Phylogenetic Supertrees pp 247-265

Part of the Computational Biology book series (COBO, volume 4)

| Cite as

Taxonomy, Supertrees, and the Tree of Life

  • Roderic D. M. Page

Abstract

Some of the main practical impediments to the application of supertrees in large-scale phylogenetic analysis are inconsistent use of taxonomic names, trees incorporating taxa of different ranks, and poor taxonomic overlap between different phylogenetic studies. This chapter considers these problems and suggests some solutions. The notion of a “classification graph” is introduced to test for consistency between higher-level classifications. One strategy for coping with poor taxonomic overlap is to use a constraint tree that specifies some taxonomic groups that must appear in the supertree.

Keywords

classification graphs cluster graphs constraints MinCutSupertree taxonomy 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adams, E. M., III. 1986. N-trees as nestings: complexity, similarity, and consensus. Journal of Classification 3:299–317.CrossRefGoogle Scholar
  2. Aho, A. V., Sagiv, Y., Szymanski, T. G., and Ullman, J. D. 1981. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. Siam Journal of Computing 10:405–421.CrossRefGoogle Scholar
  3. Alexe, G., Alexe, S., Foldes, S., Hammer, P. L., and Simeone, B. 2000. Consensus Algorithms for the Generation of all Maximal Bicliques. Technical Report 2000–14, Dimacs, Rutgers University, Piscataway, Nj 08854–8018, USA.Google Scholar
  4. Barrett, M., Donoghue, M. J., and Sober, E. 1991. Against consensus. Systematic Zoology 40:486–493.CrossRefGoogle Scholar
  5. Baum, B. R. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3–10.CrossRefGoogle Scholar
  6. Baum, B. R. and Ragan, M. A. 2004. The MRP method. In O. R. P. Bininda-Emonds (ed). Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 17–34. Kluwer Academic, Dordrecht, the Netherlands.Google Scholar
  7. Bininda-Emonds, O. R. P., Jones, K. E., Price, S. A., Cardillo, M., Grenyer, R., and Purvis, A. 2004. Garbage in, garbage out: data issues in supertree construction. In O. R. P. Bininda-Emonds (ed). Phylogenetic Supertrees: Combining Information to Reveal the Tree ofLife, pp. 267–280. Kluwer Academic, Dordrecht, the Netherlands.Google Scholar
  8. Bininda-Emonds, O. R. P. and Sanderson, M. J. 2001. Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Systematic Biology 50:565–579.PubMedCrossRefGoogle Scholar
  9. Bryant, D. 1997. Building Trees, Hunting for Trees, and Comparing Trees: Theory and Methods in Phylogenetic Analysis. Ph.D. dissertation, Department of Mathematics, University of Canterbury.Google Scholar
  10. Bryant, D. 2003. A classification of consensus methods for phylogenetics. In M. F. Janowitz, F.-J. Lapointe, F. R. McMorris, B. Mirkin, and F.S. Roberts (eds), Bioconsensus, Dimacs: Series in Discrete Mathematics and Theoretical Computer Science, volume 61, pp. 163–183. American Mathematical Society-Dimacs, Providence, Ri.Google Scholar
  11. Burleigh, J. G., Eulenstein, O., Fernandez-Baca, D., and Sanderson, M. J. 2004. MRF supertrees. In O. R. P. Bininda-Emonds (ed). Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 65–85. Kluwer Academic, Dordrecht, the Netherlands.Google Scholar
  12. Chen, D., Eulenstein, O., Fernandez-Baca, D., and Sanderson, M. J. 2002. Supertrees by Flipping. Technical Report TR02–01, Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, Ia 50011–1040, USA.Google Scholar
  13. Chu, P. C. 1995. Phylogenetic reanalysis of Strauch ’s osteological data set for the charadriiformes. Condor 97:174–196.CrossRefGoogle Scholar
  14. Coddington, J. A. 1990. Ontogeny and homology in the male palpus of orb-weaving spiders and their relatives, with comments on phylogeny (Araneoclada: Araneoidea, Deinopoidea). Smithsonian Contributions to Zoology 496:1–52.CrossRefGoogle Scholar
  15. Constantinescu, M. and Sankoff, D. 1986. Tree enumeration modulo a consensus. Journal of Classification 3:349–56.CrossRefGoogle Scholar
  16. Cormen, T. H., Leiserson, C. E., and Rivest, R. L. 1990. Introduction to Algorithms. The Mit Press, Cambridge, Massachusetts.Google Scholar
  17. Cotton, J. A. and Page, R. D. M. 2002. Going nuclear: vertebrate phylogeny and gene family evolution reconciled. Proceedings of the Royal Society of London B 269: 1555–1561.CrossRefGoogle Scholar
  18. Cotton, J. A. and Page, R. D. M. 2004. Tangled trees from molecular markers: reconciling conflict between phylogenies to build molecular supertrees. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 107–125. Kluwer Academic, Dordrecht, the Netherlands.Google Scholar
