The mariner transposable element in natural populations of Drosophila simulans.

In cosmopolitan species, geographical variations in copy number and/or level of transposition activity have been observed for several transposable elements (TEs). Environment, history and population structure can contribute to such variation in ways that are difficult to tease apart. For the mariner element, previous studies of the geographic variation of its somatic activity in natural populations of Drosophila simulans have shown contradictory results (latitudinal clines of divergent orientations or no apparent structure). To try and resolve these inconsistencies, we gathered all available data on the mariner somatic activity of worldwide natural populations. This includes previously published results by different groups and also new data. The correlations between the level of activity and several geoclimatic factors were tested. Although no general effect of temperature was found, a relationship with the invasion history was detected. It was also shown that recent invasive populations have a higher level of activity than the putative ancestral ones. Our results strongly suggest that variability of the mariner somatic activity among natural populations of D. simulans is mainly due to populational and historical factors probably related to the recent world colonization of this species. Indeed, this activity is correlated to the main route out of Africa (the Nile route) and the recent colonization of continents such as Australia and South America.

Revisiting horizontal transfer of transposable elements in Drosophila.

Horizontal transfer (HT), defined as the transfer of genetic material between species, is considered to be an essential step in the 'life cycle' of transposable elements. We present a broad overview of suspected cases of HT of transposable elements in Drosophila. Hundred-one putative events of HT have been proposed in Drosophila for 21 different elements (5.0% refer to non-long terminal repeat (LTR) retrotransposons, 42.6% to LTR retrotransposons and 52.4% to DNA transposons). We discuss the methods used to infer HT, their limits and the putative vectors of transposable elements. We outline all the alternative hypotheses and ask how we can be almost certain that phylogenetic inconsistencies are due to HT.

Highly similar piggyBac transposase-like sequences from various Bactrocera (Diptera, Tephritidae) species.

The piggyBac transposable element is currently the vector of choice for transgenesis, enhancer trapping, gene discovery and gene function determination in both insects and mammals. However, the recent discovery of sequences with similarity to piggyBac in a wide diversity of organisms suggests that piggyBac may be horizontally transferred to distantly related species. This has raised concern on the wide-range application of piggyBac-based transformation vectors and their stability. In this paper, the presence of sequences homologous to the piggyBac transposase was investigated in 17 species belonging to six genera within the Tephritidae family, including many pest species for which transformation has already been achieved. piggyBac-like sequences, with a high degree of similarity to the original Trichoplusia ni transposase sequence were identified only in six species of the Bactrocera genus.

Reversible introduction of transgenes in natural populations of insects.

The most serious challenge concerning genetically modified insects remains their invasion ability. Indeed, transgenic insects often show lower fitness than wild individuals, and the transgene does not seem able to spread through a natural population without a driving system. The use of remobilizable vectors, based on the invading properties of transposable elements, has been frequently suggested. Simulations show that this strategy can be efficient. Moreover, if the transgene is designed to use transposition machinery already present in the genome, the transgene invasion appears to be potentially reversible after a few hundred generations, leading to new experimental perspectives.

Quantitative trait analysis and geographic variability of natural populations of Zaprionus indianus, a recent invader in Brazil.

Five natural samples of a recent South America invader, the drosophilid Zaprionus indianus, were investigated with the isofemale line technique. These samples were compared to five African mainland populations, investigated with the same method. The results were also compared to data obtained on mass cultures of other populations from Africa and India. Three quantitative traits were measured on both sexes, wing and thorax length and sternopleural bristle number. We did not find any latitudinal trend among the American samples, while a significant increase in body size with latitude was observed in the Indian and, to a lesser degree, in the African populations. American populations were also characterized by their bigger size. Genetic variability, estimated by the intraclass correlation among isofemale lines, was similar in American and African populations. The intraline, nongenetic variability was significantly less in the American samples, suggesting a better developmental stability, the origin of which is unclear. A positive relationship was evident between intraline variability of size traits and the wing-thorax length correlation. Altogether, our data suggest that the colonizing propagule introduced to Brazil had a fairly large size, preventing any bottleneck effect being detected. The big body size of American flies suggests that they came from a high-latitude African country. The lack of a latitudinal dine in America seems to be related to the short time elapsed since introduction. The very rapid spread of Z. indianus all over South America suggests that it might rapidly invade North America.

