The non-equilibrium allele frequency spectrum in a Poisson random field framework
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Publication:2362548
Abstract: In population genetic studies, the allele frequency spectrum (AFS) efficiently summarizes genome-wide polymorphism data and shapes a variety of allele frequency-based summary statistics. While existing theory typically features equilibrium conditions, emerging methodology requires an analytical understanding of the build-up of the allele frequencies over time. In this work, we use the framework of Poisson random fields to derive new representations of the non-equilibrium AFS for the case of a Wright-Fisher population model with selection. In our approach, the AFS is a scaling-limit of the expectation of a Poisson stochastic integral and the representation of the non-equilibrium AFS arises in terms of a fixation time probability distribution. The known duality between the Wright-Fisher diffusion process and a birth and death process generalizing Kingman's coalescent yields an additional representation. The results carry over to the setting of a random sample drawn from the population and provide the non-equilibrium behavior of sample statistics. Our findings are consistent with and extend a previous approach where the non-equilibrium AFS solves a partial differential forward equation with a non-traditional boundary condition. Moreover, we provide a bridge to previous coalescent-based work, and hence tie several frameworks together. Since frequency-based summary statistics are widely used in population genetics, for example, to identify candidate loci of adaptive evolution, to infer the demographic history of a population, or to improve our understanding of the underlying mechanics of speciation events, the presented results are potentially useful for a broad range of topics.
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Cited in
(11)- A time-dependent Poisson random field model for polymorphism within and between two related biological species
- The joint allele frequency spectrum of multiple populations: a coalescent theory approach
- Inference of genetic forces using a Poisson random field model with non-constant population size
- Analysis of diversity-dependent species evolution using concepts in population genetics
- Moments of the frequency spectrum of a splitting tree with neutral Poissonian mutations
- Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory
- Non-equilibrium allele frequency spectra via spectral methods
- Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory
- Non-equilibrium allele frequency spectra via spectral methods
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