TY - GEN
T1 - Detecting highways of horizontal gene transfer
AU - Bansal, Mukul S.
AU - Gogarten, J. Peter
AU - Shamir, Ron
N1 - Funding Information:
Acknowledgements. MSB was supported in part by a postdoctoral fellowship from the Edmond J. Safra Bioinformatics program at Tel-Aviv University. JPG was supported in part by NSF grant DEB 0830024, the Edmond J. Safra Bioinformatics Program, and a fellowship from the Fulbright Program. RS was supported in part by the Israel Science Foundation (Grant 802/08) and by the Raymond and Beverly Sackler Chair in Bioinformatics.
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=78649918717&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-16181-0_10
DO - 10.1007/978-3-642-16181-0_10
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AN - SCOPUS:78649918717
SN - 3642161804
SN - 9783642161803
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 109
EP - 120
BT - Comparative Genomics - International Workshop, RECOMB-CG 2010, Proceedings
T2 - International Workshop on Comparative Genomics, RECOMB-CG 2010
Y2 - 9 October 2010 through 11 October 2010
ER -