The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.02 - March/April (2012 vol.9)
pp: 535-547
P. Phipps , Univ. of Texas at Dallas, Plano, TX, USA
S. Bereg , Dept. of Comput. Sci., Univ. of Texas at Dallas, Richardson, TX, USA
ABSTRACT
We address the problem of realizing a given distance matrix by a planar phylogenetic network with a minimum number of faces. With the help of the popular software SplitsTree4, we start by approximating the distance matrix with a distance metric that is a linear combination of circular splits. The main results of this paper are the necessary and sufficient conditions for the existence of a network with a single face. We show how such a network can be constructed, and we present a heuristic for constructing a network with few faces using the first algorithm as the base case. Experimental results on biological data show that this heuristic algorithm can produce phylogenetic networks with far fewer faces than the ones computed by SplitsTree4, without affecting the approximation of the distance matrix.
INDEX TERMS
Phylogeny, Measurement, Computational biology, Bioinformatics, Transmission line matrix methods, Software algorithms, History,network optimization., Computational biology, phylogenetic network, minimizing faces, split network
CITATION
P. Phipps, S. Bereg, "Optimizing Phylogenetic Networks for Circular Split Systems", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, no. 2, pp. 535-547, March/April 2012, doi:10.1109/TCBB.2011.109
REFERENCES
[1] D.H. Huson and C. Scornavacca, “A Survey of Combinatorial Methods for Phylogenetic Networks,” Genome Biology and Evolution, vol. 3, pp. 23-35, 2011.
[2] L. Bao and S. Bereg, “Clustered Splitsnetworks,” Proc. Second Ann. Int'l Conf. Combinatorial Optimization and Applications (COCOOA '08), pp. 469-478, 2008.
[3] 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.
[4] D. Gusfield and V. Bansal, “A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters,” Proc. Research in Computational Molecular Biology (RECOMB '05), pp. 217-232, 2005.
[5] D. Huson and T. Klöpper, “Beyond Galled Trees - Decomposition and Computation of Galled Networks,” Proc. the 11th Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '07), pp. 211-225, 2007.
[6] G. Jin, L. Nakhleh, S. Snir, and T. Tuller, “Molecular Phylogeny and Evolution of Primate Mitochondrial DNA,” Molecular Biology and Evolution, vol. 24, no. 1, pp. 324-337, 2007.
[7] L. Nakhleh, G. Jin, F. Zhao, and J. Mellor-Crummey, “Reconstructing Phylogenetic Networks Using Maximum Parsimony,” Proc. IEEE Computational Systems Bioinformatics Conf., pp. 93-102, 2005.
[8] J.D. Velasco and E. Sober, “Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection,” Biology and Philosophy, vol. 25, pp. 675-687, 2010.
[9] L. Wang, K. Zhang, and L. Zhang, “Perfect Phylogenetic Networks with Recombination,” J. Computational Biology, vol. 8, pp. 69-78, 2001.
[10] M. Bordewich and C. Semple, “Computing the Minimum Number of Hybridisation Events for a Consistent Evolutionary History,” Discrete Applied Math., vol. 155, no. 8, pp. 914-928, 2007.
[11] H. Bandelt and A. Dress, “A Canonical Decomposition Theory for Metrics on a Finite Set,” Advances in Math., vol. 92, pp. 47-105, 1992.
[12] H.J. Bandelt and A.W.M. Dress, “Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data,” Molecular Phylogenetics and Evolution, vol. 1, pp. 242-252, 1992.
[13] D. Bryant and V. Moulton, “Neighbornet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks,” Molecular Biology and Evolution, vol. 21, no. 2, pp. 255-265, 2004.
[14] H. Bandelt, P. Forster, B. Sykes, and M. Richards, “Mitochondrial Portraits of Human Populations Using Median Networks,” Genetics, vol. 141, no. 2, pp. 743-753, 1995.
[15] A. Dress and D. Huson, “Constructing Splits Graphs,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 1, no. 3, pp. 109-115, July-Sept. 2004.
[16] D.H. Huson and D. Bryant, “Application of Phylogenetic Networks in Evolutionary Studies,” Molecular Biology and Evolution, vol. 23, no. 2, pp. 254-267, 2006.
[17] L. Bao and S. Bereg, “Counting Faces in Split Networks,” Proc. Fifth Int'l Symp. Bioinformatics Research and Applications (ISBRA), pp. 112-123, 2009.
[18] P. Buneman, “The Recovery of Trees from Measures of Dissimlarity,” Mathematics in the Archeological and Historical Sciences, pp. 387-395, Univ. Press, 1971.
[19] S.V. Chmutov, S.V. Duzhin, and S.K. Lando, “Vassiliev Knot Invariants ii,” Advances in Soviet Math., vol. 21, pp. 127-134, 1994.
[20] T. Kashiwabara, S. Masuda, K. Nakajima, and T. Fujisawa, “Polynomial Time Algorithms on Circular-Arc Overlap Graphs,” Networks, vol. 21, pp. 195-203, 1991.
[21] D. Gusfield, “Efficient Algorithms for Inferring Evolutionary Trees,” Networks, vol. 21, no. 1, pp. 19-28, 1991.
[22] P.J. Lockhart, M.A. Steel, M.D. Hendy, and D. Penny, “Recovering Evolutionary Trees under a More Realistic Model of Sequence Evolution,” Molecular Biology and Evolution, vol. 11, pp. 605-612, 1994.
[23] K. Hayasaka, T. Gojobori, and S. Horai, “Molecular Phylogeny and Evolution of Primate Mitochondrial Dna,” Molecular Biology and Evolution, vol. 5, pp. 626-644, 1988.
7 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool