RT Journal Article SR Electronic T1 The neutral frequency spectrum of linked sites JF bioRxiv FD Cold Spring Harbor Laboratory SP 100123 DO 10.1101/100123 A1 Luca Ferretti A1 Alexander Klassmann A1 Emanuele Raineri A1 Sebastián E. Ramos-Onsins A1 Thomas Wiehe A1 Guillaume Achaz YR 2018 UL http://biorxiv.org/content/early/2018/06/01/100123.abstract 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.