2016/04/22 by Luca Ferretti, Ferretti, Luca, Alexander Klassmann +10
Biochemistry, Genetics and Molecular Biology · #FOS: Biological sciences #Fractal and DNA sequence analysis #Populations and Evolution (q-bio.PE) #Protein Structure and Dynamics #RNA and protein synthesis mechanisms #q-bio.PE
paper · pdf · doi:10.48550/arxiv.1604.06713
26 pages, 5 figures
openalex publication_date 2016/04/22 · arxiv created 2017/01/09 · arxiv updated 2017/01/11 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.