An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers

  • Jean-Philippe Doyon
  • Celine Scornavacca
  • K. Yu. Gorbunov
  • Gergely J. Szöllősi
  • Vincent Ranwez
  • Vincent Berry
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6398)


Tree reconciliation methods aim at estimating the evolutionary events that cause discrepancy between gene trees and species trees. We provide a discrete computational model that considers duplications, transfers and losses of genes. The model yields a fast and exact algorithm to infer time consistent and most parsimonious reconciliations. Then we study the conditions under which parsimony is able to accurately infer such events. Overall, it performs well even under realistic rates, transfers being in general less accurately recovered than duplications. An implementation is freely available at .


Species Tree Gene Tree Duplication Rate Optimal Receiver Rooted Binary Tree 
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  1. 1.
    Conow, C., Fielder, D., Ovadia, Y., Libeskind-Hadas, R.: Jane: a new tool for the cophylogeny reconstruction problem. Algorithms Mol. Biol. 5, 16 (2010)CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Csuros, M., Miklos, I.: Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model. Mol. Biol. Evol. 26(9), 2087–2095 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Gabaldon, T.: Computational approaches for the prediction of protein function in the mitochondrion. Am J. Physiol. Cell. Physiol. 291(6), C1121–C1128 (2006)Google Scholar
  4. 4.
    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)CrossRefGoogle Scholar
  5. 5.
    Gorbunov, K.Y., Lyubetsky, V.A.: Reconstructing genes evolution along a species tree. Mol. Biol (Mosk.) 43, 946–958 (2009)CrossRefGoogle Scholar
  6. 6.
    Gorbunov, K.Y., Lyubetsky, V.A.: An algorithm of reconciliation of gene and species trees and inferring gene duplications, losses and horizontal transfers. Information processes 10(2), 140–144 (2010) (in Russian)Google Scholar
  7. 7.
    Libeskind-Hadas, R., Charleston, M.A.: On the computational complexity of the reticulate cophylogeny reconstruction problem. JCB 16(1), 105–117 (2009)Google Scholar
  8. 8.
    Loader, S.P., Pisani, D., Cotton, J.A., Gower, D.J., Day, J.J., Wilkinson, M.: Relative time scales reveal multiple origins of parallel disjunct distributions of african caecilian amphibians. Biol. Lett., 505–508 (October 2007)Google Scholar
  9. 9.
    Merkle, D., Middendorf, M.: Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information. Theory Biosci. 123(4), 277–299 (2005)CrossRefPubMedGoogle Scholar
  10. 10.
    Merkle, D., Middendorf, M., Wieseke, N.: A parameter-adaptive dynamic programming approach for inferring cophylogenies. BMC Bioinformatics 11(suppl. 1), S60 (2010)Google Scholar
  11. 11.
    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), S3 (2009)Google Scholar
  12. 12.
    Rambaut, A.: Phylogen: phylogenetic tree simulator package (2002)Google Scholar
  13. 13.
    Tofigh, A.: Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, KTH Royal Institute of Technology, Sweden (2009)Google Scholar
  14. 14.
    Tofigh, A., Hallett, M., Lagergren, J.: Simultaneous identification of duplications and lateral gene transfers. In: IEEE/ACM TCBB, p. 99 (2010)Google Scholar
  15. 15.
    Tofigh, A., Sjöstrand, J., Sennblad, B., Arvestad, L., Lagergren, J.: Detecting LGTs using a novel probabilistic model integrating duplications, lgts, losses, rate variation, and sequence evolution (manuscript)Google Scholar
  16. 16.
    Vernot, B., Stolzer, M., Goldman, A., Durand, D.: Reconciliation with non-binary species trees. J. Comput. Biol. 15, 981–1006 (2008)CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Zhang, L.: On a mirkin-muchnik-smith conjecture for comparing molecular phylogenies. Journal of Computational Biology 4(2), 177–187 (1997)CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Jean-Philippe Doyon
    • 1
  • Celine Scornavacca
    • 2
  • K. Yu. Gorbunov
    • 3
  • Gergely J. Szöllősi
    • 4
  • Vincent Ranwez
    • 5
  • Vincent Berry
    • 1
  1. 1.LIRMMCNRS - Univ. Montpellier 2France
  2. 2.Center for Bioinformatics (ZBIT)Tuebingen Univ.Germany
  3. 3.Kharkevich IITPRussian Academy of SciencesMoscow
  4. 4.LBBE, CNRS - Univ. Lyon 1France
  5. 5.ISEM, CNRS - Univ. Montpellier 2France

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