© 2006 Society of Systematic Biologists
Fundamental Differences Between the Methods of Maximum Likelihood and Maximum Posterior Probability in Phylogenetics
1 Department of Mathematics, Uppsala University Box 480, SE-751 06 Uppsala, Sweden; E-mail: bodil.svennblad{at}math.uu.se
2 Department of Systematic Botany, Uppsala University Norbyvägen 18D, SE-75236, Uppsala, Sweden; E-mail: per.erixon{at}ebc.uu.se (P.E.); bengt.oxelman{at}ebc.uu.se (B.O.)
3 Department of Mathematics, Stockholm University SE-106 91, Stockholm, Sweden; E-mail: tom.britton{at}math.su.se
Edited by Rod Page: Associate Editor
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Abstract |
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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
Received February 1, 2005; Revised April 6, 2005; Accepted August 11, 2005
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