Haplotype frequency spectra for the top 10 peaks and extreme outliers under neutral demographic scenarios.

<p>(A) Haplotype frequency spectra for the top 10 peaks in the DGRP scan with H12 values ranging from highest to lowest. For each peak, the frequency spectrum corresponding to the analysis window with the highest H12 value is plotted, which should be the “hardest” part of any given peak. At all peaks there are multiple haplotypes present at high frequency, compatible with signatures of soft sweeps shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005004#pgen.1005004.g005" target="_blank">Fig. 5</a>. None of the cases have a single haplotype present at high frequency, as would be expected for a hard sweep. (B) In contrast, the haplotype frequency spectra corresponding to the extreme outliers under the six neutral demographic scenarios have critical H12_<i>0</i> values that are significantly lower than the H12 values at the top 10 peaks.