Abstract
AbstractWe 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.
Publisher
Cold Spring Harbor Laboratory
Reference48 articles.
1. M. Kimura , The neutral theory of molecular evolution, Cambridge University Press, Cambridge, Great Britain, 1983.
2. W. J. Ewens , Mathematical Population Genetics 1: Theoretical Introduction, volume 27, Springer, 2012.
3. L. Ferretti , A. Ledda , T. Wiehe , G. Achaz , S. E. Ramos-Onsins , De-composing the site frequency spectrum: the impact of tree topology on neutrality tests, Genetics (2017) genetics–116.
Cited by
3 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献