IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v129y2019icp148-159.html
   My bibliography  Save this article

Inductive determination of allele frequency spectrum probabilities in structured populations

Author

Listed:
  • Uyenoyama, Marcy K.
  • Takebayashi, Naoki
  • Kumagai, Seiji

Abstract

We present a method for inductively determining exact allele frequency spectrum (AFS) probabilities for samples derived from a population comprising two demes under the infinite-allele model of mutation. This method builds on a labeled coalescent argument to extend the Ewens sampling formula (ESF) to structured populations. A key departure from the panmictic case is that the AFS conditioned on the number of alleles in the sample is no longer independent of the scaled mutation rate (θ). In particular, biallelic site frequency spectra, widely-used in explorations of genome-wide patterns of variation, depend on the mutation rate in structured populations. Variation in the rate of substitution across loci and through time may contribute to apparent distortions of site frequency spectra exhibited by samples derived from structured populations.

Suggested Citation

  • Uyenoyama, Marcy K. & Takebayashi, Naoki & Kumagai, Seiji, 2019. "Inductive determination of allele frequency spectrum probabilities in structured populations," Theoretical Population Biology, Elsevier, vol. 129(C), pages 148-159.
    • Handle: RePEc:eee:thpobi:v:129:y:2019:i:c:p:148-159
    DOI: 10.1016/j.tpb.2018.10.004
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580918301035
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2018.10.004?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. Hobolth, Asger & Rivas-González, Iker & Bladt, Mogens & Futschik, Andreas, 2024. "Phase-type distributions in mathematical population genetics: An emerging framework," Theoretical Population Biology, Elsevier, vol. 157(C), pages 14-32.
    2. Uyenoyama, Marcy K. & Takebayashi, Naoki & Kumagai, Seiji, 2020. "Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent," Theoretical Population Biology, Elsevier, vol. 133(C), pages 130-140.

    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:eee:thpobi:v:129:y:2019:i:c:p:148-159. 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: Catherine Liu (email available below). General contact details of provider: https://www.journals.elsevier.com/intelligence .

    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.