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Simultaneous Identification of Duplications and Lateral Gene Transfers

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3 Author(s)
Tofigh, A. ; Dept. of Comput. Biol. (CB) & SBC, KTH R. Inst. of Technol., Stockholm, Sweden ; Hallett, M. ; Lagergren, J.

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.

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Computational Biology and Bioinformatics, IEEE/ACM Transactions on  (Volume:8 ,  Issue: 2 )