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Character-Based Cladistics and Answer Set Programming

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Practical Aspects of Declarative Languages (PADL 2005)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 3350))

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Abstract

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: to historical analysis of languages, and to 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.

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References

  1. Brooks, D.R., Mayden, R.L., McLennan, D.A.: Phylogeny and biodiversity: Conserving our evolutionary legacy. Trends in Ecology and Evolution 7, 55–59 (1992)

    Article  Google Scholar 

  2. Brooks, D.R., McLennan, D.A.: Phylogeny, Ecology, and Behavior: A Research Program in Comparative Biology. Univ. Chicago Press, Chicago (1991)

    Google Scholar 

  3. Camin, J.H., Sokal, R.R.: A method for deducing branching sequences in phylogeny. Evolution 19, 311–326 (1965)

    Article  Google Scholar 

  4. Chandler, R.M.: Phylogenetic analysis of the alcids. PhD thesis, University of Kansas (1990)

    Google Scholar 

  5. Day, W.H.E., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Systematic Zoology 35(2), 224–229 (1986)

    Article  Google Scholar 

  6. Dyen, I., Kruskal, J.B., Black, P.: An Indoeuropean classification: a lexicostatistical experiment. Transactions of the American Philosophical Society 82, 1–132 (1992)

    Article  Google Scholar 

  7. Edwards, A.W.F., Cavalli-Sforza, L.L.: Reconstruction of evolutionary trees. In: Phenetic and Phylogenetic Classification, pp. 67–76 (1964)

    Google Scholar 

  8. Erdem, E., Lifschitz, V.: Tight logic programs. TPLP 3(4-5), 499–518 (2003)

    MATH  MathSciNet  Google Scholar 

  9. Erdem, E., Lifschitz, V., Nakhleh, L., Ringe, D.: Reconstructing the evolutionary history of Indo-European languages using answer set programming. In: Dahl, V., Wadler, P. (eds.) PADL 2003. LNCS, vol. 2562, pp. 160–176. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  10. Erdem, E., Lifschitz, V., Ringe, D.: Temporal phylogenetic networks and answer set programming. In: Progress (2004)

    Google Scholar 

  11. Erdoğan, S.T., Lifschitz, V.: Definitions in answer set programming. In: Proc. of LPNMR, pp. 114–126 (2004)

    Google Scholar 

  12. Felsenstein, J.: Numerical methods for inferring evolutionary trees. The Quarterly Review of Biology 57, 379–404 (1982)

    Article  Google Scholar 

  13. Felsenstein, J.: PHYLIP (Phylogeny inference package) version 3.6

    Google Scholar 

  14. Foulds, L.R., Graham, R.L.: The Steiner tree problem in Phylogeny is NP-complete. Advanced Applied Mathematics 3, 43–49 (1982)

    Article  MATH  MathSciNet  Google Scholar 

  15. Gelfond, M., Lifschitz, V.: The stable model semantics for logic programming. In: Proc. of ICLP/SLP, pp. 1070–1080 (1988)

    Google Scholar 

  16. Gelfond, M., Lifschitz, V.: Classical negation in logic programs and disjunctive databases. New Generation Computing 9, 365–385 (1991)

    Article  Google Scholar 

  17. Hennig, W.: Grundzuege einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag (1950)

    Google Scholar 

  18. Hoberg, E.P.: Evolution and historical biogeography of a parasite-host assemblage: Alcataenia spp (Cyclophyllidea: Dilepididae) in Alcidae (Chradriiformes). Canadian Journal of Zoology 64, 2576–2589 (1986)

    Article  Google Scholar 

  19. Hoberg, E.P.: Congruent and synchronic patterns in biogeography and speciation among seabirds, pinnipeds, ans cestodes. J. Parasitology 78(4), 601–615 (1992)

    Article  Google Scholar 

  20. Lierler, Y., Maratea, M.: Cmodels-2: SAT-based answer sets solver enhanced to non-tight programs. In: Lifschitz, V., Niemelä, I. (eds.) LPNMR 2004. LNCS (LNAI), vol. 2923, pp. 346–350. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  21. Lifschitz, V.: Answer set programming and plan generation. AIJ 138, 39–54 (2002)

