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.
%0 Journal Article
%1 achaz2009frequency
%A Achaz, Guillaume
%D 2009
%I Genetics Society of America
%J Genetics
%K coalescent_theory population_genetics site_frequency_spectrum test_for_neutrality
%N 1
%P 249--258
%R 10.1534/genetics.109.104042
%T Frequency Spectrum Neutrality Tests: One for All and All for One
%U https://doi.org/10.1534%2Fgenetics.109.104042
%V 183
%X 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.
@article{achaz2009frequency,
abstract = {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.},
added-at = {2019-09-20T19:56:10.000+0200},
author = {Achaz, Guillaume},
biburl = {https://www.bibsonomy.org/bibtex/2ba4d09b89b6f7f7d92d9c8b6d1d97f87/peter.ralph},
doi = {10.1534/genetics.109.104042},
interhash = {5cae9f3148f5286b928f5344abfe2320},
intrahash = {ba4d09b89b6f7f7d92d9c8b6d1d97f87},
journal = {Genetics},
keywords = {coalescent_theory population_genetics site_frequency_spectrum test_for_neutrality},
month = jun,
number = 1,
pages = {249--258},
publisher = {Genetics Society of America},
timestamp = {2019-09-20T19:56:10.000+0200},
title = {Frequency Spectrum Neutrality Tests: {One} for All and All for One},
url = {https://doi.org/10.1534%2Fgenetics.109.104042},
volume = 183,
year = 2009
}