Signals of demographic expansion in Drosophila virilis.
ABSTRACT: BACKGROUND: The pattern of genetic variation within and among populations of a species is strongly affected by its phylogeographic history. Analyses based on putatively neutral markers provide data from which past events, such as population expansions and colonizations, can be inferred. Drosophila virilis is a cosmopolitan species belonging to the virilis group, where divergence times between different phylads go back to the early Miocene. We analysed mitochondrial DNA sequence variation among 35 Drosophila virilis strains covering the species' range in order to detect demographic events that could be used to understand the present characteristics of the species, as well as its differences from other members of the group. RESULTS: Drosophila virilis showed very low nucleotide diversity with haplotypes distributed in a star-like network, consistent with a recent world-wide exponential expansion possibly associated either with domestication or post-glacial colonization. All analyses point towards a rapid population expansion. Coalescence models support this interpretation. The central haplotype in the network, which could be interpreted as ancestral, is widely distributed and gives no information about the geographical origin of the population expansion. The species showed no geographic structure in the distribution of mitochondrial haplotypes, in contrast to results of a recent microsatellite-based analysis. CONCLUSION: The lack of geographic structure and the star-like topology depicted by the D. virilis haplotypes indicate a pattern of global demographic expansion, probably related to human movements, although this interpretation cannot be distinguished from a selective sweep in the mitochondrial DNA until nuclear sequence data become available. The particular behavioural traits of this species, including weak species-discrimination and intraspecific mate choice exercised by the females, can be understood from this perspective.
Project description:The genomic DNA sequence of a 2.4-kb region of the X-linked developmental gene fused was determined in 15 Drosophila virilis strains. One common replacement polymorphism is observed, where a negatively charged aspartic amino acid is replaced by the noncharged amino acid alanine. This replacement variant is located within the serine/threonine kinase domain of the fused gene and is present in approximately 50% of the sequences in our sample. Significant linkage disequilibrium is detected around this replacement site, although the fused gene is located in a region of the D. virilis X chromosome that seems to experience normal levels of recombination. In a 600-bp region around the replacement site, all eight alanine sequences are identical; of the six aspartic acid sequences, three are also identical. The occurrence of little or no variation within the aspartic acid and alanine haplotypes, coupled with the presence of several differences between them, is very unlikely under the usual equilibrium neutral model. Our results suggest that the fused alanine haplotypes have recently increased in frequency in the D. virilis population.
Project description:The homologue of the Drosophila melanogaster mobile element gypsy was cloned from the distantly related species D. virilis. It has three ORFs highly homologous to those of the element from D. melanogaster. gypsy from D. virilis appears to be actively transcribed and is capable of transposition. Comparison of the untranslated regions of both elements revealed conserved sequences including those which had previously been demonstrated to be important in transcription regulation. Distribution of gypsy among the different strains of D. virilis and different species within the D. virilis group was analyzed. Possible involvement of horizontal transmission in the process of spreading and evolution of gypsy is discussed.
Project description:The virilis phylad of the Drosophila virilis group consists of five closely related taxa: D. virilis, D. lummei, D. novamexicana, D. americana americana and D. americana texana. DNA sequences from a 2.1-kb pair portion of the period locus were generated in four to eight individuals from each of the five taxa. We found evidence of recombination and high levels of variation within species. We found no evidence of recent natural selection. Surprisingly there was no evidence of divergence between D. a. americana and D. a. texana, and they collectively appear to have had a large historical effective population size. The ranges of these two taxa overlap in a large hybrid zone that has been delineated in the eastern U.S. on the basis of the geographic pattern of a chromosomal fusion. Also surprisingly, D. novamexicana appears to consist of two distinct groups each with low population size and no gene flow between them.
Project description:We have isolated the homeobox gene rough (ro) from Drosophila virilis. Comparison of the predicted amino acid sequences of the D. melanogaster and D. virilis rough proteins reveals that domains of high conservation, including the homeodomain, are interspersed with highly diverged regions. Stretches of significant sequence conservation are also observed in the 5' promoter region and in the introns. The D. virilis rough gene rescues the rough mutant phenotype and is properly regulated when introduced into the D. melanogaster genome. Thus the rough protein as well as the cis-regulatory elements that ensure proper temporal and spatial regulation are functionally conserved between these Drosophila species.
Project description:Comparisons of polymorphism patterns between distantly related species are essential in order to determine their generality. However, most work on the genus Drosophila has been done only with species of the subgenus Sophophora. In the present work, we have sequenced one intron and surrounding coding sequences of 6 X-linked genes (chorion protein s36, elav, fused, runt, suppressor of sable and zeste) from 21 strains of wild-type Drosophila virilis (subgenus Drosophila). From these data, we have estimated the average level of DNA polymorphism, inferred the effective population size and population structure of this species, and compared the results with those obtained for other Drosophila species. There is no reduction in variation at two loci close to the centromeric heterochromatin, in contrast to Drosophila melanogaster.
