AI Article Synopsis
- The text introduces the concept of the conditional Site Frequency Spectrum (SFS) for a genomic region associated with a specific mutation of known frequency, detailing its expected value under a neutral model without recombination.
- It discusses the relationship between this conditional SFS and the expected SFS for two sites (2-SFS), based on the coalescent theory outlined by Fu (1995).
- Additionally, it provides straightforward formulas for analyzing linked SFS in large populations and suggests methods to adapt neutrality tests like Tajima's D for use in non-recombining genomic regions.
Article Abstract
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 multi-allelic 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.
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| http://dx.doi.org/10.1016/j.tpb.2018.06.001 | DOI Listing |
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