  19. Daniel, P. and Semple, C. 2004. A supertree algorithm for nested taxa. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 151–171. Kluwer Academic, Dordrecht, the Netherlands.Google Scholar
  20. Gatesy, J., Matthee, C., Desa L L E R., and Hayashi, C. 2002. Resolution of a supertree / supermatrix paradox. Systematic Biology 51:652 – 664.PubMedCrossRefGoogle Scholar
  21. Gatesy, J., O’grady, P., and Baker, R. H. 1999. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15:271–313.CrossRefGoogle Scholar
  22. Gatesy, J. and Springer, M. S. 2004. A critique of matrix representation with parsimony supertrees. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 369–388. Kluwer Academic, Dordrecht, the Netherlands.Google Scholar
  23. Goloboff, P. A. and Pol, D. 2002. Semi-strict supertrees. Cladistics 18:514–525.Google Scholar
  24. Lauk, C. 2002. An Attempt for a Genus-level Supertree of Birds. B.Sc. (Hons) Project Report, Deeb, Ibls, University of Glasgow.Google Scholar
  25. Liu, F.-G. R., Miyamoto, M. M., Freire, N. P., Ong, P. Q., Tennant, M. R., Young, T. S., and Gugel, K. F. 2001. Molecular and morphological supertrees for eutherian (placental) mammals. Science 291:1786–1789.PubMedCrossRefGoogle Scholar
  26. Miyamoto, M. M. 1985. Consensus classifications and general cladograms. Cladistics 1:186–189.CrossRefGoogle Scholar
  27. Novacek, M. J. 2001. Mammalian phylogeny: genes and supertrees. Current Biology 11:R573-R575.PubMedCrossRefGoogle Scholar
  28. Page, R. D. M. 2002. Modified mincut supertrees. In R. Guigó and D. Gusfield (eds), Algorithms in Bioinformatics, Second International Workshop, Wabi 2002, Rome, Italy, September 17–21, 2002, Proceedings, pp. 537–552. Springer, Berlin.Google Scholar
  29. Piel, W. H., Donoghue, M. J., and Sanderson, M. J. 2002. TreeBASE: a database of phylogenetic knowledge. In K. Shimura, K. L. Wilson, and D. Gordon (eds), To the Interoperable Catalogue of Life with Partners — Species 2000 Asia Oceania. Proceedings of 2nd International Workshop of Species 2000, pp. 41–47. National Institute of Environmental Studies (Research Report R-171–2002), Tsukuba, Japan. (http://www.nies.go.jp/kanko/kenkyu/pdf/r-171–2002.pdf)Google Scholar
  30. Pollock, D. D., Zwickl, D. J., McGuire, J. A., and Hillis, D. M. 2002. Increased taxonomic sampling is advantageous for phylogenetic inference. Systematic Biology 51:664–671.PubMedCrossRefGoogle Scholar
  31. Ragan, M. A. 1992. Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution 1:53–58.PubMedCrossRefGoogle Scholar
  32. Roshan, U., Moret, B. M. E., Williams, T. L., and Warnow, T. 2004. Performance of supertree methods on various data set decompositions. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 301–328. Kluwer Academic, Dordrecht, the Netherlands.Google Scholar
  33. Ross, H. A. and Rodrigo, A. G. 2004. An assessment of matrix representation with compatibility in supertree construction. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 35–63. Kluwer Academic, Dordrecht, the Netherlands.Google Scholar
  34. Sanderson, M. J. 1989. Confidence limits on phylogenies: the bootstrap revisited. Cladistics 5:113–129.CrossRefGoogle Scholar
  35. Sanderson, M. J., Purvis, A., and Henze, C. 1998. Phylogenetic supertrees: assembling the trees of life. Trends in Ecology and Evolution 13:105–109.PubMedCrossRefGoogle Scholar
  36. Semple, C. and Steel, M. 2000. A supertree method for rooted trees. Discrete Applied Mathematics 105:147–158.CrossRefGoogle Scholar
  37. Slowinski, J. B. and Page, R. D. M. 1999. How should species phylogenies be inferred from sequence data? Systematic Biology 48:814–825.PubMedCrossRefGoogle Scholar
  38. Steel, M. 1992. The complexity of reconstructing trees from qualitative characters and subtrees. Journal of Classification 9:91–116.CrossRefGoogle Scholar
  39. Swofford, D. L. 2002. Paup*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version4. Sinauer, Sunderland, Massachusetts.Google Scholar
  40. Wilkinson, M., Thorley, J. L., Littlewood, D. T. J., and Bray, R. A. 2001. Towards a phylogenetic supertree of Platyhelminthes? In D. T. J. Littlewood and R. A. Bray (eds), Interrelationships of the Platyhelminthes, pp. 292–301. Taylor and Francis, London.Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2004

Authors and Affiliations

  • Roderic D. M. Page

There are no affiliations available

Personalised recommendations