Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem

The small parsimony problem is studied for reconstructing recombination networks from sequence data. The small parsimony problem is polynomial-time solvable for phylogenetic trees. However, the problem is proven NP-hard even for galled recombination networks. A dynamic programming algorithm is also developed to solve the small parsimony problem. It takes <i>O</i>(<i>dn</i>2<sup>3</sup> <i> <sup>h</sup> </i>) time on an input recombination network over length-<i>d</i> sequences in which there are <i>h</i> recombination and <i>n </i>-<i>h</i> tree nodes.

[1]  Daniel H. Huson,et al.  Computing recombination networks from binary sequences , 2005, ECCB/JBI.

[2]  Kunihiko Sadakane,et al.  Computing the Maximum Agreement of Phylogenetic Networks , 2004, CATS.

[3]  Simon Tavaré,et al.  Linkage disequilibrium: what history has to tell us. , 2002, Trends in genetics : TIG.

[4]  Jessica C Kissinger,et al.  A first glimpse into the pattern and scale of gene transfer in Apicomplexa. , 2004, International journal for parasitology.

[5]  Dan Gusfield,et al.  A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters , 2005, RECOMB.

[6]  Wing-Kin Sung,et al.  Algorithms for combining rooted triplets into a galled phylogenetic network , 2005, SODA '05.

[7]  Dan Gusfield,et al.  The Fine Structure of Galls in Phylogenetic Networks , 2004, INFORMS J. Comput..

[8]  S. Salzberg,et al.  Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima , 1999, Nature.

[9]  L. Orgel,et al.  Phylogenetic Classification and the Universal Tree , 1999 .

[10]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[11]  D. Morrison,et al.  Networks in phylogenetic analysis: new tools for population biology. , 2005, International journal for parasitology.

[12]  John M. Mellor-Crummey,et al.  Reconstructing phylogenetic networks using maximum parsimony , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

[13]  Howard Ochman,et al.  Reconciling the many faces of lateral gene transfer. , 2002, Trends in microbiology.

[14]  Louxin Zhang,et al.  Models and Methods in Comparative Genomics , 2006, Adv. Comput..

[15]  Daniel H. Huson,et al.  Reconstruction of Reticulate Networks from Gene Trees , 2005, RECOMB.

[16]  Doolittle Wf.  Phylogenetic Classification and the Universal Tree , 1999 .

[17]  Daniel H. Huson,et al.  Phylogenetic super-networks from partial trees , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[18]  Wing-Kin Sung,et al.  Constructing a Smallest Refining Galled Phylogenetic Network , 2005, RECOMB.

[19]  Kaizhong Zhang,et al.  Perfect phylogenetic networks with recombination , 2001, J. Comput. Biol..

[20]  Dan Gusfield,et al.  Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination , 2004, J. Bioinform. Comput. Biol..

[21]  J. Hein.  A heuristic method to reconstruct the history of sequences subject to recombination , 1993, Journal of Molecular Evolution.

[22]  Tandy J. Warnow,et al.  Reconstructing reticulate evolution in species: theory and practice , 2004, RECOMB.

[23]  J. Hein.  Reconstructing evolution of sequences subject to recombination using parsimony. , 1990, Mathematical biosciences.