Abstract
In practice, one is often faced with incomplete phylogenetic data, such as a collection of partial trees or partial splits. This paper poses the problem of inferring a phylogenetic super-network from such data and provides an efficient algorithm for doing so, called the Z-closure method. Application to a set of five published partial gene trees relating different fungal species illustrates the usefulness of the method and an experimental study confirms its potential. The method is implemented as a plug-in for the program SplitsTree4.
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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)
Buneman, P.: The recovery of trees from measures of dissimilarity. In: Hodson, F.R., Kendall, D.G., Tautu, P. (eds.) Mathematics in the Archaeological and Historical Sciences, pp. 387–395. Edinburgh University Press (1971)
Dezulian, T., Steel, M.: Phylogenetic closure operations and homoplasy-free evolution. In: Proceedings of the 2004 International Federation of Classification Societies, Springer, Heidelberg (2004) (in press)
Dress, A.W.M., Huson, D.H.: Algorithms for drawing phylogenetic networks. In: preparation (2004)
Halperin, E., Karp, R.M.: Perfect phylogeny and haplotype assignment. In: Proceedings of the Eighth Annual Internation Conference on Research in Computational Molecular Biology, pp. 10–19. ACM Press, New York (2004)
Holland, B., Moulton, V.: Consensus networks: A method for visualizing 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.H.: SplitsTree: A program for analyzing and visualizing evolutionary data. Bioinformatics 14(10), 68–73 (1998)
Huson, D.H., Bryant, D.: SplitsTree4 - a framework for building phylogenetic trees and networks (2004), software available from http://www-ab.informatik.uni-tuebingen.de/software/splits (manuscript in preparation)
Huson, D.H., Nettles, S., Parida, L., Warnow, T., Yooseph, S.: The disk-covering method for tree reconstruction. In: Proceedings of Algorithms and Experiments (ALEX 1998), Trento, pp. 62–75 (1998)
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)
NCBI. Microbial complete genomes taxonomy (2003), http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/newmicr.html
Pryor, B.M., Bigelow, D.M.: Molecular characterization of Embellisia and Nimbya species and their relationship to Alternaria, Ulocladium and Stemphylium. Mycologia 95(6), 1141–1154 (2003)
Pryor, B.M., Gilbertson, R.L.: Phylogenetic relationships among Alternaria and related fungi based upon analysis of nuclear internal transcribed sequences and mitochondrial small subunit ribosomal DNA sequences. Mycological Research 104(11), 1312–1321 (2000)
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(6), 183 (1994)
Semple, C., Steel, M.A.: Tree recontruction via a closure operation on partial splits. In: Gascuel, O., Sagot, M.-F. (eds.) JOBIM 2000. LNCS, vol. 2066, p. 126. Springer, Heidelberg (2001)
D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis. Chapter 11: Phylogenetic inference. In D. M. Hillis, C. Moritz, and B. K. Mable, editors, Molecular Systematics, pages 407–514. Sinauer Associates, Inc., 2nd edition, 1996.
R.C. Winkworth, D. Bryant, P. Lockhart, D. Havell, and V. Moulton. Biogeographic interpretation of splits graphs: least squares optimization of branch lengths. Systematic Biology, 2004. In press.
C. R. Woese. Bacterial evolution. Microbiol. Rev., 51:221–272, 1987.
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Huson, D.H., Dezulian, T., Klöpper, T., Steel, M.A. (2004). Phylogenetic Super-networks from Partial Trees. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_33
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DOI: https://doi.org/10.1007/978-3-540-30219-3_33
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