Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer

  • Cuong Than
  • Guohua Jin
  • Luay Nakhleh
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)

Abstract

One phylogeny-based approach to horizontal gene transfer (HGT) detection entails comparing the topology of a gene tree to that of the species tree, and using their differences to locate HGT events. Another approach is based on augmenting a species tree into a phylogenetic network to improve the fitness of the evolution of the gene sequence data under an optimization criterion, such as maximum parsimony (MP). One major problem with the first approach is that gene tree estimates may have wrong branches, which result in false positive estimates of HGT events, and the second approach is accurate, yet suffers from the computational complexity of searching through the space of possible phylogenetic networks.

The contributions of this paper are two-fold. First, we present a measure that computes the support of HGT events inferred from pairs of species and gene trees. The measure uses the bootstrap values of the gene tree branches. Second, we present an integrative method to speed up the approaches for augmenting species trees into phylogenetic networks.

We conducted data analysis and performance study of our methods on a data set of 20 genes from the Amborella mitochondrial genome, in which Jeffrey Palmer and his co-workers postulated a massive amount of horizontal gene transfer. As expected, we found that including poorly supported gene tree branches in the analysis results in a high rate of false positive gene transfer events. Further, the bootstrap-based support measure assessed, with high accuracy, the support of the inferred gene transfer events. Further, we obtained very promising results, in terms of both speed and accuracy, when applying our integrative method on these data sets (we are currently studying the performance in extensive simulations). All methods have been implemented in the PhyloNet and NEPAL tools, which are available in the form of executable code from http://bioinfo.cs.rice.edu.

