Abstract
We propose a reconciliation heuristic accounting for gene duplications, losses and horizontal transfers that specifically takes into account the uncertainties in the gene tree. Rearrangements are tried for gene tree edges that are weakly supported, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dynamic programming matrix used to compute reconciliations, which allows to speed-up the tree space exploration when rearrangements are generated by Nearest Neighbor Interchanges (NNI) edit operations. Experimental results on simulated and real data confirm that running times are greatly reduced when considering the above-mentioned optimization in comparison to the naïve rearrangement procedure. Results also show that gene trees modified by such NNI rearrangements are closer to the correct (simulated) trees and lead to more correct event predictions on average. The program is available at http://www.atgc-montpellier.fr/ Mowgli/
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References
Hallett, M., Lagergren, J., Tofigh, A.: Simultaneous identification of duplications and lateral transfers. In: RECOMB 2004, pp. 347–356. ACM, New York (2004)
Górecki, P.: Reconciliation problems for duplication, loss and horizontal gene transfer. In: Bourne, P.E., Gusfield, D. (eds.) RECOMB, pp. 316–325. ACM (2004)
Conow, C., Fielder, D., Ovadia, Y., Libeskind-Hadas, R.: Jane: a new tool for the cophylogeny reconstruction problem. Algorithms Mol. Biol. 5, 16 (2010)
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)
Tofigh, A., Hallett, M., Lagergren, J.: Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM TCBB 8(2), 517–535 (2011)
David, L.A., Alm, E.J.: Rapid evolutionary innovation during an archaean genetic expansion. Nature 469(7328), 93–96 (2011)
Bansal, M.S., Alm, E.J., Kellis, M.: Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer, and loss. In: Proceeding ISBM 2012 (2012)
Goodman, M., Czelusniak, J., Moore, G.W., Herrera, R.A., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132–163 (1979)
Page, R.D.: Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. Mol. Phylogenet. Evol. 14, 89–106 (2000)
Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM Journal on Computing 30(3), 729–752 (2001)
Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species: theory and practice. In: Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, RECOMB 2004, pp. 337–346. ACM, New York (2004)
Arvestad, L., Lagergren, J., Sennblad, B.: The gene evolution model and computing its associated probabilities. J. ACM 56(2) (2009)
Doyon, J.-P., Ranwez, V., Daubin, V., Berry, V.: Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform. 12(5), 392–400 (2011)
Ovadia, Y., Fielder, D., Conow, C., Libeskind-Hadas, R.: The co phylogeny reconstruction problem is NP-complete. J. Comput. Biol. 18(1), 59–65 (2011)
Libeskind-Hadas, R., Charleston, M.A.: On the computational complexity of the reticulate cophylogeny reconstruction problem. JCB 16(1), 105–117 (2009)
Durand, D., Halldorsson, B.V., Vernot, B.: A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Comput. Biol. 13(2), 320–335 (2006)
Hahn, M.W.: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biology 8(R141) (2007)
Berglund-Sonnhammer, A.C., Steffansson, P., Betts, M.J., Liberles, D.A.: Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. J. Mol. Evol. 63(2), 240–250 (2006)
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)
Vernot, B., Stolzer, M., Goldman, A., Durand, D.: Reconciliation with non-binary species trees. J. Comput. Biol. 15, 981–1006 (2008)
Chaudhary, R., Burleigh, J.G., Eulenstein, O.: Algorithms for Rapid Error Correction for the Gene Duplication Problem. In: Chen, J., Wang, J., Zelikovsky, A. (eds.) ISBRA 2011. LNCS, vol. 6674, pp. 227–239. Springer, Heidelberg (2011)
Semple, C., Steel, M.A.: Phylogenetics. Oxford Lecture Series in Mathematics and its Applications, vol. 24. Oxford University Press (2003)
Sanderson, M.J.: Inferring absolute rates of evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301–302 (2003)
Tofigh, A.: Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, KTH Royal Institute of Technology, Sweden (2009)
Felsenstein, J.: Inferring phylogenies. Sinauer Associates, Inc. (2004)
Knuth, D.E.: The Art of Computer Programmingm, Sorting and Searching, vol. 3. Addison-Wesley (1973)
Devroye, L.: A note on the height of binary search trees. Journal of the ACM 33(3), 489–498 (1986)
Kendall, D.G.: On the generalized birth-and-death process. Ann. Math. Stat. 19, 1–15 (1948)
Stamatakis, A.: Raxml-vi-hpc: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21), 2688–2690 (2006)
Penel, S., Arigon, A.M., Dufayard, J.F., Sertier, A.S., Daubin, V., Duret, L., Gouy, M., Perriere, G.: Databases of homologous gene families for comparative genomics. BMC Bioinformatics 10(suppl. 6), 3 (2009)
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Nguyen, T.H., Doyon, JP., Pointet, S., Arigon Chifolleau, AM., Ranwez, V., Berry, V. (2012). Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. 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_10
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DOI: https://doi.org/10.1007/978-3-642-33122-0_10
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