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doi:10.1534/genetics.109.104042
A more recent version of this article appeared on September 1, 2009.
REGULAR RESEARCH PAPERS |
Frequency Spectrum Neutrality Tests, One for All and All for One
Guillaume Achaz 1*
1 Université Pierre et Marie Curie
* To whom correspondence should be addressed. E-mail: achaz{at}abi.snv.jussieu.fr.
Submitted on April 16, 2009
Accepted on 12 June 2009
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 likeliness of the standard neutral model on their dataset. 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 usefullness 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 and ultimately help to unravel scenarios of evolution.
Key Words: Coalescent Theory, Neutrality tests, Population Genetics, Tajima D
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