A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
Open accessAbstract
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The first codon models estimated parameters representing an averaged nonsynonymous-synonymous rate ratio.
“The first codon models estimated parameters representing an averaged nonsynonymous-synonymous rate ratio.”
From RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015) · cites this paper as Muse and Gaut 1994
The Probabilistic Model for Codon Evolution section says the model’s parameters determine synonymous and nonsynonymous substitution rates. But Parameter Interpretation describes the estimated parameters as products of instantaneous rates and time, not as an averaged nonsynonymous-to-synonymous rate ratio; its averaging over codons concerns expected substitution counts. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687 · see citing works
Flagged first, then by citations
Research works printed but not linked: 8
- BOUSQUET, J., S. H. STRAUSS, A. H. DOERKESEN, and R. A. PRICE. 1992. Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc. Natl. Acad. Sci. USA 89:7844-7848.
- DAHLGREEN, R. M. T., 1~. T. CLIFFORD, and P. F. YEO. 1985. The families of the Monocotyledons: structure, evolution, and taxonomy. Springer, Berlin.
- JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 2 1-132 in H. M. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
- KARLIN, S., and H. M. TAYLOR. 1975. A first course in sto- chastic processes, 2d ed. Academic Press, New York.
- PRESS, W. H., S. A. TEUKOLSKY, W. T. VETTERLING, and B. P. FLANNERY. 1992. Numerical recipes, 2d ed. Cam- bridge University Press, Cambridge.
- WOLFE, K. H., M. GOUY, Y.-W. YANG, P. M. SHARP, and W.-H. LI. 1989. Date of the monocot-dicot divergence es- timated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86:6201-6205.
- WOLFE, K. H., W.-H. LI, and P. M. SHARP. 1987. Rates of nucleotide substitution vary greatly among plant mito- chondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84:9054-9058.
- WU, C.-I., and W.-H. LI. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745.
Cited by
Sorted by citations
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879 · see citing works
Detecting Individual Sites Subject to Episodic Diversifying Selection
Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002764 · Cited by 1,811 · see citing works
The Population Genetics of dN/dS
Kryazhimskiy, S., & Plotkin, J. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000304 · Cited by 962 · see citing works
RELAX: Detecting Relaxed Selection in a Phylogenetic Framework
Wertheim, J. O., Murrell, B., Smith, M. D., Kosakovsky Pond, S. L., & Scheffler, K. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu400 · Cited by 778 · see citing works
Model Selection in Phylogenetics
Sullivan, J., & Joyce, P. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.36.102003.152633 · Cited by 412 · see citing works
The importance of proper model assumption in bayesian phylogenetics.
Lemmon, A. R., & Moriarty, E. C. (2004) · Systematic Biology · doi:10.1080/10635150490423520 · Cited by 356 · see citing works
Yang, Z., & Yoder, A. D. (2003) · Systematic Biology · doi:10.1080/10635150390235557 · Cited by 357 · see citing works
A human coronavirus evolves antigenically to escape antibody immunity
Eguia, R., Crawford, K. H. D., Stevens-Ayers, T., Kelnhofer-Millevolte, L., Greninger, A. L., Englund, J. A., Boeckh, M. J., & Bloom, J. D. (2020) · doi:10.1101/2020.12.17.423313 · Cited by 258 · see citing works
Influence of metabolic network structure and function on enzyme evolution
Vitkup, D., Kharchenko, P., & Wagner, A. (2006) · Genome biology · doi:10.1186/gb-2006-7-5-r39 · Cited by 175 · see citing works
The Evolutionary Pathway to Virulence of an RNA Virus
Stern, A., Yeh, M. T., Zinger, T., Smith, M., Wright, C., Ling, G., Nielsen, R., Macadam, A., & Andino, R. (2017) · Cell · doi:10.1016/j.cell.2017.03.013 · Cited by 127 · see citing works
Rooting the tree of life: the phylogenetic jury is still out
Gouy, R., Baurain, D., & Philippe, H. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0329 · Cited by 96 · see citing works
Fukushima, K., & Pollock, D. D. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01932-7 · Cited by 55 · see citing works
- Authors
- Muse, S. V., & Gaut, B. S.
- Affiliations
- North Carolina State University (US)
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 1994-09
- Volume
- 11
- Issue
- 5
- Pages
- 715-24
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W1881807356
- Cited by
- 920
- References
- 2
- Citations by year
- 2026: 25 · 2025: 19 · 2024: 22 · 2023: 16 · 2022: 25 · 2021: 27 · 2020: 30 · 2019: 50 · 2018: 28 · 2017: 27 · 2016: 45 · 2015: 25 · 2014: 51 · 2013: 44 · 2012: 39
- FWCI
- 3.00
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (16250)
- National Institutes of Health (16250)
- National Institute of General Medical Sciences (F32GM016250, GM-16250, F32GM015528, R01GM032518, GM15528, GM32518)
- 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
- synonymous substitution rate, nonsynonymous substitution rate, relative rate tests, likelihood ratio test, chloroplast genome, rate heterogeneity, rice, tobacco, Marchantia polymorpha
- MeSH terms
- Chloroplasts, Codon, Computer Simulation, Models, Genetic, Phylogeny, Plants, Plants, Toxic, Oryza, Sequence Homology, Nucleic Acid, Nicotiana, Likelihood Functions, Point Mutation, DNA, Chloroplast
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