Project description:Telomeres of most animals, plants, and unicellular eukaryotes are made up of tandem arrays of repeated DNA sequences produced by the enzyme telomerase. Drosophila melanogaster has an unusual variation on this theme; telomeres consist of tandem arrays of sequences produced by successive transpositions of two non-LTR retrotransposons, HeT-A and TART. To explore the phylogenetic distribution of these variant telomeres, we have looked for TART homologues in a distantly related Drosophila species, virilis. We have found elements that, despite many differences in nucleotide sequence, retain significant amino acid similarity to TART from D. melanogaster. These D. virilis TART elements have features that characterize TART elements in D. melanogaster: (i) they are found in tandem arrays on chromosome ends, (ii) they are not found in euchromatin, and (iii) they produce both sense and antisense transcripts, with the antisense RNA being in excess. The D. virilis TART elements have one surprising feature: both of the ORFs contain long stretches of the trinucleotide repeat CAX, encoding polyglutamine (with a few interspersed histidines). These long polyglutamine stretches are conserved in the three D. virilis elements sequenced. They do not interrupt any domains of known function in the TART proteins and are not seen in TART proteins from other species. Comparison of the D. virilis and D. melanogaster telomeres suggests that the retrotransposon mechanism of telomere maintenance may have arisen before the separation of the genus Drosophila.
Project description:The sevenless gene of Drosophila melanogaster encodes a transmembrane tyrosine kinase receptor required for normal eye development. We report here the isolation and DNA sequence analysis of the sevenless gene from Drosophila virilis. The predicted amino acid sequences of the sevenless proteins from these two species, which diverged approximately 60 million years ago, are compared.
Project description:Drosophila melanogaster telomeres are composed of two retrotransposons, HeT-A and TART. Drosophila virilis has recently been shown to have telomere-specific TART elements with many of the characteristics of their D. melanogaster homologues. We now report identification of the second telomere-specific retrotransposon, HeT-A, from D. virilis. These results show that HeT-A and TART have been maintaining telomeres in Drosophila for more than the 60 million years that separate D. melanogaster and D. virilis. All Drosophila species and stocks studied have both of these telomeric elements, suggesting that the elements collaborate, an assumption supported by evidence from D. melanogaster that their Gag proteins interact. Although the HeT-A sequence evolves at a high rate, the element retains the unusual structural features that characterize all HeT-A homologues. These features may be involved in the role of HeT-A at the telomere. The Gag protein from HeT-Avir is as much like TART Gag from other species as it is like HeT-A Gag, suggesting that these Gags are evolving under similar constraints, probably to maintain appropriate interactions with host telomeres and possibly to allow collaborative interactions like those seen in D. melanogaster. In addition, we have identified a chimeric element, Uvir, carrying a pol coding sequence only distantly related to sequences thus far found in any telomere arrays.
Project description:The seven in absentia (sina) gene of Drosophila encodes a nuclear protein required for normal eye development. In Drosophila melanogaster, the sina gene is located within an intron of the Rh4 opsin gene. We examine here the nucleotide sequences and chromosomal arrangements of these genes in Drosophila virilis. An interspecies comparison between D. melanogaster and D. virilis reveals that the protein-coding sequences of the sina and Rh4 genes are highly conserved, but the relative chromosomal position and structural arrangement of these genes differ between the two species. In particular, the sina and Rh4 genes are widely separated in D. virilis, and there is no intron in the Rh4 gene. Our results suggest that the Rh4 gene was translocated to another chromosomal location by a retrotransposition event.
Project description:Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation. However, reproductive genes in this group have not been characterized. Here we utilize short-read RNA sequencing of male reproductive organs to examine the evolutionary dynamics of reproductive genes in members of the virilis subgroup: D. americana, D. lummei, D. novamexicana, and D. virilis We find that the majority of male reproductive transcripts are testes-biased, accounting for ?15% of all annotated genes. Ejaculatory bulb (EB)-biased transcripts largely code for lipid metabolic enzymes, and contain orthologs of the D. melanogaster EB protein, Peb-me, which is involved in mating-plug formation. In addition, we identify 71 candidate SFPs, and show that this gene set has the highest rate of nonsynonymous codon substitution relative to testes- and EB-biased genes. Furthermore, we identify orthologs of 35 D. melanogaster SFPs that have conserved accessory gland expression in the virilis group. Finally, we show that several of the SFPs that have the highest rate of nonsynonymous codon substitution reside on chromosomal regions, which contributes to paternal gametic incompatibility between species. Our results show that SFPs rapidly diversify in the virilis group, and suggest that they likely play a role in PCSS and/or gametic isolation.