Pre-reproductive isolation as a consequence of allopatric differentiation between populations of Drosophila melanogaster.

While pre-reproductive isolations are more and more frequently described between closely related species or within species, very little is known about their conditions of emergence. In Brazzaville, two populations (Kronenbourg and Loua) of Drosophila melanogaster show a premating isolation. Two hypotheses were proposed to explain such a situation: a local sympatric differentiation or an allopatric divergence followed by a secondary contact. A microsatellite analysis, using markers on all chromosomes, strongly suggests that the Kronenbourg population has a European origin. Therefore, the allopatric divergence between Kronenbourg and Loua populations is probably responsible for the sexual isolation observed today in sympatry, after a recent introduction of a European propagule in Brazzaville.

Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences.

Retrotransposable elements and transposons are generally both found in most eukaryotes. These two classes of elements are usually distinguished on the basis of their differing mechanisms of transposition. However, their respective frequencies, their intragenomic dynamics and distributions, and the frequencies of their horizontal transfer from one species to another can also differ. The main objective of this review is to compare these two types of elements from a new perspective, using data provided by genome sequencing projects and relating this to the theoretical and observed dynamics. It is shown that the traditional division into two classes, based on the transposition mechanisms, becomes less obvious when other factors are taken into consideration. A great diversity in distribution and dynamics within each class is observed. In contrast, the impact on and the interactions with the genome can show striking similarities between families of the two classes.

Classification and nomenclature of retrotransposable elements.

The classification and nomenclature of retrotransposable elements is reviewed. A comparison is made between the initial classification summarized in Capy et al. (1997b), and the more recent proposal based on the classification of the viruses (Hull, 2001). Several problems, mainly relating to the position of elements belonging to the DIRS-like or Bel-like groups, are discussed. The first classification is now out of date, and must be revisited to take account of the discovery of new elements, however the second cannot be extended to the DNA elements. There is therefore, clear evidence of the need to adopt a general and a common classification.

Cchobo, a hobo-related sequence in Ceratitis capitata.

A hobo-related sequence, Cchobo, with high similarity to the Drosophila melanogaster HFL1 and hobo108 elements was isolated from the medfly. Thirteen PCR-derived clones, which share 97.9-100% DNA identity, were sequenced, seven of which do not show frame-shift or stop codon mutations in their conceptual translations. The consensus sequence has 99.7% DNA identity with the D. melanogaster hobo element HFLI. In a phylogenetic analysis with other hobo-related elements, Cchobo clusters with the HFL1 and hobo108 elements from D. melanogaster and hobo-related elements from D. simulans, D. mauritiana and Mamestra brassicae. These elements may have undergone horizontal transfer in the recent past. The genomic distribution of Cchobo was studied by FISH to mitotic and polytene chromosomes, which revealed that Cchobo is distributed within both the heterochromatin and euchromatin. Intra- and interstrain polymorphisms were detected both at euchromatic and heterochromatic sites. These findings suggest that active copies of the element may be present in the medfly genome.

Isofemale lines in Drosophila: an empirical approach to quantitative trait analysis in natural populations.

