BACKGROUND
genome evolution occurs by several processes, including global genome duplications, segmental duplications and the amplification/deletion of repetitive sequences.
among the repeated sequences, transposable elements , which constitute a high proportion in many genomes, play an important role in genome evolution  <cit> .
the transposition rates of these tes depend on the amount and type of the tes present in the genome; they are not constant over time, but are subject to amplification bursts in certain species and populations  <cit> .
as a result, genomes contain widely differing amounts of tes that are not directly correlated to their activity levels.
for instance, the human genome is composed of at least 50% of tes, but only very few are active, and they are responsible for less than 1% of mutations  <cit> .
in contrast, in drosophila melanogaster, only 18% of the genome is composed of tes, but a high proportion of mutations  is attributable to their transposition  <cit> .
a te life cycle can be viewed as successive waves of transposition/loss: invasion of the host genome by tes being followed by their progressive elimination  <cit> .
for example, the line- <dig>  element has colonized the entire human genome by successful waves of transposition  <cit> , and today it is the most abundant te family in this genome.
however, in humans, most of the elements have been inactivated either by structural changes or by epigenetic control, such as dna methylation  <cit> .
in d. melanogaster, the i factor has recently reinvaded this genome after being lost from the chromosome arms  <cit> .
te elimination from genomes is therefore a commonly observed phenomenon, although no real-time observation of a te extinction has ever been reported.
as tes have a considerable influence on remodeling the genome structure  <cit> , we need to understand the dynamics of changes in their copy numbers.
one way to investigate these dynamics is to analyze closely related species with differing te amounts, such as d. simulans and d. melanogaster.
these species diverged  <dig> to  <dig> million years ago  <cit>  and have differing proportions of tes: d. melanogaster contains more than 18% of tes, whereas d. simulans contains only 5%  <cit> .
d. simulans has fewer copies of most tes  <cit> , but there are a few exceptions.
the dna-transposon hobo is more abundant in d. simulans, the retrovirus-like gypsy and zam elements have the same low number of copies in both species, and the line-like element helena is present in the d. simulans genome , but has not been detected in the chromosome arms of d. melanogaster  <cit> .
the striking distribution of helena in natural populations of these two species, and the fact that degenerated copies are found in the sequenced d. melanogaster genome, make this line-like element an ideal model system to study the real time te life cycle.
petrov and colleagues  <cit>  proposed that deletions are common events in drosophila, and based this suggestion on the analysis of partial helena sequences from different drosophila species.
however, it is difficult to extrapolate this to other tes, if we take into account the fact that helena is one of the few degenerate tes in the d. melanogaster sequenced genome  <cit> .
comparing closely related species with differing te amounts, could be used to test the importance of this deletion process in regulating te genome invasions.
we analyzed the structure and activity of helena using the sequenced genomes and of  <dig> natural populations of d. melanogaster and d. simulans.
we show that the elimination of helena from its host genomes is a very quick process, and that it is mediated by massive internal deletions in the element  <cit> .
we conclude that the process of elimination of helena is far advanced in d. melanogaster.
but is still in progress in d. simulans.
RESULTS
in silico identification of a complete copy of helena in the d. simulans genome
because no full-length copy of helena had previously been described, we performed a bioinformatic search for such a copy in the draft sequence of the d. simulans genome  <cit> .
we found a 4912-bp copy of helena on the chromosome arm 3r  .
helena belongs to the jockey clade  <cit> , has a 25-bp poly a tail, and two overlapping open reading frames .
the first orf is 1737-bp and codes a 579-amino acid  protein that has high similarities to the gag protein of other line-like elements, such as x, jockey and het-a  <cit> .
the gag-like protein contains the major homology region , followed by a cysteine-rich domain .
this region is common to all gag-like proteins, and confers an rna or dna single-strain binding property on these elements, as well as being essential for gag oligomerization.
helena has a coiled-coil domain located in the 5' region of the gag protein, something that had previously only been seen in l <dig> elements from mammals  <cit>  and in some ltr retrotransposons from drosophila  <cit> .
