Molecular Biology and Evolution, Vol 11, 725-736, Copyright © 1994 by Society for Molecular Biology and Evolution
N Goldman and Z Yang
A codon-based model for the evolution of protein-coding DNA sequences is
presented for use in phylogenetic estimation. A Markov process is used to
describe substitutions between codons. Transition/transversion rate bias
and codon usage bias are allowed in the model, and selective restraints at
the protein level are accommodated using physicochemical distances between
the amino acids coded for by the codons. Analyses of two data sets suggest
that the new codon-based model can provide a better fit to data than can
nucleotide-based models and can produce more reliable estimates of certain
biologically important measures such as the transition/transversion rate
ratio and the synonymous/nonsynonymous substitution rate ratio.
ORIGINAL ARTICLE
A codon-based model of nucleotide substitution for protein-coding DNA sequences
Laboratory of Mathematical Biology, National Institute for Medical Research, United Kingdom.
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E. Betran, Y. Bai, and M. Motiwale Fast Protein Evolution and Germ Line Expression of a Drosophila Parental Gene and Its Young Retroposed Paralog Mol. Biol. Evol., November 1, 2006; 23(11): 2191 - 2202. [Abstract] [Full Text] [PDF]
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K. Scheffler, D. P. Martin, and C. Seoighe Robust inference of positive selection from recombining coding sequences Bioinformatics, October 15, 2006; 22(20): 2493 - 2499. [Abstract] [Full Text] [PDF]
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S. B. Cannon, L. Sterck, S. Rombauts, S. Sato, F. Cheung, J. Gouzy, X. Wang, J. Mudge, J. Vasdewani, T. Schiex, et al. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes PNAS, October 3, 2006; 103(40): 14959 - 14964. [Abstract] [Full Text] [PDF]
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N. Izagirre, I. Garcia, C. Junquera, C. de la Rua, and S. Alonso A Scan for Signatures of Positive Selection in Candidate Loci for Skin Pigmentation in Humans Mol. Biol. Evol., September 1, 2006; 23(9): 1697 - 1706. [Abstract] [Full Text] [PDF]
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S. Bjornerfeldt, M. T. Webster, and C. Vila Relaxation of selective constraint on dog mitochondrial DNA following domestication Genome Res., August 1, 2006; 16(8): 990 - 994. [Abstract] [Full Text] [PDF]
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J. M. Marshall and R. E. Weiss A Bayesian Heterogeneous Analysis of Variance Approach to Inferring Recent Selective Sweeps Genetics, August 1, 2006; 173(4): 2357 - 2370. [Abstract] [Full Text] [PDF]
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C. Greenman, R. Wooster, P. A. Futreal, M. R. Stratton, and D. F. Easton Statistical Analysis of Pathogenicity of Somatic Mutations in Cancer Genetics, August 1, 2006; 173(4): 2187 - 2198. [Abstract] [Full Text] [PDF]
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