Fast Local Search for Unrooted Robinson-Foulds Supertrees

A Robinson-Foulds (RF) supertree for a collection of input trees is a comprehensive species phylogeny that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maximum number of splits in the input trees. Constructing rooted and unrooted RF supertrees is NP-hard. Nevertheless, effective local search heuristics have been developed for the restricted case where the input trees and the supertree are rooted.We describe new heuristics, based on the Edge Contract and Refine (ECR) operation, that remove this restriction, thereby expanding the utility of RF supertrees. We demonstrate that our local search algorithms yield supertrees with notably better scores than those obtained from rooted heuristics.

[1]  Mark Wilkinson,et al.  Matrix representation with parsimony, taxonomic congruence, and total evidence. , 2002, Systematic biology.

[2]  Tandy J. Warnow,et al.  On contract-and-refine transformations between phylogenetic trees , 2004, SODA '04.

[3]  D. Penny,et al.  Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study. , 2003, Systematic biology.

[4]  Andy Purvis,et al.  A Modification to Baum and Ragan's Method for Combining Phylogenetic Trees , 1995 .

[5]  Mike Steel,et al.  The complexity of the median procedure for binary trees , 1994 .

[6]  David Fernández-Baca,et al.  Performance of flip supertree construction with a heuristic algorithm. , 2004, Systematic biology.

[7]  Andy Purvis,et al.  A species-level phylogenetic supertree of marsupials , 2004 .

[8]  Tandy J. Warnow,et al.  Better Hill-Climbing Searches for Parsimony , 2003, WABI.

[9]  James O. McInerney,et al.  Clann: investigating phylogenetic information through supertree analyses , 2005, Bioinform..

[10]  B. Baum.  Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees , 1992 .

[11]  Jonathan P. Bollback,et al.  Inferring the root of a phylogenetic tree. , 2002, Systematic biology.

[12]  M. Ragan.  Phylogenetic inference based on matrix representation of trees. , 1992, Molecular phylogenetics and evolution.

[13]  Michael A. Bender,et al.  The LCA Problem Revisited , 2000, LATIN.

[14]  Pablo A. Goloboff,et al.  Minority rule supertrees? MRP, Compatibility, and Minimum Flip may display the least frequent groups , 2005 .

[15]  Ward C. Wheeler,et al.  NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS , 1990, Cladistics : the international journal of the Willi Hennig Society.

[16]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[17]  Andy Purvis,et al.  Getting to the roots of matrix representation. , 2005, Systematic biology.

[18]  V. B. Yap,et al.  Rooting a phylogenetic tree with nonreversible substitution models , 2005, BMC Evolutionary Biology.

[19]  P. Goloboff.  Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima , 1999, Cladistics : the international journal of the Willi Hennig Society.

[20]  M J Sanderson,et al.  Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. , 2001, Systematic biology.

[21]  Pamela S Soltis,et al.  Darwin's abominable mystery: Insights from a supertree of the angiosperms , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Michael J Benton,et al.  A genus-level supertree of the Dinosauria , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[23]  Kate E. Jones,et al.  The delayed rise of present-day mammals , 1990, Nature.

[24]  David Fernández-Baca,et al.  Robinson-Foulds Supertrees , 2010, Algorithms for Molecular Biology.

[25]  A. Smith,et al.  Rooting molecular trees: problems and strategies , 1994 .

[26]  M. Steel,et al.  Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees , 2001 .

[27]  David Fernández-Baca,et al.  Improved Heuristics for Minimum-Flip Supertree Construction , 2006, Evolutionary bioinformatics online.

[28]  Andy Purvis,et al.  A higher-level MRP supertree of placental mammals , 2006, BMC Evolutionary Biology.

[29]  Charles Semple,et al.  On the Computational Complexity of the Rooted Subtree Prune and Regraft Distance , 2005 .