Segregation Distorter Causes Sweep Table 5. Strength of segregation distortion for African SD chromosomes. Chromosome Male transmission Female transmission SD-GN09 SD-KM87 SD-KM92 SD-KN20 SD-KY38 SD-KY91 SD-MD21 SD-NK04 SD-ZK178 SD-ZK216 SD-BN19 SD-MD31 cn bw OreR km 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 0.569 0.531 0.602 0.654 6s.e. 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.025 0.012 0.030 0.024 km* 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 0.538 0.415 0.504 0.558 6s.e. 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.025 0.012 0.033 0.026 682 1124 1092 1072 837 1544 997 1167 842 1307 1179 1531 580 912 Total progeny Total progeny kf 0.539 0.561 0.616 0.595 0.519 0.579 0.486 0.525 0.533 0.555 0.613 0.621 0.615 0.615 6s.e. 0.021 0.037 0.087 0.024 0.046 0.064 0.05 0.037 0.023 0.034 0.074 0.035 0.036 0.013 487 431 799 1020 664 230 752 457 967 813 561 1167 912 876 km and kf = proportion of progeny inheriting SD when transmitted by males and females, respectively. km* = viability-corrected estimate of proportion of progeny inheriting SD transmitted by males. doi:10.1371/journal.pgen.1000463.t005 haplotypes is star-shaped, as expected for a selective sweep, and then estimated the time back to their most recent common ancestor [52]. The expected number of segregating sites in such a sample is E(S) = ntu, where n = number of lineages, t = time in the past when the lineages coalesce into a single common ancestor, and u = the total mutation rate of the sequenced regions. Assuming that the number of mutations on the ten lineages is Poisson distributed, we numerically solved for the probability of observing zero polymor- phisms, P(S = 0) = e2ntu, for different times to the common ancestor, t. We used two different estimates of the sequence-specific mutation rate. First, we estimated the mutation rate per generation from h, which equals 4Neu under standard neutral assumptions, estimated from the wildtype sequences and assuming that Ne = 106 for D. melanogaster. Second, we estimated the mutation rate per year based on the number of fixed differences between D. melanogaster and D. simulans, assuming a divergence time of 3 Mya [53]. The two mutation rates yield qualitatively similar limits for the age of the sweep. Using the polymorphism-based estimate of u, the 95% upper confidence limit for the age of the sweep is 1,875 years. Using the divergence-based estimate of u, the 95% upper confidence limit for the age of the sweep is 3,360 years. Both estimates suggest that the major SD-Mal haplotype expanded across Africa very recently, within the last few thousand years. Accumulation of Linked Lethal Mutations We performed complementation tests among all pairwise combinations of the 12 SD chromosomes, producing 12 SDi/SDi and 66 SDi/SDj genotypes. Both minor SD chromosomes (SD- BN19 and SD-MD31) are homozygous viable, but all ten SD-Mal chromosomes are homozygous lethal (Table 6). Crosses among SD-Mal chromosomes, however, show that all ten fall into unique complementation groups—none of the lethal mutations is shared among major SD-Mal chromosomes (Table 6). This distribution of lethal mutations supports a star-shaped genealogy: all of the lethal mutations must have arisen on the external branches of the genealogical history of the SD-Mal chromosomes in our sample. These complementation data also reveal that lethal mutations are significantly over-represented on SD-Mal chromosomes relative to wildtype chromosomes: 29% of wildtype second chromosomes are lethal or semi-lethal [54] versus 100% of SD-Mal chromosomes (Fisher’s exact P = 0.0015). The large In(2R)Mal rearrangement on SD-Mal chromosomes provides a large non-recombining target for lethal mutations that can persist by hitchhiking with the SD system. Fertility in SDi/SDj Flies For the 66 viable SDi/SDj and 2 viable SDi/SDi genotypes, we tested the fertility of both sexes. None of the 68 genotypes were female-sterile, but 10 were male-sterile (Table 6). SD-ZK178 is male-sterile in combination with five other SD chromosomes; SD- KN20 is male sterile in combination with four others; and SD-NK04 is male-sterile in combination with SD-ZK216. The patterns of complementation for male fertility are complex. For instance, SD- KY38 and SD-MD21 complement one another and yet both fail to complement SD-ZK178. Similarly, SD-ZK178 and SD-NK04 complement one another and yet both fail to complement SD- ZK216. Assuming that male sterility results from male-sterile mutations on chromosome 2, the data in Table 6 require a circular complementation map with at least 10 unique lesions. A more plausible hypothesis, however, is that male sterility results not from linked male-sterile mutations but from interactions among different alleles at SD complex loci [32,55]. Indeed, previous work has shown that deletion of one copy of Sd rescues sterility in otherwise male-sterile SDi/SDj combinations, supporting a con- nection between distortion and sterility [55]. The complex patterns of fertility complementation in SDi/SDj males cannot, however, be explained by intragenic complementation at the Sd locus, as the Sd-RanGAP sequences among SD-Mal chromosomes are identical, suggesting that interactions involving other SD loci must be involved. Discussion Two major findings emerge from our analysis of the SD system. First, SD occurs in ancestral, African populations of D. melanogaster PLoS Genetics | www.plosgenetics.org 8 May 2009 | Volume 5 | Issue 5 | e1000463