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Issue No.03 - May/June (2011 vol.8)
pp: 785-796
Stephen J. Willson , Iowa State University, Ames
A rooted acyclic digraph N with labeled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T. Let Tr(N) denote the set of all trees displayed by the network N. In general, there may be many other networks M, such that Tr(M) = Tr(N). A network is regular if it is isomorphic with its cover digraph. If N is regular and {\cal D} is a collection of trees displayed by N, this paper studies some procedures to try to reconstruct N given {\cal D}. If the input is {\cal D}=Tr(N), one procedure is described, which will reconstruct N. Hence, if N and M are regular networks and Tr(N) = Tr(M), it follows that N = M, proving that a regular network is uniquely determined by its displayed trees. If {\cal D} is a (usually very much smaller) collection of displayed trees that satisfies certain hypotheses, modifications of the procedure will still reconstruct N given {\cal D}.
Phylogeny, phylogenetic, network, tree, regular, hybrid.
Stephen J. Willson, "Regular Networks Can be Uniquely Constructed from Their Trees", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 3, pp. 785-796, May/June 2011, doi:10.1109/TCBB.2010.69
[1] L. Arvestad, A.-C. Berglund, J. Lagergren, and B. Sennblad, "Gene Tree Reconstruction and Orthology Analysis Based on an Integrated Model for Duplications and Sequence Evolution," Proc. Eighth Ann. Int'l Conf. Resaerch in Computational Molecular Biology (RECOMB '04), pp. 326-335, 2004.
[2] H.-J. Bandelt and A. Dress, "Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data," Molecular Phylogenetics and Evolution, vol. 1, no. 3, pp. 242-252, 1992.
[3] M. Baroni, C. Semple, and M. Steel, "A Framework for Representing Reticulate Evolution," Annals of Combinatorics, vol. 8, no. 4, pp. 391-408, 2004.
[4] M. Baroni and M. Steel, "Accumulation Phylogenies," Annals of Combinatorics, vol. 10, no. 1, pp. 19-30, 2006.
[5] M. Bordewich and C. Semple, "Computing the Minimum Number of Hybridization Events for a Consistent Evolutionary History," Discrete Applied Math., vol. 155, no. 8, pp. 914-928, 2007.
[6] G. Cardona, F. Rossalló, and G. Valiente, "Comparison of Tree-Child Phylogenetic Networks," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 6, no. 4, pp. 552-569, Oct.-Dec. 2009, doi:10.1109/TCBB.2007.70270.
[7] G. Cardona, L. Mercè, F. Rossalló, and G. Valiente, "A Distance Metric for a Class of Tree-Sibling Phylogenetic Networks," Bioinformatics, vol. 24, no. 13, pp. 1481-1488, 2008.
[8] J. Degnan and N. Rosenberg, "Discordance of Species Trees with Their Most Likely Gene Trees," PLoS Genetics vol. 2, no. 5e68, pp. 762-768, 2006.
[9] D. Gusfield, S. Eddhu, and C. Langley, "Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination," J. Bioinformatics and Computational Biology, vol. 2, no. 1, pp. 173-213, 2004.
[10] M. Hallett and J. Lagergren, "New Algorithms for the Duplication-Loss Model," Proc. Fourth Ann. Conf. Research in Computational Molecular Biology (RECOMB '00), pp. 138-146, 2000.
[11] M. Hallett and J. Lagergren, "Efficient Algorithms for Lateral Gene Transfer Problems," Proc. Fifth Ann. Int'l Conf. Computational Biology, pp. 149-156, 2001.
[12] B. Holland, K. Huber, V. Moulton, and P. Lockhart, "Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny," Molecular Biology and Evolution vol. 21, no. 7, pp. 1459-1461, 2004.
[13] D. Huson, T. Klöpper, P. Lockhart, and M. Steel, "Reconstruction of Reticulate Networks from Gene Trees," Proc. Ninth Int'l Conf. Research in Computational Molecular Biology (RECOMB '05), S. Miyano, et al., eds., pp. 233-249, 2005.
[14] D. Huson and T. Klöpper, "Beyond Galled Trees—Decomposition and Computation of Galled Networks," Proc. Ann. Conf. Research in Computational Molecular Biology (RECOMB '07), T. Speed and H. Huong, eds., pp. 211-225, 2007.
[15] I. Kanj, L. Nakhleh, C. Than, and G. Xia, "Seeing the Trees and Their Branches in the Network is Hard," Theoretical Computer Science, vol. 401, nos. 1-3, pp. 153-164, 2008.
[16] B. Moret, L. Nakhleh, T. Warnow, C.R. Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme, "Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 1, no. 1, pp. 13-23, Jan.-Mar. 2004.
[17] L. Nakhleh, T. Warnow, C.R. Linder, and K.S. John, "Reconstructing Reticulate Evolution in Species: Theory and Practice," J. Computational Biology, vol. 12, no. 6, pp. 796-811, 2005.
[18] R.D.M. Page and M.A. Charleston, "Reconciled Trees and Incongruent Gene and Species Trees," Math. Hierarchies and Biology, B. Mirkin, F.R. McMorris, F.S. Roberts, and A. Rzhetsky, eds., pp. 57-70, Am. Math. Soc., 1997.
[19] R.D.M. Page and M.A. Charleston, "From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem," Molecular Phylogenetics and Evolution, vol. 7, no. 2, pp. 231-240, 1997.
[20] A. Rokas, B. Williams, N. King, and S. Carroll, "Genome-Scale Approaches to Resolving Incongruence in Molecular Phylogenies," Nature, vol. 425, pp. 798-804, 2003.
[21] N.A. Rosenberg, "The Probability of Topological Concordance of Gene Trees and Species Trees," Theoretical Population Biology, vol. 61, no. 2, pp. 225-247, 2002.
[22] N.A. Rosenberg, "Counting Coalescent Histories," J. Computational Biology, vol. 14, no. 3, pp. 360-377, 2007.
[23] K. Strimmer and V. Moulton, "Likelihood Analysis of Phylogenetic Networks Using Directed Graph Models," Molecular Biology and Evolution, vol. 17, no. 6, pp. 875-881, 2000.
[24] L. Wang, K. Zhang, and L. Zhang, "Perfect Phylogenetic Networks with Recombination," J. Computational Biology, vol. 8, no. 1, pp. 69-78, 2001.
[25] S.J. Willson, "Reconstruction of Certain Phylogenetic Networks from the Genomes at Their Leaves," J. Theoretical Biology, vol. 252, no. 2, pp. 338-349, 2008.
[26] S.J. Willson, "Properties of Normal Phylogenetic Networks," Bull. of Math. Biology, vol. 72, no. 2, pp. 340-358, 2010.
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