Detecting Highways of Horizontal Gene Transfer
Name
Bansal-2011-Detecting highways of horizontal gene transfer.pdf
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1.81 MB
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Author(s)
Bansal, Mukul S.
Banay, Guy
Gogarten, J. Peter
Shamir, Ron
Date Issued
September 2011
Journal
Journal of Computational Biology
Publisher
Mary Ann Liebert, Inc.
Citation
Bansal, Mukul S., Guy Banay, J. Peter Gogarten, and Ron Shamir. "Detecting Highways of Horizontal Gene Transfer." Journal of Computational Biology. September 2011, 18(9): 1087-1114. ©2011 Mary Ann Liebert, Inc.
Version
Final published version
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 + n2)-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.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1089/cmb.2011.0066
