Natural Computing

, Volume 9, Issue 2, pp 421–435 | Cite as

Beyond evolutionary trees

  • Gianluca Della VedovaEmail author
  • Riccardo Dondi
  • Tao Jiang
  • Giulio Pavesi
  • Yuri Pirola
  • Lusheng Wang


In Computational Biology, the notion of phylogeny has become synonymous with tree-like evolution. Recent advances in the Life Sciences have suggested that evolution has a much more diverse course. In this paper we will survey some of the models that have been proposed to overcome the limitations of using phylogenies to represent evolutionary histories.


Evolutionary trees Pedigrees Haplotypes Networks 



We would like to thank the anonymous referees, whose detailed suggestions have greatly contributed to the paper. GDV and YP have been partially supported by FAR grant “Computational models for phylogenetic analysis of gene variations”. TJ’s research is supported in part by NIH grant LM008991 and NSF grant IIS-0711129. LW is supported by a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (Project No. CityU 121207).


  1. Baroni M, Semple C, Steel M (2004) A framework for representing reticulate evolution. Ann Comb 8(4):391–408zbMATHCrossRefMathSciNetGoogle Scholar
  2. Bonizzoni P, Della Vedova G, Dondi R, Li J (2003) The haplotyping problem: an overview of computational models and solutions. J Comput Sci Technol 18(6):675–688zbMATHCrossRefMathSciNetGoogle Scholar
  3. Bonizzoni P, Della Vedova G, Dondi R (2005) Reconciling a gene tree to a species tree under the duplication cost model. Theor Comput Sci 347(1–2):192–216CrossRefMathSciNetGoogle Scholar
  4. Bonizzoni P, Della Vedova G, Dondi R, Mauri G (2008) The comparison of phylogenetic networks: algorithms and complexity. In: Mandoiu I, Zelikovsky A (eds) Bioinformatics algorithms: techniques and applications. Wiley-Interscience Publisher, Hoboken, NJ, pp 143–173Google Scholar
  5. Burleigh JG, Bansal MS, Wehe A, Eulenstein O (2008) Locating multiple gene duplications through reconciled trees. In: Proceedings of the 12th conference on research in computational molecular biology, (RECOMB), pp 273–284Google Scholar
  6. Chan BM-Y, Chan JW-T, Chin FYL, Fung SPY, Kao M-Y (2006) Linear-time haplotype inference on pedigrees without recombinations. In: Proceedings of the 6th workshop on algorithms in bioinformatics (WABI), pp 56–67Google Scholar
  7. Chang W-C, Eulenstein O (2006) Reconciling gene trees with apparent polytomies. In: Proceedings of the 12th conference on computing and combinatorics (COCOON), pp 235–244Google Scholar
  8. Dasgupta B, Ferrarini S, Gopalakrishnan U, Paryani NR (2006) Inapproximability results for the lateral gene transfer problem. J Comb Optim 11(4):387–405zbMATHCrossRefMathSciNetGoogle Scholar
  9. Doi K, Li J, Jiang T (2003) Minimum recombinant haplotype configuration on tree pedigrees. In: Proceedings of the 3rd workshop on algorithms in bioinformatics (WABI). Springer, pp 339–353Google Scholar
  10. Finden C, Gordon A (1985) Obtaining common pruned trees. J Classif 2:255–276CrossRefGoogle Scholar
  11. Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst Zool 28(2):132–163CrossRefGoogle Scholar
  12. Gòrecki P (2004) Reconciliation problems for duplication, loss and horizontal gene transfer. In: Proceedings of 8th conference on research in computational molecular biology, (RECOMB), pp 316–325Google Scholar
  13. Gòrecki P, Tiuryn J (2006) DLS-trees: a model of evolutionary scenarios. Theor Comput Sci 359(1–3):378–399zbMATHCrossRefGoogle Scholar
  14. Guigò R, Muchnik I, Smith T (1996) Reconstruction of ancient molecular phylogeny. Mol Phylogenet Evol 6(2):189–213CrossRefGoogle Scholar
  15. Gupta A, Manuch J, Zhao X, Stacho L (2006) Characterization of the existence of galled-tree networks. J Bioinform Comput Biol 4(6):1CrossRefGoogle Scholar
  16. Gusfield D (1997) Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press, CambridgezbMATHGoogle Scholar
  17. Gusfield D, Eddhu S, Langley CH (2004) Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J Bioinform Comput Biol 2(1):173–214CrossRefGoogle Scholar