Founding isofemale lines from wild collected females is a basic tool for investigating the genetic architecture of Drosophila natural populations. The method permits the analysis of quantitative traits under laboratory conditions, with a much broader scope than the mere evidence of a significant genetic heterogeneity among lines. Genetic variability is generally demonstrated by a significant coefficient of intraclass correlation, but several experimental precautions are needed and explained here. The relationship between classical (additive) heritability and intraclass correlation is not straightforward, presumably because the genetic bottlenecks due to the initiation of the lines unravel a significant, nonadditive genetic variance due to dominance and epistatic effects. It is thus suggested to consider intraclass correlation as a specific genetic parameter that enables comparisons between different traits, different populations or different environments. The use of isofemale lines is, however, not restricted to the calculation of an intraclass correlation. It can be used to estimate genetic correlations among traits or environments. The method is also convenient for the analysis of phenotypic plasticity in relation to an environmental gradient. A precise description of the response curves (the reaction norms) is possible, distinguishing trait parameters and plasticity parameters. A fairly general conclusion is that, for a given trait, mean value and plasticity are genetically independent. It is also possible to analyze traits, which, like sexual dimorphism, must be measured on different individuals, and even to demonstrate their genetic variability. In many cases, further empirical and theoretical analyses are possible and needed. It is argued that, in the future, isofemale lines will have an increasing significance among the various techniques appropriate to the analysis of quantitative evolutionary genetics in a diversity of species.

Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes.

The structural variants of the regulatory and coding regions of the LTR-retrotransposon 1731 are described. Two classes of genomic copies of retrotransposon 1731, with and without frameshifting strategy to express Gag and Pol proteins, were earlier revealed in the D. melanogaster genome. Copies without frameshifting are shown to be evolved from an ancient variant with frameshifting and are widespread in the genomes of the melanogaster complex species. Position of a rare codon responsible for ribosome pausing and efficient frameshifting is identified. Two structural variants of 1731 LTRs were detected in the melanogaster complex species: the predominant structural variant A1A2 of 1731 LTR in the D. melanogaster, D. simulans, and D. sechellia genomes contains duplicated and diverged copies of 28 bp in the U3 region, whereas A1 variant lacking this duplication is expanded in the D. mauritiana genome. Selective expansion of the A1A2 variant was detected in the independently established D. melanogaster cell cultures. A1A2 variant is expressed in embryos, cell culture, and testes, whereas A1 is expressed only in testes of D. melanogaster. Relief of expression of the A1A2 but not A1 variant in the ovaries as a result of mutation in the RNA interference (RNAi) spn-E gene is shown. Thus, expansion of the recently evolved genomic variants of the LTR retrotransposon 1731 possessing a new translation strategy, duplication in the U3 region, and extended profile of expression is revealed.

Comparative analysis of morphological traits among Drosophila melanogaster and D. simulans: genetic variability, clines and phenotypic plasticity.

The two sibling cosmopolitan species, Drosophila melanogaster and D. simulans, are able to proliferate under very different climatic conditions. This has resulted in local adaptations, which are often arranged in latitudinal clines. Such clines are documented for body weight, wing and thorax length, sternopleural and abdominal bristle number, ovariole number and thoracic pigmentation. The overall magnitude of geographical differentiation is, however, much less in D. simulans than in D. melanogaster, and latitudinal clines are less pronounced. The fact that natural populations live under different climates raises the problem of interaction between temperature and phenotype. The reaction norms of morphometrical traits have been investigated as a function of growth temperature. The shapes of the response curves vary according to the investigated trait. They are generally curvilinear and can be described by calculating characteristic values after polynomial adjustments. For a given trait, the reaction norms of the two species are similar in their shape, although some significant differences may be observed. Within each species, significant differences are also observed between geographic populations: reaction norms are not parallel and the divergence is better marked when more distant populations (e.g., temperate and tropical) are compared. It thus appears that besides mean trait value, phenotypic plasticity is also a target of natural selection. A specific analysis of wing shape variation according to growth temperature was also undertaken. Reaction norms with different shapes may be observed in various parts of the wing: the major effect is found between the basis and the tip of the wing, but in a similar way in the two species. By contrast, some ratios, called wing indices by taxonomists, may exhibit completely different reaction norms in the two species. For a single developmental temperature (25 degrees C) the phenotypic variability of morphometrical traits is generally similar in the two species, and also the genetic variability, estimated by the intraclass correlation. A difference exists, however, for the ovariole number which is less variable in D. simulans. Variance parameters may vary according to growth temperature, and a detailed analysis was made on wing dimensions. An increase of environmental variability at extreme, heat or cold temperatures, has been found in both species. Opposite trends were, however, observed for the genetic variability: a maximum heritability in D. simulans at middle temperatures, corresponding to a minimum heritability in D. melanogaster. Whether such a difference exists for other traits and in other populations deserves further investigations. In conclusion, morphometrical analyses reveal a large amount of significant differences which may be related to speciation and to the divergence of ecological niches. Within each species, numerous geographic variations are also observed which, in most cases, reflect some kinds of climatic adaptation.

