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New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees

  • Cedric Chauve
  • Nadia El-Mabrouk
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5541)

Abstract

Reconciliation between a set of gene trees and a species tree is the most commonly used approach to infer the duplication and loss events in the evolution of gene families, given a species tree. When a species tree is not known, a natural algorithmic problem is to infer a species tree such that the corresponding reconciliation minimizes the number of duplications and/or losses. In this paper, we clarify several theoretical questions and study various algorithmic issues related to these two problems. (1) For a given gene tree T and species tree S, we show that there is a single history explaining T and consistent with S that minimizes gene losses, and that this history also minimizes the number of duplications. We describe a simple linear-time and space algorithm to compute this parsimonious history, that is not based on the Lowest Common Ancestor (LCA) mapping approach; (2) We show that the problem of computing a species tree that minimizes the number of gene duplications, given a set of gene trees, is in fact a slight variant of a supertree problem; (3) We show that deciding if a set of gene trees can be explained using only apparent duplications can be done efficiently, as well as computing a parsimonious species tree for such gene trees. We also characterize gene trees that can be explained using only apparent duplications in terms of compatible triplets of leaves.

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References

  1. 1.
    Aho, A.V., Sagiv, Y., Szymanski, T.G., Ullman, J.D.: Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comput. 10, 405–421 (1981)CrossRefGoogle Scholar
  2. 2.
    Bansal, M.S., Burleigh, J.G., Eulenstein, O., Wehe, A.: Heuristics for the gene-duplication problem: A Θ(n) speed-up for the local search. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol. 4453, pp. 238–252. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  3. 3.
    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: RECOMB 2004, pp. 326–335 (2004)Google Scholar
  4. 4.
    Blomme, T., Vandepoele, K., De Bodt, S., Silmillion, C., Maere, S., van de Peer, Y.: The gain and loss of genes during 600 millions years of vertebrate evolution. Genome Biol. 7, R43 (2006)CrossRefGoogle Scholar
  5. 5.
    Bonizzoni, P., Della Vedova, G., Dondi, R.: Reconciling a gene tree to a species tree under the duplication cost model. Theoret. Comput. Sci. 347, 36–53 (2005)CrossRefGoogle Scholar
  6. 6.
    Bryant, D.: Hunting for trees, building trees and comparing trees: theory and methods in phylogenetic analysis. Ph.D. thesis, Dept. of Math., Univ. of Canterbury, New Zealand (1997)Google Scholar
  7. 7.
    Chauve, C., Doyon, J.-P., El-Mabrouk, N.: Gene family evolution by duplication, speciation and loss. J. Comput. Biol. 15, 1043–1062 (2008)CrossRefPubMedGoogle Scholar
  8. 8.
    Chen, K., Durand, D., Farach-Colton, M.: NOTUNG: a program for dating gene duplications and optimizing gene family trees. J. Comput. Biol. 7, 429–444 (2000)CrossRefPubMedGoogle Scholar
  9. 9.
    Constantinescu, M., Sankoff, D.: An efficient algorithm for supertrees. J. Classification 12, 101–112 (1995)CrossRefGoogle Scholar
  10. 10.
    Cotton, J.A., Page, R.D.M.: Rates and patterns of gene duplication and loss in the human genome. Proc. R. Soc. Lond. B 272, 277–283 (2005)CrossRefGoogle Scholar
  11. 11.
    Demuth, J.P., De Bie, T., Stajich, J., Cristianini, N., Hahn, M.W.: The evolution of mammalian gene families. PLoS ONE 1, e85 (2006)CrossRefGoogle Scholar
  12. 12.
