RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer
Horizontal gene transfer (HGT) plays a major role in microbial genome diversification, and is claimed to be rampant among various groups of genes in bacteria. Further, HGT is a major confounding factor for any attempt to reconstruct bacterial phylogenies. As a result, detecting and reconstructing HGT events in groups of organisms has become a major endeavor in biology. The problem of detecting HGT events based on incongruence between a species tree and a gene tree is computationally very hard (NP-hard). Efficient algorithms exist for solving restricted cases of the problem.
We propose RIATA-HGT, the first polynomial-time heuristic to handle all HGT scenarios, without any restrictions. The method accurately infers HGT events based on analyzing incongruence among species and gene trees. Empirical performance of the method on synthetic and biological data is outstanding. Being a heuristic, RIATA-HGT may overestimate the optimal number of HGT events; empirical performance, however, shows that such overestimation is very mild.
We have implemented our method and run it on biological and synthetic data. The results we obtained demonstrate very high accuracy of the method. Current version of RIATA-HGT uses the PAUP tool, and we are in the process of implementing a stand-alone version, with a graphical user interface, which will be made public. The tool, in its current implementation, is available from the authors upon request.
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- 1.Python software foundation (2005), http://www.python.org
- 2.Addario-Berry, L., Hallett, M.T., Lagergren, J.: Towards identifying lateral gene transfer events. In: Proc. 8th Pacific Symp. on Biocomputing (PSB 2003), pp. 279–290 (2003)Google Scholar
- 4.Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. In: Annals of Combinatorics, pp. 1–15 (2005) (in press)Google Scholar
- 10.Hallett, M.T., Lagergren, J.: Efficient algorithms for lateral gene transfer problems. In: Proc. 5th Ann. Int’l Conf. Comput. Mol. Biol (RECOMB 2001), pp. 149–156. ACM Press, New York (2001)Google Scholar
- 11.Ho, M.-W.: Recent evidence confirms risks of horizontal gene transfer (2002), http://www.i-sis.org.uk/FSAopenmeeting.php
- 19.Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species– theory and practice. In: Proc. 8th Ann. Int’l Conf. Comput. Mol. Biol (RECOMB 2004), pp. 337–346 (2004)Google Scholar
- 23.Salzberg, S.L., Eisen, J.A.: Lateral gene transfer or viral colonization? Science 293, 1048 (2001)Google Scholar
- 25.Sanderson, M.: r8s software package, Available from http://loco.ucdavis.edu/r8s/r8s.html
- 26.Swofford, D.L.: PAUP*: Phylogenetic analysis using parsimony (and other methods), Sinauer Associates, Underland, Massachusetts, Version 4.0 (1996)Google Scholar