Microspatial structure of Drosophila melanogaster populations in Brazzaville: evidence of natural selection acting on morphometrical traits.

Two genetically distinct habitat races of Drosophila melanogaster coexist in Brazzaville (Congo). One is the typical field type of Afrotropical populations, the other mainly breeds in beer residues in breweries. These two populations differ in their ethanol tolerance, in their allelic frequencies at several enzyme and microsatellite loci and in the composition of their cuticular hydrocarbons. The brewery population is quite similar to European temperate populations with regard to all these traits. Previous investigations of two morphological traits (ovariole number and sternopleural bristle number) failed to detect any difference between the two habitat races. Here we investigated other morphological traits (wing and thorax length, thorax pigmentation and female abdomen pigmentation). The reaction norms of these traits according to growth temperature were compared in the two Afrotropical habitat races and in a French temperate population. As expected, the French population was very different from the field African population: as a general rule, the brewery population (Kronenbourg) was intermediate in several aspects between the other two. We conclude that the strong selective forces that maintain the genetic divergence between the two habitat races also act on morphometrical traits, and the possible selective mechanisms are discussed.

[Acquisition and loss of modules: the construction set of transposable elements]. / Priobretenie i poteria modulei: nabor dlia konstruirovaniia mobil'nykh élementov.

Phylogenetic analysis of transposable elements (TEs) allows us to define the relationships between the domains or gene(s) that compose them. Moreover, modules of a few amino-acids can be detected within gag, pol, env genes or within the integrase domain of retrotransposons and transposase of DNA elements. The combination of these observations clearly shows that the evolutionary history of TEs is the outcome of the acquisition and loss of modules with differing origins and histories. This raises the question of the origin of TEs: are they derived from viruses? Are they where viruses come from? Do the basic building bricks come from the prokaryotes, and can they be assembled in the eukaryotes? Are the TEs found in prokaryotes the result of the disintegration of complex elements such as retroelements? Do they evolve from the simplest to the more complex, or are they opportunistic sequences evolving by acquiring and/or losing modules which may be either important or superfluous to their fitness (i.e., their ability to transpose). These are some of the questions that are addressed and discussed in the light of the comparative structures of TEs.

Reproductive isolation in natural populations of Drosophila melanogaster from Brazzaville (Congo).

The aim of this work is to analyze the homogamy previously detected between two natural populations of Drosophila melanogaster from Brazzaville. It is shown that mating isolation was still maintained under laboratory conditions 10 years after the populations samples were trapped. Isolation seemed to be due mainly to premating isolation and we checked for any suggestion of post-mating mortality of hybrids. Pre-mating isolation was not symmetrical, and significant chi2 values were found in 3/4 possible 3-way mating choice experiments. The only exception involved a male from the countryside and two females (one from each population) for which no significant mating preference was detected. Mortality of hybrids was intermediate between those of the parental strains showing a clear maternal effect and the existence of partial dominance. Major differences in the cuticular hydrocarbons were also found and they could account for the isolation. These findings in populations from African breweries indicate that they are closely related to European ones, suggesting that this phenomenon is not a case of sympatric speciation, but probably attributable to the reintroduction of an allopatric population.

A new basal subfamily of mariner elements in Ceratitis rosa and other tephritid flies.

