dynamics of SD comes from laborious, large-scale phenotypic assays to determine the frequency of Sd and Rsp in natural populations (e.g., [30,31]). These have revealed that in natural populations of D. melanogaster worldwide, the frequency of SD is remarkably similar (1–5%) and thus presumably stable. The stability of SD occurs because its intrinsic transmission advantage is balanced by several forces: the sterility of many SD/SD males [32]; the reduced sperm numbers in SD-bearing flies [33]; the presence of suppressors of distortion [24,30,31,34]; and selection against linked deleterious mutations that accumulate in the large non- recombining regions of SD chromosomes [1]. This apparent stability may however mask an underlying evolutionary turnover among competing SD chromosomes predicted by theory [15]. Using realistic parameters, Charlesworth and Hartl [15] showed that an inversion-free SD chromosome will invade a SD+ population and spread to a low-frequency equilibrium; this mixed population, however, is susceptible to invasion by an inversion- bearing SD chromosome that will displace the inversion-free SD and spread to the same low-frequency equilibrium. It appears, then, that SD chromosomes may evolve continuously, as a small subpopulation of second chromosomes in D. melanogaster, compet- ing with one another and evading suppressors. Fifty years of SD work has produced a rich body of genetics and theory [2,5–8], and recently the molecular basis of distortion has begun to emerge [8,35–38]. The two main SD loci have been identified: Sd is a partial, tandem duplication of the gene RanGAP, called Sd-RanGAP [37]; and Rsp is a large array of 120-bp AT-rich repeats in the centric heterochromatin of 2R [38], where alleles with #300 repeats are ‘‘insensitive’’ (Rspi), 700–1100 are ‘‘sensitive’’ (Rsps), and $1100 are ‘‘super-sensitive’’ (Rspss; [3,4,38]). Sd-RanGAP encodes truncated RanGAP (Ran-GTPase Activating Protein; [37]), a protein with essential and evolution- arily conserved functions in nuclear transport, mitosis, and chromatin processing [39–41]. The truncated Sd-RanGAP protein is enzymatically active but mislocalizes to the nucleus (normally RanGAP is cytoplasmic) where, for reasons not yet clear, it causes segregation distortion in SD/SD+ males [8,35,36]. Surprisingly, in the decade since its discovery [37], there have been no direct evolutionary analyses of Sd-RanGAP, the gene that actually causes distortion. In this paper, we study the molecular population genetics of the SD complex to investigate its evolutionary history and recent population dynamics. First, we perform the first screen for SD in populations from Africa, the ancestral range of D. melanogaster. Second, we study patterns of DNA sequence variation at the distorter, Sd-RanGAP, as well as its parent gene, RanGAP, and eight noncoding loci on chromosome 2. Finally, we characterize the strength of distortion, inversion status, and mutational load of SD chromosomes. We show that Sd- RanGAP is present in Africa and that a new SD chromosome type has spread very recently across the African continent, causing a large-scale selective sweep among SD chromosomes. These results call into question our current understanding of the timing and location of SD’s origins and suggest that, despite its remarkably stable population frequency, SD evolution is not at equilibrium. Results A Screen for SD Chromosomes in African Populations We used a three-primer PCR assay to screen 452 isofemale lines collected from 13 localities in Africa for the Sd-RanGAP duplication (Figure 1B; Table 1). We found 12 SD chromosomes from across the continent, including west (e.g., Benin, Gabon, Cameroon) and east Africa (e.g., Zimbabwe, Kenya; Table 2). Assuming that all isofemale lines are homozygous, the population frequency of SD is Segregation Distorter Causes Sweep Table 1. Isofemale lines screened for SD chromosomes. Geographic origin Lines screened SD chromosomes Benin Cameroon Congo Eritrea Gabon Ghana Kenya Malawi Niger Nigeria South Africa Uganda Zimbabwe Total 7 132 15 26 32 2 41 19 44 10 13 37 74 452 1 3 0 0 1 0 5 0 0 0 0 0 2 12 doi:10.1371/journal.pgen.1000463.t001 12/452 = 0.027; and assuming that all isofemale lines are heterozygous, the population frequency of SD is 12/904 = 0.013. These estimates suggest that SD chromosomes occur in Africa at a frequency of 1.3–2.7%, similar to its frequency in other natural populations [23]. Low Divergence between Sd-RanGAP and RanGAP After genetically extracting the SD chromosomes, we sequenced the ,4.5-kb Sd-RanGAP sequence from all 12 as well as the homologous region of the parent gene, RanGAP, from 10 wildtype (non-SD) chromosomes sampled from Zimbabwe (see Methods). RanGAP and Sd-RanGAP show typical levels of silent divergence per site from the RanGAP homolog in the outgroup species, D. simulans, with Ksil = 0.0471 and 0.0478, respectively. Silent divergence between the duplicate genes, RanGAP and Sd-RanGAP, within D. melanogaster is more than an order of magnitude lower, Ksil = 0.0027 (see also ref. [37]). These findings confirm that Sd-RanGAP arose in Table 2. SD chromosomes from Africa. SD chromosome Geographic origin SD-GN09 SD-KM87 SD-KM92 SD-KN20 SD-KY38 SD-KY91 SD-MD21 SD-NK04 SD-ZK178 SD-ZK216 SD-BN19 SD-MD31 Gabon Malindi, Kenya Malindi, Kenya Kenya Kenya Malindi, Kenya Mbalang-Djalingo, Cameroon Nkouondja, Cameroon Lake Kariba, Zimbabwe Lake Kariba, Zimbabwe Benin Mbalang-Djalingo, Cameroon Inversionsa In(2R)Mal In(2L)t+In(2R)Mal In(2R)Mal In(2R)Mal In(2R)Mal In(2R)Mal In(2R)Mal In(2L)t+In(2R)Mal In(2L)t+In(2R)Mal In(2L)t+In(2R)Mal No Inversions No Inversions aIn(2R)Mal has cytological breakpoints 44F3–12;54E3–10+51B6–11;55E3–12, and In(2L)t has breakpoints 22D3–22E1;34A8–34A9. doi:10.1371/journal.pgen.1000463.t002 PLoS Genetics | www.plosgenetics.org 3 May 2009 | Volume 5 | Issue 5 | e1000463