Who is Who in Phylogenetic Networks

Publication no #2036   Type :   Html | Bib | Both

Created: 2010-07-06 16:35:18     Modified: 2010-11-25 07:54:05

2036 Mukul S. Bansal, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10), Vol. 6398:109-120 of LNCS, springer, 2011. Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.cs.iastate.edu/~bansal/Highways_RCG10.pdf.         Toggle 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. © 2010 Springer-Verlag." @InProceedings{BGS2010,       AUTHOR = {Bansal, Mukul S. and Gogarten, J. Peter and Shamir, Ron},       TITLE = {Detecting Highways of Horizontal Gene Transfer},       YEAR = {2011},       BOOKTITLE = {Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10)},       VOLUME = {6398},       PAGES = {109-120},       SERIES = {LNCS},       PUBLISHER = {springer},       URL = {http://dx.doi.org/10.1007/978-3-642-16181-0_10},       NOTE = {http://www.cs.iastate.edu/~bansal/Highways_RCG10.pdf},       KEYWORDS = {explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction} }