Universität zu Köln

Ferretti, Luca ORCID: 0000-0001-7578-7301, Klassmann, Alexander ORCID: 0000-0002-0175-1397, Raineri, Emanuele, Ramos-Onsins, Sebastian E., Wiehe, Thomas ORCID: 0000-0002-8932-2772 and Achaz, Guillaume (2018). The neutral frequency spectrum of linked sites. Theor. Popul. Biol., 123. S. 70 - 80. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE. ISSN 1096-0325

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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 theta/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. (C) 2018 Elsevier Inc. All rights reserved.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Ferretti, Luca UNSPECIFIED orcid.org/0000-0001-7578-7301 UNSPECIFIED Klassmann, Alexander UNSPECIFIED orcid.org/0000-0002-0175-1397 UNSPECIFIED Raineri, Emanuele UNSPECIFIED UNSPECIFIED UNSPECIFIED Ramos-Onsins, Sebastian E. UNSPECIFIED UNSPECIFIED UNSPECIFIED Wiehe, Thomas UNSPECIFIED orcid.org/0000-0002-8932-2772 UNSPECIFIED Achaz, Guillaume UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-173941
DOI:	10.1016/j.tpb.2018.06.001
Journal or Publication Title:	Theor. Popul. Biol.
Volume:	123
Page Range:	S. 70 - 80
Date:	2018
Publisher:	ACADEMIC PRESS INC ELSEVIER SCIENCE
Place of Publication:	SAN DIEGO
ISSN:	1096-0325
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Institute for Genetics
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language 2-LOCUS SAMPLING DISTRIBUTIONS; VARIABLE POPULATION-SIZE; SEGREGATING SITES; LINKAGE DISEQUILIBRIUM; SELECTIVE SWEEPS; SNP DATA; MUTATION; TESTS; MODEL; RECOMBINATION Multiple languages Ecology; Evolutionary Biology; Genetics & Heredity; Mathematical & Computational Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/17394