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Reconstructing Divergence Times for Supertrees

A molecular approach

  • Chapter
Phylogenetic Supertrees

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

Abstract

Here, we present a formal approach to estimating divergence dates derived from aligned DNA sequence data on MRP supertrees, using a new supertree for the Primates as a case study. We selected 40 sequence data sets that conform under various models of sequence evolution to the molecular clock. Each of these data sets covers only a subset of the taxa on the supertree, and so composite date estimates were obtained by calibrating the data sets on common nodes and subsequently combining the estimates from different genes for the same node. The internal consistency of our estimates is high. The estimates presented here also fit well with those from Purvis ’ 1995 primate supertree, although estimates for deeper splits are progressively older.

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References

  • Adachi, J. and Hasegawa, M. 1995. Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: heterogeneity among amino acid sites. Journal of Molecular Evolution 40:622–628.

    Article  PubMed  CAS  Google Scholar 

  • Adachi, J. and Hasegawa, M. 1996. Tempo and mode of synonymous substitutions in mitochondrial DNA of Primates. Molecular Biology and Evolution 13:200–208.

    Article  PubMed  CAS  Google Scholar 

  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403–410.

    PubMed  CAS  Google Scholar 

  • Archibald, J. D. 1999. Molecular dates and the mammalian radiation. Trends in Ecology and Evolution 14:278–278.

    Article  PubMed  Google Scholar 

  • Arnason, U., Gullberg, A., Burguete, A. S., and Janke, A. 2000. Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans. Hereditas 133:217–228.

    Article  PubMed  CAS  Google Scholar 

  • Arnason, U., Gullberg, A., and Janke, A. 1998. Molecular timing of primate divergences as estimated by two nonprimate calibration points. Journal of Molecular Evolution 47:718–727.

    Article  PubMed  CAS  Google Scholar 

  • Arnason, U., Gullberg, A., Janke, A., and Xu, X. 1996a. Pattern and timing of evolutionary divergences among hominoids based on analyses of completemt DNAs. Journal of Molecular Evolution 43:650–661.

    Article  PubMed  CAS  Google Scholar 

  • Arnason, U., Xu, X. F., Gullberg, A., and Graur, D. 1996b. The “Phoca standard”: An external molecular reference for calibrating recent evolutionary divergences. Journal of Molecular Evolution 43:41–45.

    Article  PubMed  CAS  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 

  • 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 

  • Bromham, L. D., Rambaut, A., Fortey, R., Cooper, A. and Penny, D. 1998. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proceedings of the National Academy of Sciences of the United States ofAmerica 95:12386–12389

    Article  CAS  Google Scholar 

  • Bromham, L. D. and Hendy, M. D. 2000. Can fast early rates reconcile molecular dates with the Cambrian explosions? Proceedings of the Royal Society ofLondon B 267:1041–1047

    Article  CAS  Google Scholar 

  • Bryant, D., Semple, C., and Steel, M. 2004. Supertree methods for ancestral divergence dates and other applications. In O. R. P. Bininda-Emonds (ed). Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 129–150. Kluwer Academic, Dordrecht, the Netherlands.

    Google Scholar 

  • Colless, D. H. 1980. Congruence between morphometric and allozyme data for Menidia species: a reappraisal. Systematic Zoology 29:288–299.

    Article  Google Scholar 

  • Easteal, S. and Herbert, G. 1997. Molecular evidence from the nuclear genome for the time frame of human evolution. Journal of Molecular Evolution 44(Suppl. 1):S121-S132.

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368–376.

    Article  PubMed  CAS  Google Scholar 

  • Fortey, R. A., Briggs, D. E. G., and Wills, M. A. 1996. The Cambrian evolutionary “explosion”: decoupling cladogenesis from morphological disparity. Biological Journal of the Linnean Society 57:13–33.

    Google Scholar 

  • Gingerich, P. D. and Uhen, M. D. 1994. Time of origin of primates. Journal of Human Evolution 27:443–445.

    Article  Google Scholar 

  • Gittleman, J. L., Jones, K. E., and Price, S. A. 2004. Supertrees: using complete phylogenies in comparative biology. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 439–460. Kluwer Academic, Dordrecht, the Netherlands.

    Google Scholar 

  • Goodman, M., Porter, C. A., Czelusniak, J., Page, S. L., Schneider, H., Shoshani, J., Gunnell, G. F., and Groves, C. 1998. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Molecular Phylogenetics and Evolution 9:585–598.

    Article  PubMed  CAS  Google Scholar 

  • Gould, S. J. 1989. Wonderful Life. Norton, New York.

    Google Scholar 

  • Harding, E. F. 1971. The probabilities of rooted tree shapes generated by random bifurcation. Advanced Applied Probability 3:44–77.

    Article  Google Scholar 

  • Hasegawa, M., Kishino, H., and Yano, T.-A. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160–174.

    Article  PubMed  CAS  Google Scholar 

  • Jones, K. E., Purvis, A., Maclarnon, A., Bininda-Emonds, O. R. P., and Simmons, N. B. 2002. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biological Reviews 77:223–259.

    Article  PubMed  Google Scholar 

  • Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111–120.

    Article  PubMed  CAS  Google Scholar 

  • Kluge, A. and Farris, S. 1969. Quantitative phyletics and the evolution of anurans. Systematic Zoology 18:1–32.

    Article  Google Scholar 

  • Kumar, S. and Hedges, S. B. 1998. A molecular timescale for vertebrate evolution. Nature 392:917–920.

    Article  PubMed  CAS  Google Scholar 

  • Lee, M. S. Y. 1999. Molecular clock calibrations and metazoan divergence dates. Journal of Molecular Evolution 49:385–391.

