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The genealogy, site frequency spectrum and ages of two nested mutant alleles

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  • Hobolth, Asger
  • Wiuf, Carsten

Abstract

In this paper we consider the genealogy of two nested mutant alleles, assuming the constant-size neutral coalescent model with infinite sites mutation. We study the conditional genealogy and derive explicit formulas for the joint and marginal site frequency spectra for the double, single and zero mutant allele. In addition, we find the mean ages of the two mutations. We show that the age of the youngest mutation does not depend on the frequency of the single mutant allele and that the frequency spectra for the single mutant allele and the zero mutant allele are the same.

Suggested Citation

  • Hobolth, Asger & Wiuf, Carsten, 2009. "The genealogy, site frequency spectrum and ages of two nested mutant alleles," Theoretical Population Biology, Elsevier, vol. 75(4), pages 260-265.
    • Handle: RePEc:eee:thpobi:v:75:y:2009:i:4:p:260-265
    DOI: 10.1016/j.tpb.2009.02.001
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    References listed on IDEAS

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    1. Hobolth Asger & Uyenoyama Marcy K & Wiuf Carsten, 2008. "Importance Sampling for the Infinite Sites Model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-26, October.
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    Cited by:

    1. Hayman, Elizabeth & Ignatieva, Anastasia & Hein, Jotun, 2023. "Recoverability of ancestral recombination graph topologies," Theoretical Population Biology, Elsevier, vol. 154(C), pages 27-39.
    2. Ferretti, Luca & Klassmann, Alexander & Raineri, Emanuele & Ramos-Onsins, Sebastián E. & Wiehe, Thomas & Achaz, Guillaume, 2018. "The neutral frequency spectrum of linked sites," Theoretical Population Biology, Elsevier, vol. 123(C), pages 70-79.
    3. Jenkins, Paul A. & Song, Yun S., 2011. "The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele," Theoretical Population Biology, Elsevier, vol. 80(2), pages 158-173.
    4. Ganapathy, Ganeshkumar & Uyenoyama, Marcy K., 2009. "Site frequency spectra from genomic SNP surveys," Theoretical Population Biology, Elsevier, vol. 75(4), pages 346-354.
    5. Birkner, Matthias & Blath, Jochen & Steinrücken, Matthias, 2011. "Importance sampling for Lambda-coalescents in the infinitely many sites model," Theoretical Population Biology, Elsevier, vol. 79(4), pages 155-173.

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