The neutral frequency spectrum of linked sites

DOI10.1016/J.TPB.2018.06.001zbMATH Open1405.92168arXiv1604.06713OpenAlexW2809936227WikidataQ89379702 ScholiaQ89379702MaRDI QIDQ2413541FDOQ2413541

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

Publication date: 14 September 2018

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

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.

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

Recommendations

• The third moments of the site frequency spectrum
• The site-frequency spectrum of linked sites
• Experiments with the site frequency spectrum
• Multivariate phase-type theory for the site frequency spectrum
• The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele

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)

Cites Work

• On the number of segregating sites in genetical models without recombination
• The genealogy, site frequency spectrum and ages of two nested mutant alleles
• The multivariate Wright-Fisher process with mutation: moment-based analysis and inference using a hierarchical beta model
• A transition density expansion for a multi-allele diffusion model
• Title not available (Why is that?)
• Statistical properties of segregating sites
• Padé approximants and exact two-locus sampling distributions
• On the two-locus sampling distribution
• The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele
• The site-frequency spectrum of linked sites
• Transition Densities for Neutral Multi-Allele Diffusion Models
• The Distribution of Gene Frequencies Under Irreversible Mutation
• Demography-adjusted tests of neutrality based on genome-wide SNP data
• The third moments of the site frequency spectrum
• An analytical framework in the general coalescent tree setting for analyzing polymorphisms created by two mutations

Cited In (3)

• 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

This page was built for publication: The neutral frequency spectrum of linked sites

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2413541)