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Journal of Classification

, Volume 28, Issue 3, pp 390–403 | Cite as

TreeOfTrees Method to Evaluate the Congruence Between Gene Trees

Article

Abstract

A new method, TreeOfTrees, is proposed to compare X-tree structures obtained from several sets of aligned gene sequences of the same taxa. Its aim is to detect genes or sets of genes having different evolutionary histories. The comparison between sets of trees is based on several tree metrics, leading to a unique tree labelled by the gene trees. The robustness values of its edges are estimated by bootstrapping and consensus procedures that allow detecting subsets of genes having differently evolved. Simulations are performed under various evolutionary conditions to test the efficiency of the method and an application on real data is described. Tests of arboricity and various consensus algorithms are also discussed. A corresponding software package is available.

Keywords

Congruence Gene trees Phylogeny Tree of trees 

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References

  1. ALLEN, B.L., and STEEL, M. (2001), “Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees”, Annals of Combinatorics, 5, 1–15.MathSciNetCrossRefGoogle Scholar
  2. BARTHELEMY, J.P., and GUENOCHE, A. (1991), Trees and Proximity Representations, Chichester: J. Wiley.MATHGoogle Scholar
  3. DE VIENNE, D.M., GIRAUD, T., and MARTIN, O.C. (2007), “A Congruence Index for Testing Topological Similarity Between Trees”, Bioinformatics, 23, 3119–3124.CrossRefGoogle Scholar
  4. EDWARDS, S.V., LIU, L., and PEARL,D.K. (2007), “High Resolution Species TreesWithout Concatenation”, PNAS, 104(14), 5936–5941.CrossRefGoogle Scholar
  5. ESTABROOK, G.F., McMORRIS, F.R., and MEACHAM, C.A. (1985), “Comparison of Undirected Phylogenetic Trees Based on Subtrees of 4 Evolutionary Units”, Systematic Zoology, 34, 193–200.CrossRefGoogle Scholar
  6. FARRIS, J.S., KALLERJO,M., KLUGE, A.G., and BULT, C. (1994), “Testing Significance of Incongruence”, Cladistics, 10, 315–319.CrossRefGoogle Scholar
  7. FELSENSTEIN, J. (2004), Inferring Phylogenies, Sunderland (MA): Sinauer Associates.Google Scholar
  8. FINDON, C.R., and GORDON, A.D. (1985), “Obtaining Common Pruned Trees”, Journal of Classification, 2, 255–279.CrossRefGoogle Scholar
  9. GRAHAM, S.W., KOHN, J.R., MORTON, J.R., ECKENWALDER, J.E., and BARRET, S.C. (1998), “Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae”, Systematic Biology, 47, 545–567.CrossRefGoogle Scholar
  10. GUENOCHE, A. (1998), “Ordinal Properties of Tree Distances”, Discrete Mathematics, 192, 103–117.MathSciNetMATHCrossRefGoogle Scholar
  11. GUENOCHE, A., and GARRETA, H. (2001), “Can We Have Confidence in a Tree Representation?” in Computational Biology, LNCS 2066, eds. O. Gascuel and M.F. Sagot, Springer, pp. 43–53.Google Scholar
  12. GUINDON, S., and GASCUEL, O. (2003),“A Simple, Fast and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood”, Systematic Biology, 52, 696–704.CrossRefGoogle Scholar
  13. LEGENDRE, P., and LAPOINTE, F.J. (2004), “Assessing the Congruence Among Distance Matrices: Single Malt Scotch Whiskies Revisited”, Australian & New Zealand Journal of Statistics, 46, 615–629.MathSciNetMATHCrossRefGoogle Scholar
  14. MARGUSH, T., and McMORRIS F.R. (1981), “Consensus N-Trees”, Bulletin of Mathematical Biology, 43, 239–244.MathSciNetMATHGoogle Scholar
  15. NYE, T.M.W. (2008), “Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies”, Systematic Biology, 57, 785–794.CrossRefGoogle Scholar
  16. OLIVER, J.C. (2008), “AUGIST: Inferring Species TreesWhile Accommodating Gene Tree Uncertainty”, Bioinformatics, 24, 2932–2933.CrossRefGoogle Scholar
  17. PENNY, D., WATSON, E.E., and STEEL, M. (1993), “Trees from Languages and Genes Are Very Similar”, Systematic Biology, 42, 382–384.Google Scholar
  18. PHYLIP (Phylogeny Inference Package) Version 3.6 (2004), Seattle: Department of Genome Sciences, University of Washington.Google Scholar
  19. PUIGBO, P., GARCIA-VALLVE, S., and McINERNEY, J.O. (2007), “TOPD/FMTS: A New Software to Compare Phylogenetic Trees”, Bioinformatics, 23, 1556–1558.CrossRefGoogle Scholar
  20. RAMBAUT, A., and GRASSLY, N.C. (1997), “SeqGen: An Application for the Monte- Carlo Simulation of DNA Sequence Evolution Along Phylogenetic Trees”, Computer Applications in the Biosciences, 13, 235–238.Google Scholar
  21. ROKAS, A., WILLIAMS, B.L., KING, M., and CAROLL, S.B. (2003), “Genome-scale Approaches to Resolving Incongruence in Molecular Phylogenies”, Nature, 425, 798–804.CrossRefGoogle Scholar
  22. ROBINSON, D.F., and FOULDS, L.R. (1981), “Comparison of Phylogenetic Trees”, Mathematical Biosciences, 53, 131–147.MathSciNetMATHCrossRefGoogle Scholar
  23. SAITOU, N., and Nei, M. (1987), “The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees”, Molecular Biology and Evolution, 4(4), 406–425.Google Scholar
  24. SCHUBERT, S., DARLU, P., CLERMONT, O. et al. (2009), “Role of Intraspecies Recombination in the Spread of Pathogenicity Islands Within the Escherichia Coli Species”, PLoSpathogens, (5(1)e1000257).Google Scholar
  25. SEMPLE, C., and STEEL,M. (2003), Phylogenetics, Oxford: Oxford University Press.MATHGoogle Scholar
  26. SHIMODAIRA, H., and HASEGAWA, M. (1999), “Multiple Comparisons of Log-likelihoods with Applications to Phylogenetic Inference”, Molecular Biology and Evolution, 16, 1114–1116.Google Scholar
  27. STEEL M., and WARNOW T. (1993), “Kaikoura Tree Theorems: Computing the Maximum Agreement Subtree”, Information Processing Letters, 48(2), 77–82.MathSciNetMATHCrossRefGoogle Scholar
  28. THAN, C., RUTHS, D., INNAN, H., and NAKHLEH, L. (2007) “Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions”, Journal of Computational Biology, 14(4), 517–535.MathSciNetCrossRefGoogle Scholar
  29. WATERMAN, M.S., and SMITH, T.F. (1978), “On the Similarity of Dendrograms”, Journal of Theoretical Biology, 73, 789–800.MathSciNetCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.UMR 7206, MNHN, CNRSParisFrance
  2. 2.UMR 6206, CNRSMarseilleFrance

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