This Article 
 Bibliographic References 
 Add to: 
Simultaneous Identification of Duplications and Lateral Gene Transfers
March/April 2011 (vol. 8 no. 2)
pp. 517-535
Ali Tofigh, KTH Royal Institute of Technology, Stockholm
Michael Hallett, McGill University, Montreal
Jens Lagergren, KTH Royal Institute of Technology, Stockholm
The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene losses, and lateral gene transfers (also known as horizontal gene transfers). The reasonable biological constraint that a lateral gene transfer may only occur between contemporary species leads to the notion of acyclic DTL-scenarios. Parsimony methods are introduced by defining appropriate optimization problems. We show that finding most parsimonious acyclic DTL-scenarios is NP-hard. However, by dropping the condition of acyclicity, the problem becomes tractable, and we provide a dynamic programming algorithm as well as a fixed-parameter tractable algorithm for finding most parsimonious DTL-scenarios.

[1] M. Lynch and A. Force, "The Probability of Duplicate Gene Preservation by Subfunctionalization," Genetics, vol. 154, no. 1, pp. 459-473, 2000.
[2] A. Force, M. Lynch, F. Pickett, A. Amores, Y. Yan, and J. Postlethwait, "Preservation of Duplicate Genes by Complementary, Degenerative Mutations," Genetics, vol. 151, no. 4, pp. 1531-1545, Apr. 1999.
[3] M. Lynch and J. Conery, "The Evolutionary Fate and Consequences of Duplicate Genes," Science, vol. 290, no. 5494, pp. 1151-1155, Nov. 2000.
[4] M. Lynch and J. Conery, "The Evolutionary Demography of Duplicate Genes," J. Structural and Functional Genomics, vol. 3, nos. 1-4, pp. 35-44, 2003.
[5] M. Hahn, T. De Bie, J. Stajich, C. Nguyen, and N. Cristianini, "Estimating the Tempo and Mode of Gene Family Evolution from Comparative Genomic Data," Genome Research, vol. 15, no. 8, pp. 1153-1160, Aug. 2005.
[6] J. Demuth, T. De Bie, J. Stajich, N. Cristianini, and M. Hahn, "The Evolution of Mammalian Gene Families," PLoS ONE, vol. 1, p. e85, 2006.
[7] J. Cotton and R. Page, "Rates and Patterns of Gene Duplication and Loss in the Human Genome," Proc. Biological Sciences, vol. 272, no. 1560, pp. 277-283, Feb. 2005.
[8] J. Lawrence, "Horizontal and Vertical Gene Transfer: The Life History of Pathogens," Contributions to Microbiology, vol. 12, pp. 255-271, 2005.
[9] W. Doolittle and E. Bapteste, "Pattern Pluralism and the Tree of Life Hypothesis," Proc. Nat'l Academy of Sciences USA, vol. 104, no. 7, pp. 2043-2049, Feb. 2007.
[10] M. Hallett and J. Lagergren, "Efficient Algorithms for Lateral Gene Transfer Problems," Proc. Fifth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), 2001.
[11] E. Bapteste, E. Susko, J. Leigh, D. MacLeod, R. Charlebois, and W. Doolittle, "Do Orthologous Gene Phylogenies Really Support Tree-Thinking?" BMC Evolutionary Biology, vol. 5, no. 1, p. 33, 2005.
[12] M. Charleston, "Jungles: A New Solution to the Host/Parasite Phylogeny Reconciliation Problem," Math. Biosciences, vol. 149, no. 2, pp. 191-223, May 1998.
[13] L. Nakhleh, D. Ruths, and L. Wang, "Riata-hgt: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer," Proc. 11th Int'l Computing and Combinatorics Conf. (COCOON '05), pp. 84-93, 2005.
[14] V. Makarenkov and P. Legendre, "From a Phylogenetic Tree to a Reticulated Network," J. Computational Biology, vol. 11, no. 1, pp. 195-212, 2004.
[15] E. Lerat, V. Daubin, H. Ochman, and N. Moran, "Evolutionary Origins of Genomic Repertoires in Bacteria," PLoS Biology, vol. 3, no. 5, p. e130, May 2005.
[16] R. Azad and J. Lawrence, "Detecting Laterally Transferred Genes: Use of Entropic Clustering Methods and Genome Position," Nucleic Acids Research, vol. 35, no. 14, pp. 4629-4639, 2007.
[17] M. Klein, M. Friedrich, A. Roger, P. Hugenholtz, S. Fishbain, H. Abicht, L. Blackall, D. Stahl, and M. Wagner, "Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes," J. Bacteriology, vol. 183, no. 20, pp. 6028-6035, 2001.
[18] J. Archibald, M. Rogers, M. Toop, K. Ishida, and P. Keeling, "Lateral Gene Transfer and the Evolution of Plastid-Targeted Proteins in the Secondary Plastid-Containing Alga Bigelowiella Natans," Proc. Nat'l Academy of Sciences USA, vol. 100, no. 13, pp. 7678-7683, June 2003.
[19] J. Andersson, A. Sjögren, D. Horner, C. Murphy, P. Dyal, S. Svärd, J. LogsdonJr., M. Ragan, R. Hirt, and A. Roger, "A Genomic Survey of the Fish Parasite Spironucleus Salmonicida Indicates Genomic Plasticity among Diplomonads and Significant Lateral Gene Transfer in Eukaryote Genome Evolution," BMC Genomics, vol. 8, p. 51, 2007.
