Universität zu Köln

Rafajlovic, M., Klassmann, A., Eriksson, A., Wiehe, T. ORCID: 0000-0002-8932-2772 and Mehlig, B. (2014). Demography-adjusted tests of neutrality based on genome-wide SNP data. Theor. Popul. Biol., 95. S. 1 - 13. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE. ISSN 1096-0325

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Abstract

Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and the population size remains constant over time. However, it is unclear how such tests are affected if the last assumption is dropped. Here, we extend the unifying framework for tests based on the site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. Key ingredients are the first two moments of the site frequency spectrum. We show how these moments can be computed analytically if a population has experienced two instantaneous size changes in the past. We apply our method to data from ten human populations gathered in the 1000 genomes project, estimate their demographies and define demography-adjusted versions of Tajima's D, Fay & Wu's H, and Zeng's E. Our results show that demography-adjusted test statistics facilitate the direct comparison between populations and that most of the differences among populations seen in the original unadjusted tests can be explained by their underlying demographies. Upon carrying out whole-genome screens for deviations from neutrality, we identify candidate regions of recent positive selection. We provide track files with values of the adjusted and unadjusted tests for upload to the UCSC genome browser. (C) 2014 Elsevier Inc. All rights reserved.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Rafajlovic, M. UNSPECIFIED UNSPECIFIED UNSPECIFIED Klassmann, A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Eriksson, A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Wiehe, T. UNSPECIFIED orcid.org/0000-0002-8932-2772 UNSPECIFIED Mehlig, B. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-433073
DOI:	10.1016/j.tpb.2014.05.002
Journal or Publication Title:	Theor. Popul. Biol.
Volume:	95
Page Range:	S. 1 - 13
Date:	2014
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 SINGLE-NUCLEOTIDE POLYMORPHISMS; MAXIMUM-LIKELIHOOD-ESTIMATION; FREQUENCY-SPECTRUM; POSITIVE SELECTION; POPULATION PARAMETERS; STATISTICAL TESTS; NATURAL-SELECTION; SEGREGATING SITES; DNA POLYMORPHISM; HISTORY Multiple languages Ecology; Evolutionary Biology; Genetics & Heredity; Mathematical & Computational Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/43307