Molecular Biology and Evolution, Vol 10, 1073-1095, Copyright © 1993 by Society for Molecular Biology and Evolution
A Rzhetsky and M Nei
The minimum-evolution (ME) method of phylogenetic inference is based on 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 assumption has been
used without mathematical proof. Here we present the theoretical basis of
this method by showing that the expectation of the sum of branch length
estimates for the true tree is smallest among all possible trees, provided
that the evolutionary distances used are statistically unbiased and that
the branch lengths are estimated by the ordinary least-squares method. We
also present simple mathematical formulas for computing branch length
estimates and their standard errors for any unrooted bifurcating tree, with
the least-squares approach. As a numerical example, we have analyzed mtDNA
sequence data obtained by Vigilant et al. and have found the ME tree for 95
human and 1 chimpanzee (outgroup) sequences. The tree was somewhat
different from the neighbor-joining tree constructed by Tamura and Nei, but
there was no statistically significant difference between them.
ORIGINAL ARTICLE
Theoretical foundation of the minimum-evolution method of phylogenetic inference
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802.
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