Abstract
In phylogenetics it is common practice to summarize collections of partial phylogenetic trees in the form of supertrees. Recently it has been proposed to construct phylogenetic supernetworks as an alternative to supertrees as these allow the representation of conflicting information in the trees, information that may not be representable in a single tree. Here we introduce SuperQ, a new method for constructing such supernetworks. It works by breaking the input trees into quartet trees, and stitching together the resulting set to form a network. The stitching process is performed using an adaptation of the QNet method for phylogenetic network reconstruction. In addition to presenting the new method, we illustrate the applicability of SuperQ to three data sets and discuss future directions for testing and development.
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References
Bryant, D.: A classification of consensus methods for phylogenies. In: Janowitz, M., Lapointe, F.J., McMorris, F., Mirkin, B., Roberts, F. (eds.) BioConsensus. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 61, pp. 163–184. American Mathematical Society (2003)
Bininda-Emonds, O.R.P. (ed.): Phylogenetic supertrees: Combining information to reveal the tree of life. Kluwer Academic Publishers, Dordrecht (2004)
Holland, B., Conner, G., Huber, K., Moulton, V.: Imputing supertrees and supernetworks from quartets. Systematic Biology 56, 57–67 (2007)
Holland, B., Delsuc, F., Moulton, V.: Visualizing conflicting evolutionary hypotheses in large collections of trees: Using consensus networks to study the origins of placentals and hexapods. Systematic Biology 54, 66–76 (2005)
Holland, B., Jermiin, L., Moulton, V.: Improved consensus network techniques for genome-scale phylogeny. Molecular Biology and Evolution 23, 848–855 (2006)
Holland, B., Moulton, V.: Consensus networks: A method for visualising incompatibilities in collections of trees. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 165–176. Springer, Heidelberg (2003)
Huson, D., Dezulian, T., Klöpper, T., Steel, M.: Phylogenetic super-networks from partial trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 1, 151–158 (2004)
Huson, D., Bryant, D.: Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254–267 (2006)
Grünewald, S., Forslund, K., Dress, A., Moulton, V.: QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. Molecular Biology and Evolution 24, 532–538 (2007)
Grünewald, S., Moulton, V., Spillner, A.: Consistency of the QNet algorithm for generating planar split graphs from weighted quartets. Discrete Applied Mathematics (in press, 2007)
Semple, C., Steel, M.: Phylogenetics. Oxford University Press, Oxford (2003)
Bandelt, H.J., Dress, A.: A canonical decomposition theory for metrics on a finite set. Advances in Mathematics 92, 47–105 (1992)
Dress, A., Huson, D.: Constructing split graphs. IEEE Transactions on Computational Biology and Bioinformatics 1, 109–115 (2004)
Winkworth, R., Bryant, D., Lockhart, P., Moulton, V.: Biogeographic interpretation of split graphs: studying quaternary plant diversification. Systematic Biology 54, 56–65 (2005)
Lawson, C.L., Hanson, R.J.: Solving least squares problems. Prentice-Hall, Englewood Cliffs (1974)
Huson, D.: SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14, 68–73 (1998)
Banks, J.C., Whitfield, J.B.: Dissecting the ancient rapid radiation of microgastrine wasp genera using additional nuclear genes. Molecular Phylogenetics and Evolution 41, 690–703 (2006)
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)
Pryor, B.M., Gilbertson, R.L.: Phylogenetic relationships among alternaria and related funghi based upon analysis of nuclear internal transcribed sequences and mitochondrial small subunit ribosomal DNA sequences. Mycological Research 104, 1312–1321 (2000)
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Grünewald, S., Spillner, A., Forslund, K., Moulton, V. (2008). Constructing Phylogenetic Supernetworks from Quartets. 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_24
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DOI: https://doi.org/10.1007/978-3-540-87361-7_24
Publisher Name: Springer, Berlin, Heidelberg
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