SD-GN09 SD-KM87 SD-KM92 SD-KN20 SD-KY38 SD-KY91 SD-MD21 SD-NK04 SD-ZK178 SD-ZK216 SD-BN19 SD-MD31 Table 6. Complemenation tests for all SDi/SDj combinations. SD-GN09 SD-KM87 SD-KM92 SD-KN20 SD-KY38 SD-KY91 SD-MD21 SD-NK04 SD-ZK178 SD-ZK216 SD-BN19 SD-MD31 FF FF FF FF FF FF FF FF FF FF FF Lethal MF Lethal FF FF FF FF FF FF FF FF FF FF MF MF Lethal FF FF FF FF FF FF FF FF FF MF MS MF Lethal FF FF FF FF FF FF FF FF MF MF MF MS Lethal FF FF FF FF FF FF FF Lethal MF MF MF MF MF FF FF FF FF FF FF MF MF MF MS MF MF FF FF FF FF FF Lethal MF MF MF MS MF MF MS FF FF FF FF Lethal MF MF MS MF MS MS MS MF FF FF FF Lethal MF MF MF MF MF MF MF MF FF FF MS Lethal Above the diagonal, MS = male sterile and MF = male fertile; below the diagonal FF = female fertile. doi:10.1371/journal.pgen.1000463.t006 Segregation Distorter Causes Sweep MF MF MF MF MF MF MF MF MF MF MF MF MF MF MF MF MF MF MF MF FF Viable, MF, FF MF Viable, MF, FF at a frequency similar to that of other populations worldwide. This discovery raises doubts about the Mediterranean-origins hypoth- esis. Second, the evolution and rapid spread of a newer, stronger SD chromosome has left a dramatic population genetic signature: a remarkably long haplotype, spanning more than 39% of chromosome 2—roughly 30 cM—that is both free of polymor- phisms (Table 3, Figure 3) and differentiated from other chromosomes in the population (Table 4). These findings suggest that a new SD chromosome type endemic to Africa, SD-Mal, has swept across the continent sometime within the last few thousand years. SD in Africa The Mediterranean-origins hypothesis is based on the geo- graphic distribution of inversions on SD chromosomes: inversion- bearing SD chromosomes occur throughout the world; but both inversion-bearing and inversion-free, presumably ancestral, SD chromosomes occur in Spain and Italy [3,4]. The presence of ancestral SD chromosomes suggests that the complex may have arisen in Spain or Italy or nearby. Our discovery of SD chromosomes in African populations of D. melanogaster raises questions about the Mediterranean-origins hypothesis. Did SD originate in the Mediterranean and subsequently invade sub- Saharan Africa via back-migration? Or did SD originate in Africa and then make its way to Europe (and the rest of the world) as part of the D. melanogaster out-of-Africa event, ,15,000 years ago [25– 28]? The presence of inversion-free SD chromosomes in Benin and Cameroon (SD-BN19 and SD-MD31, respectively) would seem to make a sub-Saharan African origin as likely as a Mediterranean one. In either case, the fact that inversion-free SD chromosomes occur in both Africa and the Mediterranean suggests that Sd- RanGAP dispersed from one location to the other shortly after it originated and then subsequently acquired different inversions on different continents. The relative youth of the Sd-RanGAP duplication makes distinguishing between sub-Saharan African and Mediterranean origins with the present data difficult. We cannot, for instance, precisely date the origin of Sd-RanGAP from RanGAP based on the five fixed differences (1 indel, 4 nucleotide changes) by assuming a simple neutral molecular clock for two reasons. First, we cannot exclude the rapid, non-neutral fixation of changes in Sd-RanGAP. Second, some (or all) of the five fixed differences may have been segregating as the ancestral RanGAP sequence that ultimately gave rise to Sd-RanGAP. This putative ancestral RanGAP haplotype may be missing from our population sample by chance, or because it was lost from the population, or because it does not occur in African populations. Determining the time and place of origin for the SD system will therefore require deeper resequencing of Sd- RanGAP and RanGAP from both Europe and Africa. Evolutionary Turnover of SD Chromosomes The population genetic analyses revealed six striking patterns among SD chromosomes (Table 3; Figure 3): significant excesses of rare variants; significant excesses of high frequency derived variants; an unusual distribution of haplotype frequencies (10+2 or 10+1+1; Figure 3); exceedingly long-range LD; a complete absence of polymorphism in .8.1 kb spanning .39% of the length of SD-Mal chromosomes; and significant population genetic differentiation between SD-Mal and other chromosomes (Table 4). Together these observations suggest that SD-Mal has spread to high frequency among SD chromosomes in Africa sometime within the last 3,000 years. Why might one type of SD chromosome rise in frequency so quickly, apparently displacing other SD chromosomes? The answer seems straightforward: SD- Mal chromosomes distort more than SD-BN19 and SD-MD31 and recombine less over the length of 2R, perhaps preserving a favorable distortion-enhancing combination of alleles in the In(2R)Mal region. Similar displacement of one SD type (SD-5) by another (SD-72) appears to have occurred during a 30-year period in populations in Wisconsin [31]. Thus, the apparently stable equilibrium frequency of SD chromosomes in D. melanogaster populations worldwide (1–5%) appears to mask a dynamic turnover among competing SD chromosome types. There are at least two, non-exclusive explanations for the turnover of SD chromosomes. First, the SD system may be sufficiently new that it has not yet reached a stable evolutionary equilibrium: older Sd-RanGAP bearing chromosomes are still being displaced by new ones, like SD-Mal in Africa or SD-72 in North America [31], as predicted by theory [15]. Second, an ultimately stable evolutionary equilibrium for SD chromosomes may not exist: SD may be engaged in a perpetual coevolutionary conflict with the rest of the genome [17]. Indeed, there is considerable PLoS Genetics | www.plosgenetics.org 9 May 2009 | Volume 5 | Issue 5 | e1000463