Reducing Distortion in Phylogenetic Networks

  • Daniel H. Huson
  • Mike A. Steel
  • Jim Whitfield
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)

Abstract

When multiple genes are used in a phylogenetic study, the result is often a collection of incompatible trees. Phylogenetic networks and super-networks can be employed to analyze and visualize the incompatible signals in such a data set. In many situations, it is important to have control over the amount of imcompatibility that is represented in a phylogenetic network, for example reducing noise by removing splits that do not recur among the source trees. Current algorithms for computing hybridization networks from trees are based on a combinatorial analysis of the arising set of splits, and are thus sensitive to false positive splits. Here, a filter is desirable that can identify and remove splits that are not compatible with a hybridization scenario. To address these issues, the concept of the distortion of a tree relative to a split is defined as a measure of how much the tree needs to be modified in order to accommodate the split, and some of its properties are investigated. We demonstrate the usefulness of the approach by recovering a plausible hybridization scenario for buttercups from a pair of gene trees that cannot be obtained by existing methods. In a second example, a set of seven gene trees from microgastrine braconid wasps is investigated using filtered networks. A user-friendly implementation of the method is provided as a plug-in for the program SplitsTree4.

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References

  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)MATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Bandelt, H.-J., Forster, P., Sykes, B.C., Richards, M.B.: Mitochondrial portraits of human population using median networks. Genetics 141, 743–753 (1995)Google Scholar
  3. 3.
    Banks, J.C., Whitfield, J.B.: Dissecting the ancient rapid radiation of microgastrine wasp genera using additional nuclear genes. Molecular Phylogenetics and Evolution (in press, 2006)Google Scholar
  4. 4.
    Bonet, M., Steel, M.A., Warnow, T., Yooseph, S.: Better methods for solving parsimony and compatibility. In: Proc. RECOMB 1998 (1998)Google Scholar
  5. 5.
    Bryant, D.: Hunting for trees, building trees and comparing trees: theory and method in phylogenetic analysis. Ph.D. thesis, Dept. Mathematics, University of Canterbury (1997)Google Scholar
  6. 6.
    Bryant, D.: The splits in the neighbourhood of a tree. Annals of Combinatorics 8(1), 1–11 (1997)Google Scholar
  7. 7.
    Eddhu, S., Gusfield, D., Langley, C.: The fine structure of galls in phylogenetic networks. In: INFORMS J. of Computing Special Issue on Computational Biology (to appear, 2004)Google Scholar
  8. 8.
    Dress, A.W.M., Huson, D.H.: Constructing splits graphs. IEEE/ACM Transactions in Computational Biology and Bioinformatics 1(3), 109–115 (2004)CrossRefGoogle Scholar
  9. 9.
    Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Inc. (2004)Google Scholar
  10. 10.
    Gadagkar, S., Rosenberg, M.S., Kumar, S.: Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J. of Experimental Zoology (Mol. Dev. Evol.) 304B, 64–74 (2005)CrossRefGoogle Scholar
  11. 11.
    Grimaldi, D.: The co-radiations of pollinating insects and angiosperms in the Cretaceous. Ann. Missouri Bot. Garden 86, 373–406 (1999)CrossRefGoogle Scholar
  12. 12.
    Harary, F.: Graph Theory. Series in Mathematics. Addison-Wesley, Reading, MA (1969)Google Scholar
  13. 13.
    Hein, J.: Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci., 185–200 (1990)Google Scholar
  14. 14.
    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
  15. 15.
    Huson, D.H., Bryant, D.: Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254–267 (2006), Software available from: http://www.splitstree.org CrossRefGoogle Scholar
  16. 16.
    Huson, D.H., Dezulian, T., Kloepper, T., Steel, M.A.: Phylogenetic super-networks from partial trees. IEEE/ACM Transactions in Computational Biology and Bioinformatics 1(4), 151–158 (2004)CrossRefGoogle Scholar
  17. 17.
    Huson, D.H., Kloepper, T., Lockhart, P.J., Steel, M.A.: Reconstruction of reticulate networks from gene trees. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 233–249. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  18. 18.
    Huson, D.H., Kloepper, T.H.: Computing recombination networks from binary sequences. Bioinformatics 21(suppl. 2), 59–165 (2005)CrossRefGoogle Scholar
  19. 19.
    Linder, C.R., Rieseberg, L.H.: Reconstructing patterns of reticulate evolution in plants. Am. J. Bot. 91(10), 1700–1708 (2004)CrossRefGoogle Scholar
  20. 20.
    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. Garden 88, 458–477 (2001)CrossRefGoogle Scholar
  21. 21.
    Mardulyn, P., Whitfield, J.B.: Phylogenetic signal in the COI, 16S and 28S genes for inferring relationships among genera of Microgastrinae (Hymenoptera: Braconidae); evidence of a high diversification rate in this group of parasitoids. Molecular Phylogenetics and Evolution 12, 282–294 (1999)CrossRefGoogle Scholar
  22. 22.
    Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species - theory and practice. In: Proc. 8th Int’l Conf. on Research in Computational Molecular Biology RECOMB 2004, pp. 337–346 (2004)Google Scholar
  23. 23.
    Rokas, A., Williams, B.L., King, N., Carroll, S.B.: Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798–804 (2003)CrossRefGoogle Scholar
  24. 24.
    Ronquist, F., Huelsenbeck, J.P.: Mrbayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 (2003)CrossRefGoogle Scholar
  25. 25.
    Rosenberg, N.A.: The probability of topological concordance of gene trees and species trees. Theor. Pop. Biol. 61, 225–247 (2002)MATHCrossRefGoogle Scholar
  26. 26.
    Sanderson, M.J., Driskell, A.C.: The challenge of constructing large phylogenetic trees. Trends in Plant Sciences 8, 374–379 (2003)CrossRefGoogle Scholar
  27. 27.
    Sankoff, D.: Minimal mutation trees of sequences. SIAM J. of Applied Mathematics, 35–42 (1975)Google Scholar
  28. 28.
    Sankoff, D., Rousseau, P.: Locating the vertices of a Steiner tree in an arbitrary metric space. Mathematical Programming 9, 240–246 (1975)MATHCrossRefMathSciNetGoogle Scholar
  29. 29.
    Semple, C., Steel, M.A.: Phylogenetics. Oxford University Press, Oxford (2003)MATHGoogle Scholar
  30. 30.
    Swofford, D.L.: When are phylogeny estimates from molecular and morphological data incongruent? In: Miyamoto, M.M., Cracraft, J. (eds.) Phylogenetic Analysis of DNA Sequences, pp. 295–333. Oxford University Press, Oxford, UK (1991)Google Scholar
  31. 31.
    Whitfield, J.B.: Estimating the age of the polydnavirus/braconid wasp symbiosis. Proc. of the National Academy of Sciences USA 99, 7508–7513 (2002)CrossRefGoogle Scholar
  32. 32.
    Woese, C.R.: Bacterial evolution. Microbiol. Rev. 51, 221–272 (1987)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Daniel H. Huson
    • 1
  • Mike A. Steel
    • 2
  • Jim Whitfield
    • 3
  1. 1.Center for Bioinformatics (ZBIT)Tübingen UniversityGermany
  2. 2.Allan Wilson CentreUniversity of CanterburyChristchurchNew Zealand
  3. 3.Department of EntomologyUniversity of Illinois at Urbana-ChampaignUSA

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