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References

  1. 1.
    Baroni, M., Semple, C., Steel, M.: A framework for representing reticulate evolution. Annals of Combinatorics 8(4), 391–408 (2004)MATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Beiko, R.G., Hamilton, N.: Phylogenetic identification of lateral genetic transfer events. BMC Evolutionary Biology 6 (2006)Google Scholar
  3. 3.
    Bergthorsson, U., Adams, K.L., Thomason, B., Palmer, J.D.: Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424, 197–201 (2003)CrossRefGoogle Scholar
  4. 4.
    Bergthorsson, U., Richardson, A., Young, G.J., Goertzen, L., Palmer, J.D.: Massive horizontal transfer of mitochondrial genes from diverse land plant donors to basal angiosperm Amborella. Proc. Nat’l Acad. Sci., USA 101, 17747–17752 (2004)CrossRefGoogle Scholar
  5. 5.
    Galtier, N.: A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology 56(4), 633–642 (2007)CrossRefGoogle Scholar
  6. 6.
    Gogarten, J.P., Doolittle, W.F., Lawrence, J.G.: Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19(12), 2226–2238 (2002)Google Scholar
  7. 7.
    Gorecki, P.: Reconciliation problems for duplication, loss and horizontal gene transfer. In: Proc. 8th Ann. Int’l Conf. Comput. Mol. Biol. (RECOMB 2004), pp. 316–325 (2004)Google Scholar
  8. 8.
    Hallett, M.T., Lagergren, J.: Efficient algorithms for lateral gene transfer problems. In: Proc. 5th Ann. Int’l Conf. Comput. Mol. Biol. (RECOMB 2001), pp. 149–156. ACM Press, New York (2001)Google Scholar
  9. 9.
    Huson, D.H., Bryant, D.: Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23(2), 254–267 (2006)CrossRefGoogle Scholar
  10. 10.
    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)Google Scholar
  11. 11.
    Jin, G., Nakhleh, L., Snir, S., Tuller, T.: Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics 23, e123–e128 (2006); Proceedings of the European Conference on Computational Biology (ECCB 2006)CrossRefGoogle Scholar
  12. 12.
    Jin, G., Nakhleh, L., Snir, S., Tuller, T.: Maximum likelihood of phylogenetic networks. Bioinformatics 22(21), 2604–2611 (2006)CrossRefGoogle Scholar
  13. 13.
    Jin, G., Nakhleh, L., Snir, S., Tuller, T.: Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Molecular Biology and Evolution 24(1), 324–337 (2007)CrossRefGoogle Scholar
  14. 14.
    Jin, G., Nakhleh, L., Snir, S., Tuller, T.: A new linear-time heuristic algorithm for computing the the parsimony score of phylogenetic networks: theoretical bounds and empirical performance. In: Măndoiu, I.I., Zelikovsky, A. (eds.) ISBRA 2007. LNCS (LNBI), vol. 4463, pp. 61–72. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  15. 15.
    Kunin, V., Goldovsky, L., Darzentas, N., Ouzounis, C.A.: The net of life: reconstructing the microbial phylogenetic network. Genome Research 15, 954–959 (2005)CrossRefGoogle Scholar
  16. 16.
    Lerat, E., Daubin, V., Moran, N.A.: From gene trees to organismal phylogeny in prokaryotes: The case of the γ-proteobacteria. PLoS Biology 1(1), 1–9 (2003)CrossRefGoogle Scholar
  17. 17.
    MacLeod, D., Charlebois, R.L., Doolittle, F., Bapteste, E.: Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evolutionary Biology 5 (2005)Google Scholar
  18. 18.
    Makarenkov, V.: T-REX: Reconstructing and visualizing phylogenetic trees and reticulation networks. econstructing and visualizing phylogenetic trees and reticulation networks 17(7), 664–668 (2001)Google Scholar
  19. 19.
    Moret, B.M.E., Nakhleh, L., Warnow, T., Linder, C.R., Tholse, A., Padolina, A., Sun, J., Timme, R.: Phylogenetic networks: modeling, reconstructibility, and accuracy. IEEE/ACM Transactions on Computational Biology and Bioinformatics 1(1), 13–23 (2004)CrossRefGoogle Scholar
  20. 20.
    Nakamura, Y., Itoh, T., Matsuda, H., Gojobori, T.: Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nature Genetics 36(7), 760–766 (2004)CrossRefGoogle Scholar
  21. 21.
    Nakhleh, L., Jin, G., Zhao, F., Mellor-Crummey, J.: Reconstructing phylogenetic networks using maximum parsimony. In: Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB 2005), pp. 93–102 (2005)Google Scholar
  22. 22.
    Nakhleh, L., Ruths, D., Wang, L.S.: RIATA-HGT: A fast and accurate heuristic for reconstrucing horizontal gene transfer. In: Wang, L. (ed.) COCOON 2005. LNCS, vol. 3595, pp. 84–93. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  23. 23.
    Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species–theory and practice. In: Proc. 8th Ann. Int’l Conf. Comput. Mol. Biol. (RECOMB 2004), pp. 337–346 (2004)Google Scholar
  24. 24.
    Ochman, H., Lawrence, J.G., Groisman, E.A.: Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784), 299–304 (2000)CrossRefGoogle Scholar
  25. 25.
    Shimodaira, H., Hasegawa, M.: Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16, 1114–1116 (1999)Google Scholar
  26. 26.
    Suchard, M.A.: Stochastic models for horizontal gene transfer: taking a random walk through tree space. Genetics 170, 419–431 (2005)CrossRefGoogle Scholar
  27. 27.
    Than, C., Nakhleh, L.: SPR-based tree reconciliation: Non-binary trees and multiple solutions. In: Proceedings of the Sixth Asia Pacific Bioinformatics Conference, pp. 251–260 (2008)Google Scholar
  28. 28.
    Than, C., Ruths, D., Innan, H., Nakhleh, L.: Identifiability issues in phylogeny-based detection of horizontal gene transfer. In: Bourque, G., El-Mabrouk, N. (eds.) RECOMB-CG 2006. LNCS (LNBI), vol. 4205, pp. 215–219. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  29. 29.
    Than, C., Ruths, D., Innan, H., Nakhleh, L.: Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions. Journal of Computational Biology 14(4), 517–535 (2007)CrossRefMathSciNetGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Cuong Than
    • 1
  • Guohua Jin
    • 1
  • Luay Nakhleh
    • 1
  1. 1.Department of Computer ScienceRice UniversityHoustonUSA

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