Abstract
This paper presents an algorithm to detect lateral gene transfer (LGT) on the basis of pairwise evolutionary distances. The prediction is made from a likelihood ratio derived from hypotheses of LGT versus no LGT, using multivariate normal theory. In contrast to approaches based on explicit phylogenetic LGT detection, it avoids the high computational cost and pitfalls associated with gene tree inference, while maintaining the high level of characterization obtainable from such methods (species involved in LGT, direction, distance to the LGT event in the past). We validate the algorithm empirically using both simulation and real data, and compare its predictions with standard methods and other studies.
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References
Philippe, H., Douady, C.J.: Horizontal gene transfer and phylogenetics. Curr. Opin. Microbiol. 6, 498–505 (2003)
Lawrence, J.G., Ochman, H.: Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10, 1–4 (2002)
Lawrence, J.G., Ochman, H.: Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44, 383–397 (1997)
Lawrence, J.G., Ochman, H.: Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. U S A 95, 9413–9417 (1998)
Karlin, S.: Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol. 1, 598–610 (1998)
Moszer, I., Rocha, E.P., Danchin, A.: Codon usage and lateral gene transfer in Bacillus subtilis. Curr. Opin. Microbiol. 2, 524–528 (1999)
Mrazek, J., Karlin, S.: Detecting alien genes in bacterial genomes. Ann. N. Y. Acad. Sci. 870, 314–329 (1999)
Medigue, C., Rouxel, T., Vigier, P., Henaut, A., Danchin, A.: Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222, 851–856 (1991) (Comparative Study)
Hamady, M., Betterton, M.D., Knight, R.: Using the nucleotide substitution rate matrix to detect horizontal gene transfer. BMC Bioinformatics 7, 476 (2006)
Beiko, R.G., Harlow, T.J., Ragan, M.A.: Highways of gene sharing in prokaryotes. Proc. Natl. Acad. Sci. U S A 102, 14332–14337 (2005) (Comparative Study)
Gophna, U., Ron, E.Z., Graur, D.: Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312, 151–163 (2003)
Lawrence, J.G., Hartl, D.L.: Inference of horizontal genetic transfer from molecular data: an approach using the bootstrap. Genetics 131, 753–760 (1992)
Clarke, G.D.P., Beiko, R.G., Ragan, M.A., Charlebois, R.L.: Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184, 2072–2080 (2002)
Koski, L.B., Golding, G.B.: The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52, 540–542 (2001)
Pupko, T., Huchon, D., Cao, Y., Okada, N., Hasegawa, M.: Combining multiple data sets in a likelihood analysis: which models are the best?. Mol. Biol. Evol. 19, 2294–2307 (2002)
Susko, E.: Confidence regions and hypothesis tests for topologies using generalized least squares. Mol. Biol. Evol. 20, 862–868 (2003)
Felsenstein, J.: Inferring Phylogenies. Sinauer Associates Inc., Sunderland (2004)
Schneider, A., Cannarozzi, G.M., Gonnet, G.H.: Empirical codon substitution matrix. BMC Bioinformatics 6 (2005)
Kunin, V., Ouzounis, C.A.: The balance of driving forces during genome evolution in prokaryotes. Genome Res. 13, 1589–1594 (2003)
Dessimoz, C., Cannarozzi, G., Gil, M., Margadant, D., Roth, A., Schneider, A., Gonnet, G.: OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: Introduction and first achievements. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 61–72. Springer, Heidelberg (2005)
Lawrence, J.G., Hendrickson, H.: Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50, 739–749 (2003)
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O’Donovan, C., Phan, I., Pilbout, S., Schneider, M.: The swiss-prot protein knowledgebase and its supplement trembl in 2003. Nucleic Acids Res. 31, 365–370 (2003)
Lerat, E., Daubin, V., Ochman, H., Moran, N.A.: Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3, e130 (2005)
Ge, F., Wang, L.S., Kim, J.: The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol. 3, e316 (2005)
Dagan, T., Martin, W.: Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc. Natl. Acad. Sci. USA 104, 870–875 (2007)
Ragan, M.A.: On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201, 187–191 (2001)
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 Res. 16, 1099–1108 (2006)
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Dessimoz, C., Margadant, D., Gonnet, G.H. (2008). DLIGHT – Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework. In: Vingron, M., Wong, L. (eds) Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science(), vol 4955. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-78839-3_27
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DOI: https://doi.org/10.1007/978-3-540-78839-3_27
Publisher Name: Springer, Berlin, Heidelberg
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