the second orf, which starts on the last base of orf <dig>  is 2721-bp, and codes a 907-aa protein corresponding to the pol gene, which is very similar to the protein of the bs and jockey elements.
the pol-like protein contains all the domains necessary for its function: an apyrimidic endonuclease and an exonuclease , plus a reverse transcriptase domain .
both orfs are intact, could produce transcripts, and are surrounded by two untranslated regions .
because the regulatory region is often defined in the 5'utr  <cit> , we performed a bioinformatic search for transcription factors binding sites in this region.
a single region was detected containing several transcription factor binding sites, such as sp <dig> and upstream stimulating factor-like  binding domains.
this region also displays a binding site for a tata-binding protein , and an estrogen response element .
the copies of helena in the sequenced genomes of d. melanogaster and d. simulans
using the complete sequence of helena as a query, we found  <dig> helena sequences in the d. simulans genome .
twenty-eight of these copies were located on the chromosome arms, and the remaining  <dig> were in the u part of the genome, that may correspond to heterochromatin.
the copies ranged in size from  <dig> bp to  <dig> bp.
however, it is difficult to determine the exact size of some copies due to the presence of numerous undetermined bases.
two copies  were longer than the reference sequence due to insertions.
in some other cases, we may be looking at fragments of the same copy; however, the distances that separate them are too large to allow us to find out with certainty whether they come from the same copy.
the estimated number of  <dig> copies in d. simulans may therefore be an overestimation.
the average percentage identity is  <dig> % for all copies, with an average of  <dig> % for the copies in the euchromatin, and of  <dig> % for the copies in the u part.
in the sequenced genome of d. melanogaster, we found  <dig> copies of helena , which ranged in size from  <dig> bp to  <dig> bp.
the average percentage identity was  <dig> % for all copies, with an average of  <dig> % for the copies in the chromosome arms, and of  <dig> % for the copies located in the u part.
most of the copies in this genome have therefore been degraded, with numerous internal deletions or insertions.
all copies are truncated on the 5' side, and are doa  copies, apart from the 3l_ <dig> copy, although even this displays some internal deletions.
we analyzed in greater detail any copies that could correspond to the most recent insertions in both d. melanogaster and d. simulans.
we used specific blast criteria to identify these copies: we selected matches with at least 90% identity, and a length at least 50% of that of the complete copy, with e-values of less than 10e- <dig> .
in d. melanogaster, only the 3l_ <dig> copy described above met all the blast criteria.
it is obviously an inactive copy, since more than four deletions were detected within its sequence.
in d. simulans, six copies were found that matched the blast criteria, including the complete copy on the 3r chromosome ; the other five copies had internal deletions, and insertions were detected in four of them.
chromatin localization of helena copies in natural populations
we used in situ hybridization to estimate the number of helena insertion sites located on the arms  of the polytene chromosomes from salivary glands of both d. melanogaster and d. simulans.
both species had centromeric staining, but only d. simulans from natural populations presented euchromatic bands  with no fixed sites .
with this experiment we did not detect any insertions of helena in the chromosome arms, which could be explained by the short size of the elements and the divergence to the probe used.
inter-population polymorphism
we analyzed the inter-population helena copy number polymorphism by southern blot, using a restriction enzyme that does not cut inside the element.
this method detects both heterochromatic and euchromatic sequences.
as shown in figure  <dig>  d. melanogaster had  <dig> to  <dig> bands per population, and several bands were shared by different populations.
these copies could correspond to ancient and fixed heterochromatic copies in the d. melanogaster genome.
d. simulans populations contained numerous helena copies  with a high level of insertion polymorphism.
since the enzyme used for the southern blot did not cut inside the element, all bands over  <dig>  kb could correspond to a complete element.
because both species harbored bands over  <dig>  kb, they could have full-length helena copies.
pcr screening
three sets of primers were used to amplify the whole orf <dig> and two fragments of the orf <dig>  no bands corresponding to the orf <dig> were observed in any of the d. melanogaster natural populations in agreement with the absence of this orf in the sequenced genome.
there was a high level of size polymorphism for the d. melanogaster orf <dig>  corresponding to the different internal deletions already analyzed by petrov et al.
