Abstract
Reticulation events occur frequently in many types of species. Therefore, to develop accurate methods for reconstructing phylogenetic networks in order to describe evolutionary history in the presence of reticulation events is important. Previous work has suggested that constructing phylogenetic networks by merging gene trees is a biologically meaningful approach. This paper presents two new efficient algorithms for inferring a phylogenetic network from a set \(\mathcal{T}\) of gene trees of arbitrary degrees. The first algorithm solves the open problem of constructing a refining galled network for \(\mathcal{T}\) (if one exists) with no restriction on the number of hybrid nodes; in fact, it outputs the smallest possible solution. In comparison, the previously best method (SpNet) can only construct networks having a single hybrid node. For cases where there exists no refining galled network for \(\mathcal{T}\), our second algorithm identifies a minimum subset of the species set to be removed so that the resulting trees can be combined into a galled network. Based on our two algorithms, we propose two general methods named RGNet and RGNet+. Through simulations, we show that our methods outperform the other existing methods neighbor-joining, NeighborNet, and SpNet.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Bryant, D., Moulton, V.: Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution 21(2), 255–265 (2004)
Gusfield, D., Eddhu, S., Langley, C.: Efficient reconstruction of phylogenetic networks with constrained recombination. In: Proc. of Computational Systems Bioinformatics (CSB 2003), pp. 363–374 (2003)
Holland, B., Moulton, V.: Consensus networks: A method for visualising incompatibilities in collections of trees. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 165–176. Springer, Heidelberg (2003)
Huson, D.H., Dezulian, T., Klöpper, T., Steel, M.: Phylogenetic super-networks from partial trees. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 388–399. Springer, Heidelberg (2004)
Jansson, J., Nguyen, N.B., Sung, W.-K.: Algorithms for combining rooted triplets into a galled phylogenetic network. In: Proc. of the 16th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2005) (2005) (to appear)
Linder, C.R., Moret, B.M.E., Nakhleh, L., Warnow, T.: Network (reticulate) evolution: Biology, models, and algorithms. Tutorial presented at the 9th Pacific Symposium on Biocomputing (PSB 2004) (2004)
Maddison, W.P.: Gene trees in species trees. Systematic Biology 46(3), 523–536 (1997)
Nakhleh, L., Sun, J., Warnow, T., Linder, C.R., Moret, B.M.E., Tholse, A.: Towards the development of computational tools for evaluating phylogenetic reconstruction methods. In: Proc. of the 8th Pacific Symposium on Biocomputing (PSB 2003), pp. 315–326 (2003)
Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species – theory and practice. In: Proc. of the 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), pp. 337–346 (2004)
Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4), 406–425 (1987)
Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. Journal of Computational Biology 8(1), 69–78 (2001)
Zwickl, D., Hillis, D.: Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51(4), 588–598 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Huynh, T.N.D., Jansson, J., Nguyen, N.B., Sung, WK. (2005). Constructing a Smallest Refining Galled Phylogenetic Network. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_20
Download citation
DOI: https://doi.org/10.1007/11415770_20
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25866-7
Online ISBN: 978-3-540-31950-4
eBook Packages: Computer ScienceComputer Science (R0)