Estimating the Transition/Transversion Ratio from Independent Pairwise Comparisons with an Assumed Phylogeny Export

@article{citeulike:6032276, abstract = {Abstract.\ \  A method is presented for estimating the transition/transversion ratio (TI/TV), based on phylogenetically independent comparisons. TI/TV is a parameter of some models used in phylogeny estimation intended to reflect the fact that nucleotide substitutions are not all equally likely. Previous attempts to estimate TI/TV have commonly faced three problems: (1) few taxa; (2) nonindependence among pairwise comparisons; and (3) multiple hits make the apparent TI/TV between two sequences decrease over time since their divergence, giving a misleading impression of relative substitution probabilities. We have made use of the time dependency, modeling how the observed TI/TV changes over time and extrapolating to estimate the ``instantaneous'' TI/TV—the relevant parameter for phylogenetic inference. To illustrate our method, TI/TV was estimated for two mammalian mitochondrial genes. For 26 pairs of cytochrome b sequences, the estimate of TI/TV was 5.5; 16 pairs of 12s rRNA yielded an estimate of 9.5. These estimates are higher than those given by the maximum likelihood method and than those obtained by averaging all possible pairwise comparisons (with or without a two-parameter correction for multiple substitutions). We discuss strengths, weaknesses, and further uses of our method.}, author = {Purvis, Andy and Bromham, Lindell}, citeulike-article-id = {6032276}, citeulike-linkout-0 = {http://dx.doi.org/10.1007/PL00006117}, citeulike-linkout-1 = {http://www.springerlink.com/content/0er974l7jq6axhye}, day = {24}, doi = {10.1007/PL00006117}, journal = {Journal of Molecular Evolution}, keywords = {phylogenetics}, month = {January}, number = {1}, pages = {112--119}, posted-at = {2009-10-29 14:11:29}, priority = {2}, title = {Estimating the Transition/Transversion Ratio from Independent Pairwise Comparisons with an Assumed Phylogeny}, url = {http://dx.doi.org/10.1007/PL00006117}, volume = {44}, year = {1997} }

TY - JOUR ID - citeulike:6032276 L3 - citeulike-article-id:6032276 N2 - Abstract.   A method is presented for estimating the transition/transversion ratio (TI/TV), based on phylogenetically independent comparisons. TI/TV is a parameter of some models used in phylogeny estimation intended to reflect the fact that nucleotide substitutions are not all equally likely. Previous attempts to estimate TI/TV have commonly faced three problems: (1) few taxa; (2) nonindependence among pairwise comparisons; and (3) multiple hits make the apparent TI/TV between two sequences decrease over time since their divergence, giving a misleading impression of relative substitution probabilities. We have made use of the time dependency, modeling how the observed TI/TV changes over time and extrapolating to estimate the ``instantaneous'' TI/TV—the relevant parameter for phylogenetic inference. To illustrate our method, TI/TV was estimated for two mammalian mitochondrial genes. For 26 pairs of cytochrome b sequences, the estimate of TI/TV was 5.5; 16 pairs of 12s rRNA yielded an estimate of 9.5. These estimates are higher than those given by the maximum likelihood method and than those obtained by averaging all possible pairwise comparisons (with or without a two-parameter correction for multiple substitutions). We discuss strengths, weaknesses, and further uses of our method. IS - 1 JF - Journal of Molecular Evolution EP - 119 TI - Estimating the Transition/Transversion Ratio from Independent Pairwise Comparisons with an Assumed Phylogeny VL - 44 SP - 112 KW - phylogenetics AU - Purvis, Andy AU - Bromham, Lindell PY - 1997/01/24/ UR - http://dx.doi.org/10.1007/PL00006117 ER -