IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v124y2018icp41-50.html
   My bibliography  Save this article

Topological linkage disequilibrium calculated from coalescent genealogies

Author

Listed:
  • Wirtz, Johannes
  • Rauscher, Martina
  • Wiehe, Thomas

Abstract

We revisit the classical, and introduce a novel, concept of two-locus linkage disequilibrium (LD). In contrast to defining haplotypes as allele combinations at two marker loci, we concentrate on the clustering of a sample of chromosomes induced by their coalescent genealogy. The root of a binary coalescent tree defines two clusters of chromosomes, each one of them containing the left and right descendants of the root. At two different loci this assignment may be different as a result of recombination. We show that the proportion of shared chromosomes among clusters at two different loci, measured by the squared correlation, constitutes a natural measure of LD. We call this topological LD (tLD) since it is induced by the topology of the coalescent tree. We find that it is, on average, larger than classical LD for any given distance between loci. Furthermore, tLD has a smaller coefficient of variation, which should provide an advantage, compared to the use of classical LD, for any kind of mapping purposes. We conclude with a practical application to the LCT region in human populations.

Suggested Citation

  • Wirtz, Johannes & Rauscher, Martina & Wiehe, Thomas, 2018. "Topological linkage disequilibrium calculated from coalescent genealogies," Theoretical Population Biology, Elsevier, vol. 124(C), pages 41-50.
    • Handle: RePEc:eee:thpobi:v:124:y:2018:i:c:p:41-50
    DOI: 10.1016/j.tpb.2018.09.001
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580918300674
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2018.09.001?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.

    References listed on IDEAS

    as
    1. Haipeng Li & Thomas Wiehe, 2013. "Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-14, May.
    2. Luca Ferretti & Filippo Disanto & Thomas Wiehe, 2013. "The Effect of Single Recombination Events on Coalescent Tree Height and Shape," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-15, April.
    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. Haipeng Li & Thomas Wiehe, 2013. "Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-14, May.
    2. Yichen Zheng & Thomas Wiehe, 2019. "Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps," PLOS Computational Biology, Public Library of Science, vol. 15(11), pages 1-32, November.
    3. Jerome Kelleher & Alison M Etheridge & Gilean McVean, 2016. "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-22, May.

    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:124:y:2018:i:c:p:41-50. 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: 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.