Universität zu Köln

Ferretti, Luca ORCID: 0000-0001-7578-7301, Ledda, Alice, Wiehe, Thomas ORCID: 0000-0002-8932-2772, Achaz, Guillaume and Ramos-Onsins, Sebastian E. (2017). Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests. Genetics, 207 (1). S. 229 - 241. BETHESDA: GENETICS SOCIETY AMERICA. ISSN 1943-2631

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Abstract

We investigate the dependence of the site frequency spectrum on the topological structure of genealogical trees. We show that basic population genetic statistics, for instance, estimators of theta or neutrality tests such as Tajima's D, can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima's D and Fay and Wu's H depend in a direct way on a peculiar measure of tree balance, which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu's H and discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulas for these extreme values as a function of sample size and number of segregating sites.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Ferretti, Luca UNSPECIFIED orcid.org/0000-0001-7578-7301 UNSPECIFIED Ledda, Alice UNSPECIFIED UNSPECIFIED UNSPECIFIED Wiehe, Thomas UNSPECIFIED orcid.org/0000-0002-8932-2772 UNSPECIFIED Achaz, Guillaume UNSPECIFIED UNSPECIFIED UNSPECIFIED Ramos-Onsins, Sebastian E. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-220182
DOI:	10.1534/genetics.116.188763
Journal or Publication Title:	Genetics
Volume:	207
Number:	1
Page Range:	S. 229 - 241
Date:	2017
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; SEGREGATING SITES; POPULATION-SIZE; SELECTION; SEQUENCES; IMBALANCE; HISTORY Multiple languages Genetics & Heredity Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/22018