The dynamics of the roo transposable element in mutation-accumulation lines and segregating populations of Drosophila melanogaster

We estimated the number of copies for the long terminal repeat (LTR) retrotransposable element roo in a set of long-standing Drosophila melanogaster mutation-accumulation full-sib lines and in two large laboratory populations maintained with effective population size approximately 500, all of them derived from the same isogenic origin. Estimates were based on real-time quantitative PCR and in situ hybridization. Considering previous estimates of roo copy numbers obtained at earlier stages of the experiment, the results imply a strong acceleration of the insertion rate in the accumulation lines. The detected acceleration is consistent with a model where only one (maybe a few) of the approximately 70 roo copies in the ancestral isogenic genome was active and each active copy caused new insertions with a relatively high rate ( approximately 10(-2)), with new inserts being active copies themselves. In the two laboratory populations, however, a stabilized copy number or no accelerated insertion was found. Our estimate of the average deleterious viability effects per accumulated insert [E(s) < 0.003] is too small to account for the latter finding, and we discuss the mechanisms that could contain copy number.     

Transposition rate of the 412 retrotransposable element is independent of copy number in natural populations of Drosophila simulans

The transposition and excision rates of the 412 retrotransposable element were estimated in five populations of Drosophila simulans differing in their average 412 copy numbers, which ranged from 2 to 54. The transposition rate was found to equal 1 x 10(-3) to 2 x 10(-3), independently of copy number. No excision was detected. These values eliminate autoregulation as a force maintaining copy number of the 412 element in natural populations of D. simulans.      

Chromosomal distribution and population dynamics of the 412 retrotransposon in a natural population of Drosophila melanogaster

The localization of the insertion sites of the 412 retrotransposable element was analysed by in situ hybridization to the polytene chromosomes of the genomes of males from a natural population of Drosophila melanogaster. Non-parametric statistical tests do not reveal any particular distribution of the insertion sites over the chromosomes, suggesting an apparently random distribution of the 412 element. Aggregation and dispersion tests were highly significant with data of copy number (when all genomes are pooled, many copies may be at a given site), suggesting the existence of sites with high insertion frequency. Comparison with other data from the literature confirms the tendency for a low proportion of insertions on the X chromosome in comparison with the autosomes, a result in agreement with selection acting against the detrimental effect of the 412 element insertions.     

Maintenance of transposable element copy number in natural populations of Drosophila melanogaster and D. simulans

To investigate the main forces controlling the containment of transposable elements (TE) in natural populations, we analyzed the copia, mdg1, and 412 elements in various populations of Drosophila melanogaster and D. simulans. A lower proportion of insertion sites on the X chromosome in comparison with the autosomes suggests that selection against the detrimental effects of TE insertions is the major force containing TE copies in populations of Drosophila. This selection effect hypothesis is strengthened by the absence of the negative correlation between recombination rate and TE copy number along the chromosomes, which was expected under the alternative ectopic exchange model (selection against the deleterious rearrangements promoted by recombination between TE insertions). A cline in 412 copy number in relation to latitude was observed among the natural populations of D. simulans, with very high numbers existing in some local populations (around 60 copies in a sample from Canberra, Australia). An apparent absence of selection effects in this Canberra sample and a value of transposition rate equal to 1–2 × 10^-3 whatever the population and its copy number agree with the idea of recent but temporarily drastic TE movements in local populations. The high values of transposition rate in D. simulans clearly disfavor the hypothesis that the low amount of transposable elements in this species could result from a low transposition rate. This revised version was published online in August 2006 with corrections to the Cover Date.     

Geographical variation in insertion site number of retrotransposon 412 inDrosophila simulans

The insertion site number of the retrotransposable element 412 was analyzed in natural populations ofDrosophila simulans of worldwide origin by in situ hybridization. We observe a gradient in copy number ranging from as high as 23 in Europe to 1–10 in South Africa, while populations in Madagascar and the Indian Islands, which are the cradle ofD. simulans, have only 3–7 copies. We find very different copy numbers in some local populations of Australia and the Pacific Islands (with around 60 copies in 1 sample and only 5 in another), suggesting spontaneous transposition bursts in local populations. Such bursts occurring now and then in local natural populations followed by fly migration could lead to the progressive invasion of the entire species by the transposable element mobilized, explaining the gradient in 412 copy number between northern and southern hemispheres.     

