Molecular Biology and Evolution, Vol 11, 715-724, Copyright © 1994 by Society for Molecular Biology and Evolution
SV Muse and BS Gaut
A model of DNA sequence evolution applicable to coding regions is
presented. This represents the first evolutionary model that accounts for
dependencies among nucleotides within a codon. The model uses the codon, as
opposed to the nucleotide, as the unit of evolution, and is parameterized
in terms of synonymous and nonsynonymous nucleotide substitution rates. One
of the model's advantages over those used in methods for estimating
synonymous and nonsynonymous substitution rates is that it completely
corrects for multiple hits at a codon, rather than taking a parsimony
approach and considering only pathways of minimum change between homologous
codons. Likelihood-ratio versions of the relative-rate test are constructed
and applied to data from the complete chloroplast DNA sequences of Oryza
sativa, Nicotiana tabacum, and Marchantia polymorpha. Results of these
tests confirm previous findings that substitution rates in the chloroplast
genome are subject to both lineage-specific and locus-specific effects.
Additionally, the new tests suggest tha the rate heterogeneity is due
primarily to differences in nonsynonymous substitution rates. Simulations
help confirm previous suggestions that silent sites are saturated, leaving
no evidence of heterogeneity in synonymous substitution rates.
ORIGINAL ARTICLE
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
Department of Statistics, North Carolina State University.
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 A.G. CLARK, S. GLANOWSKI, R. NIELSEN, P. THOMAS, A. KEJARIWAL, M.J. TODD, D.M. TANENBAUM, D. CIVELLO, F. LU, B. MURPHY, et al. Positive Selection in the Human Genome Inferred from Human-Chimp-Mouse Orthologous Gene Alignments Cold Spring Harb Symp Quant Biol, January 1, 2003; 68(0): 479 - 486. [Abstract] [PDF]
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N. Goldman and S. Whelan A Novel Use of Equilibrium Frequencies in Models of Sequence Evolution Mol. Biol. Evol., November 1, 2002; 19(11): 1821 - 1831. [Abstract] [Full Text] [PDF]
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J. Yang, J. Huang, H. Gu, Y. Zhong, and Z. Yang Duplication and Adaptive Evolution of the Chalcone Synthase Genes of Dendranthema (Asteraceae) Mol. Biol. Evol., October 1, 2002; 19(10): 1752 - 1759. [Abstract] [Full Text] [PDF]
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L. Zhang, T. J. Vision, and B. S. Gaut Patterns of Nucleotide Substitution Among Simultaneously Duplicated Gene Pairs in Arabidopsis thaliana Mol. Biol. Evol., September 1, 2002; 19(9): 1464 - 1473. [Abstract] [Full Text] [PDF]
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B. S. W. Chang, K. Jonsson, M. A. Kazmi, M. J. Donoghue, and T. P. Sakmar Recreating a Functional Ancestral Archosaur Visual Pigment Mol. Biol. Evol., September 1, 2002; 19(9): 1483 - 1489. [Abstract] [Full Text] [PDF]
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E. Schadt and K. Lange Codon and Rate Variation Models in Molecular Phylogeny Mol. Biol. Evol., September 1, 2002; 19(9): 1534 - 1549. [Abstract] [Full Text] [PDF]
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D. L. Remington and M. D. Purugganan GAI Homologues in the Hawaiian Silversword Alliance (Asteraceae-Madiinae): Molecular Evolution of Growth Regulators in a Rapidly Diversifying Plant Lineage Mol. Biol. Evol., September 1, 2002; 19(9): 1563 - 1574. [Abstract] [Full Text] [PDF]
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 G. C. Conant and A. Wagner GenomeHistory: a software tool and its application to fully sequenced genomes Nucleic Acids Res., August 1, 2002; 30(15): 3378 - 3386. [Abstract] [Full Text] [PDF]
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Z. Yang and R. Nielsen Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages Mol. Biol. Evol., June 1, 2002; 19(6): 908 - 917. [Abstract] [Full Text] [PDF]
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C.-A. Whittle and M. O. Johnston Male-Driven Evolution of Mitochondrial and Chloroplastidial DNA Sequences in Plants Mol. Biol. Evol., June 1, 2002; 19(6): 938 - 949. [Abstract] [Full Text] [PDF]
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M. Anisimova, J. P. Bielawski, and Z. Yang Accuracy and Power of Bayes Prediction of Amino Acid Sites Under Positive Selection Mol. Biol. Evol., June 1, 2002; 19(6): 950 - 958. [Abstract] [Full Text] [PDF]
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