Reconstructing Phylogenetic Networks with One Recombination

In this paper we propose a new method for reconstructing phylogenetic networks under the assumption that recombination events have occurred rarely. For a fixed number of recombinations, we give a generalization of the maximum parsimony criterion. Furthermore, we describe an exact algorithm for one recombination event and show that in this case our method is not only able to identify the recombined sequence but also to reliably reconstruct the complete evolutionary history.

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

[2]  Andrew Rambaut,et al.  Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..

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

[4]  K. Crandall,et al.  Recombination in evolutionary genomics. , 2002, Annual review of genetics.

[5]  Tobias Polzin,et al.  Algorithms for the Steiner problem in networks , 2003 .

[6]  Sagi Snir,et al.  Efficient parsimony-based methods for phylogenetic network reconstruction , 2007, Bioinform..

[7]  Bernard M. E. Moret,et al.  NetGen: generating phylogenetic networks with diploid hybrids , 2006, Bioinform..

[8]  Kaizhong Zhang,et al.  Perfect Phylogenetic Networks with Recombination , 2001, J. Comput. Biol..

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

[10]  Luay Nakhleh,et al.  Recombination and phylogeny: effects and detection , 2005, Int. J. Bioinform. Res. Appl..

[11]  Edward C Holmes,et al.  Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. , 2003, The Journal of general virology.

[12]  Vladimir Makarenkov,et al.  Phylogenetic Network Construction Approaches , 2006 .

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

[14]  T. Tuller,et al.  Inferring phylogenetic networks by the maximum parsimony criterion: a case study. , 2006, Molecular biology and evolution.

[15]  Dan Gusfield,et al.  Efficient reconstruction of phylogenetic networks with constrained recombination , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[16]  Ernst Althaus,et al.  Computing steiner minimum trees in Hamming metric , 2006, SODA '06.

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

[18]  John D. Kececioglu,et al.  Reconstructing a history of recombinations from a set of sequences , 1994, SODA '94.

[19]  Thomas Lengauer,et al.  Recco: recombination analysis using cost optimization , 2006, Bioinform..