Drosophila melanogaster is widely used as a model in DNA variation studies. Patterns of polymorphism have, however, been affected by the history of this species, which is thought to have recently spread out of Africa to the rest of the world. We analyzed DNA sequence variation in 11 populations, including four continental African and seven non-African samples (including Madagascar), at four independent X-linked loci. Variation patterns at all four loci followed neutral expectations in all African populations, but departed from it in all non-African ones due to a marked haplotype dimorphism at three out of four loci. We also found that all non-African populations show the same major haplotypes, though in various frequencies. A parsimonious explanation for these observations is that all non-African populations are derived from a single ancestral population having undergone a substantial reduction of polymorphism, probably through a bottleneck. Less likely alternatives involve either selection at all four loci simultaneously (including balancing selection at three of them), or admixture between two divergent populations. Small but significant structure was observed among African populations, and there were indications of differentiation across Eurasia for non-African ones. Since population history may result in non-equilibrium variation patterns, our study confirms that the search for footprints of selection in the D. melanogaster genome must include a sufficient understanding of its history.

Despite having winged queens, female dispersal in the monogynous ant Cataglyphis cursor is likely to be restricted because colonies reproduce by fission. We investigated the pattern of population genetic structure of this species using eight microsatellite markers and a mitochondrial DNA (mtDNA) sequence, in order to examine the extent of female and nuclear gene flow in two types of habitat. Sampling was carried out at a large spatial scale (16 sites from 2.5 to 120 km apart) as well as at a fine spatial scale (two 4.5-km transects, one in each habitat type). The strong spatial clustering of mtDNA observed at the fine spatial scale strongly supported a restricted effective female dispersal. In agreement, patterns of the mtDNA haplotypes observed at large and fine spatial scales suggested that new sites are colonized by nearby sites. Isolation by distance and significant nuclear genetic structure have been detected at all the spatial scales investigated. The level of local genetic differentiation for mitochondrial marker was 15 times higher than for the nuclear markers, suggesting differences in dispersal pattern between the two sexes. However, male gene flow was not sufficient to prevent significant nuclear genetic differentiation even at short distances (500 m). Isolation-by-distance patterns differed between the two habitat types, with a linear decrease of genetic similarities with distance observed only in the more continuous of the two habitats. Finally, despite these low dispersal capacities and the potential use of parthenogenesis to produce new queens, no signs of reduction of nuclear genetic diversity was detected in C. cursor populations.

Transposable elements (TEs) are genomic parasites that are found in all genomes, some of which display sequence similarity to certain viruses. In insects, TEs are controlled by the Piwi-interacting small interfering RNA (piRNA) pathway in gonads, while the small interfering RNA (siRNA) pathway is dedicated to TE somatic control and defense against viruses. So far, these two small interfering RNA pathways are considered to involve distinct molecular effectors and are described as independent. Using Sindbis virus (SINV) inDrosophila, here we show that viral infections affect TE transcript amounts via modulations of the piRNA and siRNA repertoires, with the clearest effects in somatic tissues. These results suggest that viral acute or chronic infections may impact TE activity and, thus, the tempo of genetic diversification. In addition, these results deserve further evolutionary considerations regarding potential benefits to the host, the virus, or the TEs.

cEndogenous retroviruses have the ability to become permanently integrated into the genomes of their host, and they are generally transmitted vertically from parent to progeny. With the exception of gypsy, few endogenous retroviruses have been identified in insects. In this study, we describe the tirant endogenous retrovirus in a subset of Drosophila simulans natural populations. By focusing on the envelope gene, we show that the entire retroviral cycle (transcription, translation, and retrotransposition) can be completed for tirant within one population of this species. Endogenous retroviruses are genomic sequences that are widely dispersed throughout the host genome. These sequences constitute 8% of the human genome and represent the remnants of ancient infections by retroviruses (1). Some of these retroviruses were domesticated and generated cellular neogenes, such as the syncytin gene (9, 14). The structure of a canonical endogenous retrovirus consists of three open reading frames (ORFs), which are bordered by long terminal repeats (LTRs). The third ORF encodes the envelope protein (Env), which possesses fusogenic properties and is responsible for the infectious behavior of exogenous retroviruses. In insects, several endogenous retroviruses have been described, and most of them possess a complete retroviral structure. Representative insect endogenous retroviruses (IERVs) or insect ErantiViruses (24) include the following: gypsy, ZAM, Idefix, tirant, 17.6, 297, and nomad in Drosophila melanogaster; tom in Drosophila ananassae; Tv1 in Drosophila virilis; TED in Trichoplusia ni; Osvaldo in Drosophila buzzatii; and Yoyo in Ceratitis capitata (see reference 19 for a review). With the exception of nomad and Tv1, each of these displays a complete env ORF. Thus far, only the well-known gypsy element of D. melanogaster has been shown to possess infectious properties (10), as Moloney murine leukemia virus pseudotypes with the gypsy Env protein were shown to infect insect cells (25).The tirant LTR retrotransposon of D. melanogaster was previously described to share sequence similarity with the fusion proteins of certain baculoviruses (13,16,20) (see Fig. 1 for the tirant structure). In a phylogenetic study of numerous elements from insects, Terzian et al. (24) proposed that the tirant element from D. melanogaster (GenBank accession number X93507) belongs to the IERVs. Thus, the tirant element was placed into this clade of retroviruses, which uses a tRNA-Ser binding site to prime reverse transcription (RT). In the study described in this report, we examined this ERV family in Drosophila simulans using a collection of strains with variable numbers of genomic insertions (7), and we demonstrated that this family was able to produce Env proteins in the ovaries of the host. We found that tirant was capable of performing the first step required for infection, i.e., the production of a functional Env protein, which suggests that it could be classified as an active endogenous retrovirus of D. simulans. Furthermore, we demonstr...