Contrasted polymorphism patterns in a large sample of populations from the evolutionary genetics model Drosophila simulans

African populations of Drosophila simulans are thought to be ancestral in this model species and are increasingly used for testing general hypotheses in evolutionary genetics. It is often assumed that African populations are more likely to be at a neutral mutation drift equilibrium than other populations. Here we examine population structuring and the demographic profile in nine populations of D. simulans. We surveyed sequence variation in four X-linked genes (runt, sevenless, Sex-lethal, and vermilion) that have been used in a parallel study in the closely related species D. melanogaster. We found that an eastern group of populations from continental Africa and Indian Ocean islands (Kenya, Tanzania, Madagascar, and Mayotte Island) is widespread, shows little differentiation, and has probably undergone demographic expansion. The other two African populations surveyed (Cameroon and Zimbabwe) show no evidence of population expansion and are markedly differentiated from each other as well as from the populations from the eastern group. Two other populations, Europe and Antilles, are probably recent invaders to these areas. The Antilles population is probably derived from Europe through a substantial bottleneck. The history of these populations should be taken into account when drawing general conclusions from variation patterns.