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Comparisons of site- and haplotype-frequency methods for detecting positive selection
Kai Zeng1, Shuhei Mano, Suhua Shi
1State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, China. kzeng@uchicago.edu
Molecular Biology and Evolution
|April 24, 2007
Summary
This study compares statistical tests for detecting positive selection in DNA. The Ewens-Watterson (EW) test is powerful for recombining DNA, while other tests can be unreliable under recombination or demographic changes.
Area of Science:
- Population Genetics
- Molecular Evolution
- Bioinformatics
Background:
- Detecting positive selection is crucial for understanding adaptation.
- Various statistical tests exist, but their performance varies under different evolutionary scenarios.
Purpose of the Study:
- To compare the power of different site- and haplotype-frequency tests in detecting positive selection.
- To evaluate the sensitivity of these tests to recombination, background selection, and demographic forces.
Main Methods:
- Computer simulations were used to compare the power of various statistical tests.
- The study analyzed tests conditional on haplotype number (K) and segregating sites (S).
Main Results:
- Haplotype-frequency tests (like Ewens-Watterson) are suitable for recombining DNA.
- Tests conditional on segregating sites become conservative with recombination.
- The Ewens-Watterson test is powerful during selection sweeps, especially with high recombination.
- Extended haplotype homozygosity test requires prior knowledge of the selected target for high power.
Conclusions:
- The Ewens-Watterson test is a robust option for detecting positive selection in recombining populations.
- Tests can be sensitive to factors other than positive selection, necessitating careful interpretation.
- Compound tests may improve specificity and power in detecting positive selection.
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