Results
Hierarchical clustering of 206 Ag1000g haplotypes from An. gambiae s.s. from Uganda resulted in identification of a cluster of 122 haplotypes around the Cyp6aa /Cyp6p gene cluster, putatively representing a swept haplotype in this region. To characterise the signatures of selection in Ugandan haplotypes around this cluster, we examined the profile of extended haplotype homozygosity around the position of the Cyp6p4-236M SNP and around the CNV inCyp6aa1 . In both cases, we found that the putative swept haplotype had longer stretches of homozygosity than wild-type haplotypes (Figure 2). In addition, we found that An. gambiae s.s. from Uganda had reduced haplotypic diversity along the entireCyp6aa/Cyp6p gene cluster (h = 0.339746 +/- 0.005664 standard error) and a combination of Garud’s H statistics that was indicative of a hard selective sweep in this region (highH12 = 0.821867 +/- 0.006308 SE; lowH2/H1 = 0.016779 +/- 0.000228 SE)[28]. These results confirm that the haplotypes we have identified have undergone a selective sweep. We then used iterative read mapping of individuals homozygous for the sweep to search for additional mutations that might be distinctive of the haplotype. This revealed that a partial copy of a Ty3/Gypsy Zanzibar transposon insertion (termed ZZB-TE), lacking functional open reading frames, was linked to Cyp6p4-236M and Cyp6aap-Dup1 (Figure 2).