title: Maximum parsimony on subsets of taxa.
abstract: In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.
authors.affiliation: Biomathematics Research Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand. email@mareikefischer.de
authors.forename: Mareike
authors.initials: M
authors.lastname: Fischer
authors.forename: Bhalchandra D
authors.initials: BD
authors.lastname: Thatte
mesh_terms: D000465:Algorithms; D002965:Classification / Q000379:methods; D019143:Evolution, Molecular; D008954:Models, Biological; D010802:Phylogeny