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New uses for old phylogenies

An introduction to the volume

  • Chapter
Phylogenetic Supertrees

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

Abstract

What are supertrees and what is all the fuss about?

“This is a paper with an attitude problem. This may sound facetious, but is meant in all seriousness. It has in my opinion entirely the wrong attitude to phylogenetic reconstruction and indeed to the entire scientific process.”

From an anonymous review of the carnivore supertree of B ininda-Emonds et al. (1999)

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References

  • 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 on Computing 10:405–421.

    Article  Google Scholar 

  • Barthélemy, J.-P., Mcmorris, F. R., and Powers, R. C. 1995. Stability conditions for consensus functions defined on n-trees. Mathematical Computer Modeling 22:79–87.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Baum, B. R. and Ragan, M. A. 1993. Reply to A.G. Rodrigo’s “A comment on Baum’s method for combining phylogenetic trees”. Taxon 42:637–640.

    Article  Google Scholar 

  • Bininda-Emonds, O. R. P., Gittleman, J. L., and Purvis, A. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews 74:143–175.

    Article  PubMed  CAS  Google Scholar 

  • Bininda-Emonds, O. R. P., Gittleman, J. L., and Steel, M. A. 2002. The (super)tree of life: procedures, problems, and prospects. Annual Review of Ecology and Systematics 33:265–289.

    Article  Google Scholar 

  • Brooks, D. R. 1981. Hennig’s parasitological method: a proposed solution. Systematic Zoology 30:229–249.

    Article  Google Scholar 

  • Cardillo, M. and Bromham, L. 2001. Body size and risk of extinction in Australian mammals. Conservation Biology 15:1435–1440.

    Article  Google Scholar 

  • Chan, K. M. A. and Moore, B. R. 2002. Whole-tree methods for detecting differential diversification rates. Systematic Biology 51:855–865.

    Article  PubMed  Google Scholar 

  • Doyle, J. J. 1992. Gene trees and species trees: molecular systematics as one-character taxonomy. Systematic Botany 17:144–163.

    Article  Google Scholar 

  • Farris, J. S., Kluge, A. G., and Eckhardt, M. J. 1970. A numerical approach to phylogenetic systematics. Systematic Zoology 19:172–191.

    Article  Google Scholar 

  • Garland, T., Jr, Dickerman, A. W., Janis, C. M., and Jones, J. A. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265–292.

    Google Scholar 

  • Gatesy, J., Matthee, C., DeSalle, R., and Hayashi, C. 2002. Resolution of a supertree / supermatrix paradox. Systematic Biology 51:652–664.

    Article  PubMed  Google Scholar 

  • Goloboff, P. A. and Pol, D. 2002. Semi-strict supertrees. Cladistics 18:514–525.

    Google Scholar 

  • Gordon, A. D. 1986. Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves. Journal of Classification 3:31–39.

    Article  Google Scholar 

  • Hall, J. P. W. and Harvey, D. J. 2002. Basal subtribes of the Nymphidiini (Lepidoptera: Riodinidae): phylogeny and myrmecophily. Cladistics 18:539–569.

    Article  Google Scholar 

  • Harvey, P. H., Leigh Brown, A. J., Maynard Smith, J., and Nee, S. (eds) 1996. New Uses for New Phylogenies. Oxford University Press, Oxford.

    Google Scholar 

  • Huelsenbeck, J. P., Larget, B., and Swofford, D. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879–1892.

    PubMed  CAS  Google Scholar 

  • Johnson, K. P. 2001. Taxon sampling and the phylogenetic position of Passeriformes: evidence from 916 avian cytochrome b sequences. Systematic Biology 50:128–136.

    PubMed  CAS  Google Scholar 

  • Källersjö, M., Farris, J. S., Chase, M. W., Bremer, B., Fay, M. F., Humphries, C. J., Petersen, G., Seberg, O., and Bremer, K. 1998. Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Plant Systematics and Evolution 213:259–287.

    Article  Google Scholar 

  • Kennedy, M., Spencer, H. G., and Gray, R. D. 1996. Hop, step and gape: do the social displays of the Pelecaniformes reflect their phylogeny? Animal Behaviour 51:273–291.

    Article  Google Scholar 

  • Kluge, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology 38:7–25.

    Article  Google Scholar 

  • Lapointe, F.-J. and Cucumel, G. 1997. The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Systematic Biology 46:306–312.

    Article  Google Scholar 

  • McMorris, F. R. and Neumann, D. 1983. Consensus functions defined on trees. Mathematical Social Sciences 4:131–136.

    Article  Google Scholar 

  • Moore, B. R., Chan, K. M. A., and Donoghue, M. J. 2004. Detecting diversification rate variation in supertrees. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 487–533. Kluwer Academic, Dordrecht, the Netherlands.

    Google Scholar 

  • Novacek, M. J. 2001. Mammalian phylogeny: genes and supertrees. Current Biology 11:R573-R575.

    Article  PubMed  CAS  Google Scholar 

  • Ortolani, A. 1999. Spots, stripes, tail tips and dark eyes: predicting the function of carnivore colour patterns using the comparative method. Biological Journal of the Linnean Society 67:433–476.

    Article  Google Scholar 

  • 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 

  • Pennisi, E. 2003. Modernizing the Tree of Life. Science 300:1692–1697.

