Expression of achaete-scute homologues in discrete proneural clusters on the developing notum of the medfly Ceratitis capitata, suggests a common origin for the stereotyped bristle patterns of higher Diptera. (1/44)

The stereotyped positioning of sensory bristles in Drosophila has been shown to result from complex spatiotemporal regulation of the proneural achaete-scute genes, that relies on an array of cis-regulatory elements and spatially restricted transcriptional activators such as Pannier. Other species of derived schizophoran Diptera have equally stereotyped, but different, bristle patterns. Divergence of bristle patterns could arise from changes in the expression pattern of proneural genes, resulting from evolution of the cis-regulatory sequences and/or altered expression patterns of transcriptional regulators. Here we describe the isolation of achaete-scute homologues in Ceratitis capitata, a species of acalyptrate Schizophora whose bristle pattern differs slightly from that of Drosophila. At least three genes, scute, lethal of scute and asense have been conserved, thus demonstrating that gene duplication within the achaete-scute complex preceded the separation of the families Drosophilidae and Tephritidae, whose common ancestor goes back more than 100 million years. The expression patterns of these genes provide evidence for conservation of many cis-regulatory elements as well as a common origin for the stereotyped patterns seen on the scutum of many Schizophora. Some aspects of the transcriptional regulation have changed, however, and correlate in the notum with differences in the bristle pattern. The Ceratitis pannier gene was isolated and displays a conserved expression domain in the notum.  (+info)

Horizontal transfer and selection in the evolution of P elements. (2/44)

The roles of selection and horizontal transfer in the evolution of the canonical subfamily of P: elements were studied in the saltans and willistoni species groups of the genus Drosophila (subgenus Sophophora). We estimate that the common ancestor of the canonical P: subfamily dates back 2-3 Myr at the most, despite the much older age (more than 40 Myr) of the P: family as a whole. The evolution of the canonical P: subfamily is characterized by weak selection at nonsynonymous sites. These sites have evolved at three quarters the rate of synonymous sites, in which no selective constraints were detected. Their recent horizontal transfer best explains the high degree of similarity among canonical P: elements from the saltans and willistoni species groups. These results are consistent with a model of P:-element evolution in which selective constraints are imposed at the time of horizontal transfer. Furthermore, it is estimated that the spread and diversification of the canonical subfamily involved a minimum of 11 horizontal transfer events among the 18 species surveyed within the past 3 Myr. The presence of multiple P: subfamilies in the saltans and willistoni species groups is likely to be the result of multiple invasions that have previously swept through these taxa in a succession of horizontal transfer events. These results suggest that horizontal transfer among eukaryotes might be more common than anticipated.  (+info)

Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae. (3/44)

Compositional changes are a major feature of genome evolution. Overlooking nucleotide composition differences among sequences can seriously mislead phylogenetic reconstructions. Large compositional variation exists among the members of the family Drosophilidae. Until now, however, base composition differences have been largely neglected in the formulations of the nucleotide substitution process used to reconstruct the phylogeny of this important group of species. The present study adopts a maximum-likelihood framework of phylogenetic inference in order to analyze five nuclear gene regions and shows that (1) the pattern of compositional variation in the Drosophilidae does not match the phylogeny of the species; (2) accounting for the heterogeneous GC content with Galtier and Gouy's nucleotide substitution model leads to a tree that differs in significant aspects from the tree inferred when the nucleotide composition differences are ignored, even though both phylogenetic hypotheses attain strong nodal support in the bootstrap analyses; and (3) the LogDet distance correction cannot completely overcome the distorting effects of the compositional variation that exists among the species of the Drosophilidae. Our analyses confidently place the Chymomyza genus as an outgroup closer than the genus Scaptodrosophila to the Drosophila genus and conclusively support the monophyly of the Sophophora subgenus.  (+info)

Improving gene recognition accuracy by combining predictions from two gene-finding programs. (4/44)

