Inferring Phylogenetic Trees Using Answer Set Programming

  • Daniel R. Brooks
  • Esra ErdemEmail author
  • Selim T. Erdoğan
  • James W. Minett
  • Don Ringe


We describe the reconstruction of a phylogeny for a set of taxa, with a character-based cladistics approach, in a declarative knowledge representation formalism, and show how to use computational methods of answer set programming to generate conjectures about the evolution of the given taxa. We have applied this computational method in two domains: historical analysis of languages and historical analysis of parasite-host systems. In particular, using this method, we have computed some plausible phylogenies for Chinese dialects, for Indo-European language groups, and for Alcataenia species. Some of these plausible phylogenies are different from the ones computed by other software. Using this method, we can easily describe domain-specific information (e.g., temporal and geographical constraints), and thus prevent the reconstruction of some phylogenies that are not plausible.


Answer set programming Phylogeny Cladistics 


  1. 1.
    Ben Hamed, M.: Neighbour-nets portray the Chinese dialect continuum and the linguistic legacy of China’s demic history. Proc. R. Soc. Lond., B 272(1567), 1015–1022 (2005)CrossRefGoogle Scholar
  2. 2.
    Bodlaender, H.L., Fellows, M.R., Hallett, M.T., Wareham, H.T., Warnow, T.J.: The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs. Theor. Comp. Sci. 244(1–2), 167–188 (2000)zbMATHCrossRefMathSciNetGoogle Scholar
  3. 3.
    Brooks, D.R., Erdem, E., Minett, J.W., Ringe, D.: Character-based cladistics and answer set programming. In: Proceedings of the Seventh International Symposium on Practical Aspects of Declarative Languages (PADL), pp. 37–51 (2005)Google Scholar
  4. 4.
    Brooks, D.R., Mayden, R.L., McLennan, D.A.: Phylogeny and biodiversity: conserving our evolutionary legacy. Trends Ecol. Evol. 7, 55–59 (1992)CrossRefGoogle Scholar
  5. 5.
    Brooks, D.R., McLennan, D.A.: Phylogeny, Ecology, and Behavior: A Research Program in Comparative Biology. University of Chicago Press, Chicago, IL (1991)Google Scholar
  6. 6.
    Camin, J.H., Sokal, R.R.: A method for deducing branching sequences in phylogeny. Evolution 19, 311–326 (1965)CrossRefGoogle Scholar
  7. 7.
    Chandler, R.M.: Phylogenetic analysis of the alcids. Ph.D. thesis, University of Kansas (1990)Google Scholar
  8. 8.
    Day, W.H.E., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Syst. Zool. 35(2), 224–229 (1986)CrossRefGoogle Scholar
  9. 9.
    Dyen, I., Kruskal, J.B., Black, P.: An Indo-European classification: a lexicostatistical experiment. Trans. Am. Philos. Soc. 82, 1–132 (1992)CrossRefGoogle Scholar
  10. 10.
    Edwards, A.W.F., Cavalli-Sforza, L.L.: Reconstruction of evolutionary trees. In: Phenetic and Phylogenetic Classification, pp. 67–76 (1964)Google Scholar
  11. 11.
    Erdem, E., Lifschitz, V.: Tight logic programs. Theor. Pract. Log. Prog. 3(4–5), 499–518 (2003)zbMATHCrossRefMathSciNetGoogle Scholar
  12. 12.
    Erdem, E., Lifschitz, V., Nakhleh, L., Ringe, D.: Reconstructing the evolutionary history of Indo-European languages using answer set programming. In: Proceedings of the Fifth International Symposium on Practical Aspects of Declarative Languages (PADL), pp. 160–176 (2003)Google Scholar
  13. 13.
    Erdem, E., Lifschitz, V., Ringe, D.: Temporal phylogenetic networks and logic programming. Theory Pract. Log. Program. 6(5), 539–558 (2006)zbMATHCrossRefMathSciNetGoogle Scholar
  14. 14.
    Erdoğan, S.T., Lifschitz, V.: Definitions in answer set programming. In: Proceedings of the Seventh International Conference on Logic Programming and Nonmonotonic Reasoning, pp. 114–126 (2004)Google Scholar
  15. 15.
    Felsenstein, J.: Numerical methods for inferring evolutionary trees. Q. Rev. Biol. 57, 379–404 (1982)CrossRefGoogle Scholar
  16. 16.
    Felsenstein, J.: PHYLIP (phylogeny inference package) version 3.6 (2004) (Distributed by the author)Google Scholar
  17. 17.
    Ferraris, P., Lifschitz, V.: Mathematical foundations of answer set programming. In: We Will Show Them! Essays in Honour of Dov Gabbay, vol. 1, College Publications, pp. 615–664 (2005)Google Scholar
  18. 18.
    Ferraris, P., Lifschitz, V.: Weight constraints as nested expressions. Theor. Pract. Log. Prog. 5, 45–74 (2005)zbMATHCrossRefMathSciNetGoogle Scholar
  19. 19.
    Fitch, W.M.: Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20(4), 406–416 (1971)CrossRefGoogle Scholar
  20. 20.
