Cited by 1,960Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsEvolution and Genetic Dynamics

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A codon-based model of nucleotide substitution for protein-coding DNA sequences.

Nick Goldman, Ziheng Yang·1994·Molecular Biology and Evolution

DOI 10.1093/oxfordjournals.molbev.a040153

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Abstract

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.

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“(1997) and Goodman et al. (1998) suggested Otolemur and Nycticebus grouped together to the exclusion of Perodicticus using ɛ-globin and the β-globin sequences.”
BackgroundMethod
Correlation Between Ka/Ks and Ks is Related to Substitution Model and Evolutionary Lineage
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Authors: Goldman, N., & Yang, Z.
Affiliations: National Institute for Medical Research (GB)
ORCID: Nick Goldman
Ziheng Yang
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 1994-09
Volume: 11
Issue: 5
Pages: 725-36
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/oxfordjournals.molbev.a040153
OpenAlex: W1920973730
Cited by: 1,960
References: 31
Citations by year: 2026: 18 · 2025: 42 · 2024: 51 · 2023: 43 · 2022: 61 · 2021: 65 · 2020: 60 · 2019: 74 · 2018: 71 · 2017: 60 · 2016: 69 · 2015: 68 · 2014: 107 · 2013: 97 · 2012: 89
FWCI: 2.27
Type: journal article
Language: en
Open access: closed
Locations: Molecular Biology and Evolution (publishedVersion)
PubMed (publishedVersion)
Funders: National Eye Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords: Markov processes, codon usage bias, selective constraint, synonymous substitution rate, nonsynonymous substitution rate, phylogenetic estimation, nucleotide substitution models
MeSH terms: Animals, Chemistry, Physical, Codon, DNA, Genes, Globins, Mammals, Markov Chains, Models, Genetic, Nucleotidyltransferases, Phylogeny, Proteins, Likelihood Functions, Point Mutation, Glucose-1-Phosphate Adenylyltransferase, Chemical Phenomena

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A codon-based model of nucleotide substitution for protein-coding DNA sequences.

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