Segregation Distorter Causes Sweep Table 3. Summary of molecular population genetic analyses at Sd-RanGAP and eight non-coding regions on chromosome 2. locus M SD J K E F G H I gene tup Sd-RanGAP CG30497 Myd88 off-track scab staufen plexus CG34372 region p_IGR gene intron d_IGR p_IGR p_IGR p_IGR intron d_IGR cytol. location 37B 37E 43E 45C 48D6 51E 55B 58E 59E Wildtype (non-SD) n 10 - 10 10 10 10 10 10 8 L 707 - 834 824 715 612 567 728 626 S 14 (15) - 18 31 (32) 13 12 12 11 20 p 0.0092 - 0.0062 0.0124 0.0073 0.0076 0.0048 0.0042 0.0110 h 0.0075 - 0.0076 0.0137 0.0066 0.0069 0.0075 0.0053 0.0123 Tajima’s D 1.050 - 20.853 20.483 0.445 0.405 21.630 * 20.997 20.554 Fay & Wu’s H 21.067 - 1.156 4.356 0.800 20.978 23.022 21.689 20.786 ZnS 0.299 - 0.109 0.143 0.280 0.269 0.142 0.096 0.147 Ks 0.042 - 0.063 0.085 0.056 0.020 0.039 0.024 0.034 11 ** SD n 12 12 12 12 12 12 12 12 L 708 4515 865 825 700 612 567 734 626 S 17 5 11 10 12 7 0 13 (14) 24 p 0.0075 0.0003 0.0024 0.0024 0.0042 0.0021 0.0000 0.0051 0.0114 h 0.0080 0.0004 0.0042 0.0040 0.0057 0.0038 0.0000 0.0063 0.0127 Tajima’s D 20.263 20.313 21.755 * 21.705 * 21.077 21.713 * - 20.794 20.462 Fay & Wu’s H 20.818 20.242 24.697 * 27.424 * 27.242 * 24.091 * - 0.061 0.485 ZnS 0.147 1.000 0.497 0.652 0.651 0.466 - 0.088 0.162 Ks 0.042 0.048 0.064 0.084 0.057 0.018 0.037 0.025 0.034 9 ** SD-Mal only n 10 10 10 10 10 10 10 10 L 708 4515 874 825 709 614 573 737 626 S 14 0 0 0 0 0 0 13 (14) 23 p 0.0071 0 0 0 0 0 0 0.0058 0.0121 h 0.0070 0 0 0 0 0 0 0.0067 0.0130 Tajima’s D 0.047 - - - - - - 20.631 20.335 Fay & Wu’s H 21.244 - - - - - - 0.267 0.711 ZnS 0.199 - - - - - - 0.099 0.184 Ks 0.042 0.048 0.064 0.085 0.057 0.019 0.037 0.025 0.034 *P,0.05, determined by 10,000 coalescent simulations conditional on observed h and assuming no recombination. **The SD-KY38 chromosome has a lethal mutation in the staufen region (G) and thus could not be sequenced from Df(2R)Pcl7B/SD-KY38 or Df(2R)Pcl11B/SD-KY38 flies. p_IGR and d_IGR = proximal and distal intergenic region, respectively. n = number of chromosomes sampled. L = gapless length of sequenced region. S = number of segregating sites (mutations) in the sample. p = average number of pairwise differences per site. h = Watterson’s measure of variability based on the number of segregating sites. ZnS = average linkage disequilibrium among all pairwise combinations of S segregating sites in sequenced region. Ks = Jukes-Cantor corrected silent divergence per silent site between sample and D. simulans. doi:10.1371/journal.pgen.1000463.t003 African SD chromosomes possess the In(2R)NS inversion (52A2– SD-ZK178, SD-ZK216) carry the cosmopolitan In(2L)t inversion 52B1;56F9–56F13) found on most non-African SD chromosomes (22D3–D6;34A8–A9; Table 2). [2]. Indeed, SD-BN19 and SD-MD31 are inversion-free chromo- The association between major haplotype and the In(2R)Mal somes (Table 2). The other ten SD chromosomes, however, possess arrangement is perfect: all major haplotype SD chromosomes a complex chromosomal arrangement on 2R (Table 2). The carry In(2R)Mal, whereas both minor haplotype SD chromosomes cytological order (40–44F|54E–55E|51BC–44F|54E–51BC| (SD-BN19 and SD-MD31) lack In(2R)Mal (Fisher’s Exact 55E–60) shows that these SD chromosomes have recruited two P = 0.015). Hereafter, we refer to this new class of In(2R)Mal- overlapping inversions: In(2R)51BC;55E first, followed by In(2- bearing, major haplotype SD chromosomes as SD-Mal. To test the R)44F;54E (Figure 4). These inversion breakpoints match a effect of the In(2R)Mal arrangement on crossing over, we crossed previously identified, but rare, African endemic chromosomal heterozygous SD-NK04/cn bw females (SD-NK04 is a SD-Mal arrangement found in Malawi [50], hereafter called In(2R)Mal. In chromosome) to cn bw males and recorded the frequency of addition to In(2R)Mal, four SD chromosomes (SD-KN20, SD-KY87, recombination between cn (43E16) and bw (59E2). As negative PLoS Genetics | www.plosgenetics.org 6 May 2009 | Volume 5 | Issue 5 | e1000463