PT  - JOURNAL ARTICLE
AU  - Luca Ferretti
AU  - Alex Klassmann
AU  - Emanuele Raineri
AU  - Thomas Wiehe
AU  - Sebastian E. Ramos-Onsins
AU  - Guillaume Achaz
TI  - The expected neutral frequency spectrum of linked sites
AID  - 10.1101/100123
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 100123
4099  - http://biorxiv.org/content/early/2017/01/13/100123.short
4100  - http://biorxiv.org/content/early/2017/01/13/100123.full
AB  - 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.