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Molecular Biology and Evolution, Vol 16, 1079-1085, Copyright © 1999 by Society for Molecular Biology and Evolution

ORIGINAL ARTICLE

Multiple local maxima for likelihoods of phylogenetic trees: a simulation study

JS Rogers and DL Swofford
Department of Biological Sciences, University of New Orleans, Louisiana 70148, USA. jsrogers@uno.edu

Steel demonstrated that the maximum-likelihood function for a phylogenetic tree may have multiple local maxima. If this phenomenon were general, it would compromise the applicability of maximum likelihood as an optimality criterion for phylogenetic trees. In several simulation studies reported on in this paper, the true tree, and other trees of very high likelihood, rarely had multiple maxima. Our results thus provide reassurance that the value of maximum likelihood as a tree selection criterion is not compromised by the presence of multiple local maxima--the best estimates of the true tree are not likely to have them. This result holds true even when an incorrect nucleotide substitution model is used for tree selection.
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