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The third moments of the site frequency spectrum

Author

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  • Klassmann, A.
  • Ferretti, L.

Abstract

The analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-called site frequency spectrum. For neutrally evolving sequences, some classical results are available, including the expected value and variance of the spectrum in the Kingman coalescent model without recombination as calculated by Fu (1995).

Suggested Citation

  • Klassmann, A. & Ferretti, L., 2018. "The third moments of the site frequency spectrum," Theoretical Population Biology, Elsevier, vol. 120(C), pages 16-28.
    • Handle: RePEc:eee:thpobi:v:120:y:2018:i:c:p:16-28
    DOI: 10.1016/j.tpb.2017.12.002
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    References listed on IDEAS

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    1. Richard R Hudson, 2015. "A New Proof of the Expected Frequency Spectrum under the Standard Neutral Model," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-5, July.
    2. Rafajlović, M. & Klassmann, A. & Eriksson, A. & Wiehe, T. & Mehlig, B., 2014. "Demography-adjusted tests of neutrality based on genome-wide SNP data," Theoretical Population Biology, Elsevier, vol. 95(C), pages 1-12.
    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.
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    Cited by:

    1. Hobolth, Asger & Siri-Jégousse, Arno & Bladt, Mogens, 2019. "Phase-type distributions in population genetics," Theoretical Population Biology, Elsevier, vol. 127(C), pages 16-32.
    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.

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