Originally published as Genetics Published Articles Ahead of Print on June 22, 2009.

Genetics, Vol. 183, 249-258, September 2009, Copyright © 2009
doi:10.1534/genetics.109.104042

Frequency Spectrum Neutrality Tests: One for All and All for One

Guillaume Achaz1

Systématique, Adaptation et Evolution (UMR 7138) and Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris VI, Centre National de la Recherche Scientifique, Museum National d'Histoire Naturelle, Institut de Recherche pour le Développment, 75005 Paris, France

1 Address for correspondence: Atelier de Bioinformatique, Université Pierre et Marie Curie, 4 Place Jussieu, Boîte Courrier 1202, 75005 Paris, France.
E-mail: achaz{at}abi.snv.jussieu.fr

Neutrality tests based on the frequency spectrum (e.g., Tajima's D or Fu and Li's F) are commonly used by population geneticists as routine tests to assess the goodness-of-fit of the standard neutral model on their data sets. Here, I show that these neutrality tests are specific instances of a general model that encompasses them all. I illustrate how this general framework can be taken advantage of to devise new more powerful tests that better detect deviations from the standard model. Finally, I exemplify the usefulness of the framework on SNP data by showing how it supports the selection hypothesis in the lactase human gene by overcoming the ascertainment bias. The framework presented here paves the way for constructing novel tests optimized for specific violations of the standard model that ultimately will help to unravel scenarios of evolution.


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Genetics 2009 183: NP. [Full Text]