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Distance Corrections on Recombinant Sequences

  • David Bryant
  • Daniel Huson
  • Tobias Kloepper
  • Kay Nieselt-Struwe
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2812)

Abstract

Sequences that have evolved under recombination have a ‘mosaic’ structure, with different portions of the alignment having evolved on different trees. In this paper we study the effect of mosaic sequence structure on pairwise distance estimates. If we apply standard distance corrections to sequences that evolved on more than one tree then we are, in effect, correcting according to an incorrect model. We derive tight bounds on the error introduced by this model mis-specification and discuss the ramifications for phylogenetic analysis in the presence of recombination.

Keywords

Distance Matrix Branch Length Distance Matrice Weighted Distance Phylogenetic Network 
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.

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References

  1. 1.
    Atteson, K.: The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25, 251–278 (1999)zbMATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    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
  3. 3.
    Bryant, D., Moulton, V.: Neighbornet: An agglomerative algorithm for the construction of planar phylogenetic networks. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 375–391. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  4. 4.
    Bryant, D., Moulton, V.: Consistency of the neighbornet algorithm for constructing phylogenetic networks. Technical report, School of Computer Science, McGill University (2003)Google Scholar
  5. 5.
    Chang, J.: Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Mathematical Biosciences 134, 189–215 (1996)zbMATHCrossRefMathSciNetGoogle Scholar
  6. 6.
    Dress, A.W.M., Huson, D.: Computing phylogenetic networks from split systems (manuscript)Google Scholar
  7. 7.
    Gascuel, O., Bryant, D., Denis, F.: Strengths and limitations of the minimum evolution principle. Systematic Biology 50, 621–627 (2001)CrossRefGoogle Scholar
  8. 8.
    Hudson, R.R.: Properties of a neutral allele model with intragenic recombination. Theoretical Population Biology 23, 183–201 (1983)zbMATHCrossRefGoogle Scholar
  9. 9.
    Jukes, T.H., Cantor, C.R.: Evolution of protein molecules. In: Munro, H.N. (ed.) Mammalian Protein Metabolism, pp. 21–123. Academic Press, New York (1969)Google Scholar
  10. 10.
    Kuhner, M.K., Felsenstein, J.: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11, 459–468 (1994)Google Scholar
  11. 11.
    Kuhner, M.K., Yamato, J., Felsenstein, J.: Maximum likelihood estimation of recombination rates from population data. Genetics 156, 1393–1401 (2000)Google Scholar
  12. 12.
    Maynard-Smith, J.: Analyzing the mosaic structure of genes. Journal of Molecular Evolution 34, 126–129 (1992)Google Scholar
  13. 13.
    Posada, D., Crandall, K.: The effect of recombination on the accuracy of phylogeny estimation. Journal of Molecular Evolution 54, 396–402 (2002)Google Scholar
  14. 14.
    Rambaut, A., Grassly, N.C.: Seq-gen: An application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235–238 (1997)Google Scholar
  15. 15.
    Rodriguez, F., Oliver, J., Marin, A., Medina, R.: The general stochastic model of nucleotide substitution. Journal of Theoretical Biology 142, 485–501 (1990)CrossRefMathSciNetGoogle Scholar
  16. 16.
    Rzhetsky, A., Nei, M.: Theoretical foundation of the minimum evolution method of phylogenetic inference. Molecular Biology and Evolution 10, 1073–1095 (1993)Google Scholar
  17. 17.
    Schierup, M., Hein, J.: Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879–891 (2000)Google Scholar
  18. 18.
    Strimmer, K., Wiuf, C., Moulton, V.: Recombination analysis using directed graphical models. Molecular Biology and Evolution 18, 97–99 (2001)Google Scholar
  19. 19.
    Swofford, D., Olsen, G.J., Waddell, P.J., Hillis, D.M.: Phylogenetic inference. In: Hillis, D.M., Moritz, C., Mable, B.K. (eds.) Molecular Systematics, 2nd edn., pp. 407–514. Sinauer (1996)Google Scholar
  20. 20.
    Tamura, K., Nei, M.: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10, 512–526 (1993)Google Scholar
  21. 21.
    Wiuf, C., Christensen, T., Hein, J.: A simulation study of the reliability of recombination detection methods. Molecular Biology and Evolution 18, 1929–1939 (2001)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • David Bryant
    • 1
  • Daniel Huson
    • 2
  • Tobias Kloepper
    • 2
  • Kay Nieselt-Struwe
    • 2
  1. 1.McGill Centre for Bioinformatics3775 UniversityMontréalCanada
  2. 2.Center for Bioinformatics TuebingenUniversity of TuebingenTuebingenGermany

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