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Literature DB >> 25854546

How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework.

Abstract

First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast gene and a virus polymerase) are given. The formulae give much insight into the dynamics of non-synonymous substitutions and may inform the development of methods to detect adaptive evolution.

Keywords: adaptive evolution; chloroplast; influenza; non-synonymous/synonymous ratio; selection; substitution

Mesh：

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Year: 2015 PMID： 25854546 PMCID： PMC4424610 DOI： 10.1098/rsbl.2014.1031

Source DB: PubMed Journal: Biol Lett ISSN： 1744-9561 Impact factor: 3.703

11 in total

1. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.

Authors: Rasmus Nielsen; Ziheng Yang
Journal: Mol Biol Evol Date: 2003-05-30 Impact factor: 16.240

2. Evolution in Mendelian Populations.

Authors: S Wright
Journal: Genetics Date: 1931-03 Impact factor: 4.562

3. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.

Authors: Ziheng Yang; Rasmus Nielsen
Journal: Mol Biol Evol Date: 2008-01-03 Impact factor: 16.240

4. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes.

Authors: Mark T Holder; Derrick J Zwickl; Christophe Dessimoz
Journal: Philos Trans R Soc Lond B Biol Sci Date: 2008-12-27 Impact factor: 6.237

5. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.

Authors: A L Halpern; W J Bruno
Journal: Mol Biol Evol Date: 1998-07 Impact factor: 16.240

6. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.

Authors: Nicolas Rodrigue; Hervé Philippe; Nicolas Lartillot
Journal: Proc Natl Acad Sci U S A Date: 2010-02-22 Impact factor: 11.205

7. The relationship between dN/dS and scaled selection coefficients.

Authors: Stephanie J Spielman; Claus O Wilke
Journal: Mol Biol Evol Date: 2015-01-08 Impact factor: 16.240

8. A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.

Authors: Asif U Tamuri; Nick Goldman; Mario dos Reis
Journal: Genetics Date: 2014-02-14 Impact factor: 4.562

9. Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus.

Authors: Mario dos Reis; Alan J Hay; Richard A Goldstein
Journal: J Mol Evol Date: 2009-09-29 Impact factor: 2.395

10. Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.

Authors: Asif U Tamuri; Mario dos Reis; Richard A Goldstein
Journal: Genetics Date: 2011-12-29 Impact factor: 4.562

13 in total

How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework.

1. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.

2. Evolution in Mendelian Populations.

3. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.

4. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes.

5. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.

6. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.

7. The relationship between dN/dS and scaled selection coefficients.

8. A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.

9. Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus.

10. Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.

1. A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation.

2. Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint.

3. Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates.

Review 4. Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work.

5. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.

6. Finding Direction in the Search for Selection.

Review 7. Tumour Microenvironment and Immune Evasion in EGFR Addicted NSCLC: Hurdles and Possibilities.

8. Evolution of Amino Acid Propensities under Stability-Mediated Epistasis.

9. Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.

10. A Mutation-Selection Model of Protein Evolution under Persistent Positive Selection.