A Comparison of the Suitability of the Rogers, Modified Rogers, Manhattan, and Cavalli-sforza and Edwards Distances for Inferring Phylogenetic Trees from Allele Frequencies

Abstract

Theoretical considerations and the results of computer simulations demonstrate that Swofford and Berlocher's (1987, Syst. Zool. 36:293-325) reason for preferring the Manhattan metric over Rogers's distance for inferring phylogenetic trees from allele frequencies under the principle of maximum parsimony is not necessarily valid. The theoretical considerations lead to the proposal of a new general criterion for choosing between cladograms or trees of equal length for qualitative characters as well―when two trees are of equal length, the one that is consistent with more possible transformation series of the characters under consideration is preferable