    Foulds, L.R., Graham, R.L.: The Steiner tree problem in phylogeny is NP-complete. Adv. Appl. Math. 3, 43–49 (1982)zbMATHCrossRefMathSciNetGoogle Scholar
  21. 21.
    Gelfond, M., Lifschitz, V.: The stable model semantics for logic programming. In: Kowalski, R., Bowen, K. (eds.) Logic Programming: Proceedings of the Fifth International Conference and Symposium, pp. 1070–1080 (1988)Google Scholar
  22. 22.
    Gelfond, M., Lifschitz, V.: Classical negation in logic programs and disjunctive databases. New Gener. Comput. 9, 365–385 (1991)CrossRefGoogle Scholar
  23. 23.
    Hennig, W.: Grundzuege einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag (1950)Google Scholar
  24. 24.
    Hennig, W.: Phylogenetic systematics. Annu. Rev. Entomol. 10, 97–116 (1965)CrossRefGoogle Scholar
  25. 25.
    Hennig, W.: Phylogenetic Systematics. University of Illinois Press (1966) Translated from Grundzuege einer Theorie der phylogenetischen Systematik (1950) by D.D. Davis and R. ZangerlGoogle Scholar
  26. 26.
    Hoberg, E.P.: Evolution and historical biogeography of a parasite-host assemblage: Alcataenia spp. (Cyclophyllidea: Dilepididae) in Alcidae (Chradriiformes). Can. J. Zool. 64, 2576–2589 (1986)CrossRefGoogle Scholar
  27. 27.
    Hoberg, E.P.: Congruent and synchronic patterns in biogeography and speciation among seabirds, pinnipeds, and cestodes. J. Parasitol. 78(4), 601–615 (1992)CrossRefGoogle Scholar
  28. 28.
    Lifschitz, V.: Answer set programming and plan generation. Artif. Intell. 138, 39–54 (2002)zbMATHCrossRefMathSciNetGoogle Scholar
  29. 29.
    Lifschitz, V., Tang, L.R., Turner, H.: Nested expressions in logic programs. Ann. Math. Artif. Intell. 25, 369–389 (1999)zbMATHCrossRefMathSciNetGoogle Scholar
  30. 30.
    Lloyd, J.: Foundations of Logic Programming. Springer, Berlin Heidelberg New York (1984)zbMATHGoogle Scholar
  31. 31.
    Mair, V.H. (ed.): The Bronze Age and Early Iron Age Peoples of Eastern Central Asia. Institute for the Study of Man, Washington (1998)Google Scholar
  32. 32.
    Mallory, J.P.: In Search of the Indo-Europeans. Thames and Hudson, London (1989)Google Scholar
  33. 33.
    Marek, V., Truszczyński, M.: Stable models and an alternative logic programming paradigm. In: The Logic Programming Paradigm: A 25-Year Perspective, pp. 375–398. Springer, Berlin Heidelberg New York (1999)Google Scholar
  34. 34.
    Minett, J.W., Wang, W.S.-Y.: On detecting borrowing: distance-based and character-based approaches. Diachronica 20(2), 289–330 (2003)CrossRefGoogle Scholar
  35. 35.
    Moskewicz, M.W., Madigan, C.F., Zhao, Y., Zhang, L., Malik, S.: Chaff: engineering an efficient SAT solver. In: Proceedings of Design Automation Conference (DAC2001) (2001)Google Scholar
  36. 36.
    Nakhleh, L., Ringe, D., Warnow, T.: Perfect phylogenetic networks: a new methodology for reconstructing the evolutionary history of natural languages. Language 81(2), 382–420 (2005)CrossRefGoogle Scholar
  37. 37.
    Rexova, K., Frynta, D., Zrzavý, J.: Cladistic analysis of languages: Indo-European classification based on lexicostatistical data. Cladistics 19, 120–127 (2003)CrossRefGoogle Scholar
  38. 38.
    Ringe, D., Warnow, T., Taylor, A.: Indo-European and computational cladistics. Trans. Philol. Soc. 100(1), 59–129 (2002)CrossRefGoogle Scholar
  39. 39.
    Roberts, R.G., Jones, R.M., Smith, M.A.: Thermoluminescence dating of a 50,000-year-old human occupation site in Northern Australia. Science 345, 153–156 (1990)Google Scholar
  40. 40.
    Simons, P., Niemelä, I., Soininen, T.: Extending and implementing the stable model semantics. Artif. Intell. 138, 181–234 (2002)zbMATHCrossRefGoogle Scholar
  41. 41.
    Swofford, D.L.: PAUP*: phylogenetic analysis under parsimony (and other methods), version 4.0. Sinauer Associates, Sunderland, MA (2003)Google Scholar
  42. 42.
    White, J.P., O’Connell, J.F.: A Prehistory of Australia, New Guinea, and Sahul. Academic, San Diego, CA (1982)Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Daniel R. Brooks
    • 1
  • Esra Erdem
    • 2
    Email author
  • Selim T. Erdoğan
    • 3
  • James W. Minett
    • 4
  • Don Ringe
    • 5
  1. 1.Department of Ecology and Evolutionary BiologyUniversity of TorontoOntarioCanada
  2. 2.Faculty of Engineering and Natural SciencesSabancı UniversityIstanbulTurkey
  3. 3.Department of Computer SciencesUniversity of Texas at AustinAustinUSA
  4. 4.Department of Electronic EngineeringChinese University of Hong KongShatinHong Kong
  5. 5.Department of LinguisticsUniversity of PennsylvaniaPhiladelphiaUSA

Personalised recommendations