Ferretti, Luca ORCID: 0000-0001-7578-7301, Ledda, Alice, Wiehe, Thomas, 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:
CreatorsEmailORCIDORCID Put Code
Ferretti, LucaUNSPECIFIEDorcid.org/0000-0001-7578-7301UNSPECIFIED
Ledda, AliceUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wiehe, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Achaz, GuillaumeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ramos-Onsins, Sebastian E.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
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: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
STATISTICAL TESTS; SEGREGATING SITES; POPULATION-SIZE; SELECTION; SEQUENCES; IMBALANCE; HISTORYMultiple languages
Genetics & HeredityMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/22018

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