Detecting Highways of Horizontal Gene Transfer

  • Mukul S. Bansal
  • J. Peter Gogarten
  • Ron Shamir
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6398)

Abstract

In a horizontal gene transfer (HGT) event a gene is transferred between two species that do not share an ancestor-descendant relationship. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. We present a method for inferring such highways. Our method is based on the fact that the evolutionary histories of horizontally transferred genes disagree with the corresponding species phylogeny. Specifically, given a set of gene trees and a trusted rooted species tree, each gene tree is first decomposed into its constituent quartet trees and the quartets that are inconsistent with the species tree are identified. Our method finds a pair of species such that a highway between them explains the largest (normalized) fraction of inconsistent quartets. For a problem on n species, our method requires O(n4) time, which is optimal with respect to the quartets input size. An application of our method to a dataset of 1128 genes from 11 cyanobacterial species, as well as to simulated datasets, illustrates the efficacy of our method.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Mukul S. Bansal
    • 1
  • J. Peter Gogarten
    • 2
  • Ron Shamir
    • 1
  1. 1.The Blavatnik School of Computer ScienceTel-Aviv UniversityIsrael
  2. 2.Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsUSA

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