Accumulation of transposable elements in laboratory lines of Drosophila melanogaster

It is recognized that a stable number of transposable element (TE) copies per genome is maintained in natural populations of D. melanogaster as a result of the dynamic equilibrium between transposition to new sites and natural selection eliminating copies. The force of natural selection opposing TE multiplication is partly relaxed in inbred laboratory lines of flies. The average rate of TE transposition is from 2.6 × 10 ^-4 to 5.0 ×10 ^-4 per copy per generation, and the average rate of excision is at least two orders of magnitude lower; therefore inbred lines accumulate increasing numbers of copies with time. Correlations between the rate of transposition and TE copy number have been determined for copia, Doc, roo, and 412 and found to be either zero or positive. Because the rate of transposition is not a decreasing function of TE copy number, TE accumulation in inbred lines is self-accelerating. Transpositions cause a substantial fraction of mutations in D. melanogaster, therefore the mutation rate should increase with time in laboratory lines of this species. Inferences about the properties of spontaneous mutations from studies of mutation accumulation in laboratory lines should be reevaluated, because they are based on the assumption of a constant mutation rate. This revised version was published online in August 2006 with corrections to the Cover Date.     

Retrotransposon mdg3 is transferred between somatic cells of unrelated species in coculture

Since retrovirus-like particles of gypsy (mdg4) are capable of interspecific transfer, other Drosophila melanogaster gypsy-related retrotransposons were tested for this property. As a donor and a recipient, D. melanogaster and D. virilis cultured cells were used. Recipient cell DNA was analyzed with probes directed to mdg1, mdg3, 17.6, 297, 412, or B104/roo. Transfer was demonstrated for mdg3, which lacks env. The possible mechanism of transfer is discussed.     

Mechanisms regulating the copy numbers of six LTR retrotransposons in the genome of Drosophila melanogaster

There has been debate over the mechanisms that control the copy number of transposable elements in the genome of Drosophila melanogaster. Target sites in D. melanogaster populations are occupied at low frequencies, suggesting that there is some form of selection acting against transposable elements. Three main theories have been proposed to explain how selection acts against transposable elements: insertions of a copy of a transposable element are selected against; chromosomal rearrangements caused by ectopic exchange between element copies are selected against; or the process of transposition itself is selected against. The three theories give different predictions for the pattern of transposable element insertions in the chromosomes of D. melanogaster. We analysed the abundance of six LTR (long terminal repeat) retrotransposons on the X and fourth chromosomes of multiple strains of D. melanogaster, which we compare with the predictions of each theory. The data suggest that no one theory can account for the insertion patterns of all six retrotransposons. Comparing our results with earlier work using these transposable element families, we find a significant correlation between studies in the particular model of copy number regulation supported by the proportion of elements on the X for the different transposable element families. This suggests that different retrotransposon families are regulated by different mechanisms.     

Insertion polymorphism of retrotransposable elements in populations of the insular, endemic species Drosophila madeirensis

The insertion site numbers of the retrotransposable elements (TE) 412, gypsy and bilbo were determined in individuals of five distinct natural populations of the endemic species Drosophila madeirensis from the island of Madeira. The TE distributions were compared to those of the paleartic, widespread and phylogenetically closely related species, D. subobscura. In situ hybridization and Southern blots showed that in D. madeirensis the number of insertion sites ranged between 10 and 15, three and six, and 35 and 42 for elements 412, gypsy and bilbo, respectively. The corresponding values for D. subobscura were similar. Two of these elements, 412 and gypsy, had very few insertions in the heterochromatin, unlike bilbo, which displayed a high heterochromatic insertion number. The Southern band polymorphism was very high, leading to within-population variation of 97.2%, whatever the population and the TE concerned. Using the polymorphic TE insertion sites as markers to analyse population structure by AMOVA, adapted for RAPD (Randomly Amplified Polymorphic DNA) data, we found small but significant genetic differences between the populations on Madeira. This slight differentiation, coupled with similar copy numbers for each TE between populations, suggests that the D. madeirensis species consists of a single, only slightly subdivided population. These data also show that insular populations and endemic species of Drosophila can have as many copies of TEs as more widespread species.     

