Simultaneous identification of duplications and lateral gene transfers

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):517-35. doi: 10.1109/TCBB.2010.14.

Abstract

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.

MeSH terms

  • Algorithms*
  • Evolution, Molecular
  • Gene Duplication*
  • Gene Transfer, Horizontal / genetics*
  • Models, Genetic