IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v556y2018i7702d10.1038_s41586-018-0043-0.html
   My bibliography  Save this article

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Author

Listed:
  • F. Lemoine

    (Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS
    Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS)

  • J.-B. Domelevo Entfellner

    (University of the Western Cape
    South African National Bioinformatics Institute, University of the Western Cape)

  • E. Wilkinson

    (School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal)

  • D. Correia

    (Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS)

  • M. Dávila Felipe

    (Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS)

  • T. Oliveira

    (School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal
    University of KwaZulu-Natal)

  • O. Gascuel

    (Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Université de Montpellier & CNRS)

Abstract

Felsenstein’s application of the bootstrap method to evolutionary trees is one of the most cited scientific papers of all time. The bootstrap method, which is based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies based on hundreds or thousands of taxa are becoming routine. With phylogenies of this size Felsenstein’s bootstrap tends to yield very low supports, especially on deep branches. Here we propose a new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual ‘transfer’ distance rather than the binary presence or absence index used in Felsenstein’s original version. The resulting supports are higher and do not induce falsely supported branches. The application of our method to large mammal, HIV and simulated datasets reveals their phylogenetic signals, whereas Felsenstein’s bootstrap fails to do so.

Suggested Citation

  • F. Lemoine & J.-B. Domelevo Entfellner & E. Wilkinson & D. Correia & M. Dávila Felipe & T. Oliveira & O. Gascuel, 2018. "Renewing Felsenstein’s phylogenetic bootstrap in the era of big data," Nature, Nature, vol. 556(7702), pages 452-456, April.
    • Handle: RePEc:nat:nature:v:556:y:2018:i:7702:d:10.1038_s41586-018-0043-0
    DOI: 10.1038/s41586-018-0043-0
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41586-018-0043-0
    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/s41586-018-0043-0?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. Marie-Claire Daugeron & Sophia Missoury & Violette Cunha & Noureddine Lazar & Bruno Collinet & Herman Tilbeurgh & Tamara Basta, 2023. "A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Alessandro Boverio & Neelam Jamil & Barbara Mannucci & Maria Laura Mascotti & Marco W. Fraaije & Andrea Mattevi, 2024. "Structure, mechanism, and evolution of the last step in vitamin C biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    3. Tomoyuki Hatano & Saravanan Palani & Dimitra Papatziamou & Ralf Salzer & Diorge P. Souza & Daniel Tamarit & Mehul Makwana & Antonia Potter & Alexandra Haig & Wenjue Xu & David Townsend & David Rochest, 2022. "Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    4. Gautier Bailleul & Guang Yang & Callum R. Nicoll & Andrea Mattevi & Marco W. Fraaije & Maria Laura Mascotti, 2023. "Evolution of enzyme functionality in the flavin-containing monooxygenases," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    5. Joao A. Ascensao & Kelly M. Wetmore & Benjamin H. Good & Adam P. Arkin & Oskar Hallatschek, 2023. "Quantifying the local adaptive landscape of a nascent bacterial community," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    6. Matthew Goulty & Gaelle Botton-Amiot & Ezio Rosato & Simon G. Sprecher & Roberto Feuda, 2023. "The monoaminergic system is a bilaterian innovation," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    7. Octavio R. Salazar & Ke Chen & Vanessa J. Melino & Muppala P. Reddy & Eva Hřibová & Jana Čížková & Denisa Beránková & Juan Pablo Arciniegas Vega & Lina María Cáceres Leal & Manuel Aranda & Lukasz Jare, 2024. "SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    8. Michael P. Andreas & Tobias W. Giessen, 2024. "The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    9. Heather R. Kates & Brian C. O’Meara & Raphael LaFrance & Gregory W. Stull & Euan K. James & Shui-Yin Liu & Qin Tian & Ting-Shuang Yi & Daniel Conde & Matias Kirst & Jean-Michel Ané & Douglas E. Soltis, 2024. "Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    10. Fares Boudjouan & Walid Zeghbib & João Carneiro & Raquel Silva & João Morais & Vitor Vasconcelos & Graciliana Lopes, 2022. "Comparison Study on Wild and Cultivated Opuntia sp.: Chemical, Taxonomic, and Antioxidant Evaluations," Agriculture, MDPI, vol. 12(11), pages 1-21, October.
    11. Ya Gao & Daisylyn Senna Tan & Mathias Girbig & Haoqing Hu & Xiaomin Zhou & Qianwen Xie & Shi Wing Yeung & Kin Shing Lee & Sik Yin Ho & Vlad Cojocaru & Jian Yan & Georg K. A. Hochberg & Alex Mendoza & , 2024. "The emergence of Sox and POU transcription factors predates the origins of animal stem cells," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

    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:556:y:2018:i:7702:d:10.1038_s41586-018-0043-0. 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.