Skip to main content
SpringerLink
Log in

Minimum Leaf Removal for Reconciliation: Complexity and Algorithms

  • Conference paper
Combinatorial Pattern Matching (CPM 2012)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7354))

Included in the following conference series:

Abstract

Reconciliation is a well-known method for studying the evolution of a gene family through speciation, duplication, and loss. Unfortunately, the inferred history strongly depends on the considered gene tree for the gene family, as a few misplaced leaves can lead to a completely different history, possibly with significantly more duplications and losses. It is therefore essential to develop methods that are able to preprocess and correct gene trees prior to reconciliation. In this paper, we consider a combinatorial problem, known as the Minimum Leaf Removal problem, that has been proposed to remove errors from a gene tree by deleting some of its leaves. We prove that the problem is APX-hard, even in the restricted case of a gene family with at most two copies per genome. On the positive side, we present fixed-parameter algorithms where the parameters are the size of the solution (minimum number of leaf removals) and the number of genomes containing multiple gene copies.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Alimonti, P., Kann, V.: Some APX-completeness results for cubic graphs. Theor. Comput. Sci. 237(1-2), 123–134 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  2. Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410 (1990)

    Google Scholar 

  3. Arvestad, L., Berglung, A.C., Lagergren, J., Sennblad, B.: Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In: Gusfield, D. (ed.) RECOMB 2004, pp. 326–335. ACM, New York (2004)

    Chapter  Google Scholar 

  4. Blin, G., Bonizzoni, P., Dondi, R., Rizzi, R., Sikora, F.: Complexity Insights of the Minimum Duplication Problem. In: Bieliková, M., Friedrich, G., Gottlob, G., Katzenbeisser, S., Turán, G. (eds.) SOFSEM 2012. LNCS, vol. 7147, pp. 153–164. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  5. Blomme, T., Vandepoele, K., Bodt, S.D., Silmillion, C., Maere, S., van de Peer, Y.: The gain and loss of genes during 600 millions years of vertebrate evolution. Genome Biology 7, R43 (2006)

    Google Scholar 

  6. Bonizzoni, P., Della Vedova, G., Dondi, R.: Reconciling a gene tree to a species tree under the duplication cost model. Theoretical Computer Science 347, 36–53 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  7. Chang, W.-C., Eulenstein, O.: Reconciling Gene Trees with Apparent Polytomies. In: Chen, D.Z., Lee, D.T. (eds.) COCOON 2006. LNCS, vol. 4112, pp. 235–244. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  8. Chauve, C., El-Mabrouk, N.: New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 46–58. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  9. Chen, K., Durand, D., Farach-Colton, M.: Notung: Dating gene duplications using gene family trees. Journal of Computational Biology 7, 429–447 (2000)

    Article  Google Scholar 

  10. Cotton, J., Page, R.: Rates and patterns of gene duplication and loss in the human genome. Proceedings of the Royal Society of London. Series B 272, 277–283 (2005)

    Article  Google Scholar 

  11. Demuth, J., Bie, T.D., Stajich, J., Cristianini, N., Hahn, M.: The evolution of mammalian gene families. PLoS ONE 1, e85 (2006)

    Google Scholar 

  12. Doroftei, A., El-Mabrouk, N.: Removing Noise from Gene Trees. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS (LNBI), vol. 6833, pp. 76–91. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  13. Durand, D., Haldórsson, B., Vernot, B.: A hybrid micro-macroevolutionary approach to gene tree reconstruction. Journal of Computational Biology 13, 320–335 (2006)

    Article  MathSciNet  Google Scholar 

  14. Eichler, E., Sankoff, D.: Structural dynamics of eukaryotic chromosome evolution. Science 301, 793–797 (2003)

    Article  Google Scholar 

  15. Goodman, M., Czelusniak, J., Moore, G., Romero-Herrera, A., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28, 132–163 (1979)

    Article  Google Scholar 

  16. Górecki, P., Eulenstein, O.: A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees. In: Chen, J., Wang, J., Zelikovsky, A. (eds.) ISBRA 2011. LNCS, vol. 6674, pp. 148–159. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  17. Gorecki, P., Tiuryn, J.: DLS-trees: a model of evolutionary scenarios. Theoretical Computer Science 359, 378–399 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  18. Guigó, R., Muchnik, I., Smith, T.: Reconstruction of ancient molecular phylogeny. Molecular Phylogenetics and Evolution 6, 189–213 (1996)

    Article  Google Scholar 

  19. Hahn, M.: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biology 8(R141) (2007)

    Google Scholar 

  20. Hahn, M., Han, M., Han, S.G.: Gene family evolution across 12 drosophilia genomes. PLoS Genetics 3, e197 (2007)

    Google Scholar 

  21. Kristensen, D., Wolf, Y., Mushegian, A., Koonin, E.: Computational methods for gene orthology inference. Briefings in Bioinformatics 12(5), 379–391 (2011)

    Article  Google Scholar 

  22. Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM J. on Comput. 30, 729–752 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  23. Niedermeier, R.: Invitation to Fixed-Parameter Algorithms. Oxford University Press, Oxford (2006)

    Book  MATH  Google Scholar 

  24. Ohno, S.: Evolution by gene duplication. Springer, Berlin (1970)

    Google Scholar 

  25. Page, R.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology 43, 58–77 (1994)

    Google Scholar 

  26. Page, R.: Genetree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 14, 819–820 (1998)

    Article  Google Scholar 

  27. Page, R., Charleston, M.: Reconciled trees and incongruent gene and species trees. DIMACS Series in Discrete Mathematics and Theoretical Computer Science 37, 57–70 (1997)

    MathSciNet  Google Scholar 

  28. Page, R., Cotton, J.: Vertebrate phylogenomics: reconciled trees and gene duplications. In: Pacific Symposium on Biocomputing, pp. 536–547 (2002)

    Google Scholar 

  29. Sanderson, M., McMahon, M.: Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evolutionary Biology 7, S3 (2007)

    Google Scholar 

  30. Vernot, B., Stolzer, M., Goldman, A., Durand, D.: Reconciliation with non-binary species trees. Journal of Computational Biology 15, 981–1006 (2008)

    Article  MathSciNet  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dipartimento di Scienze dei Linguaggi, della Comunicazione e degli Studi Culturali, Universit‘a degli Studi di Bergamo, Bergamo, Italy

    Riccardo Dondi

  2. Départment d’Informatique et Recherche Opérationnelle, Université de Montréal, Montréal, Canada

    Nadia El-Mabrouk

Authors
  1. Riccardo Dondi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nadia El-Mabrouk
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Helsinki, Gustaf Hällström Katu 2b, P.O. Box 68, 00014, Helsinki, Finland

    Juha Kärkkäinen

  2. Faculty of Technology, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany

    Jens Stoye

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Dondi, R., El-Mabrouk, N. (2012). Minimum Leaf Removal for Reconciliation: Complexity and Algorithms. In: Kärkkäinen, J., Stoye, J. (eds) Combinatorial Pattern Matching. CPM 2012. Lecture Notes in Computer Science, vol 7354. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31265-6_32

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-31265-6_32

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-31264-9

  • Online ISBN: 978-3-642-31265-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation