IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0034572.html
   My bibliography  Save this article

Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics

Author

Listed:
  • Oscar Westesson
  • Gerton Lunter
  • Benedict Paten
  • Ian Holmes

Abstract

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.

Suggested Citation

  • Oscar Westesson & Gerton Lunter & Benedict Paten & Ian Holmes, 2012. "Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-12, April.
    • Handle: RePEc:plo:pone00:0034572
    DOI: 10.1371/journal.pone.0034572
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034572
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0034572&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0034572?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
    ---><---

    References listed on IDEAS

    as
    1. Katherine S. Pollard & Sofie R. Salama & Nelle Lambert & Marie-Alexandra Lambot & Sandra Coppens & Jakob S. Pedersen & Sol Katzman & Bryan King & Courtney Onodera & Adam Siepel & Andrew D. Kern & Cole, 2006. "An RNA gene expressed during cortical development evolved rapidly in humans," Nature, Nature, vol. 443(7108), pages 167-172, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Noah Dukler & Mehreen R. Mughal & Ritika Ramani & Yi-Fei Huang & Adam Siepel, 2022. "Extreme purifying selection against point mutations in the human genome," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Kazi Abdul, Mannan, 2020. "The Theory of Matriarchism: The Universal Origin of Human," MPRA Paper 101353, University Library of Munich, Germany, revised 2020.
    3. Su Yeon Kim & Jonathan K Pritchard, 2007. "Adaptive Evolution of Conserved Noncoding Elements in Mammals," PLOS Genetics, Public Library of Science, vol. 3(9), pages 1-15, September.
    4. Xinru Zhang & Bohao Fang & Yi-Fei Huang, 2023. "Transcription factor binding sites are frequently under accelerated evolution in primates," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    5. Kirsten E Eilertson & James G Booth & Carlos D Bustamante, 2012. "SnIPRE: Selection Inference Using a Poisson Random Effects Model," PLOS Computational Biology, Public Library of Science, vol. 8(12), pages 1-14, December.
    6. Kazi Abdul, Mannan, 2020. "A Theory of Matriarchism: The Universal Origins of Humanity," MPRA Paper 105016, University Library of Munich, Germany, revised 2020.

    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:plo:pone00:0034572. 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.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.