MOTIVATION: Despite constant improvements in prediction accuracy, gene-finding programs are still unable to provide automatic gene discovery with desired correctness. The current programs can identify up to 75% of exons correctly and less than 50% of predicted gene structures correspond to actual genes. New approaches to computational gene-finding are clearly needed. RESULTS: In this paper we have explored the benefits of combining predictions from already existing gene prediction programs. We have introduced three novel methods for combining predictions from programs Genscan and HMMgene. The methods primarily aim to improve exon level accuracy of gene-finding by identifying more probable exon boundaries and by eliminating false positive exon predictions. This approach results in improved accuracy at both the nucleotide and exon level, especially the latter, where the average improvement on the newly assembled dataset is 7.9% compared to the best result obtained by Genscan and HMMgene. When tested on a long genomic multi-gene sequence, our method that maintains reading frame consistency improved nucleotide level specificity by 21.0% and exon level specificity by 32.5% compared to the best result obtained by either of the two programs individually. AVAILABILITY: The scripts implementing our methods are available from http://www.cs.ubc.ca/labs/beta/genefinding/  (+info)

First occurrence of parasitoid Spalangia endius (Walker) (Hymenoptera: Pteromalidae) in pupae of Zaprionus indianus Gupta (Diptera: Drosophilidae) in Brazil. (5/44)

This paper reports the first occurrence of the parasitoid Spalangia endius collected in pupae of Zaprionus indianus using traps with fruit bait. The experiment was carried out at the University of Lavras in Lavras, Minas Gerais, Brazil, from November to December, 2001. A total of 4 Spalangia endius specimens were obtained from 105 Zaprionus indianus pupae. The overall prevalence of parasitism was 3.8%.  (+info)

A minisatellite with fold-back structure is included in the 5'-flanking region of the Adh gene of Scaptodrosophila lebanonensis. (6/44)

A tandem repetitive sequence with a repeat unit of 12 bp has been found 1.3 kb upstream of the Adh gene of Scaptodrosophila lebanonensis. This repetitive sequence extends over 4.3 kb and consists of two inverted arrays (a fold-back segment). The repeated unit with a consensus sequence GAATACAGAATA is highly conserved and the nucleotide substitutions are not distributed randomly among the 12 bp. In situ hybridization in S. lebanonensis polytene chromosomes revealed two signals, one at the 60A section, the Adh locus, and a second site in the same chromosome at the 60C section close to the telomere. This same pattern of hybridization is obtained in all the analyzed strains including the subspecies S. lebanonensis casteeli. The minisatellite sequence accounts for about 0.03-0.04% of the S. lebanonensis genome and showed intraspecific variability in tandem repeat numbers. Possible functions of this sequence are discussed.  (+info)

Complex evolution of gypsy in Drosophilid species. (7/44)

In an endeavor to contribute to the comprehension of the evolution of transposable elements (TEs) in the genome of host species, we investigated the phylogenetic relationships of sequences homologous to the retrotransposon gypsy of Drosophila melanogaster in 19 species of Drosophila, in Scaptodrosophila latifasciaeformis, and in Zaprionus indianus. This phylogenetic study was based on approximately 500 base pairs of the env gene. Our analyses showed considerable discrepancy between the phylogeny of gypsy elements and the relationship of their host species, and they allow us to infer a complex evolutionary pattern that could include ancestral polymorphism, vertical transmission, and several cases of horizontal transmission.  (+info)

Population structure and host-plant specialization in two Scaptodrosophila flower-breeding species. (8/44)

In contrast to phytophagous insect species, little attention has been paid to the possibility of host races in the Drosophilidae, although flower-breeding species, where courtship and mating take place on the flowers, are likely candidates. Two species of Scaptodrosophila, S. hibisci and S. aclinata, are restricted to flowers of Hibiscus species (section Furcaria), and the Furcaria specialization likely predated the separation of S. hibisci and S. aclinata. In all, 20 microsatellite loci were analysed in nine populations of S. hibisci and five of S. aclinata. For two pairs of S. hibisci populations in close proximity, but breeding on different Hibiscus species, differentiation between the populations of each of these pairs was similar to that between the populations that were from the same Hibiscus species, but geographically distant, suggesting the early stages of host-race formation. Genetic variability was significantly less in S. aclinata than in S. hibisci, suggesting greater drift effects in the former. However, of 253 alleles detected, 82 were present in both species, 160 in S. hibisci only and 11 in S. aclinata only, indicating that S. aclinata was derived from S. hibisci, following a strong bottleneck at the time of separation--possibly 40,000 years BP. Analyses and interpretation of Hardy-Weinberg equilibrium and F statistics needed to account for null alleles known to be present at eight loci in S. hibisci, and possibly present at other loci. The results emphasize the need for caution in studies where the presence of null alleles is inferred only from population data.  (+info)

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