[20] M. Goodman, J. Czelusniak, G. Moore, A. Romero-Herrera, and G. Matsuda, "Fitting the Gene Lineage into Its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences," Systematic Zoology, vol. 28, no. 2, pp. 132-163, 1979.
[21] R. Guigó, I. Muchnik, and T. Smith, "Reconstruction of Ancient Molecular Phylogeny," Molecular Phylogenetics and Evolution, vol. 6, no. 2, pp. 189-213, Oct. 1996.
[22] B. Ma, M. Li, and L. Zhang, "From Gene Trees to Species Trees," SIAM J. Computing, vol. 30, no. 3, pp. 729-752, 2000.
[23] M. Hallett and J. Lagergren, "New Algorithms for the Duplication-Loss Model," Proc. Fourth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 138-146, 2000.
[24] I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev, "Natural History and Evolutionary Principles of Gene Duplication in Fungi," Nature, vol. 449, no. 7158, pp. 54-61, Sept. 2007.
[25] L. Arvestad, A. 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. Research in Computational Molecular Biology (RECOMB), pp. 326-335, 2004.
[26] L. Arvestad, J. Lagergren, and B. Sennblad, "The Gene Evolution Model and Computing Its Associated Probabilities," J. ACM, vol. 56, no. 2, pp. 1-44, 2009.
[27] B. Sennblad and J. Lagergren, "Probabilistic Orthology Analysis," Systematic Biology, vol. 58, no. 4, pp. 411-424, 2008.
[28] Ö. Åkerborg, B. Sennblad, L. Arvestad, and J. Lagergren, "Simultaneous Bayesian Gene Tree Reconstruction and Reconciliation Analysis," Proc. Nat'l Academy of Sciences USA, vol. 106, no. 14, pp. 5714-5719, Apr. 2009.
[29] J. Lawrence and H. Ochman, "Molecular Archaeology of the Escherichia Coli Genome," Proc. Nat'l Academy of Sciences USA, vol. 95, no. 16, pp. 9413-9417, Aug. 1998.
[30] D. Gevers, K. Vandepoele, C. Simillon, and Y. Van de Peer, "Gene Duplication and Biased Functional Retention of Paralogs in Bacterial Genomes," Trends in Microbiology, vol. 12, no. 4, pp. 148-154, Apr. 2004.
[31] A. Retchless and J. Lawrence, "Temporal Fragmentation of Speciation in Bacteria," Science, vol. 317, no. 5841, pp. 1093-1096, Aug. 2007.
[32] F. Ronquist, "Parsimony Analysis of Coevolving Species Associations," Tangled Trees: Phylogeny, Cospeciation and Coevolution, Univ. of Chicago Press, pp. 22-64, 2002.
[33] M. Csűrös and I. Miklós, "A Probabilistic Model for Gene Content Evolution with Duplication, Loss and Horizontal Transfer," Proc. 10th Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 206-220, 2006.
[34] P. Górecki, "Reconciliation Problems for Duplication, Loss and Horizontal Gene Transfer," Proc. Eighth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 316-325, 2004.
[35] M. Hallett, J. Lagergren, and A. Tofigh, "Simultaneous Identification of Duplications and Lateral Transfers," Proc. Eighth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 347-356, 2004.
[36] L. Addario-Berry, M. Hallett, and J. Lagergren, "Towards Identifying Lateral Gene Transfer Events," Proc. Eighth Pacific Symp. Biocomputing (PSB '03), pp. 279-290, 2003.
[37] R.D.M. Page, "Maps between Trees and Cladistic Analysis of Historical Associations among Genes, Organisms, and Areas," Systematic Biology, vol. 43, no. 1, pp. 58-77, 1994.
[38] B. Mirkin, I. Muchnik, and T. Smith, "A Biologically Consistent Model for Comparing Molecular Phylogenies," J. Computational Biology, vol. 2, no. 4, p. 493-507, 1995.
[39] M.R. Garey and D.S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman & Co., 1979.
[40] M.A. Bender, M. Farach-Colton, G. Pemmasani, S. Skiena, and P. Sumazin, "Lowest Common Ancestors in Trees and Directed Acyclic Graphs," J. Algorithms, vol. 57, no. 2, pp. 75-94, 2005.
[41] O. Matte-Tailliez, C. Brochier, P. Forterre, and H. Philippe, "Archaeal Phylogeny Based on Ribosomal Proteins," Molecular Biology and Evolution, vol. 19, no. 5, pp. 631-639, May 2002.
[42] G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "Maximum Likelihood of Phylogenetic Networks," Bioinformatics, vol. 22, no. 21, pp. 2604-2611, Nov. 2006.
[43] F. Ronquist and J. Huelsenbeck, "MrBayes 3: Bayesian Phylogenetic Inference under Mixed Models," Bioinformatics, vol. 19, no. 12, pp. 1572-1574, Aug. 2003.

Index Terms:
Trees, biology and genetics, combinatorial algorithms, graph algorithms.
Ali Tofigh, Michael Hallett, Jens Lagergren, "Simultaneous Identification of Duplications and Lateral Gene Transfers," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 2, pp. 517-535, March-April 2011, doi:10.1109/TCBB.2010.14
Usage of this product signifies your acceptance of the Terms of Use.