Least Common Ancestor Based Method for Efficiently Constructing Rooted Supertrees

Phylogenetic supertree is a collection of different phylogenetic trees combined into a single tree forming a tree of life. The smaller overlapping phylogenetic trees are combined in such a way that no branching information is lost. This problem is important for several biological applications. Yet the solution is difficult as exponentially large number of supertrees exists for a given set of trees and the optimal tree has to be selected based upon some optimality criteria. In this paper, we propose a polynomial time algorithm for combining phylogenetic trees, which makes use of least common ancestor information as optimality criterion. The algorithm satisfies the desirable properties of a phylogenetic supertree method as mentioned in literature, and constructs a single phylogenetic supertree even for incompatible input trees which is difficult to solve. Experimental results and comparisons with other works show the superiority of our algorithm.

[1]  J. L. Gittleman,et al.  The (Super)Tree of Life: Procedures, Problems, and Prospects , 2002 .

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

[3]  Sydney Anne Cameron,et al.  Molecular Evolution: A Phylogenetic Approach.—Roderic D. M. Page and Edward C. Holmes. , 2002 .

[4]  Kunihiko Sadakane,et al.  Rooted Maximum Agreement Supertrees , 2004, LATIN.

[5]  S. J. Willson,et al.  Constructing rooted supertrees using distances , 2004, Bulletin of mathematical biology.

[7]  M. Steel,et al.  Extension Operations on Sets of Leaf-Labeled Trees , 1995 .

[8]  Robert R. Sokal,et al.  A statistical method for evaluating systematic relationships , 1958 .

[9]  Robert E. Tarjan,et al.  Fast Algorithms for Finding Nearest Common Ancestors , 1984, SIAM J. Comput..

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

[11]  M. Steel.  The complexity of reconstructing trees from qualitative characters and subtrees , 1992 .

[12]  David Bryant,et al.  A classification of consensus methods for phylogenetics , 2001, Bioconsensus.

[13]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[14]  Roderic D. M. Page,et al.  Modified Mincut Supertrees , 2002, WABI.

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

[16]  M Steel,et al.  Simple but fundamental limitations on supertree and consensus tree methods. , 2000, Systematic biology.

[17]  E. N. Adams,et al.  N-trees as nestings: Complexity, similarity, and consensus , 1986 .

[18]  A. D. Gordon.  Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labeled leaves , 1986 .

[19]  Nicholas C. Wormald,et al.  Reconstruction of Rooted Trees From Subtrees , 1996, Discret. Appl. Math..

[20]  R. Graham,et al.  Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time , 1982 .

[21]  Charles Semple,et al.  Supertree Methods for Ancestral Divergence Dates and other Applications , 2004 .

[22]  Uzi Vishkin,et al.  On Finding Lowest Common Ancestors: Simplification and Parallelization , 1988, AWOC.

[23]  Charles Semple,et al.  A supertree method for rooted trees , 2000, Discret. Appl. Math..