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bioRxiv · 10.1101/100123

The expected neutral frequency spectrum of linked sites

Ferretti, L.·Klassmann, A.·Raineri, E.·Wiehe, T.·Ramos-Onsins, S. E.·Achaz, G.
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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 multiallelic Kolmogorov equations. These formulae are the immediate extensions of the well known single site{theta} /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 Tajimas D and other SFS-based neutrality tests to a non-recombining region containing a neutral marker is presented.

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Ferretti, L., Klassmann, A., Raineri, E., Wiehe, T., Ramos-Onsins, S. E., Achaz, G.. 2017-01-13. The expected neutral frequency spectrum of linked sites. https://doi.org/10.1101/100123

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