Detecting highways of horizontal gene transfer

Mukul S. Bansal, J. Peter Gogarten, Ron Shamir

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

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(n 4) 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.

Original languageEnglish
Title of host publicationComparative Genomics - International Workshop, RECOMB-CG 2010, Proceedings
Pages109-120
Number of pages12
DOIs
StatePublished - 2010
EventInternational Workshop on Comparative Genomics, RECOMB-CG 2010 - Ottawa, ON, Canada
Duration: 9 Oct 201011 Oct 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6398 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

ConferenceInternational Workshop on Comparative Genomics, RECOMB-CG 2010
Country/TerritoryCanada
CityOttawa, ON
Period9/10/1011/10/10

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