Journal Article

Fundamental Differences Between the Methods of Maximum Likelihood and Maximum Posterior Probability in Phylogenetics

Bodil Svennblad, Per Erixon, Bengt Oxelman and Tom Britton

Edited by Rod Page

in Systematic Biology

Volume 55, issue 1, pages 116-121
Published in print February 2006 | ISSN: 1063-5157
Published online February 2006 | e-ISSN: 1076-836X | DOI: https://dx.doi.org/10.1080/10635150500481648
Fundamental Differences Between the Methods of Maximum Likelihood and Maximum Posterior Probability in Phylogenetics

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Using a four-taxon example under a simple model of evolution, we show that the methods of maximum likelihood and maximum posterior probability (which is a Bayesian method of inference) may not arrive at the same optimal tree topology. Some patterns that are separately uninformative under the maximum likelihood method are separately informative under the Bayesian method. We also show that this difference has impact on the bootstrap frequencies and the posterior probabilities of topologies, which therefore are not necessarily approximately equal. Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429–13434, 1996) stated that bootstrap frequencies can, under certain circumstances, be interpreted as posterior probabilities. This is true only if one includes a noninformative prior distribution of the possible data patterns, and most often the prior distributions are instead specified in terms of topology and branch lengths.

Keywords: Bayesian inference; maximum likelihood method; Phylogeny; support

Journal Article.  4686 words.  Illustrated.

Subjects: Biological Sciences ; Evolutionary Biology ; Genetics and Genomics

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