New methods for detecting positive selection at single amino acid sites

Journal of Molecular Evolution
Yoshiyuki Suzuki

Abstract

Inferring positive selection at single amino acid sites is of particular importance for studying evolutionary mechanisms of a protein. For this purpose, Suzuki and Gojobori (1999) developed a method (SG method) for comparing the rates of synonymous and nonsynonymous substitutions at each codon site in a protein-coding nucleotide sequence, using ancestral codons at interior nodes of the phylogenetic tree as inferred by the maximum parsimony method. In the SG method, however, selective neutrality of nucleotide substitutions cannot be tested at codon sites, where only termination codons are inferred at any interior node or the number of equally parsimonious inferences of ancestral codons at all interior nodes exceeds 10,000. Here I present a modified SG method which is free from these problems. Specifically, I use the distance-based Bayesian method for inferring the single most likely ancestral codon from 61 sense codons at each interior node. In the computer simulation and real data analysis, the modified SG method showed a higher overall efficiency of detecting positive selection than the original SG method, particularly at highly polymorphic codon sites. These results indicate that the modified SG method is useful for inferring...Continue Reading

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Citations

Oct 28, 2008·Journal of Molecular Evolution·J R CavatortaM M Jahn
Mar 31, 2007·Proceedings of the National Academy of Sciences of the United States of America·Arthur Chun-Chieh ShihWen-Hsiung Li
Apr 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Masafumi NozawaMasatoshi Nei
Aug 27, 2005·Molecular Biology and Evolution·Masatoshi Nei
May 4, 2005·Journal of Bacteriology·Burkhard Tümmler, Pierre Cornelis
May 21, 2005·BMC Evolutionary Biology·Colin A M SempleJulia R Dorin
Jun 23, 2006·PLoS Computational Biology·Sergei L Kosakovsky PondAndrew J Leigh Brown
Jan 18, 2005·Genetics·Tim Massingham, Nick Goldman
Apr 9, 2008·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Michael J StanhopeHeather Amrine-Madsen
Oct 20, 2006·Experimental Gerontology·Eva TerzibasiAlessandro Cellerino
Oct 7, 2005·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·K L HaagF J Ayala
Feb 14, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Yoshiyuki Suzuki
Jul 7, 2012·PloS One·Linn Fenna GroeneveldLinda Vigilant
Jun 14, 2012·PloS One·Oscar Westesson, Ian Holmes
Jan 24, 2013·PloS One·Adrian M AltenhoffChristophe Dessimoz
Oct 21, 2014·PloS One·Emanuel MaldonadoAgostinho Antunes
Mar 3, 2012·PloS One·Yann BertrandMagnus Johansson
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Sep 18, 2013·Biochemical and Biophysical Research Communications·Arindam DuttaTapan K Dutta
Aug 4, 2016·Molecular Biology and Evolution·Joseph MingroneJoseph Bielawski
Oct 17, 2008·Molecular Biology and Evolution·Maria Anisimova, Carolin Kosiol
Jul 5, 2006·Molecular Biology and Evolution·Yoshiyuki Suzuki
Feb 11, 2005·Molecular Biology and Evolution·Sergei L Kosakovsky Pond, Simon D W Frost
Jul 1, 2005·Molecular Biology and Evolution·Michael J B Krieger, Kenneth G Ross
Apr 20, 2019·Scientific Reports·Thorsten R KlingenAlice C McHardy
Nov 14, 2020·Current Opinion in HIV and AIDS·Ramon Lorenzo-RedondoJudd F Hultquist

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