Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests

Genetics
Luca FerrettiSebastian Ramos-Onsins

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 θ 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.

References

Apr 1, 1975·Theoretical Population Biology·G A Watterson
Oct 1, 1995·Theoretical Population Biology·Y X Fu
May 17, 2005·Mathematical Biosciences·Michael G B Blum, Olivier François
Sep 15, 2006·Systematic Biology·Michael G B Blum, Olivier François
Aug 22, 2008·Genetics·Daniel Zivković, Thomas Wiehe
Jul 9, 2010·Genetics·Luca FerrettiSebastian Ramos-Onsins
Apr 13, 2011·Molecular Ecology Resources·Simon Y W Ho, Beth Shapiro
May 23, 2013·PLoS Computational Biology·Haipeng Li, Thomas Wiehe
Apr 12, 2014·PLoS Computational Biology·Remco BouckaertAlexei J Drummond
Apr 8, 2015·Nature Genetics·Xiaoming Liu, Yun-Xin Fu
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Jan 1, 1984·Evolution; International Journal of Organic Evolution·Joseph Felsenstein

Citations

Oct 2, 2018·Genes & Genetic Systems·Naoko T FujitoNaoyuki Takahata
Jul 23, 2019·Theoretical Population Biology·Johannes Wirtz, Thomas Wiehe
Nov 4, 2020·Proceedings of the National Academy of Sciences of the United States of America·Jaehee KimJulia A Palacios

Related Concepts

Phylogeny
Selection, Genetic
Anatomy, Regional
Equilibrium
Neutralization Tests
Trees (plant)
Site
Shapes
Size
Structure

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