Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics.
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 π. Overall, Watterson's was found to contribute the most information for distinguishing between bottlenecks and selection.
CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Kao
K
Lin
Haipeng
H
Li
Christian
C
Schlötterer
Andreas
A
Futschik
D000465:Algorithms; D001499:Bayes Theorem; D019143:Evolution, Molecular; D023281:Genomics; D006801:Humans; D012641:Selection, Genetic; D013223:Statistics as Topic / Q000379:methods*