The neutral frequency spectrum of linked sites

DOI10.1016/J.TPB.2018.06.001MaRDI QIDQ2413541zbMATH OpenOpenAlexWikidataFDO

Authors Luca Ferretti, Alexander Klassmann, E. Raineri, Guillaume Achaz, Sebástian E. Ramos-Onsins, Thomas Wiehe

Publication date 14 September 2018

Published in Theoretical Population Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1604.06713

zbMATH Keywords

linkage disequilibriumsite frequency spectrumKingman coalescentneutral evolution

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Abstract: We present an exact, closed expression for the expected neutral Site Frequency Spectrum for two neutral sites, 2-SFS, without recombination. This spectrum is the immediate extension of the well known single site $heta/f$ neutral SFS. Similar formulae are also provided for the case of the expected SFS of sites that are linked to a focal neutral mutation of known frequency. Formulae for finite samples are obtained by coalescent methods and remarkably simple expressions are derived for the SFS of a large population, which are also solutions of the multi-allelic Kolmogorov equations. Besides the general interest of these new spectra, they relate to interesting biological cases such as structural variants and introgressions. As an example, we present the expected neutral frequency spectrum of regions with a chromosomal inversion.

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Cites work

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Cited in

(13)

• The site frequency spectrum of dispensable genes
• Inductive determination of allele frequency spectrum probabilities in structured populations
• Experiments with the site frequency spectrum
• An almost infinite sites model
• The third moments of the site frequency spectrum
• An efficient algorithm for generating the internal branches of a Kingman coalescent
• Developments in coalescent theory from single loci to chromosomes
• The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele
• Demography-adjusted tests of neutrality based on genome-wide SNP data
• Joint effect of changing selection and demography on the site frequency spectrum
• The site-frequency spectrum of linked sites
• Exact site frequency spectra of neutrally evolving tumors: a transition between power laws reveals a signature of cell viability
• Multivariate phase-type theory for the site frequency spectrum

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