PT  - JOURNAL ARTICLE
AU  - Luca Ferretti
AU  - Alexander Klassmann
AU  - Emanuele Raineri
AU  - Sebastián E. Ramos-Onsins
AU  - Thomas Wiehe
AU  - Guillaume Achaz
TI  - The neutral frequency spectrum of linked sites
AID  - 10.1101/100123
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 100123
4099  - http://biorxiv.org/content/early/2018/06/01/100123.short
4100  - http://biorxiv.org/content/early/2018/06/01/100123.full
AB  - 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.