Abstract
Reticulate networks are a type of phylogenetic network that are used to represent reticulate evolution involving hybridization, horizontal gene transfer or recombination. The simplest form of these networks are galled trees, in which all reticulations are independent of each other. This paper introduces a more general class of reticulate networks, that we call galled networks, in which reticulations are not necessarily independent, but may overlap in a tree-like manner. We prove a Decomposition Theorem for these networks that has important consequences for their computation, and present a fixed-parameter-tractable algorithm for computing such networks from trees or binary sequences. We provide a robust implementation of the algorithm and illustrate its use on two biological datasets, one based on a set of three gene-trees and the other based on a set of binary characters obtained from a restriction site map.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bandelt, H.J., Dress, A.W.M.: A canonical decomposition theory for metrics on a finite set. Advances in Mathematics 92, 47–105 (1992)
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
Sang, T., Zhong, Y.: Testing hybrization hypotheses based on incongruent gene trees. System. Biol. 49, 422–424 (2000)
Linder, C.R., Rieseberg, L.H.: Reconstructing patterns of reticulate evolution in plants. Am. J. Bot. 91, 1700–1708 (2004)
Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species - theory and practice. In: Proceedings of the Eighth International Conference on Research in Computational Molecular Biology (RECOMB), pp. 337–346 (2004)
Huson, D., Kloepper, T., Lockhart, P., Steel, M.: Reconstruction of reticulate networks from gene trees. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P., Waterman, M. (eds.) Research in Computational Molecular Biology. LNCS (LNBI), vol. 3500, pp. 233–249. Springer, Heidelberg (2005)
Bordewich, M., Semple, C.: Computing the minimum number of hybridisation events for a consistent evolutionary history (in press, 2006)
Hallett, M., Largergren, J., Tofigh, A.: Simultaneous identification of duplications and lateral transfers. In: Proceedings of the Eight International Conference on Research in Computational Molecular Biology (RECOMB), pp. 347–356 (2004)
Hudson, R.R.: Properties of the neutral allele model with intergenic recombination. Theoretical Population Biology 23, 183–201 (1983)
Hein, J.: Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci., 185–200 (1990)
Griffiths, R.C., Marjoram, P.: Ancestral inference from samples of DNA sequences with recombination. J. Computational Biology 3, 479–502 (1996)
Gusfield, D., Eddhu, S., Langley, C.: Efficient reconstruction of phylogenetic networks with constrained recombination. In: Proceedings of the IEEE Computer Society Conference on Bioinformatics, p. 363. IEEE, Los Alamitos (2003)
Song, Y., Hein, J.: Parsimonious reconstruction of sequence evolution and haplotype blocks: Finding the minimum number of recombination events. In: Proceedings of the Workshop on Algorithms in Bioinformatics, pp. 287–302 (2003)
Gusfield, D., Eddhu, S., Langley, C.: The fine structure of galls in phylogenetic networks. INFORMS J. of Computing, Special Issue on Computational Biology 16, 459–469 (2004)
Song, Y., Hein, J.: On the minimum number of recombination events in the evolutionary history of DNA sequences. J. Math. Biol. 48, 160–186 (2004)
Gusfield, D., Bansal, V.: A fundamental decomposition theory for phylogenetic networks and incompatible characters. In: Proceedings of the Ninth International Conference on Research in Computational Molecular Biology (RECOMB), pp. 217–232 (2005)
Huson, D., Kloepper, T.: Computing recombination networks from binary sequences. Bioinformatics 21, ii159–ii165. ECCB (2005)
Song, Y., Hein, J.: Constructing minimal ancestral recombination graphs. J. Comp. Biol. 12, 147–169 (2005)
Lyngsø, R.B., Song, Y.S., Hein, J.: Minimum recombination histories by branch and bound. In: WABI, pp. 239–250 (2005)
Baroni, M., Semple, C., Steel, M.A.: A framework for representing reticulate evolution. Annals of Combinatorics (In press)
Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. Journal of Computational Biology 8, 69–78 (2001)
Pryor, B.M., Bigelow, D.M.: Molecular characterization of Embellisia and Nimbya species and their relationship to Alternaria, Ulocladium and Stemphylium. Mycologia 95, 1141–1154 (2003)
Kumar, A., Black, W., Rai, K.: An estimate of phylogenetic relationships among culicine mosquitoes using a restriction map of the rDNA cistron. Insect Molecular Biology 7, 367–373 (1998)
Kimura, M.: The number of heterozygous nucleotide sites maintained in a finite population due to the steady flux of mutations. Genetics 61, 893–903 (1969)
Dress, A.W.M., Huson, D.H.: Constructing splits graphs. IEEE/ACM Transactions in Computational Biology and Bioinformatics 1, 109–115 (2004)
Sanderson, M.J., Donoghue, M.J., Piel, W., Eriksson, T.: Treebase: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Amer. Jour. Bot. 81, 183 (1994)
Huson, D., Steel, M., Whitfield, J.: Reducing distortion in phylogenetic networks. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 150–161. Springer, Heidelberg (2006)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Huson, D.H., Klöpper, T.H. (2007). Beyond Galled Trees - Decomposition and Computation of Galled Networks. In: Speed, T., Huang, H. (eds) Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science(), vol 4453. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71681-5_15
Download citation
DOI: https://doi.org/10.1007/978-3-540-71681-5_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-71680-8
Online ISBN: 978-3-540-71681-5
eBook Packages: Computer ScienceComputer Science (R0)