Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.

<h4>Background</h4>A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and e...

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Autor principal:	Sanzo Miyazawa
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/17b0b699298e47288983f63bd919f1ab
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spelling	oai:doaj.org-article:17b0b699298e47288983f63bd919f1ab2021-11-18T07:31:18ZAdvantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.1932-620310.1371/journal.pone.0028892https://doaj.org/article/17b0b699298e47288983f63bd919f1ab2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22220197/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated.<h4>Results</h4>The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that assuming variable mutation rates over sites lead to the overestimation of branch lengths.Sanzo MiyazawaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 12, p e28892 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sanzo Miyazawa Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
description	<h4>Background</h4>A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated.<h4>Results</h4>The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that assuming variable mutation rates over sites lead to the overestimation of branch lengths.
format	article
author	Sanzo Miyazawa
author_facet	Sanzo Miyazawa
author_sort	Sanzo Miyazawa
title	Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
title_short	Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
title_full	Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
title_fullStr	Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
title_full_unstemmed	Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
title_sort	advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/17b0b699298e47288983f63bd919f1ab
work_keys_str_mv	AT sanzomiyazawa advantagesofamechanisticcodonsubstitutionmodelforevolutionaryanalysisofproteincodingsequences
_version_	1718423333203083264

Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.

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