  18. Gusfield D, Bansal V, Bafna V, Song YS (2007) A decomposition theory for phylogenetic networks and incompatible characters. J Comput Biol 14(10):1247–1272CrossRefMathSciNetGoogle Scholar
  19. Hallett M, Lagergren J (2001) Efficient algorithms for lateral gene transfer problems. In: Proceedings of 5th annual international conference on research in computational molecular biology, (RECOMB), pp 149–156Google Scholar
  20. Hallett M, Lagergren J, Tofigh A (2004) Simultaneous identification of duplications and lateral transfers. In: Proceedings of 8th annual international conference on research in computational molecular biology, (RECOMB), pp 347–356Google Scholar
  21. Hamel A, Steel MA (1996) Finding a common compatible tree is NP-hard for sequences and trees. Appl Math Lett 9(2):55–60zbMATHCrossRefMathSciNetGoogle Scholar
  22. Li J, Jiang T (2003) Efficient inference of haplotypes from genotypes on a pedigree. J Bioinform Comput Biol 1(1):41–69CrossRefGoogle Scholar
  23. Liu L, Chen X, Xiao J, Jiang T (2007) Complexity and approximation of the minimum recombinant haplotype configuration problem. Theor Comput Sci 378(3):316–330zbMATHCrossRefMathSciNetGoogle Scholar
  24. Ma B, Li M, Zhang L (2000) From gene trees to species trees. SIAM J Comput 30(3):729–752zbMATHCrossRefMathSciNetGoogle Scholar
  25. Moret BME, Nakhleh L, Warnow T, Linder CR, Tholse A, Padolina A, Sun J, Timme RE (2004) Phylogenetic networks: modeling, reconstructibility, and accuracy. IEEE/ACM Trans Comput Biol Bioinform 1(1):13–23CrossRefGoogle Scholar
  26. Nakhleh L, Ruths DA, Wang L-S (2005a) RIATA-HGT: a fast and accurate heuristic for reconstructing horizontal gene transfer. In: Proceedings of the 11th conference on computing and combinatorics (COCOON), pp 84–93Google Scholar
  27. Nakhleh L, Warnow T, Linder CR, John KS (2005b) Reconstructing reticulate evolution in species: theory and practice. J Comput Biol 12(6):796–811CrossRefGoogle Scholar
  28. Page R (1994) Maps between trees and cladistic analysis of historical associations among genes. Syst Biol 43:58–77Google Scholar
  29. Steel M, Böcker S, Dress A (2000) Simple but fundamental limits for supertree and consensus tree methods. Syst Biol 49(2):363–368CrossRefGoogle Scholar
  30. Than C, Nakhleh L (2008) SPR-based tree reconciliation: non-binary trees and multiple solutions. In: Proceedings of the 6th Asia-Pacific bioinformatics conference (APBC), pp 251–260Google Scholar
  31. Than C, Ruths D, Innan H, Nakhleh L (2007) Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions. J Comput Biol 14(4):517–535CrossRefMathSciNetGoogle Scholar
  32. van Iersel L, Keijsper J, Kelk S, Stougie L, Hagen F, Boekhout T (2008) Constructing level-2 phylogenetic networks from triplets. In: Proceedings of 5th annual international conference on computational molecular biology, (RECOMB), pp 450–462Google Scholar
  33. Wang L, Zhang K, Zhang L (2001) Perfect phylogenetic networks with recombination. J Comput Biol 8(1):69–78CrossRefGoogle Scholar
  34. Xiao J, Liu L, Xia L, Jiang T (2007) Fast elimination of redundant linear equations and reconstruction of recombination-free mendelian inheritance on a pedigree. In: Proceedings of the 18th symposium on discrete algorithms (SODA), pp 655–664Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Gianluca Della Vedova
    • 1
    Email author
  • Riccardo Dondi
    • 2
  • Tao Jiang
    • 3
  • Giulio Pavesi
    • 4
  • Yuri Pirola
    • 5
  • Lusheng Wang
    • 6
  1. 1.Dipartimento di StatisticaUniversità degli Studi di Milano-BicoccaMilanoItaly
  2. 2.Dipartimento di Scienze dei Linguaggi, della Comunicazione e degli Studi CulturaliUniversità degli Studi di BergamoBergamoItaly
  3. 3.Department of Computer ScienceUniversity of California at RiversideRiversideUSA
  4. 4.Dipartimento di Informatica e ComunicazioneUniversità degli Studi di MilanoMilanoItaly
  5. 5.Dipartimento di Informatica, Sistemistica e ComunicazioneUniversità degli Studi di Milano-BicoccaMilanoItaly
  6. 6.Department of Computer ScienceCity University of Hong KongKowloonHong Kong

Personalised recommendations