How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the fisher-wright mutation-selection framework

Biology Letters

Volumn 11, Issue 4, 2015, Pages

  Dos Reis, Mario ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Adaptive evolution; Chloroplast; Influenza; Non synonymous synonymous ratio; Selection; Substitution

Indexed keywords

ADAPTATION; CHLOROPLAST; GENE; MUTATION; POPULATION GENETICS; PROTEIN; SELECTION;

CODON; PB2 PROTEIN, INFLUENZA VIRUS; PLANT PROTEIN; PROTEIN; VIRAL PROTEIN;

ANGIOSPERM; ANIMAL; BIOLOGICAL MODEL; CHLOROPLAST; CODON; GENETIC SELECTION; GENETICS; HUMAN; MOLECULAR EVOLUTION; MUTATION; ORTHOMYXOVIRIDAE; POPULATION GENETICS; STATISTICAL MODEL;

ANGIOSPERMS; ANIMALS; CHLOROPLASTS; CODON; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; ORTHOMYXOVIRIDAE; PLANT PROTEINS; PROTEINS; SELECTION, GENETIC; VIRAL PROTEINS;

EID: 84929095318     PISSN: 17449561     EISSN: 1744957X     Source Type: Journal    
DOI: 10.1098/rsbl.2014.1031     Document Type: Article

References (14)

1. Halpern AL, Bruno WJ. 1998 Evolutionary distances for protein-coding sequences: modeling sitespecific residue frequencies. Mol. Biol. Evol. 15, 910-917. (doi:10.1093/oxfordjournals.molbev. a025995)
2. Fisher R. 1930 The genetic theory of natural selection. Oxford, UK: Clarendon Press
3. Wright S. 1931 Evolution in Mendelian populations. Genetics 16, 97-159
4. Holder MT, Zwickl DJ, Dessimoz C. 2008 Evaluating the robustness of phylogenetic methods to amongsite variability in substitution processes. Phil. Trans. R. Soc. B 363, 4013-4021. (doi:10.1098/rstb. 2008.0162)
5. Spielman SJ, Wilke CO. 2015 The relationship between dN/dS and scaled selection coefficients. Mol. Biol. Evol.,32,(10.1093/molbev/msv003)
6. Yang Z, Nielsen R. 2008 Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol. Biol. Evol. 25, 568-579. (doi:10.1093/molbev/ msm284)
7. Rodrigue N, Philippe H, Lartillot N. 2010 Mutation- selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc. Natl Acad. Sci. USA 107, 4629-4634. (doi:10.1073/ pnas.0910915107)
8. Tamuri AU, dos Reis M, Goldstein RA. 2012 Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models. Genetics 190, 1101-1115. (doi:10.1534/genetics.111. 136432)
9. Tamuri AU, Goldman N, dos Reis M. 2014 A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data. Genetics 197, 257-271. (doi:10. 1534/genetics.114.162263)
10. dos Reis M. 2013 Population genetics and substitution models of adaptive evolution. (http:// arxiv.org/abs/1311.6682)
11. Tamuri AU, dos Reis M, Hay AJ, Goldstein RA. 2009 Identifying changes in selective constraints: host shifts in influenza. PLoS Comput. Biol. 5, e1000564. (doi:10.1371/journal.pcbi.1000564)
12. dos Reis M, Hay AJ, Goldstein RA. 2009 Using nonhomogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus. J. Mol. Evol. 69, 333-345. (doi:10.1007/s00239-009-9282-x)
13. Nielsen R, Yang Z. 2003 Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol. Biol. Evol. 20, 1231-1239. (doi:10.1093/molbev/msg147)
14. Bustamante CD. 2005 Population genetics of molecular evolution. In Statistical methods in molecular evolution (ed. R Nielsen), pp. 63-99. New York, NY: Springer.