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Joint effect of changing selection and demography on the site frequency spectrum

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  • Jain, Kavita
  • Kaushik, Sachin

Abstract

The site frequency spectrum (SFS) is an important statistic that summarizes the molecular variation in a population, and is used to estimate population-genetic parameters and detect natural selection. Here, we study the SFS in a randomly mating, diploid population in which both the population size and selection coefficient vary periodically with time using a diffusion theory approach, and derive simple analytical expressions for the time-averaged SFS in slowly and rapidly changing environments. We show that for strong selection and in slowly changing environments where the population experiences both positive and negative cycles of the selection coefficient, the time-averaged SFS differs significantly from the equilibrium SFS in a constant environment. The deviation is found to depend on the time spent by the population in the deleterious part of the selection cycle and the phase difference between the selection coefficient and population size, and can be captured by an effective population size.

Suggested Citation

  • Jain, Kavita & Kaushik, Sachin, 2022. "Joint effect of changing selection and demography on the site frequency spectrum," Theoretical Population Biology, Elsevier, vol. 146(C), pages 46-60.
    • Handle: RePEc:eee:thpobi:v:146:y:2022:i:c:p:46-60
    DOI: 10.1016/j.tpb.2022.07.001
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    References listed on IDEAS

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    1. Živković, Daniel & Stephan, Wolfgang, 2011. "Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory," Theoretical Population Biology, Elsevier, vol. 79(4), pages 184-191.
    2. Koopmann, Bendix & Müller, Johannes & Tellier, Aurélien & Živković, Daniel, 2017. "Fisher–Wright model with deterministic seed bank and selection," Theoretical Population Biology, Elsevier, vol. 114(C), pages 29-39.
    3. Toni I Gossmann & David Waxman & Adam Eyre-Walker, 2014. "Fluctuating Selection Models and Mcdonald-Kreitman Type Analyses," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-5, January.
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