Journal
GENETICS
Volume 187, Issue 1, Pages 229-244Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.110.122614
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Funding
- Shanghai Pujiang Program [08PJ14104]
- Bairen Program
- Fonds zur Forderung der wissenschaftlichen Forschung
- Wiener-, Wissenschafts-, Forschungs- und Technologiefonds
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The summary statistics are widely used in population genetics, but they suffer from the drawback that no simple sufficient summary statistic exists, which captures all information required to distinguish different evolutionary hypotheses. Here, we apply boosting, a recent statistical method that combines simple classification rules to maximize their joint predictive performance. We show that our implementation of boosting has a high power to detect selective sweeps. Demographic events, such as bottlenecks, do not result in a large excess of false positives. A comparison to other neutrality tests shows that our boosting implementation performs well compared to other neutrality tests. Furthermore, we evaluated the relative contribution of different summary statistics to the identification of selection and found that for recent sweeps integrated haplotype homozygosity is very informative whereas older sweeps are better detected by Tajima's pi. Overall, Watterson's theta was found to contribute the most information for distinguishing between bottlenecks and selection.
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