstract] [Full Text] [PDF]

				A. Wagner Periodic Extinctions of Transposable Elements in Bacterial Lineages: Evidence from Intragenomic Variation in Multiple Genomes Mol. Biol. Evol., April 1, 2006; 23(4): 723 - 733. [Abstract] [Full Text] [PDF]

				B. A. Chapman, J. E. Bowers, F. A. Feltus, and A. H. Paterson Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication PNAS, February 21, 2006; 103(8): 2730 - 2735. [Abstract] [Full Text] [PDF]

				Z. Su, J. Wang, J. Yu, X. Huang, and X. Gu Evolution of alternative splicing after gene duplication Genome Res., February 1, 2006; 16(2): 182 - 189. [Abstract] [Full Text] [PDF]

				M. A. Fares, K. P. Byrne, and K. H. Wolfe Rate Asymmetry After Genome Duplication Causes Substantial Long-Branch Attraction Artifacts in the Phylogeny of Saccharomyces Species Mol. Biol. Evol., February 1, 2006; 23(2): 245 - 253. [Abstract] [Full Text] [PDF]

				K. D. Crow, P. F. Stadler, V. J. Lynch, C. Amemiya, and G. P. Wagner The "Fish-Specific" Hox Cluster Duplication Is Coincident with the Origin of Teleosts Mol. Biol. Evol., January 1, 2006; 23(1): 121 - 136. [Abstract] [Full Text] [PDF]

				C. D. Jones and D. J. Begun Parallel evolution of chimeric fusion genes PNAS, August 9, 2005; 102(32): 11373 - 11378. [Abstract] [Full Text] [PDF]

				J. Gough Convergent evolution of domain architectures (is rare) Bioinformatics, April 15, 2005; 21(8): 1464 - 1471. [Abstract] [Full Text] [PDF]

				J. B. Pereira-Leal and S. A. Teichmann Novel specificities emerge by stepwise duplication of functional modules Genome Res., April 1, 2005; 15(4): 552 - 559. [Abstract] [Full Text] [PDF]

				K. Bomblies and J. F. Doebley Molecular Evolution of FLORICAULA/LEAFY Orthologs in the Andropogoneae (Poaceae) Mol. Biol. Evol., April 1, 2005; 22(4): 1082 - 1094. [Abstract] [Full Text] [PDF]

				X. Gu, Z. Zhang, and W. Huang Rapid evolution of expression and regulatory divergences after yeast gene duplication PNAS, January 18, 2005; 102(3): 707 - 712. [Abstract] [Full Text] [PDF]

				R. C. Moore, S. R. Grant, and M. D. Purugganan Molecular Population Genetics of Redundant Floral-Regulatory Genes in Arabidopsis thaliana Mol. Biol. Evol., January 1, 2005; 22(1): 91 - 103. [Abstract] [Full Text] [PDF]

				G. P. Wagner, C. Fried, S. J. Prohaska, and P. F. Stadler Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests Mol. Biol. Evol., November 1, 2004; 21(11): 2116 - 2121. [Abstract] [Full Text] [PDF]

				C. I. Castillo-Davis, D. L. Hartl, and G. Achaz cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes Genome Res., August 1, 2004; 14(8): 1530 - 1536. [Abstract] [Full Text] [PDF]

				G. Blanc and K. H. Wolfe Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution PLANT CELL, July 1, 2004; 16(7): 1679 - 1691. [Abstract] [Full Text] [PDF]

				Z. Zhang and H. Kishino Genomic Background Predicts the Fate of Duplicated Genes: Evidence From the Yeast Genome Genetics, April 1, 2004; 166(4): 1995 - 1999. [Abstract] [Full Text] [PDF]