Abstract
The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss, and lateral gene transfer (LGT). The extent of LGT, particularly in prokaryotes, and its implications for creating a ‘network of life’ rather than a ‘tree of life’ is controversial. In this paper, we formally model the problem of quantifying LGT, and provide exact mathematical bounds, and new computational results. In particular, we investigate the computational complexity of quantifying the extent of LGT under the simple models of gene genesis, loss, and transfer on which a recent heuristic analysis of biological data relied. Our approach takes advantage of a relationship between LGT optimization and graph-theoretical concepts such as tree width and network flow.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Andersson, J.O., 2005. Lateral gene transfer in eukaryotes. Cell. Mol. Life Sci. 62(11), 1182–1197.
Dagan, T., Martin, W., 2007. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc. Natl. Acad. Sci. USA 104, 870–875.
Dagan, T., Artzy-Randrup, Y., Martin, W., 2008. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc. Natl. Acad. Sci. USA 105, 10039–10044.
Diestel, R., 2006. Graph Theory, 3rd edn. Springer, Berlin.
Doolittle, W.F., Bapteste, E., 2007. Pattern pluralism and the Tree of Life hypothesis. Proc. Natl. Acad. Sci. USA 104, 2043–2049.
Doolittle, W.F., Boucher, Y., Nesbø, C., Douady, C.J., Andersson, J.O., Roger, A.J., 2003. How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos. Trans. R. Soc. B 358, 39–58.
Goldberg, A.V., Rao, S., 1998. Beyond the flow decomposition barrier. J. ACM 45(5), 783–797.
Even, S., Itai, A., Shamir, A., 1972. On the complexity of timetable and multi-commodity flow problems. SIAM J. Comput. 1(2), 188–202.
Felsenstein, J., 2004. Inferring Phylogenies. Sinauer Press, Sunderland.
Fortune, S., Hopcroft, J., Wyllie, J., 1980. The directed subgraph homeomorphism problem. Theor. Comput. Sci. 10, 111–121.
Gusfield, D., Eddhu, S., Langley, C., 2004. Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinform. Comput. Biol. 2, 173–213.
Jin, G., Nakhleh, L., Snir, S., Tamir, T., 2007. Inferring phylogenetic networks by the maximum parsimony criterion: A case study. Mol. Biol. Evol. 24, 324–337.
Kimura, M., 1983. The Neutral Theory of Evolution. Cambridge University Press, Cambridge.
Mirkin, B.G., Fenner, T.I., Galperin, M.Y., Koonin, E.V., 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of lateral gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3, 2.
Spencer, M., Susko, E., Roger, A.J., 2006. Modelling prokaryote gene content. Evol. Bioinf. Online 2, 157–178.
Author information
Authors and Affiliations
Corresponding author
Additional information
We thank the Allan Wilson Centre for Molecular Ecology and Evolution, and the New Zealand Marsden Fund for helping fund this work.
Rights and permissions
About this article
Cite this article
van Iersel, L., Semple, C. & Steel, M. Quantifying the Extent of Lateral Gene Transfer Required to Avert a ‘Genome of Eden’. Bull. Math. Biol. 72, 1783–1798 (2010). https://doi.org/10.1007/s11538-010-9506-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11538-010-9506-7