Gene Trees and Species Trees: The Gene-Duplication Problem is Fixed-Parameter Tractable

  • Ulrike Stege
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1663)


Gene Duplication is the problem of computing an optimal species tree for a given set of gene trees under the Gene-Duplication Model (first introduced by Goodman et al.). The problem is known to be NP-complete. We give a fixed-parameter-tractable algorithm solving the problem parameterized by the number of gene duplications necessary to rectify the gene trees with respect to the species tree.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    S. Benner and A. Ellington. Evolution and Structural Theory. The frontier between chemistry and biochemistry. Bioorg. Chem. Frontiers 1 (1990), 1–70.CrossRefGoogle Scholar
  2. 2.
    R. G. Downey and M. R. Fellows. Parameterized Complexity, Springer, 1998.Google Scholar
  3. 3.
    R. Downey, M. Fellows, and U. Stege. “Parameterized Complexity: A Framework for Systematically Confronting Computational Intractability,” in The Future of Discr. Mathem.: Proc. of the 1st DIMATIA Symp., AMS-DIMACS, to appear.Google Scholar
  4. 4.
    R. G. Downey, M. R. Fellows, and U. Stege. Computational Tractability: The View From Mars, to appear in the Bulletin of the EATCS.Google Scholar
  5. 5.
    J. Felsenstein. Phylogenies from Molecular Sequences: Inference and Reliability. Annu. Rev. Genet. (1988), 22, 521–65.CrossRefGoogle Scholar
  6. 6.
    M. Fellows, M. Hallett, and U. Stege. “On the Multiple Gene Duplication Problem”, Algorithms and Computation, 9th International Symposium, ISAAC’98, LNCS 1533 (December 1998).Google Scholar
  7. 7.
    W. Fitch, E. Margoliash. “Construction of Phylogenetic Tree,” Sci. 155 (1967).Google Scholar
  8. 8.
    M. Goodman, J. Czelusniak, G. Moore, A. Romero-Herrera, G. Matsuda. “Fitting the Gene Lineage into its Species Lineage: A parsimony strategy illustrated by cladograms constructed from globin sequences,” Syst. Zool. (1979), 28.Google Scholar
  9. 9.
    R. Guigó, I. Muchnik, and T. F. Smith. “Reconstruction of Ancient Molecular Phylogeny,” Molec. Phylogenet. and Evol. (1996),6:2, 189–213.CrossRefGoogle Scholar
  10. 10.
    J. Hein, T. Jiang, L. Wang, and K. Zhang. “On the Complexity of Comparing Evolutionary Trees”, DAMATH: Discrete Applied Mathematics and Combinatorial Operations Research and Computer Science 71 (1996).Google Scholar
  11. 11.
    B. Ma, M. Li, and L. Zhang. “On Reconstructing Species Trees from Gene Trees in Term of Duplications and Losses,” Recomb 98.Google Scholar
  12. 12.
    R. D. M. Page. “Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas,” Syst. Biol. 43 (1994), 58–77.Google Scholar
  13. 13.
    D. L. Swofford. “When are phylogeny estimates from molecular and morphological data incongruent?” in Phylogenetic analysis of DNA sequences, Oxford Univ. Press (1991), pp. 295–333Google Scholar
  14. 14.
    L. Zhang. “On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies,” Journal of Comp. Biol. (1997) 4:2, 177–187.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1999

Authors and Affiliations

  • Ulrike Stege
    • 1
  1. 1.CBRG, Department of Computer ScienceZürich

Personalised recommendations