Abstract
Supertree algorithms combine smaller phylogenetic trees into a single, comprehensive phylogeny, or supertree. Most supertree problems are NP-hard, and often heuristics identify supertrees with anomalous or unwanted relationships. We introduce knowledge-enhanced supertree problems, which seek an optimal supertree for a collection of input trees that can only be assembled from a set of given, possibly incompatible, phylogenetic relationships. For these problems we introduce efficient algorithms that, in a special setting, also provide exact solutions for the original supertree problems. We describe our algorithms and verify their performance based on the Robinson Foulds (RF) supertree problem. We demonstrate that our algorithms (i) can significantly improve upon estimates of existing RF-heuristics, and (ii) can compute exact RF supertrees with up to 17 taxa.
This is a preview of subscription content, log in via an institution to check access.
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
Bansal, M.S., Burleigh, J.G., Eulenstein, O., Fernández-Baca, D.: Robinson-foulds supertrees. Algor. Mol. Biol. 5, 18 (2010)
Barthelemy, J.P., McMorris, F.R.: The median procedure for n-trees. Journal of Classification 3, 329–334 (1986)
Bininda-Emonds, O.R.P.: The evolution of supertrees. Trends Ecol. Evol. 19, 315–322 (2004)
Bininda-Emonds, O.R.P., Gittleman, J.L., Steel, M.A.: The (super) tree of life: procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33, 265–289 (2002)
Burleigh, J.G., Barbazuk, W.B., Davis, J.M., Morse, A.M., Soltis, P.S.: Exploring diversification and genome size evolution in extant gymnosperms through phylogenetic synthesis. Journal of Botany, 292857 (2012)
Cardillo, M., Bininda-Emonds, O.R.P., Boakes, E., Purvis, A.: A species-level phylogenetic supertree of marsupials. Journal of Zoology 264, 11–31 (2004)
Chang, W., Burleigh, J.G., Fernandez-Baca, D.F., Eulenstein, O.: An ILP solution for the gene duplication problem. BMC Bioinformatics 12(suppl.1), S14 (2011)
Chaudhary, R., Burleigh, J.G., Fernández-Baca, D.: Fast Local Search for Unrooted Robinson-Foulds Supertrees. In: Chen, J., Wang, J., Zelikovsky, A. (eds.) ISBRA 2011. LNCS, vol. 6674, pp. 184–196. Springer, Heidelberg (2011)
Davies, T.J., Fritz, S.A., Grenyer, R., Orme, C.D.L., Bielby, J., Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., Gittleman, J.L., Mace, G.M., Purvis, A.: Phylogenetic trees and the future of mammalian biodiversity. Proc. Natl. Acad. Sci. USA 105, 11556–11563 (2008)
Edwards, E.J., Still, C.J., Donoghue, M.J.: The relevance of phylogeny to studies of global change. Trends Ecol. Evol. 22, 243–249 (2007)
Forest, F., Grenyer, R., Rouget, M., Davies, T.J., et al.: Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445, 757–760 (2007)
Hallett, M.T., Lagergren, J.: New algorithms for the duplication-loss model. In: RECOMB, pp. 138–146 (2000)
Hartmann, S., Lu, D., Phillips, J., Vision, T.J.: Phytome: A platform for plant comparative genomics. Nucleic Acids Research 34, D724–D730 (2006)
Jones, D.T., Taylor, W.R., Thornton, J.M.: The rapid generation of mutation data matrices from protein sequences. Comp. Appl. Biosci. 8, 25–282 (1992)
Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM J. Comput. 30, 729–752 (2000)
Robinson, D.F., Foulds, L.R.: Comparison of phylogenetic trees. Mathematical Biosciences 53, 131–147 (1981)
Sanderson, M.J., Purvis, A., Henze, C.: Phylogenetic supertrees: Assembling the trees of life. Trends Ecol. Evol. 13, 105–109 (1998)
Stamatakis, A.: Raxml-vi-hpc: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006)
Stamatakis, A., Hoover, P., Rougemont, J.: A fast bootstrapping algorithm for the raxml web-servers. In Systematic Biology 57(5), 758–771 (2008)
Swofford, D.L.: PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10 (2002)
Than, C., Nakhleh, L.: Species tree inference by minimizing deep coalescences. PLoS Comput. Biol. 5(9), e1000501 (2009)
Thuiller, W., Lavergne, S., Roquet, C., Boulangeat, I., Lafourcade, B., Araujo, M.B.: Consequences of climate change on the tree of life in europe. Nature 470, 531–534 (2011)
Wehe, A., Bansal, M.S., Burleigh, J.G., Eulenstein, O.: Duptree: A program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13), 1540–1541 (2008)
Willis, C.G., Ruhfel, B., Primack, R.B., Miller-Rushing, A.J., Davis, C.C.: Phylogenetic patterns of species loss in thoreauś woods are driven by climate change. Proc. Nat. Acad Sci. USA 105, 17029–17033 (2009)
Yu, Y., Warnow, L., Nakhleh, T.: Algorithms for mdc-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles. J. Comput Biol. 18(11), 1543–1559 (2011)
Zhang, L.: Inferring a species tree from gene trees under the deep coalescence cost. In: RECOMB, pp. 192–193 (2000)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Wehe, A., Burleigh, J.G., Eulenstein, O. (2012). Algorithms for Knowledge-Enhanced Supertrees. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science(), vol 7292. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30191-9_25
Download citation
DOI: https://doi.org/10.1007/978-3-642-30191-9_25
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-30190-2
Online ISBN: 978-3-642-30191-9
eBook Packages: Computer ScienceComputer Science (R0)