Abstract
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and costly process. Therefore, decision criteria would be desirable to decide a priori which data might contribute new information to the supertree which is not explicitly displayed by any input tree. A new concept, the so-called groves, to identify taxon sets with the potential to construct such informative supertrees was suggested by Ané et al. in 2009. But the important conjecture that maximal groves can easily be identified in a database remained unproved and was published on the Isaac Newton Institute’s list of open phylogenetic problems. In this paper, we show that the conjecture does not generally hold, but also introduce a new concept, namely, the 2-overlap groves, which overcomes this problem.
Similar content being viewed by others
References
Ané C., Eulenstein O., Piaggio-Talice R., Sanderson M: Groves of phylogenetic trees. Ann. Combin. 13(2), 139–167 (2009)
Baum B.R: Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41(1), 3–10 (1992)
Bininda-Emonds O.R.P.: Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Kluwer Academic Publishers, Dordrecht (2004)
Bryant D., Steel M: Extension operations on sets of leaf-labelled trees. Adv. Appl.Math. 16(4), 425–453 (1995)
Chor B., Tuller T: Finding a maximum likelihood tree is hard. J. ACM 53(5), 722–744 (2006)
Driskell A. et al.: Prospects for building the tree of life from large sequence databases. Science, 306(5699), 1172–1174 (2004)
Foulds L.R., Graham R.L: The Steiner problem in phylogeny is NP-complete. Adv. Appl. Math. 3(1), 43–49 (1982)
Gordon A.D: Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves. J. Classification 3(2), 335–348 (1986)
McMahon M.M., Sanderson M.J: Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Syst. Biol. 55(5), 818–836 (2006)
Roch S: A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE/ACMTrans. Comput. Biol. Bioinform. 3(1), 92–94 (2006)
Sanderson M.J., Purvis A., Henze C: Phylogenetic supertrees: assembling the trees of life. Trends Ecology & Evol. 13(3), 105–109 (1998)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Fischer, M. Mathematical Aspects of Phylogenetic Groves. Ann. Comb. 17, 295–310 (2013). https://doi.org/10.1007/s00026-013-0179-4
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00026-013-0179-4