Molecular Biology and Evolution, Vol 11, 261-277, Copyright © 1994 by Society for Molecular Biology and Evolution
Y Tateno, N Takezaki and M Nei
The relative efficiencies of the maximum-likelihood (ML), neighbor- joining
(NJ), and maximum-parsimony (MP) methods in obtaining the correct topology
and in estimating the branch lengths for the case of four DNA sequences
were studied by computer simulation, under the assumption either that there
is variation in substitution rate among different nucleotide sites or that
there is no variation. For the NJ method, several different distance
measures (Jukes-Cantor, Kimura two- parameter, and gamma distances) were
used, whereas for the ML method three different transition/transversion
ratios (R) were used. For the MP method, both the standard unweighted
parsimony and the dynamically weighted parsimony methods were used. The
results obtained are as follows: (1) When the R value is high, dynamically
weighted parsimony is more efficient than unweighted parsimony in obtaining
the correct topology. (2) However, both weighted and unweighted parsimony
methods are generally less efficient than the NJ and ML methods even in the
case where the MP method gives a consistent tree. (3) When all the
assumptions of the ML method are satisfied, this method is slightly more
efficient than the NJ method. However, when the assumptions are not
satisfied, the NJ method with gamma distances is slightly better in
obtaining the correct topology than is the ML method. In general, the two
methods show more or less the same performance. The NJ method may give a
correct topology even when the distance measures used are not unbiased
estimators of nucleotide substitutions. (4) Branch length estimates of a
tree with the correct topology are affected more easily than topology by
violation of the assumptions of the mathematical model used, for both the
ML and the NJ methods. Under certain conditions, branch lengths are
seriously overestimated or underestimated. The MP method often gives
serious underestimates for certain branches. (5) Distance measures that
generate the correct topology, with high probability, do not necessarily
give good estimates of branch lengths. (6) The likelihood-ratio test and
the confidence-limit test, in Felsenstein's DNAML, for examining the
statistical of branch length estimates are quite sensitive to violation of
the assumptions and are generally too liberal to be used for actual data.
Rzhetsky and Nei's branch length test is less sensitive to violation of the
assumptions than is Felsenstein's test. (7) When the extent of sequence
divergence is < or = 5% and when > or = 1,000 nucleotides are used,
all three methods show essentially the same efficiency in obtaining the
correct topology and in estimating branch lengths.(ABSTRACT TRUNCATED AT
400 WORDS)
ORIGINAL ARTICLE
Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
National Institute of Genetics, Mishima.
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