D. melanogaster well after the split from D. simulans [29]. Using D. simulans RanGAP as an outgroup sequence, we polarized the substitutions between D. melanogaster RanGAP and Sd-RanGAP. Of five fixed differences between RanGAP and Sd-RanGAP, all were fixed in the common ancestor of the Sd-RanGAP sequences: three noncoding changes, one fixed 6-bp deletion, and a single nonsynonymous change (Figure 2). The first intron of RanGAP contains the gene, Hs2st, raising the possibility that some ‘‘silent’’ changes in one gene are not silent in the other. However, of the five fixed substitutions occurring in Sd-RanGAP, only four affect Hs2st: two are noncoding and two are synonymous. DNA Sequence Variation at RanGAP and Sd-RanGAP The amount and distribution of DNA sequence variability at RanGAP is not unusual for an autosomal locus sampled from African populations of D. melanogaster. First, among the 10 wildtype RanGAP sequences, we detect 29 segregating sites (Figure 2), with two measures of DNA sequence polymorphism per site, p = 0.0020 and h = 0.0023. These values show that RanGAP harbors less variability than the average autosomal locus in African populations (p = 0.0104 and h = 0.0114; ref. [27]), but this is not unexpected as RanGAP resides in a centromere-proximal region (37E) with a relatively low rate of crossing over and is thus especially susceptible to background selection and hitchhiking effects [42,43]. Three polymorphisms are synonymous, two are nonsynonymous, and 23 are noncoding, with 66% falling in the large first intron (3.2 kb). The site frequency spectrum at RanGAP does not deviate significantly from standard neutral expectations (Tajima’s D = 20.606, P = 0.297; Fay and Wu’s H = 24.711, P = 0.127 [44,45]), where significance was evaluated from 10,000 coalescent simulations conditioning on the observed h and assuming no recombination). The moderately negative Tajima’s D is consistent with recent expansion in the African D. melanogaster populations as inferred from other autosomal loci [27]. Sd-RanGAP is less variable than RanGAP: among the 12 Sd- RanGAP sequences, we detect only five segregating sites (Figure 2), with p = 0.0003 and h = 0.0004, and a site frequency spectrum Segregation Distorter Causes Sweep skewed towards a moderate excess of rare variants, although not significantly (Tajima’s D = 20.313, P = 0.395; Fay and Wu’s H = 20.242, P = 0.250). Of the five polymorphisms, two are synonymous and three are noncoding. The lower variability at Sd- RanGAP relative to RanGAP is, of course, expected as Sd-RanGAP is present on only ,2% of second chromosomes. There are no shared polymorphisms between RanGAP and Sd-RanGAP and hence no evidence for recent gene conversion due to ectopic recombination [46]. The lack of recombination between the two loci implies that Sd-RanGAP evolves as an isolated subpopulation of sequences with a distinct genealogical history. Unusual Haplotype Structure at Sd-RanGAP We found six haplotypes among the ten wildtype RanGAP sequences, with levels of linkage disequilibrium (LD) typical of an autosomal locus in Africa (ZnS = 0.247; [27,47]). In contrast, the spatial distribution of polymorphic sites in the 4.5-kb Sd-RanGAP sequences is unusual: mutations at five segregating sites are in perfect linkage disequilibrium (ZnS = 1.0), forming just two haplotypes (K = 2). The major haplotype occurs ten times in the sample (M = 10) and the minor haplotype twice. We used coalescent-based haplotype configuration tests to estimate the probability of observing such unusual haplotype structure under standard neutral model assumptions [48]. We performed 100,000 coalescent simulations without recombination (a conservative assumption), assuming a sample size of n = 12 and five segregating sites (S = 5). The cumulative probability that the observed haplotype configuration, or one more extreme, occurs by chance is P = 0.0378. Two features of the haplotype configuration, in particular, differ significantly from the expec- tations of a neutral genealogical process: the major haplotype is too common in the sample, P(M$10|n = 12, S = 5) = 0.0313; and there are too few kinds of haplotypes, P(K#2|n = 12, S = 5) = 0.0285. Both features of the data are consistent with an incomplete selective sweep in which the major haplotype has quickly and recently risen to high frequency, but not fixation, among SD chromosomes [49]. Figure 2. Variation in 12 Sd-RanGAP and 10 RanGAP sequences from African populations of D. melanogaster. Sd-RanGAP and RanGAP show four nucleotide differences and one indel difference. (N = nonsynonymous; S = synonymous; all other changes are noncoding.) doi:10.1371/journal.pgen.1000463.g002 PLoS Genetics | www.plosgenetics.org 4 May 2009 | Volume 5 | Issue 5 | e1000463