THEORETICAL FOUNDATION OF THE MINIMUM-EVOLUTION METHOD OF PHYLOGENETIC INFERENCE

The minimum-evolution (ME) method of phylogenetic inference is based o n the assumption that the tree with the smallest sum of branch length estimates is most likely to be the true one. In the past this assumpti on has been used without mathematical proof. Here we present the theor etical basis of this method by showing that the expectation of the sum of branch length estimates for the true tree is smallest among all po ssible trees, provided that the evolutionary distances used are statis tically unbiased and that the branch lengths are estimated by the ordi nary least-squares method. We also present simple mathematical formula s for computing branch length estimates and their standard errors for any unrooted bifurcating tree, with the least-squares approach. As a n umerical example, we have analyzed mtDNA sequence data obtained by Vig ilant et al. and have found the ME tree for 95 human and 1 chimpanzee (outgroup) sequences. The tree was somewhat different from the neighbo r-joining tree constructed by Tamura and Nei, but there was no statist ically significant difference between them.