IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v425y2003i6960d10.1038_nature02053.html
   My bibliography  Save this article

Genome-scale approaches to resolving incongruence in molecular phylogenies

Author

Listed:
  • Antonis Rokas

    (University of Wisconsin-Madison)

  • Barry L. Williams

    (University of Wisconsin-Madison)

  • Nicole King

    (University of Wisconsin-Madison)

  • Sean B. Carroll

    (University of Wisconsin-Madison)

Abstract

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.

Suggested Citation

  • Antonis Rokas & Barry L. Williams & Nicole King & Sean B. Carroll, 2003. "Genome-scale approaches to resolving incongruence in molecular phylogenies," Nature, Nature, vol. 425(6960), pages 798-804, October.
    • Handle: RePEc:nat:nature:v:425:y:2003:i:6960:d:10.1038_nature02053
    DOI: 10.1038/nature02053
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature02053
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature02053?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Wang Yuancheng & Degnan James H, 2011. "Performance of Matrix Representation with Parsimony for Inferring Species from Gene Trees," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-39, May.
    2. Alexei J Drummond & Simon Y W Ho & Matthew J Phillips & Andrew Rambaut, 2006. "Relaxed Phylogenetics and Dating with Confidence," PLOS Biology, Public Library of Science, vol. 4(5), pages 1-1, March.
    3. Roch, Sebastien & Steel, Mike, 2015. "Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent," Theoretical Population Biology, Elsevier, vol. 100(C), pages 56-62.
    4. Sergio Consoli & Jan Korst & Steffen Pauws & Gijs Geleijnse, 2020. "Improved metaheuristics for the quartet method of hierarchical clustering," Journal of Global Optimization, Springer, vol. 78(2), pages 241-270, October.
    5. Haque Md Rejuan & Kubatko Laura, 2024. "A global test of hybrid ancestry from genome-scale data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 23(1), pages 1-18, January.
    6. David Peris & Emily J. Ubbelohde & Meihua Christina Kuang & Jacek Kominek & Quinn K. Langdon & Marie Adams & Justin A. Koshalek & Amanda Beth Hulfachor & Dana A. Opulente & David J. Hall & Katie Hyma , 2023. "Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    7. Martín Espariz & Federico A Zuljan & Luis Esteban & Christian Magni, 2016. "Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case," PLOS ONE, Public Library of Science, vol. 11(9), pages 1-17, September.
    8. Rahul Siddharthan & Eric D Siggia & Erik van Nimwegen, 2005. "PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny," PLOS Computational Biology, Public Library of Science, vol. 1(7), pages 1-23, December.
    9. Siewert Elizabeth A & Kechris Katerina J, 2009. "Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-36, September.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:425:y:2003:i:6960:d:10.1038_nature02053. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.