Phylogenetic Super-networks from Partial Trees

  • Daniel H. Huson
  • Tobias Dezulian
  • Tobias Klöpper
  • Mike A. Steel
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)


In practice, one is often faced with incomplete phylogenetic data, such as a collection of partial trees or partial splits. This paper poses the problem of inferring a phylogenetic super-network from such data and provides an efficient algorithm for doing so, called the Z-closure method. Application to a set of five published partial gene trees relating different fungal species illustrates the usefulness of the method and an experimental study confirms its potential. The method is implemented as a plug-in for the program SplitsTree4.


Molecular evolution phylogeny partial trees networks closure operations 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Bandelt, H.-J., Dress, A.W.M.: A canonical decomposition theory for metrics on a finite set. Advances in Mathematics 92, 47–105 (1992)zbMATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Buneman, P.: The recovery of trees from measures of dissimilarity. In: Hodson, F.R., Kendall, D.G., Tautu, P. (eds.) Mathematics in the Archaeological and Historical Sciences, pp. 387–395. Edinburgh University Press (1971)Google Scholar
  3. 3.
    Dezulian, T., Steel, M.: Phylogenetic closure operations and homoplasy-free evolution. In: Proceedings of the 2004 International Federation of Classification Societies, Springer, Heidelberg (2004) (in press) Google Scholar
  4. 4.
    Dress, A.W.M., Huson, D.H.: Algorithms for drawing phylogenetic networks. In: preparation (2004)Google Scholar
  5. 5.
    Halperin, E., Karp, R.M.: Perfect phylogeny and haplotype assignment. In: Proceedings of the Eighth Annual Internation Conference on Research in Computational Molecular Biology, pp. 10–19. ACM Press, New York (2004)CrossRefGoogle Scholar
  6. 6.
    Holland, B., Moulton, V.: Consensus networks: A method for visualizing incompatibilities in collections of trees. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 165–176. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  7. 7.
    Huson, D.H.: SplitsTree: A program for analyzing and visualizing evolutionary data. Bioinformatics 14(10), 68–73 (1998)CrossRefGoogle Scholar
  8. 8.
    Huson, D.H., Bryant, D.: SplitsTree4 - a framework for building phylogenetic trees and networks (2004), software available from (manuscript in preparation)
  9. 9.
    Huson, D.H., Nettles, S., Parida, L., Warnow, T., Yooseph, S.: The disk-covering method for tree reconstruction. In: Proceedings of Algorithms and Experiments (ALEX 1998), Trento, pp. 62–75 (1998)Google Scholar
  10. 10.
    Meacham, C.A.: Theoretical and computational considerations of the compatibility of qualitative taxonomic characters. In: Felsenstein, J. (ed.) Numerical Taxonomy. NATO ASI Series, vol. G1, Springer, Berlin (1983)Google Scholar
  11. 11.
    NCBI. Microbial complete genomes taxonomy (2003),
  12. 12.
    Pryor, B.M., Bigelow, D.M.: Molecular characterization of Embellisia and Nimbya species and their relationship to Alternaria, Ulocladium and Stemphylium. Mycologia 95(6), 1141–1154 (2003)CrossRefGoogle Scholar
  13. 13.
    Pryor, B.M., Gilbertson, R.L.: Phylogenetic relationships among Alternaria and related fungi based upon analysis of nuclear internal transcribed sequences and mitochondrial small subunit ribosomal DNA sequences. Mycological Research 104(11), 1312–1321 (2000)CrossRefGoogle Scholar
  14. 14.
    Sanderson, M.J., Donoghue, M.J., Piel, W., Eriksson, T.: Treebase: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Amer. Jour. Bot. 81(6), 183 (1994)Google Scholar
  15. 15.
    Semple, C., Steel, M.A.: Tree recontruction via a closure operation on partial splits. In: Gascuel, O., Sagot, M.-F. (eds.) JOBIM 2000. LNCS, vol. 2066, p. 126. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  16. 16.
    D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis. Chapter 11: Phylogenetic inference. In D. M. Hillis, C. Moritz, and B. K. Mable, editors, Molecular Systematics, pages 407–514. Sinauer Associates, Inc., 2nd edition, 1996. Google Scholar
  17. 17.
    R.C. Winkworth, D. Bryant, P. Lockhart, D. Havell, and V. Moulton. Biogeographic interpretation of splits graphs: least squares optimization of branch lengths. Systematic Biology, 2004. In press. Google Scholar
  18. 18.
    C. R. Woese. Bacterial evolution. Microbiol. Rev., 51:221–272, 1987.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Daniel H. Huson
    • 1
  • Tobias Dezulian
    • 1
  • Tobias Klöpper
    • 1
  • Mike A. Steel
    • 2
  1. 1.Center for Bioinformatics (ZBIT)Tübingen UniversityTübingenGermany
  2. 2.Biomathematics Research CentreUniversity of CanterburyChristchurchNew Zealand

Personalised recommendations