<cit> .
in contrast, d. simulans displayed low size polymorphism for helena orf <dig> and orf <dig>  indeed, only one population out of twenty had two sets of orf <dig> .
all d. simulans populations had two to three sets of orf <dig>
analysis of helena copies in d. simulans populations
pcr fragments obtained from the d. simulans population screening mentioned above were cloned and sequenced.
surprisingly several common indels were detected at the same positions in different sequences from all the populations analyzed.
phylogenetic reconstructions based on the orf <dig> and orf <dig>  showed that the sequences that displayed the same indels are grouped in the tree.
this suggests that the deletion or insertion events were produced before the amplification of these sequences.
some copies had only a few insertions, and might be inactive since their reading frames were not preserved.
however, the amplification of some of these copies could have been promoted in trans.
we did not find any population that had both complete orfs.
nevertheless, some orfs had no internal stop codons in their sequence, suggesting that copies bearing them could be active despite the deletions.
the percentage identity between the reference copy and orf <dig> ranges between 96% and 99%, meaning that these copies have not diverged much.
no relationship was detected between the size and location of the deletions, and the percentage identity.
for the orf <dig>  we found copies with a percentage identity of more than 93% that reached 100% for some copies.
a common 401-bp deletion was found in copies with 93% identity with the complete helena copy, but no correlation was observed with the percentage identity for the other deletions or insertions.
based on the age estimation of each copy, we found that most of the oldest orf <dig> fragments had the 401-bp deletion.
several young copies of both orf <dig> and orf <dig> displayed major internal deletions, showing that the mechanism leading to these deletions is much more powerful than copy divergence in inactivating them.
transcript analysis in d. simulans
to test the transcriptional potential of helena in d. simulans, we performed northern blot and rt-pcr in various populations .
since the sequenced genome was obtained from strains from north america, we added three populations from this continent .
no transcripts were found by northern blot in any of the populations.
however, the rt-pcr method detected transcripts of both orf <dig> and orf <dig> in the valence population, an extremely low signal for orf <dig> and orf <dig> in three of the american populations, and orf <dig> transcripts in the amieu population.
none of the other populations had any transcript for helena, implying that this element is extinct in these populations.
since the northern blot technique is less sensitive than rt-pcr, these findings suggest that helena is transcribed at extremely low levels in the populations in which some transcripts were detected by rt-pcr.
discussion
our in silico and experimental analyses of the d. melanogaster genome show that helena copies are mostly doa, devoid of orf <dig>  and therefore unable to transpose autonomously.
all these features have been associated with elements that are in the process of inactivation  <cit> .
the scenario for the helena copies in d. simulans is quite different.
analysis of the sequenced genome of this species allowed us to identify a full-length copy of helena with the structures required for an active element: two intact orfs, a poly-a tail, and regulatory regions.
the high level of insertion polymorphism detected in the natural populations suggests that helena is an active element or has been active recently.
however, sequence analysis of the two orfs of helena in the natural populations revealed two main points: first, both orfs are intact in only very few populations; second, even though the sequences of helena are very similar at the nucleotide level, their deletion features differ.
the first point was strengthened by the almost total absence of helena transcripts in all natural populations of d. simulans, which means that very few copies were involved in transcription.
because a single master copy is enough to maintain te transposition  <cit> , the putative activity of helena in this species could reside in the full-length copy probably present in some populations such as valence, where we did observe transcripts.
hence, we would expect sequences that are still similar at nucleotide level to differ only in the 5' end truncation size, as usually observed for line-like elements.
however, as mentioned in the second point, we actually observed many other kinds of internal deletions that occurred throughout the length of the element.
intriguingly this deletion-promoting process appears to be quite powerful in inactivating the elements, and could be even more powerful than other mutation processes such as point mutations.
this means that a real-time loss of helena is ongoing in all d. simulans populations.
the nature of the mechanisms leading to internally deleted copies is still unknown.
in humans, line elements can be spliced  <cit> , a process that creates internal deletions.
