variation among populations in the frequency of insensitive Rspi alleles [30,31] and other unlinked genetic variants that affect distortion (e.g., [24,34]). Under this scenario, the rise of SD-Mal and decline of SD-BN19 and SD-MD31 could reflect a transitional phase in the genetic conflict in Africa: SD-BN19 and SD-MD31 may no longer cause distortion because they have come under the effective control of unlinked suppressors in the genome, whereas adaptive changes specific to SD-Mal chromosomes allow them to escape suppression. The discovery of two Sd-RanGAP bearing chromosomes that fail to cause distortion is surprising—indeed, classical phenotypic screens for segregation distortion undoubtedly would have misclassified SD-BN19 and SD-MD31 as wildtype chromosomes. While these chromosomes may now be suppressed, there are four other possibilities. One is that SD-BN19 and SD-MD31 have experienced mutations causing a loss of distortion. Mutational disruption of the Sd-RanGAP sequence seems unlikely, however, as all five differences that distinguish SD-BN19 and SD-MD31 from SD-Mal are silent. A second possibility is that recombination has stripped SD-BN19 and SD-MD31 chromosomes of essential modifiers required for distortion. Wildtype chromosomes that carry Sd-RanGAP transgenes but lack upward modifiers cause either very weak or even no distortion [37]. However, both of these scenarios—disruption by mutation or recombination— require that we explain the seemingly improbable coincidental loss of distortion by two identical, and relatively rare, Sd-RanGAP haplotypes. A third possibility is that SD-BN19 and SD-MD31 are not ‘‘SD chromosomes’’ but rather ancestral Sd-RanGAP-bearing chromosomes that never caused drive. This scenario would imply that SD chromosomes evolved from a neutral, non-driving ancestral haplotype: Sd-RanGAP arose as new duplication, drifted to sufficiently high frequency to become established via migration in Europe and in Africa, and then subsequently recruited genetic modifiers that conferred distortion. This history, if true, implies that African and non-African SD chromosomes independently acquired convergent distorting gene complexes. A final possibility is that SD-BN19 and SD-MD31 may cause distortion but not in the particular genetic backgrounds used in our assay. Further genetic analyses are required to distinguish these possibilities. Epistatic Selection Shapes Variation on SD-Mal Chromosomes The long SD-Mal haplotype spans Sd-RanGAP, region 43E (locus J), and the In(2R)Mal inversions (K, E, F, and G; Figure 3) but does not extend distal to Sd-RanGAP on 2L or distal to In(2R)Mal on 2R. The structure of the SD-Mal haplotype probably reflects the hitchhiking effects of epistatic selection. First, consistent with the lack of loci known to affect distortion distal to Sd-RanGAP, SD and SD+ chromosomes are free to recombine without consequence on the distal part of 2L, preventing LD there [4,29]. Second, although In(2R)Mal suppresses recombination within the inverted regions, there is opportunity for crossing over in the interval between the SD complex loci (Sd, E(SD), and Rsp) and the proximal breakpoint of the In(2R)Mal. The perfect LD across this interval suggests that strong epistatic selection maintains the association between the SD loci and the In(2R)Mal inversions. In principle, double-recombi- nants in the interval between centromeric SD loci and In(2R)Mal could preserve their association, but these may be rare events relative to the strength of epistatic selection favoring SD-Mal. Thus, positive epistatic selection on the SD-In(2R)Mal genotype may have caused hitchhiking effects to dominate the intervening sequence between them, explaining the skewed frequency spectrum, LD and lack of variability on SD-Mal chromosomes in region 43E (locus J). It is also possible that epistatic selection Segregation Distorter Causes Sweep directly preserves an association with a M(SD) allele in the SD- In(2R)Mal interval [20], but we do not yet know if SD-Mal carries M(SD). Third, inversions on 2R have been interpreted as tightening the association between SD and St(SD), a modifier (or region of polygenic modifiers; ref. [56]) that increases the strength of distortion, putatively located near the tip of 2R [21,22]. The fact that we fail to detect LD between SD and loci in cytological regions 58–59 (H and I; Figure 3) suggests that either no St(SD) loci reside in (or distal to) regions 58–59 as previously reported [22] or that no such St(SD) loci enhance distortion on SD-Mal chromo- somes. It is important to note that St(SD), like M(SD), was characterized from non-African SD chromosomes; African SD chromosomes may carry a distinct set of linked modifiers. Explaining the Global SD Equilibrium Although there appears to be competition among SD chromo- somes, the overall frequency of SD in populations throughout the world is remarkably similar (1–5%; but see ref. [24]). Considering that different populations have experienced different environ- ments, genetic backgrounds, and demographic histories, the seemingly stable frequency of SD suggests that its equilibrium is the result of strong deterministic forces. What prevents SD from reaching higher frequencies or even fixation? Three factors limit the spread of SD. First, as SD frequency increases, so does selection for insensitive Rspi alleles and other genetic suppressors. Second, as SD frequency increases, intrinsically male-sterile SDi/SDj geno- types become more common, placing an upper-limit on the spread of SD (Table 6; ref. [32]). Third, SD/SD+ males have been shown to suffer reduced male fertility, as might be expected when 50% of sperm are destroyed [9]. Finally, many SD chromosomes worldwide, including the new SD-Mal chromosomes, carry linked recessive lethal and other deleterious mutations (Table 6). The large non-recombining, inverted blocks of chromosome that become associated with SD present a large mutational target. Without recombination, linked recessive lethal and other delete- rious mutations are able to persist by hitchhiking with SD. It remains unclear if these factors are sufficient to explain the distortion-selection balance that causes the frequency of SD to settle at 1–5% in D. melanogaster populations worldwide. Conclusions The hitchhiking effects of selfish meiotic drive gene complexes have shaped patterns of DNA sequence variability in at least five other cases: four selfish X chromosome systems (one in Drosophila pseudoobscura [57], two in Drosophila simulans [58,59], and one in Drosophila recens [60]) that drive in the male germline and a selfish autosomal centromere that drives in the female germline of the monkeyflower, Mimulus guttatus [61]. Like SD, all five of these drive systems are associated with haplotypes of reduced variability and three show long-range LD—the signatures of partial selective sweeps. Notably, all five are balanced polymorphisms in which the drive elements are prevented from going to fixation by modifiers or countervailing selection. It is important to note that these well characterized drive systems may not be representative, as there is a clear detection bias: to be discovered and characterized, drive systems must be conspicuous (e.g., causing strong drive or distorting sex ratios) and segregate within populations (i.e., balanced) [7]. But what about those drive elements that are not balanced and thus able to spread to fixation? These would also invade when concentrated in the centromeric regions of autosomes or on sex chromosomes (little or no crossing over occurs between the X and Y) and then sweep through populations, causing complete rather than partial selective sweeps. The extent to which hitchhiking effects of selfish meiotic drive systems contribute to PLoS Genetics | www.plosgenetics.org 10 May 2009 | Volume 5 | Issue 5 | e1000463