Ty1 copy number dynamics in Saccharomyces

To understand long terminal repeat (LTR)-retrotransposon copy number dynamics, Ty1 elements were reintroduced into a "Ty-less" Saccharomyces strain where elements had been lost by LTR-LTR recombination. Repopulated strains exhibited alterations in chromosome size that were associated with Ty1 insertions, but did not become genetically isolated. The rates of element gain and loss under genetic and environmental conditions known to affect Ty1 retrotransposition were determined using genetically tagged reference elements. The results show that Ty1 retrotransposition varies with copy number, temperature, and cell type. In contrast to retrotransposition, Ty1 loss by LTR-LTR recombination was more constant and not markedly influenced by copy number. Endogenous Ty1 cDNA was poorly utilized for recombination when compared with LTR-LTR recombination or ectopic gene conversion. Ty1 elements also appear to be more susceptible to copy number fluctuation in haploid cells. Ty1 gain/loss ratios obtained under different conditions suggest that copy number oscillates over time by altering the rate of retrotransposition, resulting in the diverse copy numbers observed in Saccharomyces.     

Mdg-1 mobile element polymorphism in selected Drosophila melanogaster populations

The changes in mdg-1 mobile element polymorphism that followed artificial selection for either high or low egg-to-adult viability in a Drosophila melanogaster population were investigated. The two selected subpopulations were thus characterized for fecundity, wing length, and number and location of the mdg-1 mobile element by in situ hybridization of the biotinylated-DNA on salivary gland chromosomes. The selected populations that differed greatly in egg-to-adult viability showed the same mean fecundity and identical values for intra and inter components of variances, intraclass correlation coefficient, and fluctuating asymmetry estimated on the wing length measurement. This indicates a non-correlated effect between deleterious mutations affecting viability and other fitness components. However, the two selected populations differed in their pattern of mdg-1 location, although the mean number of insertions per genome was not different from that of the initial population hence, the number of insertions of the mdg-1 mobile element was independent of the effective population size. These results suggest that the mdg-1 copy number was regulated, and that during the selection process, drift and inbreeding made up new insertion patterns of the mdg-1 element in the selected populations. The results are discussed in the light of some recent theoretical models of the population dynamics of transposable elements.     

Transiently beneficial insertions could maintain mobile DNA sequences in variable environments

The maintenance of mobile DNA sequences in clonal organisms has been seen as a paradox. If selfish mobile sequences spread through genomes only by overreplication in transposition, then sexuality is necessary for their spread through populations. The persistence of bacterial transposable elements without obvious dominant selectable markers has previously been explained by horizontal transfer. However, advantageous insertions of mobile DNAs are known in bacteria. Here we model maintenance of an otherwise selfish mobile DNA element in a clonal species in which selection for null mutations occurs during one of two temporally alternating environments. Large areas of parameter space permit maintenance of mobile DNAs where, without selection, they would have gone extinct. Horizontal transfer diminishes, rather than enhances, mean copy number. In finite populations, effective population sizes are greatly reduced by selective sweeps, and mean copy number can be increased as the reduced variance in copy number results in reduced selection.     

Retrotransposon mdg3 Is Transferred between Somatic Cells of Unrelated Species in Mixed Culture

Since retrovirus-like particles of gypsy (mdg4) are capable of interspecific transfer, other Drosophila melanogaster gypsy-related retrotransposons were tested for this property. As a donor and a recipient, D. melanogaster and D. virilis cultured cells were used. Recipient cell DNA was analyzed with probes directed to mdg1, mdg3, 17.6, 297, 412, or B104/roo. Transfer was demonstrated for mdg3, which lacks env. The possible mechanism of transfer is discussed.     