    MATH  MathSciNet  Google Scholar 

  22. Lifschitz, V.: Introduction to answer set programming. Unpublished draft (2004)

    Google Scholar 

  23. Lloyd, J.: Foundations of Logic Programming. Springer, Heidelberg (1984)

    MATH  Google Scholar 

  24. Mair, V.H.: The Bronze Age and Early Iron Age Peoples of Eastern Central Asia. Institute for the Study of Man, Washington (1998)

    Google Scholar 

  25. Mallory, J.P.: In Search of the Indo-Europeans. Thames and Hudson, London (1989)

    Google Scholar 

  26. Marek, V., Truszczyński, M.: Stable models and an alternative logic programming paradigm. In: The Logic Programming Paradigm: a 25-Year Perspective, pp. 375–398 (1999)

    Google Scholar 

  27. Minett, J.W., Wang, W.S.-Y.: On detecting borrowing: distance-based and character-based approaches. Diachronica 20(2), 289–330 (2003)

    Article  Google Scholar 

  28. Moskewicz, M.W., Madigan, C.F., Zhao, Y., Zhang, L., Malik, S.: Chaff: Engineering an efficient SAT solver. In: Proc. of DAC (2001)

    Google Scholar 

  29. Nakhleh, L., Ringe, D., Warnow, T.: Perfect phylogenetic networks: A new methodology for reconstructing the evolutionary history of natural languages. In: Language (2005) (to appear)

    Google Scholar 

  30. Rexova, K., Frynta, D., Zrzavý, J.: Cladistic analysis of languages: Indo-European classification based on lexicostatistical data. Cladistics 19, 120–127 (2003)

    Article  Google Scholar 

  31. Ringe, D., Warnow, T., Taylor, A.: Indo-European and computational cladistics. Transactions of the Philological Society 100(1), 59–129 (2002)

    Article  Google Scholar 

  32. Roberts, R.G., Jones, R., Smith, M.A.: Thermoluminescence dating of a 50,000-year-old human occupation site in Northern Australia. Science 345, 153–156 (1990)

    Google Scholar 

  33. Simons, P., Niemelä, I., Soininen, T.: Extending and implementing the stable model semantics. AIJ 138, 181–234 (2002)

    MATH  Google Scholar 

  34. Swofford, D.L.: PAUP* (Phylogenetic analysis under parsimony) version 4.0

    Google Scholar 

  35. White, J.P., O’Connell, J.F.: A Prehistory of Australia, New Guinea, and Sahul. Academic Press, New York (1982)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Zoology, University of Toronto, Toronto, Canada

    Daniel R. Brooks

  2. Institute of Information Systems, Vienna University of Technology, Vienna, Austria

    Esra Erdem

  3. Department of Electronic Engineering, Chinese University of Hong Kong, Shatin, Hong Kong

    James W. Minett

  4. Department of Linguistics, University of Pennsylvania, Philadelphia, USA

    Donald Ringe

Authors
  1. Daniel R. Brooks
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  2. Esra Erdem
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  3. James W. Minett
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  4. Donald Ringe
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Editor information

Editors and Affiliations

  1. IMDEA Institute for Software Development Technology, Universidad Politécnica de Madrid, University of New Mexico Universidad Complutense de Madrid,  

    Manuel V. Hermenegildo

  2. School of Computer Science, T.U. Madrid (UPM), Spain

    Daniel Cabeza

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© 2005 Springer-Verlag Berlin Heidelberg

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Brooks, D.R., Erdem, E., Minett, J.W., Ringe, D. (2005). Character-Based Cladistics and Answer Set Programming. In: Hermenegildo, M.V., Cabeza, D. (eds) Practical Aspects of Declarative Languages. PADL 2005. Lecture Notes in Computer Science, vol 3350. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30557-6_5

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  • DOI: https://doi.org/10.1007/978-3-540-30557-6_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-24362-5

  • Online ISBN: 978-3-540-30557-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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