    Article  PubMed  Google Scholar 

  • Pisani, D. 2002. Comparing and Combining Data and Trees in Phylogenetic Analysis. Ph.D. dissertation, Department of Earth Sciences, University of Bristol, United Kingdom.

    Google Scholar 

  • Pisani, D. and Wilkinson, M. 2002. Matrix representation with parsimony, taxonomic congruence, and total evidence. Systematic Biology 51:151–155.

    Article  PubMed  Google Scholar 

  • Purvis, A. 1995a. A composite estimate of primate phylogeny. Philosophical Transactions of the Royal Society of London B 348:405–421.

    Article  CAS  Google Scholar 

  • Purvis, A. 1995b. A modification to Baum and Ragan’s method for combining phylogenetic trees. Systematic Biology 44:251–255.

    Google Scholar 

  • Purvis, A., Nee, S., and Harvey, P. H. 1995. Macroevolutionary inferences from primate phylogeny. Proceedings of the Royal Society of London B 260:329–333.

    Article  CAS  Google Scholar 

  • Purvis, A. and Webster, A. J. 1999. Phylogenetically independent comparisons and primate phylogeny. In P. C. Lee (ed.), Comparative Primate Socioecology, pp. 44–70. Cambridge University Press, Cambridge.

    Chapter  Google Scholar 

  • Ragan, M. A. 1992. Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution 1:53–58.

    Article  PubMed  CAS  Google Scholar 

  • Rambaut, A. and Bromham, L. 1998. Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15:442–448.

    Article  PubMed  CAS  Google Scholar 

  • Rodrigo, A. G. 1996. On combining cladograms. Taxon 45:267–274.

    Article  Google Scholar 

  • Salamin, N., Hodkinson, T. R., and Savolainen, V. 2002. Building supertrees: an empirical assessment using the grass family (Poaceae). Systematic Biology 51:136–150.

    Article  PubMed  Google Scholar 

  • Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 19:101–109.

    Article  PubMed  CAS  Google Scholar 

  • Sanderson, M. J., Purvis, A., and Henze, C. 1998. Phylogenetic supertrees: assembling the trees of life. Trends in Ecology and Evolution 13:105–109.

    Article  PubMed  CAS  Google Scholar 

  • Semple, C. and Steel, M. 2000. A supertree method for rooted trees. Discrete Applied Mathematics 105:147–158.

    Article  Google Scholar 

  • Slowinski, J. B. and Page, R. D. M. 1999. How should species phylogenies be inferred from sequence data? Systematic Biology 48:814–825.

    Article  PubMed  CAS  Google Scholar 

  • Soltis, P. S. and Souris, D. E. 2001. Molecular systematics: assembling and using the Tree of Life. Taxon 50:663–677.

    Article  Google Scholar 

  • Springer, M. S. and De Jong, W. W. 2001. Phylogenetics. Which mammalian supertree to bark up? Science 291:1709–1711.

    Article  PubMed  CAS  Google Scholar 

  • Steel, M., Dress, A. W. M., and Böcker, S. 2000. Simple but fundamental limitations on supertree and consensus tree methods. Systematic Biology 49:363–368.

    Article  PubMed  CAS  Google Scholar 

  • Thorley, J. L. and Page, R. D. 2000. RadCon: phylogenetic tree comparison and consensus. Bioinformatics 16:486–7.

    Article  PubMed  CAS  Google Scholar 

  • Thorne, J. L., Kishino, H., and Painter, I. S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15:1647–1657.

    Article  PubMed  CAS  Google Scholar 

  • Thorne, J. L. and Kishino, H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51:689–702.

    Article  PubMed  Google Scholar 

  • Vos, R. A. and Mooers, A. O. 2004. Reconstructing divergence times for supertrees. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 281–299. Kluwer Academic, Dordrecht, the Netherlands.

    Google Scholar 

  • Webb, C. O. 2000. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. American Naturalist 156:145–155.

    Article  PubMed  Google Scholar 

  • Willson, S. J. 1999. Building phylogenetic trees from quartets by using local inconsistency measures. Molecular Biology and Evolution 16:685–693.

    Article  CAS  Google Scholar 

  • Willson, S. J. 2001. An error correcting map for quartets can improve the signals for phylogenetic trees. Molecular Biology and Evolution 18:344–351.

    Article  PubMed  CAS  Google Scholar 

  • Yoder, A. D. and Yang, Z. H. 2000. Estimation of speciation dates using local molecular clocks. Molecular Biology and Evolution 17:1081–1090.

    Article  PubMed  CAS  Google Scholar 

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Authors
  1. Olaf R. P. Bininda-Emonds
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Editors and Affiliations

  1. Lehrstuhl für Tierzucht, Technische Universität München, Freising- Weihenstephan, Germany

    Olaf R. P. Bininda-Emonds

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Bininda-Emonds, O.R.P. (2004). New uses for old phylogenies. In: Bininda-Emonds, O.R.P. (eds) Phylogenetic Supertrees. Computational Biology, vol 4. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-2330-9_1

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  • DOI: https://doi.org/10.1007/978-1-4020-2330-9_1

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-1-4020-2329-3

  • Online ISBN: 978-1-4020-2330-9

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