Molecular Biology and Evolution 17:32-43 (2000)
© 2000 Society for Molecular Biology and Evolution
Article |
Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models
*Department of Biology, University College London, England;
and
Department of Organismic and Evolutionary Biology, Harvard University
Approximate methods for estimating the numbers of synonymous and nonsynonymous substitutions between two DNA sequences involve three steps: counting of synonymous and nonsynonymous sites in the two sequences, counting of synonymous and nonsynonymous differences between the two sequences, and correcting for multiple substitutions at the same site. We examine complexities involved in those steps and propose a new approximate method that takes into account two major features of DNA sequence evolution: transition/transversion rate bias and base/codon frequency bias. We compare the new method with maximum likelihood, as well as several other approximate methods, by examining infinitely long sequences, performing computer simulations, and analyzing a real data set. The results suggest that when there are transition/transversion rate biases and base/codon frequency biases, previously described approximate methods for estimating the nonsynonymous/synonymous rate ratio may involve serious biases, and the bias can be both positive and negative. The new method is, in general, superior to earlier approximate methods and may be useful for analyzing large data sets, although maximum likelihood appears to always be the method of choice.
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C. E. Popescu, T. Borza, J. P. Bielawski, and R. W. Lee Evolutionary Rates and Expression Level in Chlamydomonas Genetics, March 1, 2006; 172(3): 1567 - 1576. [Abstract] [Full Text] [PDF]
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F.-C. Chen, S.-S. Wang, C.-J. Chen, W.-H. Li, and T.-J. Chuang Alternatively and Constitutively Spliced Exons Are Subject to Different Evolutionary Forces Mol. Biol. Evol., March 1, 2006; 23(3): 675 - 682. [Abstract] [Full Text] [PDF]
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S.-Y. Jiang and S. Ramachandran Comparative and evolutionary analysis of genes encoding small GTPases and their activating proteins in eukaryotic genomes Physiol Genomics, February 23, 2006; 24(3): 235 - 251. [Abstract] [Full Text] [PDF]
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G. M. Wilson, S. Flibotte, P. I. Missirlis, M. A. Marra, S. Jones, K. Thornton, A. G. Clark, and R. A. Holt Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla Genome Res., February 1, 2006; 16(2): 173 - 181. [Abstract] [Full Text] [PDF]
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M. T. Sweeney, M. J. Thomson, B. E. Pfeil, and S. McCouch Caught Red-Handed: Rc Encodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice PLANT CELL, February 1, 2006; 18(2): 283 - 294. [Abstract] [Full Text] [PDF]
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H. Khan, A. Smit, and S. Boissinot Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates Genome Res., January 1, 2006; 16(1): 78 - 87. [Abstract] [Full Text] [PDF]
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M. Csuros and I. Miklos Statistical Alignment of Retropseudogenes and Their Functional Paralogs Mol. Biol. Evol., December 1, 2005; 22(12): 2457 - 2471. [Abstract] [Full Text] [PDF]
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S. Zhang, C. Chen, L. Li, L. Meng, J. Singh, N. Jiang, X.-W. Deng, Z.-H. He, and P. G. Lemaux Evolutionary Expansion, Gene Structure, and Expression of the Rice Wall-Associated Kinase Gene Family Plant Physiology, November 1, 2005; 139(3): 1107 - 1124. [Abstract] [Full Text] [PDF]
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K. P. Byrne and K. H. Wolfe The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species Genome Res., October 1, 2005; 15(10): 1456 - 1461. [Abstract] [Full Text] [PDF]
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B. Giardine, C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, J. Taylor, et al. Galaxy: A platform for interactive large-scale genome analysis Genome Res., October 1, 2005; 15(10): 1451 - 1455. [Abstract] [Full Text] [PDF]
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S.-M. Chang, Y. Lu, and M. D. Rausher Neutral Evolution of the Nonbinding Region of the Anthocyanin Regulatory Gene Ipmyb1 in Ipomoea Genetics, August 1, 2005; 170(4): 1967 - 1978. [Abstract] [Full Text] [PDF]
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L. Rowen, E. Williams, G. Glusman, E. Linardopoulou, C. Friedman, M. E. Ahearn, J. Seto, C. Boysen, S. Qin, K. Wang, et al. Interchromosomal Segmental Duplications Explain the Unusual Structure of PRSS3, the Gene for an Inhibitor-Resistant Trypsinogen Mol. Biol. Evol., August 1, 2005; 22(8): 1712 - 1720. [Abstract] [Full Text] [PDF]
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B. E. Pfeil, J. A. Schlueter, R. C. Shoemaker, and J. J. Doyle Placing Paleopolyploidy in Relation to Taxon Divergence: A Phylogenetic Analysis in Legumes Using 39 Gene Families Syst Biol, June 1, 2005; 54(3): 441 - 454. [Abstract] [Full Text] [PDF]
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