TY - JOUR T1 - The expected neutral frequency spectrum of linked sites JF - bioRxiv DO - 10.1101/100123 SP - 100123 AU - Luca Ferretti AU - Alex Klassmann AU - Emanuele Raineri AU - Thomas Wiehe AU - Sebastian E. Ramos-Onsins AU - Guillaume Achaz Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/01/13/100123.abstract N2 - We present an exact, closed expression for the expected neutral Site Frequency Spectrum for two neutral sites, 2-SFS, without recombination. This spectrum is the immediate extension of the well known single site θ/f neutral SFS. Similar formulae are also provided for the case of the expected SFS of sites that are linked to a focal neutral mutation of known frequency. Formulae for finite samples are obtained by coalescent methods and remarkably simple expressions are derived for the SFS of a large population, which are also solutions of the multi-allelic Kolmogorov equations. Besides the general interest of these new spectra, they relate to interesting biological cases such as structural variants and introgressions. As an example, we present the expected neutral frequency spectrum of regions with a chromosomal inversion. ER -