Molecular Biology and Evolution, Vol 9, 537-551, Copyright © 1992 by Society for Molecular Biology and Evolution
RW DeBry
A phylogenetic method is a consistent estimator of phylogeny if and only if
it is guaranteed to give the correct tree, given that sufficient (possibly
infinite) independent data are examined. The following methods are examined
for consistency: UPGMA (unweighted pair- group method, averages), NJ
(neighbor joining), MF (modified Farris), and P (parsimony). A
two-parameter model of nucleotide sequence substitution is used, and the
expected distribution of character states is calculated. Without perfect
correction for superimposed substitutions, all four methods may be
inconsistent if there is but one branch evolving at a faster rate than the
other branches. Partial correction of observed distances improves the
robustness of the NJ method to rate variation, and perfect correction makes
the NJ method a consistent estimator for all combinations of rates that
were examined. The sensitivity of all the methods to unequal rates varies
over a wide range, so relative-rate tests are unlikely to be a reliable
guide for accepting or rejecting phylogenies based on parsimony analysis.
ORIGINAL ARTICLE
The consistency of several phylogeny-inference methods under varying evolutionary rates
Department of Chemistry, Florida State University, Tallahassee 32306.
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