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.

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.

The strange phylogenies of transposable elements: are horizontal transfers the only explantation?

Analyses of the evolution of transposable elements reveal some inconsistencies when the phylogenies of such elements are compared to conventional phylogenies of the host species. Such discrepancies are generally interpreted as resulting from occasional horizontal transfers of transposable elements across species boundaries. This phenomenon has been clearly demonstrated for only a few elements and both its frequency and the mechanism by which it occurs remain unknown. Moreover, in many cases, the hypothesis of horizontal transfer must be compared with alternative evolutionary scenarios.

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.

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.

Estimation of the allele number in a natural population by the method of isofemale lines.

The number of alleles present in a natural population of unknown structure is estimated using a sequential sampling procedure applied to isofemale lines. Two questions are raised: how many individuals per isofemale line must be assayed and how many isofemale lines must be sampled to get an adequate sample to estimate the number of alleles, at a given risk, of the natural population? On the one hand, we show that when wild females are inseminated once, only two individuals per line are required. On the other hand, the number of isofemale lines that must be sampled depends on the risk chosen of losing an allele, on the number of alleles present in the population and on their drawing probabilities. When the population structure is known, an accurate answer can be provided. For an unknown population structure, one general sequential sampling previously described by J. Rouault and P. Capy is proposed to estimate the number of alleles in the population from data on isofemale lines.

Sequence analysis of active mariner elements in natural populations of Drosophila simulans.

Active and inactive mariner elements from natural and laboratory populations of Drosophila simulans were isolated and sequenced in order to assess their nucleotide variability and to compare them with previously isolated mariner elements from the sibling species Drosophila mauritiana and Drosophila sechellia. The active elements of D. simulans are very similar among themselves (average 99.7% nucleotide identity), suggesting that the level of mariner expression in different natural populations is largely determined by position effects, dosage effects and perhaps other factors. Furthermore, the D. simulans elements exhibit nucleotide identities of 98% or greater when compared with mariner elements from the sibling species. Parsimony analysis of mariner elements places active elements from the three species into separate groups and suggests that D. simulans is the species from which mariner elements in D. mauritiana and D. sechellia are most likely derived. This result strongly suggests that the ancestral form of mariner among these species was an active element. The two inactive mariner elements sequenced from D. simulans are very similar to the inactive peach element from D. mauritiana. The similarity may result from introgression between D. simulans and D. mauritiana or from selective constraints imposed by regulatory effects of inactive elements.

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.

Somatic activity of the mariner transposable element in natural populations of Drosophila simulans.

The characteristics of the mariner transposable element in natural populations of Drosophila simulans from different parts of the world were analysed. The somatic excision rate (estimated from a test-cross with a reference strain), the average number of copies (determined by Southern blots), and the presence of deleted copies (detected by polymerase chain reaction amplification) were estimated for each population. There was a great variability in the somatic excision rate, measured as the percentage of mosaic males, both within and between populations. The population effect was highly significant. The average copy number also varied widely and was correlated with the excision rate. Rare deleted elements were detected by polymerase chain reaction and Southern blots. Percentage of mosaic males increased in strains kept for a long time at low temperature, and the somatic excision rate increased with the latitude of origin of populations. Therefore, these results strongly suggest that temperature could be involved in the regulation of mariner somatic excision in D. simulans.

Active mariner transposable elements are widespread in natural populations of Drosophila simulans.

The occurrence of active, or autonomous, mariner elements was investigated by crossing white-peach mutant Drosophila simulans females with wild-type males from various geographic origins. From a total of 194 experimental crosses only 17 failed to produce progeny with eye mosaicism (MOS, i.e. pigmented spots in otherwise white-peach eyes). Therefore, active mariner elements inducing somatic excision of the copy inserted at the white locus are abundant in all populations sampled. In the experimental crosses the frequency of mosaic offspring ranged from 0 to 100%, showing that the phenotypic expression is highly variable. The MOS phenotype, measured by the number of spots on the eyes, is quite variable within the progeny of single crosses. Although a difference was observed in the average MOS score (percentage of mosaic flies) between northern and southern populations of France, there was no indication of long range variation between geographic populations. Neither was there a systematic difference between recently collected populations and samples kept several years as isofemale lines.

[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.

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.

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.

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.

Retrotransposons and retroviruses: analysis of the envelope gene.

Retroviruses and long terminal repeat (LTR) retrotransposons share a common structural organization. The main difference between these retroelements is the presence of a functional envelope (env) gene in retroviruses, which is absent or nonfunctional in LTR retrotransposons. Several similarities between these two groups of retroelements have been detected for the reverse transcriptase, gag, and integrase domains. Assuming that each of these domains shares a common ancestral sequence, several hypotheses could account for the emergence of retroviruses from LTR retrotransposons. In this context, the positions of elements such as gypsy and the members of the Ty3 subfamily are not clear, since they are classified as retroviruses but phylogenetically they are assigned to the LTR retrotransposon group. We compared the env gene products of these retroelements and identified two similar motifs in retroviruses and LTR retrotransposons. These two regions do not occur in the same order. If we assume that they are derived from the same ancestral sequence, this could result from independent acquisition of the various domains rather than the single acquisition of the whole env gene. However, we cannot exclude the possibility that the env gene was reorganized after being acquired. Trees based on these regions show that these two groups of elements are clearly distinguished. These trees are similar to those obtained from reverse transcriptase or integrase. In trees based on reverse transcriptase, the retroviruses with complete or partial env genes can be distinguished from the other LTR retrotransposons.