Molecular Biology and Evolution, Vol 3, 418-426, Copyright © 1986 by Society for Molecular Biology and Evolution
M Nei and T Gojobori
Two simple methods for estimating the numbers of synonymous and
nonsynonymous nucleotide substitutions are presented. Although they give no
weights to different types of codon substitutions, these methods give
essentially the same results as those obtained by Miyata and Yasunaga's and
by Li et al.'s methods. Computer simulation indicates that estimates of
synonymous substitutions obtained by the two methods are quite accurate
unless the number of nucleotide substitutions per site is very large. It is
shown that all available methods tend to give an underestimate of the
number of nonsynonymous substitutions when the number is large.
ORIGINAL ARTICLE
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
Center for Demographic and Population Genetics, University of Texas at Houston 77225.
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X. Wang, H. Tang, J. E. Bowers, F. A. Feltus, and A. H. Paterson Extensive Concerted Evolution of Rice Paralogs and the Road to Regaining Independence Genetics, November 1, 2007; 177(3): 1753 - 1763. [Abstract] [Full Text] [PDF]
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M. T. Levine, A. K. Holloway, U. Arshad, and D. J. Begun Pervasive and Largely Lineage-Specific Adaptive Protein Evolution in the Dosage Compensation Complex of Drosophila melanogaster Genetics, November 1, 2007; 177(3): 1959 - 1962. [Abstract] [Full Text] [PDF]
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 N. J. Maness, L. E. Valentine, G. E. May, J. Reed, S. M. Piaskowski, T. Soma, J. Furlott, E. G. Rakasz, T. C. Friedrich, D. A. Price, et al. AIDS virus specific CD8+ T lymphocytes against an immunodominant cryptic epitope select for viral escape J. Exp. Med., October 29, 2007; 204(11): 2505 - 2512. [Abstract] [Full Text] [PDF]
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C. Carrillo, Z. Lu, M. V. Borca, A. Vagnozzi, G. F. Kutish, and D. L. Rock Genetic and Phenotypic Variation of Foot-and-Mouth Disease Virus during Serial Passages in a Natural Host J. Virol., October 15, 2007; 81(20): 11341 - 11351. [Abstract] [Full Text] [PDF]
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T. P. Tourova, E. M. Spiridonova, I. A. Berg, N. V. Slobodova, E. S. Boulygina, and D. Yu. Sorokin Phylogeny and evolution of the family Ectothiorhodospiraceae based on comparison of 16S rRNA, cbbL and nifH gene sequences Int J Syst Evol Microbiol, October 1, 2007; 57(10): 2387 - 2398. [Abstract] [Full Text] [PDF]
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 M. Ingman and U. Gyllensten Rate variation between mitochondrial domains and adaptive evolution in humans Hum. Mol. Genet., October 1, 2007; 16(19): 2281 - 2287. [Abstract] [Full Text] [PDF]
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L. R. Saraiva and S. I. Korsching A novel olfactory receptor gene family in teleost fish Genome Res., October 1, 2007; 17(10): 1448 - 1457. [Abstract] [Full Text] [PDF]
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D. T. Gerrard and A. Meyer Positive Selection and Gene Conversion in SPP120, a Fertilization-Related Gene, during the East African Cichlid Fish Radiation Mol. Biol. Evol., October 1, 2007; 24(10): 2286 - 2297. [Abstract] [Full Text] [PDF]
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 S. K. Bag, S. Paul, S. Ghosh, and C. Dutta Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human Mouse Orthologs of Two Compositional Extrema DNA Res, September 25, 2007; (2007) dsm015v1. [Abstract] [Full Text] [PDF]
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T. Kuwata, R. Byrum, S. Whitted, R. Goeken, A. Buckler-White, R. Plishka, R. Iyengar, and V. M. Hirsch A Rapid Progressor-Specific Variant Clone of Simian Immunodeficiency Virus Replicates Efficiently In Vivo Only in the Absence of Immune Reponses J. Virol., September 1, 2007; 81(17): 8891 - 8904. [Abstract] [Full Text] [PDF]
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A. L. V. Cohen, J. D. Oliver, A. DePaola, E. J. Feil, and E. Fidelma Boyd Emergence of a Virulent Clade of Vibrio vulnificus and Correlation with the Presence of a 33-Kilobase Genomic Island Appl. Envir. Microbiol., September 1, 2007; 73(17): 5553 - 5565. [Abstract] [Full Text] [PDF]
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H. Ogata and J.-M. Claverie Unique genes in giant viruses: Regular substitution pattern and anomalously short size Genome Res., September 1, 2007; 17(9): 1353 - 1361. [Abstract] [Full Text] [PDF]
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N. L. Clark, G. D. Findlay, X. Yi, M. J. MacCoss, and W. J. Swanson Duplication and Selection on Abalone Sperm Lysin in an Allopatric Population Mol. Biol. Evol., September 1, 2007; 24(9): 2081 - 2090. [Abstract] [Full Text] [PDF]
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 Y. Radhakrishnan, M. A. Fares, F. S. French, and S. H. Hall Comparative genomic analysis of a mammalian {beta}-defensin gene cluster Physiol Genomics, August 20, 2007; 30(3): 213 - 222. [Abstract] [Full Text] [PDF]
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 J.-M. Escobar-Restrepo, N. Huck, S. Kessler, V. Gagliardini, J. Gheyselinck, W.-C. Yang, and U. Grossniklaus The FERONIA Receptor-like Kinase Mediates Male-Female Interactions During Pollen Tube Reception Science, August 3, 2007; 317(5838): 656 - 660. [Abstract] [Full Text] [PDF]
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