H12 and <i>iHS</i> scan in DGRP data along the four autosomal arms.

<p>(A) H12 scan. Each data point represents the H12 value calculated over an analysis window of size 400 SNPs centered at the particular genomic position. Grey points indicate regions in the genome with recombination rates lower than 5×10^–7 cM/bp we excluded from our analysis. The orange line represents the 1-per-genome FDR line calculated under a neutral demographic model with a constant population size of 10⁶ and a recombination rate of 5×10^–7 cM/bp. Red and blue points highlight the top 50 H12 peaks in the DGRP data relative to the 1-per-genome FDR line. Red points indicate the peaks that overlap the top 10% of 100Kb windows with an enrichment of SNPs with |iHS| > 2 in B. We identify three well-characterized cases of selection in <i>D</i>. <i>melanogaster</i> at <i>Ace</i>, <i>CHKov1</i>, and <i>Cyp6g1</i> as the three highest peaks. (B) <i>iHS</i> scan. Plotted are the number of SNPs in 100Kb windows with |<i>iHS</i>| > 2. Highlighted in red and blue are the top 10%100Kb windows (a total of 95 windows). Red points correspond to those windows that overlap the top 50 peaks in the H12 scan. The positive controls, <i>Ace</i>, <i>CHKov1</i>, and <i>Cyp6g1</i> are all among the top 10% windows.