Klassmann, A. and Ferretti, L. (2018). The third moments of the site frequency spectrum. Theor. Popul. Biol., 120. S. 16 - 29. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE. ISSN 1096-0325

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Abstract

The analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-called site frequency spectrum. For neutrally evolving sequences, some classical results are available, including the expected value and variance of the spectrum in the Kingman coalescent model without recombination as calculated by Fu (1995). In this work, we use similar techniques to compute the third moments of the frequencies of three linked sites. Based on these results, we derive analytical results for the bias of Tajima's D and other neutrality tests. As a corollary, we obtain the second moments of the frequencies of two linked mutations conditional on the presence of a third mutation with a certain frequency. These moments can be used for the normalisation of new neutrality tests relying on these spectra. (C) 2017 The Authors. Published by Elsevier Inc.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Klassmann, A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ferretti, L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-194254
DOI: 10.1016/j.tpb.2017.12.002
Journal or Publication Title: Theor. Popul. Biol.
Volume: 120
Page Range: S. 16 - 29
Date: 2018
Publisher: ACADEMIC PRESS INC ELSEVIER SCIENCE
Place of Publication: SAN DIEGO
ISSN: 1096-0325
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
STATISTICAL TESTS; SEGREGATING SITES; DNA POLYMORPHISM; NEUTRALITY; MUTATION; MODELS; RECOMBINATION; COALESCENT; SELECTION; GENOMESMultiple languages
Ecology; Evolutionary Biology; Genetics & Heredity; Mathematical & Computational BiologyMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/19425

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