Abstract
The result of a multiple gene tree analysis is usually a number of different tree topologies that are each supported by a significant proportion of the genes. We introduce the concept of a cluster network that can be used to combine such trees into a single rooted network, which can be drawn either as a cladogram or phylogram. In contrast to split networks, which can grow exponentially in the size of the input, cluster networks grow only quadratically. A cluster network is easily computed using a modification of the tree-popping algorithm, which we call network-popping. The approach has been implemented as part of the Dendroscope tree-drawing program and its application is illustrated using data and results from three recent studies on large numbers of gene trees.
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References
King, N., Rokas, A., Williams, B.L., Carroll, S.B.: Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425(6960), 798–804 (2003)
Bandelt, H.-J., Dress, A.W.M.: A canonical decomposition theory for metrics on a finite set. Advances in Mathematics 92, 47–105 (1992)
Bordewich, M., Semple, C.: Computing the minimum number of hybridization events for a consistent evolutionary history. Discrete Appl. Math. 155(8), 914–928 (2007)
Doolittle, W.F., Bapteste, E.: Pattern pluralism and the tree of life hypothesis. PNAS 104, 2043–2049 (2007)
Ebersberger, I., Galgoczy, P., Taudien, S., Taenzer, S., Platzer, M., von Haeseler, A.: Mapping Human Genetic Ancestry. Mol. Biol. Evol. 24(10), 2266–2276 (2007)
Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Inc. (2004)
Gascuel, O.: BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14, 685–695 (1997)
Gusfield, D.: Algorithms on Strings, Trees and Sequences. Cambridge University Press, Cambridge (1997)
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 (2003)
Holland, B., Huber, K., Moulton, V., Lockhart, P.J.: Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution 21, 1459–1461 (2004)
Huson, D.H.: SplitsTree: A program for analyzing and visualizing evolutionary data. Bioinformatics 14(10), 68–73 (1998)
Huson, D.H., Bryant, D.: Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254–267 (2006), www.splitstree.org
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)
Huson, D.H., Kloepper, T.H.: Computing recombination networks from binary sequences. Bioinformatics 21(suppl. 2), ii159–ii165 (2005)
Huson, D.H., Richter, D.C., Rausch, C., Dezulian, T., Franz, M., Rupp, R.: Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8, 460 (2007), www.dendroscope.org , doi:10.1186/1471-2105-8-460
Huson, D.H., Steel, M.A., 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)
Leebens-Mack, J., Raubeson, L.A., Cui, L., Kuehl, J.V., Fourcade, M.H., Chumley, T.W., Boore, J.L., Jansen, R.K., de Pamphilis, C.W.: Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One’s Way Out of the Felsenstein Zone. Mol. Biol. Evol. 22(10), 1948–1963 (2005)
Meacham, C.A.: Theoretical and computational considerations of the compatibility of qualitative taxonomic characters. In: Felsenstein, J. (ed.) Numerical Taxonomy. NATO ASI Series, vol. G1, Springer, Berlin (1983)
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)
Patterson, N., Richter, D.J., Gnerre, S., Lander, E.S., Reich, D.: Genetic evidence for complex speciation of humans and chimpanzees. Nature 441, 1103–1108 (2006)
Steel, M.A.: Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett. 7(2), 19–24 (1994)
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Huson, D.H., Rupp, R. (2008). Summarizing Multiple Gene Trees Using Cluster Networks. In: Crandall, K.A., Lagergren, J. (eds) Algorithms in Bioinformatics. WABI 2008. Lecture Notes in Computer Science(), vol 5251. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87361-7_25
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DOI: https://doi.org/10.1007/978-3-540-87361-7_25
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