The excess of transitions among nucleotide substitutions: New methods of estimating transition bias underscore its significance

Estimates of transition bias provide insight into the process of nucleotide substitution, and are required in some commonly used phylogenetic methods. Transitions are favored over transversions among spontaneous mutations, and the direction and strength of selection on proteins and RNA appears to depend on mutation type. As the complexity of the nucleotide-substitution process has become apparent, problems with classical methods of estimating transition bias have been recognized, These problems arise because there is a fundamental difference between ratios of numbers of differences among sequences and ratios of rates, and because classical methods are not easily generalized. Several new methods are now available.