Skip to main content
SpringerLink
Log in

Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees

  • Conference paper
Algorithms in Bioinformatics (WABI 2003)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 2812))

Included in the following conference series:

Abstract

We present a method for summarising collections of phylogenetic trees that extends the notion of consensus trees. Each branch in a phylogenetic tree corresponds to a bipartition or split of the set of taxa labelling its leaves. Given a collection of phylogenetic trees, each labelled by the same set of taxa, all those splits that appear in more than a predefined threshold proportion of the trees are displayed using a median network. The complexity of this network is bounded as a function of the threshold proportion. We demonstrate the method for a collection of 5000 trees resulting from a Monte Carlo Markov Chain analysis of 37 mammal mitochondrial genomes, and also for a collection of 80 equally parsimonious trees resulting from a heuristic search on 53 human mitochondrial sequences.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Amenta, N., Klingner, J.: Case Study: Visualizing Sets of Evolutionary Trees. In: 8th IEEE Symposium on Information Visualization, InfoVIs 2002 (2002)

    Google Scholar 

  2. Bandelt, H.-J., Dress, A.: Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Molecular Phylogenetics and Evolution 1(3), 242–252 (1992)

    Article  Google Scholar 

  3. Bandelt, H.-J.: Phylogenetic Networks. Verhandl. Naturwiss. Vereins Hamburg (NF) 34, 51–71 (1994)

    Google Scholar 

  4. Bandelt, H.-J., Forster, P., Sykes, B.C., Richards, M.B.: Mitochondrial portraits of human populations using median networks. Genetics 14, 743–753 (1995)

    Google Scholar 

  5. Bandelt, H.-J., Huber, K.T., Moulton, V.: Quasi-median graphs from sets of partitions. Discrete Applied Mathematics 122, 23–35 (2002)

    Article  MATH  MathSciNet  Google Scholar 

  6. Bryant, D.: A classification of consensus methods for phylogenetics. In: Janowitz, M., Lapointe, F.J., McMorris, F., Mirkin, B., Roberts, F. (eds.) Bioconsensus. DIMACSAMS. 2003, pp. 1–21 (2003)

    Google Scholar 

  7. Bryant, D., Moulton, V.: NeighborNet: an agglomerative method for the construction of planar phylogenetic networks. In: the proceedings of WABI, pp. 375–391 (2002)

    Google Scholar 

  8. Dress, A., Klucznik, M., Koolen, J., Moulton, V.: A note on extremal combinatorics of cyclic split systems. Seminaire Lotharingien de Combinatoire 47 (2001), http://www.mat.univie.ac.at/slc

  9. Felsenstein, J.: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791 (1985)

    Article  Google Scholar 

  10. Hendy, M.D., Steel, M.A., Penny, D., Henderson, I.M.: Families of trees and consensus. In: Bock, H.H. (ed.) Classification and Related Methods of Data Analysis, pp. 355–362. Elsevier Science Publ, North Holland (1988)

    Google Scholar 

  11. Huber, K.T., Langton, M., Penny, D., Moulton, V., Hendy, M.: Spectronet: A package for computing spectra and median networks. Applied Bioinformatics 1, 159–161 (2002)

    Google Scholar 

  12. Huber, K.T., Moulton, V., Lockhart, P., Dress, A.: Pruned median networks: a technique for reducing the complexity of median networks. Molecular Phylogenetics and Evolution 19, 302–310 (2001)

    Article  Google Scholar 

  13. Huelsenbeck, J.P., Larget, B., Miller, R.E., Ronquist, F.: Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51, 673–688 (2002)

    Article  Google Scholar 

  14. Huelsenbeck, J.P., Ronquist, F.: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755 (2001)

    Article  Google Scholar 

  15. Huelsenbeck, J.P., Ronquist, F., Nielsen, R., Bollback, J.P.: Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310–2314 (2001)

    Article  Google Scholar 

  16. Huson, D.: SplitsTree: a program for analyzing and visualizing evolutionary data. Bioinformatics 14, 68–73 (1998), http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html

    Article  Google Scholar 

  17. Ingman, M., Kaessmann, H., Paabo, S., Gyllensten, U.: Mitochondrial genome variation and the origin of modern humans. Science 408, 708–713 (2000)

    Google Scholar 

  18. Klingner, J.: Visualizing Sets of Evolutionary Trees. The University of Texas at Austin, Department of Computer Sciences. Technical Report CS-TR-01-26 (2001)

    Google Scholar 

  19. Lin, Y.-H., McLenachan, P.A., Gore, A.R., Phillips, M.J., Ota, R., Hendy, M.D., Penny, D.: Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Molecular Biology and Evolution 19, 2060–2070 (2002)

    Google Scholar 

  20. Lin, Y.-H., Waddell, P.J., Penny, D.: Pika and Vole mitochondrial genomes add support to both rodent monophyly and glires. Gene 294, 119–129 (2002)

    Article  Google Scholar 

  21. Semple, C., Steel, M.: Phylogenetics. Oxford University Press, Oxford (2003)

    MATH  Google Scholar 

  22. Swofford, D.L.: PAUP* - Phylogenetic Analysis Using Parsimony (*and other methods) Version 4. Sinauer Associates, Sunderland, Mass. (1998)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, New Zealand

    Barbara Holland

  2. The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, 751 24, Uppsala, Sweden

    Vincent Moulton

Authors
  1. Barbara Holland
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vincent Moulton
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Biomathematical Sciences, The Mount Sinai School of Medicine, 10029-6574, New York, NY

    Gary Benson

  2. Institute of Biomedical and Life Sciences, Division of Environmental and Evolutionary Biology, University of Glasgow, G12 8QQ, Glasgow, Scotland

    Roderic D. M. Page

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Holland, B., Moulton, V. (2003). Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees. In: Benson, G., Page, R.D.M. (eds) Algorithms in Bioinformatics. WABI 2003. Lecture Notes in Computer Science(), vol 2812. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39763-2_13

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-39763-2_13

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20076-5

  • Online ISBN: 978-3-540-39763-2

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation