title: Towards improving searches for optimal phylogenies.
abstract: Finding the optimal evolutionary history for a set of taxa is a challenging computational problem, even when restricting possible solutions to be "tree-like" and focusing on the maximum-parsimony optimality criterion. This has led to much work on using heuristic tree searches to find approximate solutions. We present an approach for finding exact optimal solutions that employs and complements the current heuristic methods for finding optimal trees. Given a set of taxa and a set of aligned sequences of characters, there may be subsets of characters that are compatible, and for each such subset there is an associated (possibly partially resolved) phylogeny with edges corresponding to each character state change. These perfect phylogenies serve as anchor trees for our constrained search space. We show that, for sequences with compatible sites, the parsimony score of any tree [Formula: see text] is at least the parsimony score of the anchor trees plus the number of inferred changes between [Formula: see text] and the anchor trees. As the maximum-parsimony optimality score is additive, the sum of the lower bounds on compatible character partitions provides a lower bound on the complete alignment of characters. This yields a region in the space of trees within which the best tree is guaranteed to be found; limiting the search for the optimal tree to this region can significantly reduce the number of trees that must be examined in a search of the space of trees. We analyze this method empirically using four different biological data sets as well as surveying 400 data sets from the TreeBASE repository, demonstrating the effectiveness of our technique in reducing the number of steps in exact heuristic searches for trees under the maximum-parsimony optimality criterion.
authors.affiliation: Department of Computer Science, Graduate Center, CUNY, New York, NY, 10016, USA; Department of Mathematics and Computer Science, Lehman College, CUNY, Bronx, NY, 10468, USA; and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA;
authors.forename: Eric
authors.initials: E
authors.lastname: Ford
authors.affiliation: Department of Computer Science, Graduate Center, CUNY, New York, NY, 10016, USA; Department of Mathematics and Computer Science, Lehman College, CUNY, Bronx, NY, 10468, USA; and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA; Department of Computer Science, Graduate Center, CUNY, New York, NY, 10016, USA; Department of Mathematics and Computer Science, Lehman College, CUNY, Bronx, NY, 10468, USA; and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA; stjohn@lehman.cuny.edu.
authors.forename: Katherine
authors.initials: K
authors.lastname: St John
authors.affiliation: Department of Computer Science, Graduate Center, CUNY, New York, NY, 10016, USA; Department of Mathematics and Computer Science, Lehman College, CUNY, Bronx, NY, 10468, USA; and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA;
authors.forename: Ward C
authors.initials: WC
authors.lastname: Wheeler
mesh_terms: D000465:Algorithms; D000818:Animals; D002965:Classification / Q000379:methods*; D005658:Fungi / Q000145:classification; D019684:Magnoliopsida / Q000145:classification; D010802:Phylogeny
keywords: Character compatibility; exact search; maximum-parsimony optimality criterion; phylogenetic islands; tree search