In DNA barcoding, a short standardized DNA sequence is used to assign unknown individuals to species and aid in the discovery of new species. A fragment of the mitochondrial gene cytochrome c oxidase subunit 1 is emerging as the standard barcode region for animals. However, patterns of mitochondrial variability can be confounded by the spread of maternally transmitted bacteria that cosegregate with mitochondria. Here, we investigated the performance of barcoding in a sample comprising 12 species of the blow fly genus Protocalliphora, known to be infected with the endosymbiotic bacteria Wolbachia. We found that the barcoding approach showed very limited success: assignment of unknown individuals to species is impossible for 60% of the species, while using the technique to identify new species would underestimate the species number in the genus by 75%. This very low success of the barcoding approach is due to the non-monophyly of many of the species at the mitochondrial level. We even observed individuals from four different species with identical barcodes, which is, to our knowledge, the most extensive case of mtDNA haplotype sharing yet described. The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly results from introgressive hybridization associated with Wolbachia infection. Given that Wolbachia is known to infect between 15 and 75% of insect species, we conclude that identification at the species level based on mitochondrial sequence might not be possible for many insects. However, given that Wolbachia-associated mtDNA introgression is probably limited to very closely related species, identification at the genus level should remain possible.

While workers of almost all subspecies of honeybee are able to lay only haploid male eggs, Apis mellifera capensis workers are able to produce diploid female eggs by thelytokous parthenogenesis. Cytological analyses have shown that during parthenogenesis, egg diploidy is restored by fusion of the two central meiotic products. This peculiarity of the Cape bee preserves two products of a single meiosis in the daughters and can be used to map centromere positions using half-tetrad analysis. In this study, we use the thelytokous progenies of A. m. capensis workers and a sample of individuals from a naturally occurring A. m. capensis thelytokous clone to map centromere position for most of the linkage groups of the honeybee. We also show that the recombination rate is reduced by Ͼ10-fold during the meiosis of A. m. capensis workers. This reduction is restricted to thelytokous parthenogenesis of capensis workers and is not observed in the meiosis of queen within the same subspecies or in arrhenotokous workers of another subspecies. The reduced rate of recombination seems to be associated with negative crossover interference. These results are discussed in relation to evolution of thelytokous parthenogenesis and maintenance of heterozygosity and female sex after thelytoky.

Summary Microsatellites are currently considered the most useful genetic markers with wide applications in genomics, quantitative and population genetics. We present here the structure of the core sequence of 552 microsatellites, together with the sequences of the primers and the length of the sequenced allele. These microsatellites were isolated from several libraries constructed from either fractions of total genomic DNA or from clones of a bacterial artificial chromosome (BAC) library. All 552 loci are polymorphic in the honeybee. Many of them were also successfully amplified in three other species of Apis: A. cerana (58%), A. dorsata (59%) and A. florea (38%). A summary of the variability of 36 loci in the three main evolutionary lineages of A. mellifera is given.

The honeybee (Apis mellifera) queen mates during nuptial £ights, in the so-called drone congregation area where many males from surrounding colonies gather. Using 20 highly polymorphic microsatellite loci, we studied a sample of 142 drones captured in a congregation close to Oberursel (Germany). A parentage test based on lod score showed that this sample contained one group of four brothers, six groups of three brothers, 20 groups of two brothers and 80 singletons. These values are very close to a Poisson distribution. Therefore, colonies were apparently equally represented in the drone congregation, and calculations showed that the congregation comprised males that originated from about 240 di¡erent colonies. This ¢gure is surprisingly high. Considering the density of colonies around the congregation area and the average £ight range of males, it suggests that most colonies within the recruitment perimeter delegated drones to the congregation with an equal probability, resulting in an almost perfect panmixis. Consequently, the relatedness between a queen and her mates, and hence the inbreeding coe¤cient of the progeny, should be minimized. The relatedness among the drones mated to the same queen is also very low, maximizing the genetic diversity among the di¡erent patrilines of a colony.

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.

-Variability of mitochondrial deoxyribonucleic acid (mtDNA)

The genetic variability and differentiation of west European honey bee populations (Apis mellifera mellifera and A. m. iberica) have been investigated using 11 microsatellite loci. These two subspecies are characterised by a lower genetic variability than most other studied subspecies and several tests are indicative of a recent increase of the population size. Moreover, the genetic profiles are rather homogeneous from southern Spain to Scandinavia. French populations are more or less introgressed (a few percent up to 57 %) by genes from the north Mediterranean lineage which provides most of the imported queens. The inferred percentage of introgressed nuclear genes is generally well correlated with the proportion of alien mitochondrial deoxyribonucleic acid (mtDNA) haplotypes detected in the same populations. The level of introgression is the main source of genetic distances among populations. When introgressed genes are disregarded, however, populations cluster in two groups which correspond to both subspecies (iberica and mellifera), giving full support to the taxonomy of this lineage. © Inra/Elsevier, Paris honey bee / microsatellites / population genetics / introgression / conservation * Correspondence and reprints Résumé -Diversité génétique de l'abeille ouest européenne (Apis mellifera mellifera et A. m. iberica). II. Locus microsatellites. La variabilité génétique et la différenciation entre populations a été étudiée pour 11 locus microsatellites dans 15 populations de l'abeille ouest européenne. Les deux sous-espèces qui constituent ce rameau (Apis mellifera mellifera et A. m. iberica) ont une variabilité génétique

A linkage map for the honeybee (Apis mellifera) was constructed mainly from the progeny of two hybrid queens (A. m. ligustica ϫ A. m. mellifera). A total of 541 loci were mapped; 474 were microsatellite loci; a few were additional bands produced during PCRs, one of the two rDNA loci (using ITS), the MDH locus, and three sex-linked markers (Q and FB loci and one RAPD band). Twenty-four linkage groups were estimated of which 5 were minute (between 7.1 and 22.8 cM) and 19 were major groups (Ͼ76.5 cM). The number of major linkage groups exceeded by three the number of chromosomes of the complement (n ϭ 16). The sum of the lengths of all linkage groups amounts to 4061 cM to which must be added at least 320 cM to link groups in excess, making a total of at least 4381 cM. The length of the largest linkage group I was 630 cM. The average density of markers was 7.5 cM and the average resolution was about one marker every 300 kb. For most of the large groups, the centromeric region was determined genetically, as described in Baudry et al. (2004, accompanying article in this issue), using half-tetrad analysis of thelytokous parthenogens in which diploid restoration occurs through central fusion. Several cases of segregation distortion that appreared to result from deleterious recessives were discovered. A low positive interference was also detected.