Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions.

@article{citeulike:835239, abstract = {Rates and patterns of synonymous and nonsynonymous substitutions have important implications for the origin and maintenance of mammalian isochores and the effectiveness of selection at synonymous sites. Previous studies of mammalian nuclear genes largely employed approximate methods to estimate rates of nonsynonymous and synonymous substitutions. Because these methods did not account for major features of DNA sequence evolution such as transition/transversion rate bias and unequal codon usage, they might not have produced reliable results. To evaluate the impact of the estimation method, we analyzed a sample of 82 nuclear genes from the mammalian orders Artiodactyla, Primates, and Rodentia using both approximate and maximum-likelihood methods. Maximum-likelihood analysis indicated that synonymous substitution rates were positively correlated with GC content at the third codon positions, but independent of nonsynonymous substitution rates. Approximate methods, however, indicated that synonymous substitution rates were independent of GC content at the third codon positions, but were positively correlated with nonsynonymous rates. Failure to properly account for transition/transversion rate bias and unequal codon usage appears to have caused substantial biases in approximate estimates of substitution rates.}, address = {Department of Biology, University College London, London NW1 2HE, United Kingdom. j.bielawski@ucl.ac.uk}, author = {Bielawski, J. P. and Dunn, K. A. and Yang, Z. }, citeulike-article-id = {835239}, issn = {0016-6731}, journal = {Genetics}, keywords = {adaptation, positive, selection, w}, month = {November}, number = {3}, pages = {1299--1308}, posted-at = {2006-09-08 10:51:12}, priority = {2}, title = {Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/11063703}, volume = {156}, year = {2000} }

TY - JOUR ID - citeulike:835239 L3 - citeulike-article-id:835239 TI - Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions. JF - Genetics VL - 156 IS - 3 SP - 1299 EP - 1308 AD - Department of Biology, University College London, London NW1 2HE, United Kingdom. j.bielawski@ucl.ac.uk SN - 0016-6731 N2 - Rates and patterns of synonymous and nonsynonymous substitutions have important implications for the origin and maintenance of mammalian isochores and the effectiveness of selection at synonymous sites. Previous studies of mammalian nuclear genes largely employed approximate methods to estimate rates of nonsynonymous and synonymous substitutions. Because these methods did not account for major features of DNA sequence evolution such as transition/transversion rate bias and unequal codon usage, they might not have produced reliable results. To evaluate the impact of the estimation method, we analyzed a sample of 82 nuclear genes from the mammalian orders Artiodactyla, Primates, and Rodentia using both approximate and maximum-likelihood methods. Maximum-likelihood analysis indicated that synonymous substitution rates were positively correlated with GC content at the third codon positions, but independent of nonsynonymous substitution rates. Approximate methods, however, indicated that synonymous substitution rates were independent of GC content at the third codon positions, but were positively correlated with nonsynonymous rates. Failure to properly account for transition/transversion rate bias and unequal codon usage appears to have caused substantial biases in approximate estimates of substitution rates. KW - adaptation KW - positive KW - selection KW - w AU - Bielawski, JP AU - Dunn, KA AU - Yang, Z PY - 2000/11// UR - http://view.ncbi.nlm.nih.gov/pubmed/11063703 ER -