Reconstruction of Reticulate Networks from Gene Trees

  • Daniel H. Huson
  • Tobias Klöpper
  • Pete J. Lockhart
  • Mike A. Steel
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3500)

Abstract

One of the simplest evolutionary models has molecular sequences evolving from a common ancestor down a bifurcating phylogenetic tree, experiencing point-mutations along the way. However, empirical analyses of different genes indicate that the evolution of genomes is often more complex than can be represented by such a model. Thus, the following problem is of significant interest in molecular evolution: Given a set of molecular sequences, compute a reticulate network that explains the data using a minimal number of reticulations. This paper makes four contributions toward solving this problem. First, it shows that there exists a one-to-one correspondence between the tangles in a reticulate network, the connected components of the associated incompatibility graph and the netted components of the associated splits graph. Second, it provides an algorithm that computes a most parsimonious reticulate network in polynomial time, if the reticulations contained in any tangle have a certain overlapping property, and if the number of reticulations contained in any given tangle is bounded by a constant. Third, an algorithm for drawing reticulate networks is described and a robust and flexible implementation of the algorithms is provided. Fourth, the paper presents a statistical test for distinguishing between reticulations due to hybridization, and ones due to other events such as lineage sorting or tree-estimation error.

Keywords

Gene Tree Horizontal Gene Transfer Phylogenetic Network Tree Edge Recombination Node 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Holland, B., Huber, K., Moulton, V., Lockhart, P.J.: Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution 21, 1459–1461 (2004)CrossRefGoogle Scholar
  2. 2.
    Rieseberg, L.H., Raymond, O., Rosenthal, D.M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J.L., Schwarzbach, A.E., Donovan, L.A., Lexer, C.: Major ecological transitions in annual sunflowers facilitated by hybridization. Science 301, 1211–1216 (2003)CrossRefGoogle Scholar
  3. 3.
    Hein, J.: Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci., 185–200 (1990)Google Scholar
  4. 4.
    Hein, J.: A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36, 396–405 (1993)CrossRefGoogle Scholar
  5. 5.
    Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. Journal of Computational Biology 8, 69–78 (2001)CrossRefGoogle Scholar
  6. 6.
    Gusfield, D., Eddhu, S., Langley, C.: Efficient reconstruction of phylgenetic networks with constrained recombination. In: Proceedings of the 2003 IEEE CSB Bioinformatics Conference (2003)Google Scholar
  7. 7.
    Gusfield, D., Eddhu, S., Langley, C.: The fine structure of galls in phylogenetic networks. INFORMS J. of Computing Special Issue on Computational Biology (2004) (to appear)Google Scholar
  8. 8.
    Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species - theory and practice. In: RECOMB 2004, pp. 337–346 (2004)Google Scholar
  9. 9.
    Hudson, R.R., Kaplan, N.L.: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147–164 (1985)Google Scholar
  10. 10.
    Myers, S.R., Griffiths, R.C.: Bounds on the minimal number of recombination events in a sample history. Genetics 163, 375–394 (2003)Google Scholar
  11. 11.
    Bafna, V., Bansal, V.: The number of recombination events in a sample history: conflict graph and lower bounds. IEEE/ACM Transactions in Computational Biology and Bioinformatics 1, 78–90 (2004)CrossRefGoogle Scholar
  12. 12.
    Bandelt, H.J., Dress, A.W.M.: A canonical decomposition theory for metrics on a finite set. Advances in Mathematics 92, 47–105 (1992)MATHCrossRefMathSciNetGoogle Scholar
  13. 13.
    Dress, A.W.M., Huson, D.H.: Constructing splits graphs. IEEE/ACM Transactions in Computational Biology and Bioinformatics 1, 109–115 (2004)CrossRefGoogle Scholar
  14. 14.
    Gusfield, D., Bansal, V.: A fundamental decomposition theory for phylogenetic networks and incompatible characters. To appear in: Proceedings of RECOMB 2005 (2004)Google Scholar
  15. 15.
    Huson, D.H., Bryant, D.: Estimating phylogenetic trees and networks using SplitsTree 4. Manuscript in preparation (2004), software available from http://www-ab.informatik.uni-tuebingen.de/software
  16. 16.
    Lockhart, P.J., McLenachan, P.A., Havell, D., Glenny, D., Huson, D.H., Jensen, U.: Phylogeny, dispersal and radiation of New Zealand alpine buttercups: molecular evidence under split decomposition. Ann. Missouri. Bot. Gard. 88, 458–477 (2001)CrossRefGoogle Scholar
  17. 17.
    Kreitman, M.: Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Genetics 11, 147–164 (1985)Google Scholar
  18. 18.
    Semple, C., Steel, M.A.: Phylogenetics. Oxford University Press, Oxford (2003)MATHGoogle Scholar
  19. 19.
    Jukes, T.H., Cantor, C.R.: Evolution of protein molecules. In: Munro, H.N. (ed.) Mammalian Protein Metabolism, pp. 21–132. Academic Press, London (1969)Google Scholar
  20. 20.
    Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46, 523–536 (1997)CrossRefGoogle Scholar
  21. 21.
    Baroni, M., Semple, C., Steel, M.A.: A framework for representing reticulate evolution. Annals of Combinatorics (in press)Google Scholar
  22. 22.
    Huson, D.H., Dezulian, T., Kloepper, T., Steel, M.A.: Phylogenetic super-networks from partial trees. IEEE/ACM Transactions in Computational Biology and Bioinformatics (2004) (in press)Google Scholar
  23. 23.
    Rosenberg, N.A.: The probability of topological concordance of gene trees and species trees. Theor. Pop. Biol. 61, 225–247 (2002)MATHCrossRefGoogle Scholar
  24. 24.
    Sang, T., Zhong, Y.: Testing hybrization hypotheses based on incongruent gene trees. System. Biol. 49, 422–424 (2000)CrossRefGoogle Scholar
  25. 25.
    Steel, M.A., Lockhart, P., Penny, D.: Confidence in evolutionary trees from biological sequence data. Nature 364, 440–442 (1993)CrossRefGoogle Scholar
  26. 26.
    Tajima, F.: Evolutionary relationships of DNA sequences in finite populations. Genetics 105, 437–460 (1983)Google Scholar
  27. 27.
    Alon, N., Spencer, J.H.: The Probabilistic Method, 2nd edn. John Wiley, Chichester (2000)MATHCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Daniel H. Huson
    • 1
  • Tobias Klöpper
    • 1
  • Pete J. Lockhart
    • 2
  • Mike A. Steel
    • 3
  1. 1.Center for Bioinformatics (ZBIT)Tübingen UniversityTübingenGermany
  2. 2.Institute of Molecular BioSciencesMassey UniversityPalmerston NorthNew Zealand
  3. 3.Biomathematics Research CentreUniversity of CanterburyChristchurchNew Zealand

Personalised recommendations