Abstract
Reconciliation is a method widely used to infer the evolutionary relationship between the members of a gene family. It consists of comparing a gene tree with a species tree, and interpreting the incongruence between the two trees as evidence of duplication and loss. In the case of binary rooted trees, linear-time algorithms have been developed for the duplication, loss, and mutation (duplication + loss) costs. However, a strict prerequisite to reconciliation is to have a gene tree free from error, as few misplaced edges may lead to a completely different result in terms of the number and position of inferred duplications and losses. How should the weak edges be handled? One reasonable answer is to transform the binary gene tree into a non-binary tree by removing each weak edge and collapsing its two incident vertices into one. The created polytomies are “apparent” as they do not reflect a true simultaneous divergence of many copies from a common ancestor, but rather a lack of resolution. In this paper, we consider the problem of reconciling a non-binary rooted gene tree G with a binary rooted species tree S, were polytomies of G are assumed to be apparent. We give a linear-time algorithm that infers a reconciliation of minimum mutation cost between a binary refinement of a polytomy and S, improving on the best known result, which is cubic. This implies a straightforward generalization to a gene tree G with nodes of arbitrary degree, that runs in time O(|S||G|), which is shown to be an optimal algorithm.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Akerborg, O., Sennblad, B., Arvestad, L., Lagergren, J.: Simultaneous bayesian gene tree reconstruction and reconciliation analysis. Proceedings of the National Academy of Sciences USA 106(14), 5714–5719 (2009)
Arvestad, L., Berglung, A.-C., Lagergren, J., Sennblad, B.: Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In: Gusfield, D. (ed.) RECOMB 2004: Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, pp. 326–335. ACM, New York (2004)
Chang, W.-C., Eulenstein, O.: Reconciling Gene Trees with Apparent Polytomies. In: Chen, D.Z., Lee, D.T. (eds.) COCOON 2006. LNCS, vol. 4112, pp. 235–244. Springer, Heidelberg (2006)
Chang, W.C., Eulenstein, O.: Reconciling gene trees with apparent polytomies, technical report. Department of Computer Science, Iowa State University (2006)
Chauve, C., El-Mabrouk, N.: New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 46–58. Springer, Heidelberg (2009)
Chen, K., Durand, D., Farach-Colton, M.: Notung: Dating gene duplications using gene family trees. Journal of Computational Biology 7, 429–447 (2000)
Csűrös, M.: Ancestral reconstruction by asymmetric wagner parsimony over continuous characteand squared parsimony over distributions. In: Sixth RECOMB Satellite Workshop on Comparative Genomics, pp. 72–86 (2008)
Doroftei, A., El-Mabrouk, N.: Removing Noise from Gene Trees. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS (LNBI), vol. 6833, pp. 76–91. Springer, Heidelberg (2011)
Doyon, J.-P., Ranwez, V., Daubin, V., Berry, V.: Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform. 12, 392–400 (2011)
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)
Durand, D., Haldórsson, B.V., Vernot, B.: A hybrid micro-macroevolutionary approach to gene tree reconstruction. Journal of Computational Biology 13, 320–335 (2006)
Fang, G., Bhardwaj, N., Robilotto, R., Gerstein, M.B.: Getting started in gene orthology and functional analysis. PLoS Comput. Biol. 6(3), e1000703 (2010)
Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A.E., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28, 132–163 (1979)
Gorecki, P., Tiuryn, J.: DLS-trees: a model of evolutionary scenarios. Theoretical Computer Science 359, 378–399 (2006)
Hahn, M.W.: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biology 8(R141) (2007)
Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM J. on Comput. 30, 729–752 (2000)
Slowinski, J.B.: Molecular polytomies. Molecular Phylogenetics and Evolution 19(1), 114–120 (2001)
Tofigh, A., Hallett, M., Lagergren, J.: Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans. Comput. Biol. Bioinform. 8, 517–535 (2011)
Zhang, J.: Evolution by gene duplication: an update. Trends in Ecology and Evolution 18(6), 292–298 (2003)
Zhang, L.X.: On Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. Journal of Computational Biology 4, 177–188 (1997)
Zheng, Y., Wu, T., Zhang, L.: Reconciliation of gene and species trees with polytomies, eprint arXiv:1201.3995 (2012)
Zmasek, C.M., Eddy, S.R.: A simple algorithm to infer gene duplication and speciiation events on a gene tree. Bioinformatics 17, 821–828 (2001)
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
Lafond, M., Swenson, K.M., El-Mabrouk, N. (2012). An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. In: Raphael, B., Tang, J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science(), vol 7534. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33122-0_9
Download citation
DOI: https://doi.org/10.1007/978-3-642-33122-0_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-33121-3
Online ISBN: 978-3-642-33122-0
eBook Packages: Computer ScienceComputer Science (R0)