we used bioinformatic analyses, but were unable to find splice sites in the full-length helena sequence.
also, although recombination between mrnas can produce internal deletions  <cit> , helena sequences are not sufficiently divergent to allow us to infer the origin of a single copy.
helena appears to be extinct in d. melanogaster, and this recalls the i element, which also disappeared from the d. melanogaster genome in the past, and reinvaded it only recently  <cit> .
the i and helena elements are both line-like elements, leading us to wonder whether amplification/loss of copies could be a characteristic of this type of element.
waves of amplification/loss have been observed in humans, where only the youngest l <dig> subfamily is active, perhaps as a result of competition between different l <dig> subfamilies  <cit> .
our data show that helena has been almost entirely removed from the d. melanogaster genome, and was not subjected to the recent wave of transpositions reported for other elements  <cit> .
in d. simulans, we did observe an insertion site polymorphism of helena, but this corresponds to copies that are being internally deleted by an efficient mechanism.
this may be generalized on the basis of data on the ltr retrotransposons  <dig> and tirant, which have also internal deletions  <cit> .
we still do not clearly understand which mechanisms lead to a low copy number in the d. simulans genome, but a mechanism promoting internal deletions could be a major force at work  <cit> .
CONCLUSIONS
tes are major players in genome evolution, and the way they are controlled by the host genome is one of the most fundamental questions in evolutionary genomics.
here we show that two closely related species of drosophila have a te family at different stages in its life cycle.
the mechanism by which this is achieved in d. simulans implies that a very efficient internal deletion mechanism is acting on tes, which is more powerful than the simple neutral evolution of non-active elements.
the difference in the amount of tes between d. melanogaster and d. simulans could be explained by such a process, that doesn't seem to be very active in d. melanogaster present populations.

 genome evolution occurs by several processes, including global genome duplications, segmental duplications and the amplification/deletion of repetitive sequences. among the repeated sequences, transposable elements, which constitute a high proportion in many genomes, play an important role in genome evolution. the transposition rates of these tes depend on the amount and type of the tes present in the genome; they are not constant over time, but are subject to amplification bursts in certain species and populations. as a result, genomes contain widely differing amounts of tes that are not directly correlated to their activity levels. for instance, the human genome is composed of at least 50% of tes, but only very few are active, and they are responsible for less than 1% of mutations. in contrast, in drosophila melanogaster, only 18% of the genome is composed of tes, but a high proportion of mutations is attributable to their transposition. a te life cycle can be viewed as successive waves of transposition/loss: invasion of the host genome by tes being followed by their progressive elimination. for example, the line- element has colonized the entire human genome by successful waves of transposition, and today it is the most abundant te family in this genome. however, in humans, most of the elements have been inactivated either by structural changes or by epigenetic control, such as dna methylation. in d. melanogaster, the i factor has recently reinvaded this genome after being lost from the chromosome arms. te elimination from genomes is therefore a commonly observed phenomenon, although no real-time observation of a te extinction has ever been reported. as tes have a considerable influence on remodeling the genome structure, we need to understand the dynamics of changes in their copy numbers. one way to investigate these dynamics is to analyze closely related species with differing te amounts, such as d. simulans and d. melanogaster. these species diverged to million years ago and have differing proportions of tes: d. melanogaster contains more than 18% of tes, whereas d. simulans contains only 5%. d. simulans has fewer copies of most tes, but there are a few exceptions. the dna-transposon hobo is more abundant in d. simulans, the retrovirus-like gypsy and zam elements have the same low number of copies in both species, and the line-like element helena is present in the d. simulans genome, but has not been detected in the chromosome arms of d. melanogaster. the striking distribution of helena in natural populations of these two species, and the fact that degenerated copies are found in the sequenced d. melanogaster genome, make this line-like element an ideal model system to study the real time te life cycle. petrov and colleagues proposed that deletions are common events in drosophila, and based this suggestion on the analysis of partial helena sequences from different drosophila species. however, it is difficult to extrapolate this to other tes, if we take into account the fact that helena is one of the few degenerate tes in the d. melanogaster sequenced genome. comparing closely related species with differing te amounts, could be used to test the importance of this deletion process in regulating te genome invasions. we analyzed the structure and activity of helena using the sequenced genomes and of natural populations of d. melanogaster and d. simulans. we show that the elimination of helena from its host genomes is a very quick process, and that it is mediated by massive internal deletions in the element. we conclude that the process of elimination of helena is far advanced in d. melanogaster. but is still in progress in d. simulans.  