Non-hereditary Maximum Parsimony trees

J Math Biol. 2012 Aug;65(2):293-308. doi: 10.1007/s00285-011-0458-9. Epub 2011 Aug 13.

Abstract

In this paper, we investigate a conjecture by Arndt von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a Maximum Parsimony tree for a particular (DNA) alignment necessarily has subtrees of all possible sizes which are most parsimonious for the corresponding subalignments. We answer the conjecture affirmatively for binary alignments on 5 taxa but also show how to construct examples for which Maximum Parsimony trees are not hereditary. Apart from showing that a most parsimonious tree cannot generally be reduced to a most parsimonious tree on fewer taxa, we also show that compatible most parsimonious quartets do not have to provide a most parsimonious supertree. Last, we show that our results can be generalized to Maximum Likelihood for certain nucleotide substitution models.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Likelihood Functions
  • Models, Genetic*
  • Phylogeny*
  • Sequence Alignment
  • Sequence Analysis, DNA / statistics & numerical data*