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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Atteson, K.: The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25, 251–278 (1999)
Bandelt, H.-J., Dress, A.W.M.: A canonical decomposition theory for metrics on a finite set. Advances in Mathematics 92, 47–105 (1992)
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)
Bryant, D., Moulton, V.: Consistency of the neighbornet algorithm for constructing phylogenetic networks. Technical report, School of Computer Science, McGill University (2003)
Chang, J.: Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Mathematical Biosciences 134, 189–215 (1996)
Dress, A.W.M., Huson, D.: Computing phylogenetic networks from split systems (manuscript)
Gascuel, O., Bryant, D., Denis, F.: Strengths and limitations of the minimum evolution principle. Systematic Biology 50, 621–627 (2001)
Hudson, R.R.: Properties of a neutral allele model with intragenic recombination. Theoretical Population Biology 23, 183–201 (1983)
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)
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)
Kuhner, M.K., Yamato, J., Felsenstein, J.: Maximum likelihood estimation of recombination rates from population data. Genetics 156, 1393–1401 (2000)
Maynard-Smith, J.: Analyzing the mosaic structure of genes. Journal of Molecular Evolution 34, 126–129 (1992)
Posada, D., Crandall, K.: The effect of recombination on the accuracy of phylogeny estimation. Journal of Molecular Evolution 54, 396–402 (2002)
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)
Rodriguez, F., Oliver, J., Marin, A., Medina, R.: The general stochastic model of nucleotide substitution. Journal of Theoretical Biology 142, 485–501 (1990)
Rzhetsky, A., Nei, M.: Theoretical foundation of the minimum evolution method of phylogenetic inference. Molecular Biology and Evolution 10, 1073–1095 (1993)
Schierup, M., Hein, J.: Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879–891 (2000)
Strimmer, K., Wiuf, C., Moulton, V.: Recombination analysis using directed graphical models. Molecular Biology and Evolution 18, 97–99 (2001)
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)
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)
Wiuf, C., Christensen, T., Hein, J.: A simulation study of the reliability of recombination detection methods. Molecular Biology and Evolution 18, 1929–1939 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bryant, D., Huson, D., Kloepper, T., Nieselt-Struwe, K. (2003). Distance Corrections on Recombinant Sequences. In: Benson, G., Page, R.D.M. (eds) Algorithms in Bioinformatics. WABI 2003. Lecture Notes in Computer Science(), vol 2812. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39763-2_21
Download citation
DOI: https://doi.org/10.1007/978-3-540-39763-2_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-20076-5
Online ISBN: 978-3-540-39763-2
eBook Packages: Springer Book Archive