Deriving Phylogenetic Trees from Allele Frequencies: A Comparison of Nine Genetic Distances

Abstract

An iterative procedure for deriving minimum-length phylogenetic trees form allele frequencies using Rogers'' genetic distance as the measure of branch length is extended to include eight additional distances: a modified Rogers'' distance; Nei''s standard, maximum and minimum distances; Cavalli-Sforza and Edwards'' chord and arc distances; and modified forms of the chord and arc distances. The derivation of such trees is defended as a parsimony procedure, and I conclude that any distance used in this procedure must be metric. The nine genetic distances are compared on the criteria of: metricity; ability to produce ancestral allele frequencies with heterozygosity approximating that of the terminal taxa; convergence to a stable solution; and computer time. The modified Cavalli-Sforza and Edwards'' chord distance is equal or superior to the other distances on the first three criteria, but requires more computer time than most. Rogers'' distance has the properties of metricity and convergence, and ranks below the modified chord distance on ancestral heterozygosity, but generally requires about one-half as much computer time as the modified chord distance.