Several copies of highly related transposable elements, Crmar2, Almar1, and Asmar1, are described from the genomes of Ceratitis rosa, Anastrepha ludens, and A. suspensa, respectively. One copy from C. rosa, Crmar2.5, contains a full-length, uninterrupted ORF. All the other copies, from the three species contain a long deletion within the putative ORF. The consensus Crmar2 element has features typical of the mariner/Tc1 superfamily of transposable elements. In particular, the Crmar2 consensus encodes a D,D41D motif, a variant of the D,D34D catalytic domain of mariner elements. Phylogenetic analysis of the relationships of these three elements and other members of the mariner/Tc1 superfamily, based on their encoded amino acid sequences, suggests that they form a new basal subfamily of mariner elements, the rosa subfamily. BLAST analyses identified sequences from other diptera, including Drosophila melanogaster, which appear to be members of the rosa subfamily of mariner elements. Analyses of their molecular evolution suggests that Crmar2 entered the genome of C. rosa in the recent past, a consequence of horizontal transfer.

Molecular evolution of the AMP-forming Acetyl-CoA synthetase.

Acetyl-CoA-Synthetase (ACS) is involved in the production of acetate, a major metabolite in numerous organisms. There are two forms of this enzyme: ADP-forming ACS and ATP-forming ACS. We focus mainly on the AMP-forming ACS gene, which is relatively well conserved in eubacteria, archeaebacteria, and eukaryotes. BLAST searches in databases showed 30 protein sequences significantly related to the ACS. Most of these sequences were identified as ACS but three of them, belonging to the mammalian species, were annotated as another gene named: the SA gene, which is involved in the essential hypertension. The ACS and SA genes probably derived from a duplication of an ancestral gene but have acquired different functions. Six conserved regions of the ACS protein were defined across the three domains of life. While the precise function of the conserved regions remains unknown, they are probably involved in the enzymatic activity. Among eukaryotes, we found a high variability with respect to the number and the position of introns. However, some positions are conserved between fungi and a nematode. A maximum likelihood tree based upon the conserved regions showed that all sequences except the one from B. subtilis, belong to two basic groups: one the SA-like group including sequences from Archaeoglobus fulgidus and Streptomyces coelicolor, and second, the ACS group. The later can be further divided in two parts: a prokaryotic one including eubacteria and an archaebacterium, and a eukaryotic group within which two proteobacterial sequences branch including ACS from the alpha-proteobacterium Rhodobacter capsulatus. Within the eukaryotic group, bootstrap support is very low, but overall the data are consistent with the view that eukaryotes acquired their ACS gene from the ancestors of mitochondria. The localization of this enzyme in eukaryotic mitochondria is the additional evidence in favor of this interpretation.

Stress and transposable elements: co-evolution or useful parasites?

The activity of transposable elements can be induced by environmental and population factors and in particular by stresses in various organisms. A consequence of the increase in transposable element mobility is the creation of new genetic variability that can be useful in the face of stressful conditions. In this review, results supporting this hypothesis are presented and discussed. The main question is how stress induces the activity of transposable elements. We discuss hypotheses based upon the existence of promoters or fixation sites of transcription activators in the untranslated regions of transposable elements, similar to those found in regulatory regions of host defence genes.

Sexual isolation of genetically differentiated sympatric populations of Drosophila melanogaster in Brazzaville, Congo: the first step towards speciation?

Two sympatric populations of Drosophila melanogaster were collected in the Brazzaville area in Congo, one from the suburban countryside and the other from a brewery located in the city. They were compared for several genetically determined traits including morphology, allozymes, microsatellites, cuticular hydrocarbons, and sexual behaviour. The two populations were similar to other African populations for morphological traits, but differed significantly from each other for all other characters. The countryside population resembled other African populations, whereas the urban population was consistently similar to European populations. Mating choice experiments showed incipient reproductive separation between the populations. In agreement with the hypothesis that D. melanogaster originated in Africa and spread to the rest of the world by invading human-modified habitats, we suggest that man-adapted fruit fly populations have returned 'back to Africa', and remained partially isolated from older native stocks.