    Doyon, J.-P., Chauve, C., Hamel, S.: Algorithms for exploring the space of gene tree/species tree reconciliations. In: Nelson, C.E., Vialette, S. (eds.) RECOMB-CG 2008. LNCS (LNBI), vol. 5267, pp. 1–13. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  13. 13.
    Durand, D., Haldórsson, B.V., Vernot, B.: A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Comput. Biol. 13, 320–3354 (2006)CrossRefPubMedGoogle Scholar
  14. 14.
    Eichler, E.E., Sankoff, D.: Structural dynamics of eukaryotic chromosome evolution. Science 301, 793–797 (2003)CrossRefPubMedGoogle Scholar
  15. 15.
    Eulenstein, O., Mirkin, B., Vingron, M.: Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees. In: Mathematical hierarchies and biology. DIMACS Series Discrete Math. Theoret. Comput. Sci., vol. 37, pp. 71–93 (1997)Google Scholar
  16. 16.
    Gorecki, P., Tiutyn, J.: DLS-trees: a model of evolutionary scenarios. Theoret. Comput. Sci. 359, 378–399 (2006)CrossRefGoogle Scholar
  17. 17.
    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. Syst. Zool. 28, 132–163 (1979)CrossRefGoogle Scholar
  18. 18.
    Hallett, M.T., Lagergren, J.: New algorithms for the duplication-loss model. In: RECOMB 2000, pp. 138–146 (2000)Google Scholar
  19. 19.
    Hahn, M.W., Han, M.V., Han, S.-G.: Gene family evolution across 12 Drosophilia genomes. PLoS Genet. 3, e197 (2007)CrossRefGoogle Scholar
  20. 20.
    Henzinger, M.R., King, V., Warnow, T.: Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology. Algorithmica 24, 1–13 (1999)CrossRefGoogle Scholar
  21. 21.
    Lynch, M., Conery, J.S.: The evolutionary fate and consequences of duplicate genes. Science 290, 1151–1155 (2000)CrossRefPubMedGoogle Scholar
  22. 22.
    Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM J. Comput. 30, 729–752 (2000)CrossRefGoogle Scholar
  23. 23.
    Ohno, S.: Evolution by gene duplication. Springer, Heidelberg (1970)CrossRefGoogle Scholar
  24. 24.
    Page, R.D.M.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43, 58–77 (1994)Google Scholar
  25. 25.
    Page, R.D.M., Charleston, M.A.: Reconciled trees and incongruent gene and species trees. Mathematical hierarchies and biology. DIMACS Series Discrete Math. Theoret. Comput. Sci. 37, 57–70 (1997)CrossRefGoogle Scholar
  26. 26.
    Page, R.D.M.: GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 14, 819–820 (1998)CrossRefPubMedGoogle Scholar
  27. 27.
    Page, R.D.M.: Modified mincut supertrees. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 537–551. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  28. 28.
    Sanderson, M.J., McMahon, M.M.: Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol. Biol. 7, S3 (2007)CrossRefGoogle Scholar
  29. 29.
    Semple, C., Steel, M.: A supertree method for rooted trees. Discrete Appl. Math. 105, 147–158 (2000)CrossRefGoogle Scholar
  30. 30.
    Snir, S., Rao, S.: Using max cut to enhance rooted trees consistency. IEEE/ACM Trans. Comput. Biol. and Bioinform. 3, 323–333 (2006)CrossRefGoogle Scholar
  31. 31.
    Steel, M.: The complexity of reconstructing trees from qualitative characters and subtrees. J. Classification 9, 91–116 (1992)CrossRefGoogle Scholar
  32. 32.
    Wapinski, I., Pfeffer, A., Friedman, N., Regev, A.: Natural history and evolutionary principles of gene duplication in fungi. Nature 449, 54–61 (2007)CrossRefPubMedGoogle Scholar
  33. 33.
    Zhang, L.X.: On Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J. Comput. Biol. 4, 177–188 (1997)CrossRefPubMedGoogle Scholar
  34. 34.
    Zmasek, C.M., Eddy, S.R.: A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17, 821–828 (2001)CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Cedric Chauve
    • 1
  • Nadia El-Mabrouk
    • 2
  1. 1.Department of MathematicsSimon Fraser UniversityBurnaby (BC)Canada
  2. 2.Département Informatique et Recherche OpérationnelleUniversité de MontréalMontréal (QC)Canada

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