Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

The mojavensis cluster of the repleta species group of Drosophila (Drosophilidae: Diptera) consists of three species. One is newly described as D. navojoa. A second species, described here as D. arizonae, replaces D. arizonensis, which has become a junior subjective synonym for D. mojavensis, the third species in the cluster. A phylogeny of the three species is presented, based on chromosomal inversions, morphology, and the ability to produce hybrids. Breakage points are assigned for all inversions, and male genitalia are figured; 186 crosses were made from 225 possible combinations among 15 geographic strains from the southwestern United States, Mexico, and Guatemala. It is confirmed that D. mojavensis and D. arizonae are very closely related and shown that D. navojoa is more distantly related in regard to all criteria. This relationship is supported by the geographical positions of the ancestral gene sequences in each species, which show a sequential northwest movement (D. navojoa----D. arizonae----D. mojavensis) from southern Mexico to southern California and northern Arizona. The relationship is also supported by the fact that D. navojoa breeds in Opuntia cactus, an ancestral behavior, whereas the other two species breed chiefly in Stenocereus cacti, a derived behavior. The possible role of this host plant shift in speciation is discussed.

The salivary gland chromosomes of 10 species in the Drosophila mullen subgroup (repleta group) have been re-analysed. These include the eight members of the South American buzzatii and martensis clusters, previously ascribed to the mullen complex, and the two Caribbean species D. staikeni and D. nichardsoni, previously comprising the stalkeri complex. The chief results can be summarized as follows. Inversion 3a is not present in the inartensis cluster. Hence, there is no cytological link between this cluster, or the buzzatii cluster, and the rest of the mullen complex. Accordingly, a new species complex, the buzzatii complex, is established with the two South American clusters. D. stalkeni and D. richardsoni share at least two inversions with all the species in the buzzatii and martensis clusters, and produce hybrids in interspecific crosses with many of them.This indicates a close phylogenetic relationship. Therefore, D. stalkeri and D. richardsoni are incorporated as a cluster within the newly erected buzzatii complex. A phylogenetic tree illustrating the chromosomal evolution of the buzzatii complex is presented and all the previous cytological information concerning its members is reviewed.

During the evolution of the genus Drosophila, the molecular organization of the major chromosomal elements has been repeatedly rearranged via the fixation of paracentric inversions. Little detailed information is available, however, on the extent and effect of these changes at the molecular level. In principle, a full description of the rate and pattern of change could reveal the limits, if any, to which the eukaryotic genome can accommodate reorganizations. We have constructed a high-density physical map of the largest chromosomal element in Drosophila repleta (chromosome 2) and compared the order and distances between the markers with those on the homologous chromosomal element (3R) in Drosophila melanogaster. The two species belong to different subgenera (Drosophila and Sophophora, respectively), which diverged 40-62 million years (Myr) ago and represent, thus, the farthest lineages within the Drosophila genus. The comparison reveals extensive reshuffling of gene order from centromere to telomere. Using a maximum likelihood method, we estimate that 114 ± 14 paracentric inversions have been fixed in this chromosomal element since the divergence of the two species, that is, 0.9-1.4 inversions fixed per Myr. Comparison with available rates of chromosomal evolution, taking into account genome size, indicates that the Drosophila genome shows the highest rate found so far in any eukaryote. Twenty-one small segments (23-599 kb) comprising at least two independent (nonoverlapping) markers appear to be conserved between D. melanogaster and D. repleta. These results are consistent with the random breakage model and do not provide significant evidence of functional constraint of any kind. They support the notion that the Drosophila genome is extraordinarily malleable and has a modular organization. The high rate of chromosomal change also suggests a very limited transferability of the positional information from the Drosophila genome to other insects.[The sequence data described in this paper have been submitted to the GenBank data library under accession no, AF319441.]Comparative genomics allows us to infer the rates and patterns of genome evolution. The comparison of genomes between distantly related species is made possible by the construction of high-density linkage and/ or physical maps and will be greatly facilitated and accelerated by the sequencing of entire genomes in a handful of archetypal species. Critical to this approach is that the analysis of linkage (synteny) and order (colinearity) relationships must be based on orthologous coding markers (Type I markers; O'Brien et al. 1997). Comparative mapping has already yielded important insights into how the genomes of plants and mammals have evolved (Paterson et al. 1996;Gale and Devos 1998; O' Brien et al. 1999).Drosophila melanogaster was the subject of the first genetic map (Sturtevant 1913) and the first interspecific comparative study (Sturtevant 1921), and is currently the genetically best-characterized insect. Its relatively small (180 Mb) genome, whose e...

Transposable elements (TEs) have been implicated in the generation of genetic rearrangements, but their potential to mediate changes in the organization and architecture of host genomes could be even greater than previously thought. Here, we describe the naturally occurring structural and nucleotide variation around two TE insertions in the genome of Drosophila buzzatii. The studied regions correspond to the breakpoints of a widespread chromosomal inversion generated by ectopic recombination between oppositely oriented copies of a TE namedGalileo. A detailed molecular analysis by Southern hybridization, PCR amplification, and DNA sequencing of 7.1 kb surrounding the inversion breakpoints in 39 D. buzzatii lines revealed an unprecedented degree of restructuring, consisting of 22 insertions of ten previously undescribed TEs, 13 deletions, 1 duplication, and 1 small inversion. All of these alterations occurred exclusively in inverted chromosomes and appear to have accumulated after the insertion of the Galileo elements, within or close to them. The nucleotide variation at the studied regions is six times lower in inverted than in noninverted chromosomes, suggesting that most of the observed changes originated in only 84,000 years.Galileo elements thus seemed to promote the transformation of these, otherwise normal, chromosomal regions in genetically unstable hotspots and highly efficient traps for transposon insertions. The particular features of two new Galileo copies found indicate that this TE belongs to the Foldback family. Together, our results strengthen the importance of TEs, and especially DNA transposons, as inducers of genome plasticity in evolution.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AF368842–AF368859 and AF368861–AF368900. In addition, sequences submitted under accession nos. AF162796–AF162799 were used as a basis for this study.]