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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
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)
Gray, G., Fitch, W.: Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus. Mol. Biol. Evol. 1(1), 57–66 (1983)
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)
Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Annals of combinatorics 8(4), 409–423 (2005)
Hallett, M.T., Lagergren, J.: Efficient algorithms for lateral gene transfer problems. In: RECOMB, pp. 149–156 (2001)
Boc, A., Makarenkov, V.: New efficient algorithm for detection of horizontal gene transfer events. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 190–201. Springer, Heidelberg (2003)
Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species: theory and practice. In: RECOMB, pp. 337–346 (2004)
Nakhleh, L., Ruths, D.A., Wang, L.S.: Riata-hgt: A fast and accurate heuristic for reconstructing horizontal gene transfer. In: Wang, L. (ed.) COCOON 2005. LNCS, vol. 3595, pp. 84–93. Springer, Heidelberg (2005)
Beiko, R.G., Harlow, T.J., Ragan, M.A.: Highways of gene sharing in prokaryotes. Proc. Natl. Acad. Sci. USA 102(40), 14332–14337 (2005)
Than, C., Ruths, D.A., Innan, H., Nakhleh, L.: Confounding factors in hgt detection: Statistical error, coalescent effects, and multiple solutions. Journal of Computational Biology 14(4), 517–535 (2007)
Jin, G., Nakhleh, L., Snir, S., Tuller, T.: Parsimony score of phylogenetic networks: Hardness results and a linear-time heuristic. IEEE/ACM Trans. Comput. Biology Bioinform. 6(3), 495–505 (2009)
Boc, A., Philippe, H., Makarenkov, V.: Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity. Syst. Biol. 59(2), 195–211 (2010)
Gary, M.W.: Origin and evolution of organelle genomes. Curr. Opin. Genet. Dev. 3, 884–890 (1993)
Huang, J., Gogarten, J.: Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biology 8(6), R99 (2007)
Lake, J.A.: Evidence for an early prokaryotic endosymbiosis. Nature 460, 967–971 (2009)
Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F., Papke, R.T.: Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Research 16(9), 1099–1108 (2006)
Hein, J.: Reconstructing evolution of sequences subject to recombination using parsimony. Mathematical Biosciences 98(2), 185–200 (1990)
Bender, M.A., Farach-Colton, M.: The LCA problem revisited. In: Gonnet, G.H., Viola, A. (eds.) LATIN 2000. LNCS, vol. 1776, pp. 88–94. Springer, Heidelberg (2000)
Zhaxybayeva, O., Doolittle, W.F., Papke, R.T., Gogarten, J.P.: Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus. Genome Biol. Evol. 1, 325–339 (2009)
Fournier, G.P., Gogarten, J.P.: Rooting the Ribosomal Tree of Life. Mol. Biol. Evol. (2010), (Epub ahead of print) msq057
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bansal, M.S., Gogarten, J.P., Shamir, R. (2010). Detecting Highways of Horizontal Gene Transfer. In: Tannier, E. (eds) Comparative Genomics. RECOMB-CG 2010. Lecture Notes in Computer Science(), vol 6398. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16181-0_10
Download citation
DOI: https://doi.org/10.1007/978-3-642-16181-0_10
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16180-3
Online ISBN: 978-3-642-16181-0
eBook Packages: Computer ScienceComputer Science (R0)