Molecular Biology and Evolution, Vol 7, 82-102, Copyright © 1990 by Society for Molecular Biology and Evolution
L Jin and M Nei
Lake's evolutionary parsimony (EP) method of constructing a phylogenetic
tree is primarily applied to four DNA sequences. In this method, three
quantities--X, Y, and Z--that correspond to three possible unrooted trees
are computed, and an invariance property of these quantities is used for
choosing the best tree. However, Lake's method depends on a number of
unrealistic assumptions. We therefore examined the theoretical basis of his
method and reached the following conclusions: (1) When the rates of two
transversional changes from a nucleotide are unequal, his invariance
property breaks down. (2) Even if the rates of two transversional changes
are equal, the invariance property requires some additional conditions. (3)
When Kimura's two- parameter model of nucleotide substitution applies and
the rate of nucleotide substitution varies greatly with branch, the EP
method is generally better than the standard maximum-parsimony (MP) method
in recovering the correct tree but is inferior to the neighbor-joining (NJ)
and a few other distance matrix methods. (4) When the rate of nucleotide
substitution is the same or nearly the same for all branches, the EP method
is inferior to the MP method even if the proportion of transitional changes
is high. (5) When Lake's assumptions fail, his chi2 test may identify an
erroneous tree as the correct tree. This happens because the test is not
for comparing different trees. (6) As long as a proper distance measure is
used, the NJ method is better than the EP and MP methods whether there is a
transition/transversion bias or whether there is variation in substitution
rate among different nucleotide sites.
ORIGINAL ARTICLE
Limitations of the evolutionary parsimony method of phylogenetic analysis [published erratum appears in Mol Biol Evol 1990 Mar;7(2):201]
Center for Demographic and Population Genetics, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston 77225.
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