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

Molecular Biology and Evolution
Z Yang, Rasmus Nielsen

Abstract

Current models of codon substitution are formulated at the levels of nucleotide substitution and do not explicitly consider the separate effects of mutation and selection. They are thus incapable of inferring whether mutation or selection is responsible for evolution at silent sites. Here we implement a few population genetics models of codon substitution that explicitly consider mutation bias and natural selection at the DNA level. Selection on codon usage is modeled by introducing codon-fitness parameters, which together with mutation-bias parameters, predict optimal codon frequencies for the gene. The selective pressure may be for translational efficiency and accuracy or for fine-tuning translational kinetics to produce correct protein folding. We apply the models to compare mitochondrial and nuclear genes from several mammalian species. Model assumptions concerning codon usage are found to affect the estimation of sequence distances (such as the synonymous rate d(S), the nonsynonymous rate d(N), and the rate at the 4-fold degenerate sites d(4)), as found in previous studies, but the new models produced very similar estimates to some old ones. We also develop a likelihood ratio test to examine the null hypothesis that codon ...Continue Reading

Citations

Mar 25, 2009·Journal of Molecular Evolution·Alexis Criscuolo, Christian J Michel
Apr 29, 2010·Journal of Molecular Evolution·Daniel B Sloan, Douglas R Taylor
Sep 15, 2011·Journal of Molecular Evolution·Mikio C Aoi, Bryan C Rourke
Nov 18, 2008·Human Genetics·David A HughesMark Stoneking
Feb 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Nicolas RodrigueNicolas Lartillot
Oct 31, 2008·Briefings in Bioinformatics·Wayne DelportCathal Seoighe
Jul 14, 2010·Genome Biology and Evolution·Kate E RidoutDmitry A Filatov
Jul 25, 2009·The Journal of Heredity·Arlin Stoltzfus, Lev Y Yampolsky
Oct 17, 2008·Molecular Biology and Evolution·Maria Anisimova, Carolin Kosiol
Nov 27, 2008·Molecular Biology and Evolution·Mario dos Reis, Lorenz Wernisch
Dec 20, 2008·Molecular Biology and Evolution·Alan M Moses, Richard Durbin
Jan 20, 2009·Molecular Biology and Evolution·Sankar Subramanian
Apr 23, 2009·Molecular Biology and Evolution·Nicolas RodrigueNicolas Lartillot
Nov 26, 2009·Molecular Biology and Evolution·Diana Cumings Outlaw, Robert E Ricklefs
Mar 17, 2010·Molecular Biology and Evolution·Tong ZhouClaus O Wilke
Nov 27, 2010·Molecular Biology and Evolution·Mario dos ReisRichard A Goldstein
Aug 30, 2011·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Apr 12, 2012·Molecular Biology and Evolution·Tanya Renner, Chelsea D Specht
Apr 12, 2012·Molecular Biology and Evolution·Wanjun GuTong Zhou
Jun 27, 2012·Molecular Biology and Evolution·Lorenzo Carretero-Paulet, Mario A Fares
Mar 16, 2013·Molecular Biology and Evolution·Edward W J WallaceD Allan Drummond
May 24, 2013·Molecular Biology and Evolution·Laurent GuéguenJulien Y Dutheil
Jul 26, 2013·Molecular Biology and Evolution·Aoife Doherty, James O McInerney
Aug 3, 2013·Molecular Biology and Evolution·Nicola De MaioCarolin Kosiol
Mar 28, 2009·Journal of the Royal Society, Interface·Mark WelchJeremy Minshull
Jul 24, 2008·Proceedings. Biological Sciences·Sergey KryazhimskiyJonathan Dushoff
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Sang Chul ChoiJeffrey L Thorne
Mar 20, 2009·Journal of Virology·Eleca J DunhamJeffery K Taubenberger
Nov 6, 2008·Annual Review of Genetics·Ruth Hershberg, Dmitri A Petrov
Sep 13, 2012·BMC Evolutionary Biology·Michael P ScherrerClaus O Wilke
Sep 11, 2009·BMC Evolutionary Biology·Cécile BonnardNicolas Lartillot
Dec 10, 2009·BMC Evolutionary Biology·Yosef PratMichal Linial
Jan 9, 2009·BMC Evolutionary Biology·David A HughesMartin Klingenspor
Jul 9, 2013·Virology Journal·Mario TelloEugenio Spencer
Jan 1, 2010·Genes & Genetic Systems·Yoshiyuki Suzuki
Dec 17, 2008·PLoS Genetics·Sergey Kryazhimskiy, Joshua B Plotkin
Jun 6, 2013·PLoS Genetics·David S LawrieDmitri A Petrov

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