title: Non-hereditary Maximum Parsimony trees.
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.
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr Gasse 9, 1030, Vienna, Austria. email@mareikefischer.de
authors.forename: Mareike
authors.initials: M
authors.lastname: Fischer
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*