    Article  PubMed  CAS  Google Scholar 

  • Li, W.-H., Wolfe, K. H., Soudis, J., and Sharp, P. 1987. Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution. Cold Spring Harbor Symposia on Quantitative Biology 52:847–856.

    Article  PubMed  CAS  Google Scholar 

  • Lipps, J. H. and Signor, P. W. 1992. Origin and Early Evolution of Metazoa. Plenum, New York.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Maddison, D. R., Swofford, D. L., and Maddison, W. P. 1997. Nexus: an extensible file format for systematic information. Systematic Biology 46:590–621.

    Article  PubMed  CAS  Google Scholar 

  • Mooers, A.O., Heard, S. B., and E. Chrostowski, E. In press. Evolutionary heritage as a metric for conservation. In A. Purvis, T. L. Brooks, and J. L. Gittleman (eds), Phylogeny and Conservation. Oxford University Press, Oxford.

    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 

  • Nee, S. 2001. Inferring speciation rates from phylogenies. Evolution 55:661–668.

    Article  PubMed  CAS  Google Scholar 

  • Nee, S., Mooers, A. O., and Harvey, P. H. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proceedings of the National Academy of Sciences of the United States ofAmerica 89:8322–8326.

    Article  CAS  Google Scholar 

  • Nei, M. and Glazko, G. V. 2002. Estimation of divergence times for a few mammalian and several primate species. Journal of Heredity 93:157–164.

    Article  PubMed  CAS  Google Scholar 

  • Nixon, K. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15:407–414.

    Article  Google Scholar 

  • Novacek, M. J. and Wheeler, Q. D. 1992. Introduction: extinct taxa. In: Novacek M. J. and Q. D. Wheeler (eds), Extinction and Phylogeny. New York: Columbia University Press, 1–16.

    Google Scholar 

  • Pisani, D., Yates, A. M., Langer, M. C., and Benton, M. J. 2002. A genus-level supertree of the Dinosauria. Proceedings of the Royal Society ofLondon B 269:915–921.

    Article  Google Scholar 

  • Porter, C. A., Page, S. L., Czelusniak, J., Schneider, H., Schneider, M. P. C., Sampaio, I., and Goodman, M. 1997. Phylogeny and evolution of selected primates as determined by sequences of the ε-globin locus and 5 ’ flanking regions. International Journal of Primatology 18:261–295.

    Article  Google Scholar 

  • Posada, D. and Crandall, K. A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818.

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  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 

  • Ridley, M. 1996. Evolution, 2nd edition. Blackwell Science, Inc., Cambridge, Massachusetts.

    Google Scholar 

  • Rodríguez, F., Oliver, J. L., Marín, A., and Medina, J. R. 1990. The general stochastic model of nucleotide substitution. Journal of Theoretic Biology 142:485–501.

    Article  Google Scholar 

  • Salamin, N., Hodkinson, T. R., and Savolainen, V. 2002. Building supertrees: an empirical assessment using the grass family (Poaceae). Systematic Biology 51:112–126.

    Article  Google Scholar 

  • Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14:1218–1231.

    Article  CAS  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 

  • Stauffer, R. L., Walker, A., Ryder, O. A., Lyons-Weiler, M., and Hedges, S. B. 2001. Human and ape molecular clocks and constraints on paleontological hypotheses. Journal of Heredity 92:469–474.

    Article  PubMed  CAS  Google Scholar 

  • Swofford, D. L. 2002. Paup Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sinauer, Sunderland, Massachusetts.

    Google Scholar 

  • Thompson, J. D., Higgins, D. G., T. J. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22:4673–4680.

    Article  PubMed  CAS  Google Scholar 

  • Thorley, J. L. and Page, R. D. M. 2000. Rad Con: phylogenetic tree comparison and consensus. Bioinformatics 16:486–487.

    Article  PubMed  CAS  Google Scholar 

  • Wilson, D. E. and Reeder, D. M. (eds). 1993. Mammal Species of the World. Smithsonian Institution Press, Washington Dc.

    Google Scholar 

  • Wojciechowski, M. F., Sanderson, M. J., Steel, K. P., and Liston, A. 2000. Molecular phylogeny of the “temperate herbaceous tribes” of papilionoid legumes: a supertree approach. In P. Herendeen and A. Bruneau (eds), Advances in Legume Systematics 9:277–298. Royal Botanic Garden, Kew.

    Google Scholar 

  • Xun, G. 1998. Early metazoan divergence was about 830 million years ago. Journal of Molecular Evolution 47:369–371.

    Article  Google Scholar 

  • Yang, Z., Goldman, N., and Friday, A. 1994. Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Molecular Biology and Evolution 11:316–324.

    PubMed  CAS  Google Scholar 

  • Yang, Z. 1996. Among-site variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution 11:367–371.

    Article  PubMed  CAS  Google Scholar 

  • Yoder, A. D. 1997. Back to the future: a synthesis of strepsirhine systematics. Evolutionary Anthropology: Issues, News, and Reviews 6:11–22.

    Article  Google Scholar 

  • Zuckercandl, E. and Pauling, L. 1965. Evolutionary divergence and convergence in proteins. In V. Bryson and H. J. Vogel (eds), pp. 97–165 in Evolving Genes and Proteins. Academic Press, New York.

    Google Scholar 

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Authors
  1. Rutger A. Vos
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  2. Arne Ø. Mooers
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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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Vos, R.A., Mooers, A.Ø. (2004). Reconstructing Divergence Times for Supertrees. 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_14

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  • DOI: https://doi.org/10.1007/978-1-4020-2330-9_14

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-1-4020-2329-3

  • Online ISBN: 978-1-4020-2330-9

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