The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Models of amino acid substitution and applications to mitochondrial protein evolution
Abstract
Models of amino acid substitution were developed and compared using maximum likelihood. Two kinds of models are considered. "Empirical" models do not explicitly consider factors that shape protein evolution, but attempt to summarize the substitution pattern from large quantities of real data. "Mechanistic" models are formulated at the codon level and separate mutational biases at the nucleotide level from selective constraints at the amino acid level. They account for features of sequence evolution, such as transition-transversion bias and base or codon frequency biases, and make use of physicochemical distances between amino acids to specify nonsynonymous substitution rates. A general approach is presented that transforms a Markov model of codon substitution into a model of amino acid replacement. Protein sequences from the entire mitochondrial genomes of 20 mammalian species were analyzed using different models. The mechanistic models were found to fit the data better than empirical models derived from large databases. Both the mutational distance between amino acids (determined by the genetic code and mutational biases such as the transition-transversion bias) and the physicochemical distance are found to have strong effects on amino acid substitution rates. A significant proportion of amino acid substitutions appeared to have involved more than one codon position, indicating that nucleotide substitutions at neighboring sites may be correlated. Rates of amino acid substitution were found to be highly variable among sites.
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Citations
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
Evolutionary divergence and convergence in proteins.
ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
Self-citationEstimating the pattern of nucleotide substitution
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178256 · Cited by 1,076
Self-citation
Cited by
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
Self-citationWhelan, S., & Goldman, N. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003851 · Cited by 2,849
dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.0683 · Cited by 526
Self-citationPhylogenetic tree building in the genomic age
Kapli, P., Yang, Z., & Telford, M. J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0233-0 · Cited by 533
Self-citationEstimation of primate speciation dates using local molecular clocks.
Yoder, A. D., & Yang, Z. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026389 · Cited by 494
Self-citationThe Rooting of the Universal Tree of Life Is Not Reliable
Philippe, H., & Forterre, P. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006573 · Cited by 267
On Reduced Amino Acid Alphabets for Phylogenetic Inference
Susko, E., & Roger, A. J. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm144 · Cited by 177
Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study
Rota-Stabelli, O., Lartillot, N., Philippe, H., & Pisani, D. (2013) · Systematic Biology · doi:10.1093/sysbio/sys077 · Cited by 155
Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs.
Matsui, A., Rakotondraparany, F., Munechika, I., Hasegawa, M., & Horai, S. (2009) · Gene · doi:10.1016/j.gene.2008.08.024 · Cited by 121
“(1979) amino acid distance with geometric formulae was used in calculating the acceptance rate of amino acid substitution (Yang et al., 1998).”
MethodA methodological bias toward overestimation of molecular evolutionary time scales
Rodríguez-Trelles, F., Tarrío, R., & Ayala, F. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.122231299 · Cited by 116
Hansmann, S., & Martin, W. (2000) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/00207713-50-4-1655 · Cited by 99
Dahlbäck, M., Rask, T. S., Andersen, P. H., Nielsen, M. A., Ndam, N. T., Resende, M., Turner, L., Deloron, P., Hviid, L., Lund, O., et al. (2006) · PLoS Pathogens · doi:10.1371/journal.ppat.0020124 · Cited by 98
A new criterion and method for amino acid classification
Kosiol, C., Goldman, N., & H. Buttimore, N. (2004) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2003.12.010 · Cited by 70
Genes underlying the evolution of tetrapod testes size
Baker, J., Meade, A., & Venditti, C. (2021) · BMC Biology · doi:10.1186/s12915-021-01107-z · Cited by 6
Decomposing information into copying versus transformation
Kolchinsky, A., & Corominas-Murtra, B. (2020) · Journal of The Royal Society Interface · doi:10.1098/rsif.2019.0623 · Cited by 5
Metadata
- Authors
- Yang, Z., Nielsen, R., & Hasegawa, M.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 1998-12-01
- Volume
- 15
- Issue
- 12
- Pages
- 1600-1611
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W1973101413
- Cited by
- 419
- References
- 4
- FWCI
- 2.48
- Type
- journal article
- Language
- en
- Open access
- closed
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