PMID: 9541535Apr 29, 1998Paper

Synonymous and nonsynonymous rate variation in nuclear genes of mammals

Journal of Molecular Evolution
Z Yang, R Nielsen

Abstract

A maximum likelihood approach was used to estimate the synonymous and nonsynonymous substitution rates in 48 nuclear genes from primates, artiodactyls, and rodents. A codon-substitution model was assumed, which accounts for the genetic code structure, transition/transversion bias, and base frequency biases at codon positions. Likelihood ratio tests were applied to test the constancy of nonsynonymous to synonymous rate ratios among branches (evolutionary lineages). It is found that at 22 of the 48 nuclear loci examined, the nonsynonymous/synonymous rate ratio varies significantly across branches of the tree. The result provides strong evidence against a strictly neutral model of molecular evolution. Our likelihood estimates of synonymous and nonsynonymous rates differ considerably from previous results obtained from approximate pairwise sequence comparisons. The differences between the methods are explored by detailed analyses of data from several genes. Transition/transversion rate bias and codon frequency biases are found to have significant effects on the estimation of synonymous and nonsynonymous rates, and approximate methods do not adequately account for those factors. The likelihood approach is preferable, even for pairwi...Continue Reading

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Citations

Dec 2, 1999·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·S Easteal
Feb 8, 2005·Journal of Molecular Evolution·Sidney DelgadoJean-Yves Sire
Feb 8, 2005·Journal of Molecular Evolution·Alexander N YatsenkoJames R Lupski
Jun 7, 2006·Journal of Molecular Evolution·Nina M Talyzina, Pär K Ingvarsson
Mar 25, 2009·Journal of Molecular Evolution·Alexis Criscuolo, Christian J Michel
Jun 12, 2009·Journal of Molecular Evolution·Philippe Gayral, Marie-Line Iskra-Caruana
Mar 30, 2010·Journal of Molecular Evolution·Yuichi NaritaTakashi Kageyama
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Aug 15, 2009·Molecular Biology and Evolution·Tom ViaeneKoen Geuten
Mar 20, 2010·Molecular Biology and Evolution·Lesheng KongChris P Ponting

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