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The neutral frequency spectrum of linked sites

View ORCID ProfileLuca Ferretti, Alexander Klassmann, Emanuele Raineri, Sebastián E. Ramos-Onsins, Thomas Wiehe, Guillaume Achaz
doi: https://doi.org/10.1101/100123
Luca Ferretti
aThe Pirbright Institute, Woking, United Kingdom
bInstitut de Systématique, Evolution, Biodiversité, UMR 7205, MNHN and Centre Interdisciplinaire de Recherche en Biologie, UMR 7241, Collége de France
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Alexander Klassmann
cInstitut für Genetik, Universität zu Köln, 50674 Köln, Germany
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Emanuele Raineri
dCNAG-CRG, Centre for Genomic Regulation (CRG) and UPF, Barcelona, Spain
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Sebastián E. Ramos-Onsins
eCentre for Research in Agricultural Genomics (CRAG), Bellaterra, Barcelona, Spain
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Thomas Wiehe
cInstitut für Genetik, Universität zu Köln, 50674 Köln, Germany
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Guillaume Achaz
bInstitut de Systématique, Evolution, Biodiversité, UMR 7205, MNHN and Centre Interdisciplinaire de Recherche en Biologie, UMR 7241, Collége de France
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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 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted June 01, 2018.
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The neutral frequency spectrum of linked sites
Luca Ferretti, Alexander Klassmann, Emanuele Raineri, Sebastián E. Ramos-Onsins, Thomas Wiehe, Guillaume Achaz
bioRxiv 100123; doi: https://doi.org/10.1101/100123
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The neutral frequency spectrum of linked sites
Luca Ferretti, Alexander Klassmann, Emanuele Raineri, Sebastián E. Ramos-Onsins, Thomas Wiehe, Guillaume Achaz
bioRxiv 100123; doi: https://doi.org/10.1101/100123

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