Fast algorithm to reconstruct a species supertree from a set of protein trees
Purchase on Springer.com
$39.95 / €34.95 / £29.95*
Rent the article at a discountRent now
* Final gross prices may vary according to local VAT.
The problem of reconstructing a species supertree from a given set of protein, gene, and regulatorysite trees is the subject of this study. Under the traditional formulation, this problem is proven to be NP-hard. We propose a reformulation: to seek for a supertree, most of the clades of which contribute to the original protein trees. In such a variant, the problem seems to be biologically natural and a fast algorithm can be developed for its solution. The algorithm was tested on artificial and biological sets of protein trees, and it proved to be efficient even under the assumption of horizontal gene transfer. When horizontal transfer is not allowed, the algorithm correctness is proved mathematically; the time necessary for repeating the algorithm is assessed, and, in the worst case scenario, it is of the order n 3 · |V 0|3, where n is the number of gene trees and |V 0| is the number of tree species. Our software for supertree construction, examples of computations, and instructions can be freely accessed at http://lab6.iitp.ru/ru/super3gl/. Events associated with horizontal gene transfer are not included either in this study or in any variant of the software. A general case is described in the authors’ report (journal Problems of Information Transmission, 2011).
- Ma B., Li M., Zhang L., et al. 1998. On reconcstructing species trees from gene trees in term of duplications and losses. Proc. Second Annu. Int. Conf. Res. Computat. Mol. Biol. NY: ACM, pp. 182–191. CrossRef
- Phylogenetic Supertrees. Combining Information to Reveal the Tree of Life. 2004. Ed. Bininda-Emonds O.R.P. Dordrecht: Kluwer.
- Bansal M.S., Burleigh J.G., Eulenstein O., Fernández-Baca D. 2010. Robinson-Foulds Supertrees. Algorithms Mol. Biol. 5, 18. CrossRef
- Lyubetsky V.A., Gorbunov K.Yu., Rusin L.Y., V’yugin V.V. 2006. Algorithms to reconstruct evolutionary events at molecular level and infer species phylogeny. In: Bioinformatics of Genome Regulation and Structure II. Eds. Kolchanov N., Hofestaedt R., Milanesi L. Springer, pp. 189–204.
- Gorbunov K.Yu., Lyubetsky V.A. 2009. Reconstructing the evolution of genes along the species tree. Mol. Biol. (Moscow). 43, 881–893. CrossRef
- Gorbunov K.Yu., Lyubetsky V.A. 2010. An algorithm of reconciliation of gene and species trees and inferring gene duplications, losses and horizontal transfers. Inform. Protsesses. 10, 140–144.
- Gorbunov K.Yu., Lyubetsky V. A. 2011. The tree nearest on average to a given set of trees. Probl. Inform. Trans. 47, 274–288. CrossRef
- Doyon J.-P., Scornavacca C., Gorbunov K.Yu., Szöllösi G.J., Ranwez V., Berry V. 2010. Lecture Notes Comp. Sci. 6398, 93–108. CrossRef
- V’yugin V.V., Gelfand M.S., Lyubetsky V.A. 2002. Identification of horizontal gene transfer from phylogenetic gene trees. Mol. Biol. (Moscow). 37, 650–658. CrossRef
- Bansal M.S., Burleigh J.G., Eulenstein O., Wehe A. 2007. Heuristics for the gene-duplication problem: A θ(n) speed-up for the local search. Lecture Notes Comp. Sci. 4453, 238–252. CrossRef
- Pisani D., Cotton J.A., McInerney J.O. 2007. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol. Biol. Evol. 24, 1752–1760. CrossRef
- Guigo R., Muchnik I., Smith T.F. 1996. Reconstruction of ancient molecular phylogeny. Mol. Phylogenet. Evol. 6, 189–213. CrossRef
- Wu D., Hugenholtz P., Mavromatis K., et al. 2009. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature. 462, 1056–1060. doi:10.1038/ nature08656. CrossRef
- Wehe A., Bansal M.S., Burleigh J.G., Eulenstein O. 2008. DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics. 24, 1540–1541. CrossRef
- Gorbunov K.Yu. and Lyubetsky V.A. 2005. Identification of ancestral genes that introduce incongruence between protein- and species trees. Mol. Biol. (Moscow). 39, 741–751. CrossRef
- Fast algorithm to reconstruct a species supertree from a set of protein trees
Volume 46, Issue 1 , pp 161-167
- Cover Date
- Print ISSN
- Online ISSN
- SP MAIK Nauka/Interperiodica
- Additional Links
- species tree
- species supertree
- new formulation of the problem of supertree reconstruction; fast algorithm to reconstruct a supertree
- generation of a gene set from a supertree
- modeling the gene evolution along a species tree