Improving the analysis of phylogenetic data

Methods of phylogenetic analysis are presented that result in corrections of highly biased data sets, particularly those in which there are great differences between mutation and/or substitution rates from one nucleotide site to another along a DNA sequence. Two approaches are discussed. In the first, pairwise comparisons of a set of sequences are used to determine whether the most recent substitutions take place at the sites that are most polymorphic--that is, where the mutational "hot spots" are located. In the second, a "topiary pruning" method is used to remove selectively the bases in the data set that are most likely to occupy these hot spots and therefore to result in homoplastic substitutions. The two methods combined yield new and substantially older estimates of the time at which the mitochondrial Eve lived, and increase the likelihood that she lived in Africa. In these data, transversions provide a more satisfactory yardstick for phylogenetic analysis than transitions, because there is no detectable tendency for transversions to occur at mutational hot spots.