Universität zu Köln

Yang, Zongfeng, Li, Junrui, Wiehe, Thomas ORCID: 0000-0002-8932-2772 and Li, Haipeng (2018). Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree. Genetics, 208 (2). S. 791 - 806. BETHESDA: GENETICS SOCIETY AMERICA. ISSN 1943-2631

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Abstract

Many population genomic studies have been conducted in the past to search for traces of recent events of positive selection. These traces, however, can be obscured by temporal variation of population size or other demographic factors. To reduce the confounding impact of demography, the coalescent tree topology has been used as an additional source of information for detecting recent positive selection in a population or a species. Based on the branching pattern at the root, we partition the hypothetical coalescent tree, inferred from a sequence sample, into two subtrees. The reasoning is that positive selection could impose a strong impact on branch length in one of the two subtrees while demography has the same effect on average on both subtrees. Thus, positive selection should be detectable by comparing statistics calculated for the two subtrees. Simulations demonstrate that the proposed test based on these principles has high power to detect recent positive selection even when DNA polymorphism data from only one locus is available, and that it is robust to the confounding effect of demography. One feature is that all components in the summary statistics (Du) can be computed analytically. Moreover, misinference of derived and ancestral alleles is seen to have only a limited effect on the test, and it therefore avoids a notorious problem when searching for traces of recent positive selection.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Yang, Zongfeng UNSPECIFIED UNSPECIFIED UNSPECIFIED Li, Junrui UNSPECIFIED UNSPECIFIED UNSPECIFIED Wiehe, Thomas UNSPECIFIED orcid.org/0000-0002-8932-2772 UNSPECIFIED Li, Haipeng UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-198126
DOI:	10.1534/genetics.117.300401
Journal or Publication Title:	Genetics
Volume:	208
Number:	2
Page Range:	S. 791 - 806
Date:	2018
Publisher:	GENETICS SOCIETY AMERICA
Place of Publication:	BETHESDA
ISSN:	1943-2631
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 STATISTICAL TESTS; NATURAL-SELECTION; NEUTRALITY TESTS; POPULATION-SIZE; SPURIOUS SIGNATURES; GENOMIC SCANS; HITCHHIKING; DEMOGRAPHY; SWEEPS; RECOMBINATION Multiple languages Genetics & Heredity Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/19812