Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Export

@article{citeulike:3088443, abstract = {The ratio of radical to conservative amino acid replacements is frequently used to infer positive Darwinian selection. This method is based on the assumption that radical replacements are more likely than conservative replacements to improve the function of a protein. Therefore, if positive selection plays a major role in the evolution of a protein, one would expect the radical-conservative ratio to exceed the expectation under neutrality. Here, we investigate the possibility that factors unrelated to selection, i.e., transition-transversion ratio, codon usage, genetic code, and amino acid composition, influence the radical-conservative replacement ratio. All factors that have been studied were found to affect the radical-conservative replacement ratio. In particular, amino acid composition and transition-transversion ratio are shown to have the most profound effects. Because none of the studied factors had anything to do with selection (positive or otherwise) and also because all of them (singly or in combination) affected a measure that was supposed to be indicative of positive selection, we conclude that selectional inferences based on radical-conservative replacement ratios should be treated with suspicion.}, address = {Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University. tali@kimura.tau.ac.il}, author = {Dagan, T. and Talmor, Y. and Graur, D.}, citeulike-article-id = {3088443}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12082122}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12082122}, issn = {0737-4038}, journal = {Molecular biology and evolution}, keywords = {ka\_ks}, month = {July}, number = {7}, pages = {1022--1025}, posted-at = {2008-08-05 16:43:03}, priority = {2}, title = {Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/12082122}, volume = {19}, year = {2002} }

TY - JOUR ID - citeulike:3088443 L3 - citeulike-article-id:3088443 N2 - The ratio of radical to conservative amino acid replacements is frequently used to infer positive Darwinian selection. This method is based on the assumption that radical replacements are more likely than conservative replacements to improve the function of a protein. Therefore, if positive selection plays a major role in the evolution of a protein, one would expect the radical-conservative ratio to exceed the expectation under neutrality. Here, we investigate the possibility that factors unrelated to selection, i.e., transition-transversion ratio, codon usage, genetic code, and amino acid composition, influence the radical-conservative replacement ratio. All factors that have been studied were found to affect the radical-conservative replacement ratio. In particular, amino acid composition and transition-transversion ratio are shown to have the most profound effects. Because none of the studied factors had anything to do with selection (positive or otherwise) and also because all of them (singly or in combination) affected a measure that was supposed to be indicative of positive selection, we conclude that selectional inferences based on radical-conservative replacement ratios should be treated with suspicion. IS - 7 JF - Molecular biology and evolution SN - 0737-4038 AD - Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University. tali@kimura.tau.ac.il EP - 1025 TI - Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. VL - 19 SP - 1022 KW - ka_ks AU - Dagan, T AU - Talmor, Y AU - Graur, D PY - 2002/07// UR - http://view.ncbi.nlm.nih.gov/pubmed/12082122 ER -