Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks

J Bioinform Comput Biol. 2009 Aug;7(4):597-623. doi: 10.1142/s0219720009004308.

Abstract

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network determines how non-treelike the evolution can be, with level-0 networks being trees. We study the problem of constructing level-k phylogenetic networks from triplets, i.e. phylogenetic trees for three leaves (taxa). We give, for each k, a level-k network that is uniquely defined by its triplets. We demonstrate the applicability of this result by using it to prove that (1) for all k > or = 1 it is NP-hard to construct a level-k network consistent with all input triplets, and (2) for all k > or = 0 it is NP-hard to construct a level-k network consistent with a maximum number of input triplets, even when the input is dense. As a response to this intractability, we give an exact algorithm for constructing level-1 networks consistent with a maximum number of input triplets.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Computer Simulation
  • Gene Transfer, Horizontal / genetics*
  • Genetics, Population*
  • Humans
  • Models, Genetic*
  • Pedigree*
  • Phylogeny*