Heuristics for the Gene-duplication Problem : A Θ ( n ) Speed-up for the Local Search

The gene-duplication problem is to infer a species supertree from a collection of gene trees that are confounded by complex histories of gene duplications. This problem is NP-hard and thus requires efficient and effective heuristics. Existing heuristics perform a stepwise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. We show how this local search problem can be solved efficiently by reusing previously computed information. This improves the running time of the current solution by a factor of n, where n is the number of species in the resulting supertree solution, and makes the gene-duplication problem more tractable for large-scale phylogenetic analyses. We verify the exceptional performance of our solution in a comparison study using sets of large randomly generated gene trees. Furthermore, we demonstrate the utility of our solution by incorporating large genomic data sets from GenBank into a supertree analysis of

[1]  Bin Ma,et al.  On reconstructing species trees from gene trees in term of duplications and losses , 1998, RECOMB '98.

[2]  A. Knight,et al.  Inferring species trees from gene trees: a phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins. , 1997, Molecular phylogenetics and evolution.

[3]  G. Moore,et al.  Fitting the gene lineage into its species lineage , 1979 .

[4]  M. Sanderson,et al.  Inferring angiosperm phylogeny from EST data with widespread gene duplication , 2007, BMC Evolutionary Biology.

[5]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[6]  Roderic D. M. Page,et al.  GeneTree: comparing gene and species phylogenies using reconciled trees , 1998, Bioinform..

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

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

[9]  Temple F. Smith,et al.  Reconstruction of ancient molecular phylogeny. , 1996, Molecular phylogenetics and evolution.

[10]  Jerzy Tiuryn,et al.  On the Structure of Reconciliations , 2004, Comparative Genomics.

[11]  R. Page.  Maps between trees and cladistic analysis of historical associations among genes , 1994 .

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

[13]  J. G. Burleigh,et al.  Prospects for Building the Tree of Life from Large Sequence Databases , 2004, Science.

[14]  Roderic D. M. Page,et al.  Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications , 2001, Pacific Symposium on Biocomputing.

[15]  Paola Bonizzoni,et al.  Reconciling Gene Trees to a Species Tree , 2003, CIAC.

[16]  Michael R. Fellows,et al.  Analogs & duals of the MAST problem for sequences & trees , 2003, J. Algorithms.

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

[18]  Dannie Durand,et al.  NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees , 2000, J. Comput. Biol..

[19]  Ilya B. Muchnik,et al.  A Biologically Consistent Model for Comparing Molecular Phylogenies , 1995, J. Comput. Biol..

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

[21]  Michael T. Hallett,et al.  New algorithms for the duplication-loss model , 2000, RECOMB '00.

[22]  Louxin Zhang,et al.  On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies , 1997, J. Comput. Biol..

[23]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[24]  M. P. Cummings,et al.  PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4 , 2000 .

[25]  Ulrike Stege,et al.  Gene Trees and Species Trees: The Gene-Duplication Problem in Fixed-Parameter Tractable , 1999, WADS.

[26]  R. Page.  Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. , 2000, Molecular phylogenetics and evolution.