Detecting Highways of Horizontal Gene Transfer
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(n4) 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.
Unable to display preview. Download preview PDF.
- 1.Ochiai, K., Yamanaka, T., Kimura, K., Sawada, O.: Inheritance of drug resistance (and its transfer) between Shigella strains and Between Shigella and E.coli strains. Hihon Iji Shimpor 1861, 34–46 (1959) (in Japanese)Google Scholar
- 3.Zhaxybayeva, O.: Detection and Quantitative Assessment of Horizontal Gene Transfer. In: Horizontal gene Transfer: Genomes in Flux. Methods in Molecular Biology, vol. 532, pp. 195–213. Humana Press (2009)Google Scholar
- 5.Hallett, M.T., Lagergren, J.: Efficient algorithms for lateral gene transfer problems. In: RECOMB, pp. 149–156 (2001)Google Scholar
- 7.Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species: theory and practice. In: RECOMB, pp. 337–346 (2004)Google Scholar
- 20.Fournier, G.P., Gogarten, J.P.: Rooting the Ribosomal Tree of Life. Mol. Biol. Evol. (2010), (Epub ahead of print) msq057Google Scholar