TOPIARY PRUNING AND WEIGHTING REINFORCE AN AFRICAN ORIGIN FOR THE HUMAN MITOCHONDRIAL DNA TREE.

Abstract

A method is presented for removing recent homoplastic events from a phylogenetic tree. This "topiary pruning" method produces a series of progressively modified duplicates of the original set of data, from which more and more of the most recent substitutions have been removed. The edited sets of data have increased amounts of information per remaining taxon, while similar but randomized data sets subjected to topiary pruning do not. The ability of topiary pruning to "unscramble" artificial data sets that have high levels of homoplasy is demonstrated, and is shown to be similar in its effects to the weighting method of Kluge and Farris (1969), although with the additional advantage of reducing the number of taxa to the point where bootstrapping is feasible. Pruning and weighting used together produce closer approximations to the "true" tree than either method used separately. It is further shown that in these artificial data sets midpoint rooting is more likely to be accurate than outgroup rooting. When pruning and weighting are applied to the extensive sets of mitochondrial DNA data of Cann et al. (1987) and Vigilant et al. (1991), trees result that have deep branch points, some of which lead to entirely African branches. In the case of the Vigilant et al. data, the three African branches have bootstrap values between 0.94 and 1.0, and the consensus and bootstrap midpoint roots also have high bootstrap values and occur on these African branches near their junction. An African origin of the human mitochondrial tree is not proved by this approach, particularly since sequences from non-African groups are underrepresented in current data sets, but it is rendered more likely.