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

Author

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  • 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
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    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. 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.
    7. 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.

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