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Bulletin of Mathematical Biology

, Volume 72, Issue 1, pp 208–220 | Cite as

Revisiting an Equivalence Between Maximum Parsimony and Maximum Likelihood Methods in Phylogenetics

  • Mareike Fischer
  • Bhalchandra Thatte
Original Article

Abstract

Tuffley and Steel (Bull. Math. Biol. 59:581–607, 1997) proved that maximum likelihood and maximum parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been widely cited ever since. We show that small changes to the model assumptions suffice to make the two methods inequivalent. In particular, we analyze the case of bounded substitution probabilities as well as the molecular clock assumption. We show that in these cases, even under no common mechanism, maximum parsimony and maximum likelihood might make conflicting choices. We also show that if there is an upper bound on the substitution probabilities which is ‘sufficiently small’, every maximum likelihood tree is also a maximum parsimony tree (but not vice versa).

Keywords

Phylogenetics Maximum parsimony Maximum likelihood Molecular clock 

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Copyright information

© Society for Mathematical Biology 2009

Authors and Affiliations

  1. 1.Allan Wilson Centre for Molecular Ecology and Evolution, Biomathematics Research CentreUniversity of CanterburyChristchurchNew Zealand
  2. 2.Department of StatisticsUniversity of OxfordOxfordUK

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