Reconciling Gene Trees to a Species Tree (original) (raw)

Abstract

In this paper we deal with the general problem of recombining the information from evolutionary trees representing the relationships between distinct gene families. First we solve a problem from [8] regarding the construction of a minimum reconciled tree by giving an efficient algorithm. Then we show that the exemplar problem, arising from the exemplar analysis of multigene genomes [2], is NP-hard even when the number of copies of a given label is at most two. Finally we introduce two novel formulations for the problem of recombining evolutionary trees, extending the notion of the gene duplication problem studied in [88,11,9,10,6], and we give an exact algorithm (via dynamic programming) for one of the formulations given.

Preview

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest and Clifford Stein Introduction to Algorithms, Second Edition. The MIT Press and McGraw-Hill Book Company, 2001.
    Google Scholar
  2. N. El-Mabrouk, D. Sankoff Duplication, Rearrangement and Reconciliation. In Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map alignment and the Evolution of Gene Families. Computational Biology Series. Kluwer Academic Publishers. Vol 1. pages 537–550 (2000), 2000.
    Google Scholar
  3. M. R. Fellows, M. T. Hallett, U. Stege. On the Multiple Gene Duplication Problem. In Proccedings of International Symposium on Algorithms and Computation 1998 (ISAAC 1998), pages 347–356, 1998.
    Google Scholar
  4. M. R. Garey, D. S. Johnson. Computer and Intractability: A Guide to NP-Completeness. W. H. Freeman, 1979.
    Google Scholar
  5. M. Goodman, J. Czelusniak, G.W. Moore, A.E. Romero-Herrera, and G. Matsuda. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology, (28):132–163, 1979.
    Google Scholar
  6. R. Guigò, I. Muchnik, and T. Smith. Reconstruction of ancient molecular phylogeny. Mol. Phy. and Evol., 6(2):189–213, 1996.
    Article Google Scholar
  7. M. T. Hallett, and J. Lagergren. New algorithms for the duplication-loss model. In Proceedings of the Fourth Annual International Conference on Computational Biology 2000 (RECOMB 2000), pages 138–146, 2000.
    Google Scholar
  8. B. Ma, M. Li, and L. Zhang. From gene trees to species trees. SIAM Journal on Computing, 30(3):729–752, 2000.
    Article MATH MathSciNet Google Scholar
  9. R.D. M. Page. Maps between trees and cladistic analysis of historical associations among genes. Systematic Biology, 43:58–77, 1994.
    Article Google Scholar
  10. R.D. M. Page and J. Cotton. Vertebrate phylogenomics: reconciled trees and gene duplications. In Proceedings of Pacific Symposium on Biocomputing 2002 (PSB2002), pages 536–547, 2002.
    Google Scholar
  11. U. Stege. Gene Trees and Species Trees: The Gene-Duplication Problem is Fixed-Parameter Tractable. In Proceedings of Workshop on Algorithms And Data Structures 1999 (WADS’99), pages 288–293, 1999
    Google Scholar

Download references

Author information

Authors and Affiliations

  1. Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Milano, Italy
    Paola Bonizzoni & Riccardo Dondi
  2. Dipartimento di Statistica, Universitä degli Studi di Milano-Bicocca, Milano, Italy
    Gianluca Della Vedova

Authors

  1. Paola Bonizzoni
    You can also search for this author inPubMed Google Scholar
  2. Gianluca Della Vedova
    You can also search for this author inPubMed Google Scholar
  3. Riccardo Dondi
    You can also search for this author inPubMed Google Scholar

Editor information

Editors and Affiliations

  1. Dipartimento di Infornatica, Università di Roma “La Sapienza”, Via Salaria 113, 00198, Rome, Italy
    Rossella Petreschi & Riccardo Silvestri &
  2. Dipartimento di Infornatica ed Applicazioni “R.M. Capocelli”, Università di Salerno, Via S. Allende 2, 84081, Baronissi, SA, Italy
    Giuseppe Persiano

Rights and permissions

© 2003 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Bonizzoni, P., Della Vedova, G., Dondi, R. (2003). Reconciling Gene Trees to a Species Tree. In: Petreschi, R., Persiano, G., Silvestri, R. (eds) Algorithms and Complexity. CIAC 2003. Lecture Notes in Computer Science, vol 2653. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44849-7\_18

Download citation

Publish with us