Detecting highways of horizontal gene transfer

Mukul S. Bansal, Guy Banay, J. Peter Gogarten, Ron Shamir*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

In a horizontal gene transfer (HGT) event, a gene is transferred between two species that do not have 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 and m input quartet trees, we give an efficient O(m+n 2)-time algorithm for detecting highways, 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.

Original languageEnglish
Pages (from-to)1087-1114
Number of pages28
JournalJournal of Computational Biology
Volume18
Issue number9
DOIs
StatePublished - 1 Sep 2011

Keywords

  • Algorithms
  • horizontal gene transfer
  • microbial evolution
  • quartets

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