The neutral frequency spectrum of linked sites

Luca Ferretti, Alexander Klassmann, Emanuele Raineri, Ramos-Onsins, Sebastián E., Thomas Wiehe and Guillaume Achaz

Theoretical Population Biology, 2018, vol. 123, issue C, 70-79

Abstract: We introduce the conditional Site Frequency Spectrum (SFS) for a genomic region linked to a focal mutation of known frequency. An exact expression for its expected value is provided for the neutral model without recombination. Its relation with the expected SFS for two sites, 2-SFS, is discussed. These spectra derive from the coalescent approach of Fu (1995) for finite samples, which is reviewed. Remarkably simple expressions are obtained for the linked SFS of a large population, which are also solutions of the multi-allelic Kolmogorov equations. These formulae are the immediate extensions of the well known single site θ∕f neutral SFS. Besides the general interest in these spectra, they relate to relevant biological cases, such as structural variants and introgressions. As an application, a recipe to adapt Tajima’s D and other SFS-based neutrality tests to a non-recombining region containing a neutral marker is presented.

Keywords: Site frequency spectrum; Linkage disequilibrium; Neutral evolution; Kingman coalescent (search for similar items in EconPapers)
Date: 2018
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Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:123:y:2018:i:c:p:70-79

DOI: 10.1016/j.tpb.2018.06.001

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