Who is Who in Phylogenetic Networks

Publication no #2136   Type :   Html | Bib | Both

Created: 2011-09-08 02:04:18     Modified: 2012-01-15 11:11:44

2136 Mukul S. Bansal, Guy Banay, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In JCB, Vol. 18(9):1087-1114, 2011. Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://people.csail.mit.edu/mukul/HighwayFull_preprint.pdf.         Toggle 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. © 2011, Mary Ann Liebert, Inc." @Article{BBGS2011,       AUTHOR = {Bansal, Mukul S. and Banay, Guy and Gogarten, J. Peter and Shamir, Ron},       TITLE = {Detecting Highways of Horizontal Gene Transfer},       YEAR = {2011},       JOURNAL = {JCB},       VOLUME = {18},       NUMBER = {9},       PAGES = {1087-1114},       URL = {http://dx.doi.org/10.1089/cmb.2011.0066},       NOTE = {http://people.csail.mit.edu/mukul/HighwayFull_preprint.pdf},       KEYWORDS = {explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction} }