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. 2018 Sep:123:70-79.
doi: 10.1016/j.tpb.2018.06.001. Epub 2018 Jun 28.

The neutral frequency spectrum of linked sites

Luca Ferretti  1 , Alexander Klassmann  2 , Emanuele Raineri  3 , Sebastián E Ramos-Onsins  4 , Thomas Wiehe  2 , Guillaume Achaz  5
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Free article

The neutral frequency spectrum of linked sites

Luca Ferretti et al. Theor Popul Biol. 2018 Sep.
Free article

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: Kingman coalescent; Linkage disequilibrium; Neutral evolution; Site frequency spectrum.

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