The population biology and evolutionary significance of Ty elements in Saccharomyces cerevisiae

The basic structure and properties of Ty elements are considered with special reference to their role as agents of evolutionary change. Ty elements may generate genetic variation for fitness by their action as mutagens, as well as by providing regions of portable homology for recombination. The mutational spectra generated by Ty 1 transposition events may, due to their target specificity and gene regulatory capabilities, possess a higher frequency of adaptively favorable mutations than spectra resulting from other types of mutational processes. Laboratory strains contain between 25–35 elements, and in both these and industrial strains the insertions appear quite stable. In contrast, a wide variation in Ty number is seen in wild isolates, with a lower average number/genome. Factors which may determine Ty copy number in populations include transposition rates (dependent on Ty copy number and mating type), and stabilization of Ty elements in the genome as well as selection for and against Ty insertions in the genome. Although the average effect of Ty transpositions are deleterious, populations initiated with a single clone containing a single Ty element steadily accumulated Ty elements over 1,000 generations. Direct evidence that Ty transposition events can be selectively favored is provided by experiments in which populations containing large amounts of variability for Ty1 copy number were maintained for 100 generations in a homogeneous environment. At their termination, the frequency of clones containing 0 Ty elements had decreased to 0.0, and the populations had became dominated by a small number of clones containing >0 Ty elements. No such reduction in variability was observed in populations maintained in a structured environment, though changes in Ty number were observed. The implications of genetic (mating type and ploidy) changes and environmental fluctuations for the long-term persistence of Ty elements within the S. cerevisiae species group are discussed.     

Fitness Effects of Ty Transposition in Saccharomyces Cerevisiae

It has been suggested that the primary evolutionary role of transposable elements is negative and parasitic. Alternatively, the target specificity and gene regulatory capabilities of many transposable elements raise the possibility that transposable element-induced mutations are more likely to be adaptively favorable than other types of mutations. Populations of Saccharomyces cerevisiae containing large amounts of variation for Ty1 genomic insertions were constructed, and the effects of Ty1 copy number on two components of fitness, yield and growth rate were determined. Although mean stationary phase density decreased with increased Ty1 copy number, the variance and range increased. The distributions of stationary phase densities indicate that many Ty1 insertions have negative effects on fitness, but also that some may have positive effects. To test directly for adaptively favorable Ty1 insertions, populations containing large amounts of variability for Ty1 copy number were grown in continuous culture. After 98-112 generations the frequency of clones containing zero Ty1 elements had decreased to approximately 0.0, and specific Ty1-containing clone families had predominated. Considering that most of the genetic variation in the populations was due to Ty1 transposition, and that Ty1 insertions had, on average, a negative effect on fitness, we conclude that Ty1 transposition events were directly responsible for the production of adaptive mutations in the clones that predominated in the populations.     

Chromosomal Distribution of Transposable Elements in Drosophila Melanogaster: Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number

Data of insertion site localization and site occupancy frequency of P, hobo, I, copia, mdg1, mdg3, 412, 297, and roo transposable elements (TEs) on the polytene chromosomes of Drosophila melanogaster were extracted from the literature. We show that TE insertion site number per chromosomal division was significantly correlated with the amount of DNA. The insertion site number weighted by DNA content was not correlated with recombination rate for all TEs except hobo, for which a positive correlation was detected. No global tendency emerged in the relationship between TE site occupancy frequency, weighted by DNA content, and recombination rate; a strong negative correlation was, however, found for the 3L arm. A possible dominant deleterious effect of chromosomal rearrangements due to recombination between TE insertions is thus not the main factor explaining the dynamics of TEs, since this hypothesis implies a negative relationship between recombination rate and both TE insertion site number and site occupancy frequency. The alternative hypothesis of selection against deleterious effects of insertional mutations is discussed.