Robustness of the Parsimonious Reconciliation Method in Cophylogeny
The aim of this paper is to explore the robustness of the parsimonious host-symbiont tree reconciliation method under editing or small perturbations of the input. The editing involves making different choices of unique symbiont mapping to a host in the case where multiple associations exist. This is made necessary by the fact that no tree reconciliation method is currently able to handle such associations. The analysis performed could however also address the problem of errors. The perturbations are re-rootings of the symbiont tree to deal with a possibly wrong placement of the root specially in the case of fast-evolving species. In order to do this robustness analysis, we introduce a simulation scheme specifically designed for the host-symbiont cophylogeny context, as well as a measure to compare sets of tree reconciliations, both of which are of interest by themselves.
KeywordsCophylogeny Parsimony Event-based methods Robustness Measure for tree reconciliation comparison
The authors would like to express their gratitude to Christian Gautier for fruitful preliminary discussions on this work.
- 5.Conow, C., Fielder, D., Ovadia, Y., Libeskind-Hadas, R.: Jane: a new tool for the cophylogeny reconstruction problem. Algo. Mol. Biol. 5(16), 1–10 (2010)Google Scholar
- 7.Doyon, J.-P., Scornavacca, C., Gorbunov, K.Y., Szöllősi, G.J., Ranwez, V., Berry, V.: An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 93–108. Springer, Heidelberg (2010)CrossRefGoogle Scholar
- 10.Keller-Schmidt, S., Wieseke, N., Klemm, K., Middendorf, M.: Evaluation of host parasite reconciliation methods using a new approach for cophylogeny generation. Technical report, University of Leipzig (2011). https://www.bioinf.uni-leipzig.de/Publications/PREPRINTS/11-013.pdf
- 14.Nei, M., Kumar, S.: Molecular evolution and phylogenetics. Oxford Univ, Press (2000)Google Scholar
- 17.Paterson, A.M., Gray, R.D., Clayton, D.H., Moore, J.: Host-parasite co-speciation, host switching, and missing the boat. In: Clayton, D.H., Moore, J. (eds.) Host-parasite evolution: general principles and avian models, pp. 236–250. Oxford University Press, Oxford (1997)Google Scholar
- 22.Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M.: Phylogenetic inference. In: Hillis, D.M., Moritz, C., Mable, B.K. (eds.) Molecular systematics, pp. 407–514. Sinauer Associates Inc, Sunderland (1996)Google Scholar
Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 2.5 International License (http://creativecommons.org/licenses/by-nc/2.5/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.
The images or other third party material in this chapter are included in the chapter's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.