Large-Scale Selective Sweep among African SD Chromosomes If the major African SD haplotype has indeed risen to high frequency due to positive selection or superior segregation distortion, then the haplotype structure may extend beyond the Sd-RanGAP region. To test this possibility, we sequenced eight noncoding regions across chromosome 2 from all 12 African SD chromosomes and from 10 wildtype chromosomes (Figure 3; Table 3). The amount and distribution of DNA sequence variation among wildtype chromosomes was typical for African D. melanogaster populations [27], with h ranging from 0.0053 to 0.0137 and Tajima’s D ranging from 21.630 to 0.445 (P = 0.045 for locus G, but $0.05 for other loci; Table 3). In addition, there is ample evidence for recombination in all but one of the loci (region E has an unusual lack of variability and a small number of haplotypes, though not significantly so; Table 3; Figure 3). The distribution of variation among SD chromosomes differs strikingly from wildtype chromosomes in two ways. First, the frequency spectra at several loci show patterns consistent with a recent selective sweep. Of the eight noncoding regions surveyed, three loci (J, K, and F) show significant excesses of rare variants (Tajima’s D; Table 3), four contiguous loci (J, K, E and F) show significant excesses of high-frequency derived variants (Fay and Wu’s H; Table 3), and a fifth contiguous locus (G) possesses no variability at all. The three loci whose frequency spectra do not deviate from neutral expectations include the most distal locus on 2L (M at 37B) and the two most distal loci on 2R (H and I at 58E and 59E, respectively). Second, and more striking, the haplotype structure seen at Sd-RanGAP extends across most of chromosome arm 2R: the 10 major Sd-RanGAP chromosomes possess a single identical haplotype that extends from cytological region 37E on 2L (Sd-RanGAP) to region 55B on 2R (locus G; Table 3; Figure 3). The long distance LD does not extend to the most distal locus on 2L Segregation Distorter Causes Sweep (locus M) or the two most distal loci on 2R (H and I; Table 3; Figure 3). Among all 12 SD chromosomes, forty-five segregating sites occur at Sd-RanGAP and the six regions extending to cytological subdivision 55B. Remarkably, all are differences between the major and minor SD chromosomes (17) or between the two minor SD chromosomes (28). The 10 major SD haplotypes are identical—there is not a single polymorphism in .8.1 kb of sequence. A haplotype configuration test assuming n = 12, S = 45, and no recombination confirms that this haplotype configuration (M = 10, K = 3) is highly unusual under a standard neutral genealogical process (P = 0.00002): the major haplotype is too common in the sample (P[M$10|n = 12, S = 45]#0.00001) and there are too few kinds of haplotypes (P[K#3|n = 12, S = 34] = 0.00002). The chromosomal region between Sd-RanGAP and region 55B (G) spans $14 Mb and ,30 cM, comprising more than 39% of the euchromatic length of chromosome 2. Taken together, the significantly skewed frequency spectra and the existence of an extraordinarily long, high-frequency, mutation-free haplotype suggest a large-scale selective sweep in progress among SD chromosomes [49]. The Major SD Haplotype Recombines Less and Distorts More The magnitude of a selective sweep is determined by two key parameters: the local rate of recombination and the strength of selection driving the major haplotype to high frequency. The SD chromosomes carrying the major haplotype are unique in both respects. First, recombination is suppressed along much of the major SD haplotype. We cytogenetically characterized the 12 African SD chromosomes by crossing SD/SD or SD/CyO males to virgin cn bw females (which are homozygous for standard- arrangement second chromosomes) and examined polytene chromosome squashes from larval salivary glands. None of the Figure 3. Distribution of DNA sequence variation at Sd-RanGAP and eight non-coding regions in Africa. Sequences were sampled from 12 SD and 10 wildtype second chromosomes from African populations of D. melanogaster. The positions of the two overlapping inversions, In(2R)Mal, and the sequenced loci are shown on chromosome 2 (only part of 2L is shown). Sequence variants are arbitrarily coded: gray matches SD-GN09, white does not. The red box highlights the long, mutation-free haplotype that spans from Sd-RanGAP on 2L to locus G (55B) on 2R. doi:10.1371/journal.pgen.1000463.g003 PLoS Genetics | www.plosgenetics.org 5 May 2009 | Volume 5 | Issue 5 | e1000463