in silico identification of a complete copy of helena in the d. simulans genome because no full-length copy of helena had previously been described, we performed a bioinformatic search for such a copy in the draft sequence of the d. simulans genome. we found a 4912-bp copy of helena on the chromosome arm 3r. helena belongs to the jockey clade, has a 25-bp poly a tail, and two overlapping open reading frames. the first orf is 1737-bp and codes a 579-amino acid protein that has high similarities to the gag protein of other line-like elements, such as x, jockey and het-a. the gag-like protein contains the major homology region, followed by a cysteine-rich domain. this region is common to all gag-like proteins, and confers an rna or dna single-strain binding property on these elements, as well as being essential for gag oligomerization. helena has a coiled-coil domain located in the 5' region of the gag protein, something that had previously only been seen in l elements from mammals and in some ltr retrotransposons from drosophila. the second orf, which starts on the last base of orf is 2721-bp, and codes a 907-aa protein corresponding to the pol gene, which is very similar to the protein of the bs and jockey elements. the pol-like protein contains all the domains necessary for its function: an apyrimidic endonuclease and an exonuclease, plus a reverse transcriptase domain. both orfs are intact, could produce transcripts, and are surrounded by two untranslated regions. because the regulatory region is often defined in the 5'utr, we performed a bioinformatic search for transcription factors binding sites in this region. a single region was detected containing several transcription factor binding sites, such as sp and upstream stimulating factor-like binding domains. this region also displays a binding site for a tata-binding protein, and an estrogen response element. the copies of helena in the sequenced genomes of d. melanogaster and d. simulans using the complete sequence of helena as a query, we found helena sequences in the d. simulans genome. twenty-eight of these copies were located on the chromosome arms, and the remaining were in the u part of the genome, that may correspond to heterochromatin. the copies ranged in size from bp to bp. however, it is difficult to determine the exact size of some copies due to the presence of numerous undetermined bases. two copies were longer than the reference sequence due to insertions. in some other cases, we may be looking at fragments of the same copy; however, the distances that separate them are too large to allow us to find out with certainty whether they come from the same copy. the estimated number of copies in d. simulans may therefore be an overestimation. the average percentage identity is % for all copies, with an average of % for the copies in the euchromatin, and of % for the copies in the u part. in the sequenced genome of d. melanogaster, we found copies of helena, which ranged in size from bp to bp. the average percentage identity was % for all copies, with an average of % for the copies in the chromosome arms, and of % for the copies located in the u part. most of the copies in this genome have therefore been degraded, with numerous internal deletions or insertions. all copies are truncated on the 5' side, and are doa copies, apart from the 3l_ copy, although even this displays some internal deletions. we analyzed in greater detail any copies that could correspond to the most recent insertions in both d. melanogaster and d. simulans. we used specific blast criteria to identify these copies: we selected matches with at least 90% identity, and a length at least 50% of that of the complete copy, with e-values of less than 10e-. in d. melanogaster, only the 3l_ copy described above met all the blast criteria. it is obviously an inactive copy, since more than four deletions were detected within its sequence. in d. simulans, six copies were found that matched the blast criteria, including the complete copy on the 3r chromosome; the other five copies had internal deletions, and insertions were detected in four of them. chromatin localization of helena copies in natural populations we used in situ hybridization to estimate the number of helena insertion sites located on the arms of the polytene chromosomes from salivary glands of both d. melanogaster and d. simulans. both species had centromeric staining, but only d. simulans from natural populations presented euchromatic bands with no fixed sites. with this experiment we did not detect any insertions of helena in the chromosome arms, which could be explained by the short size of the elements and the divergence to the probe used. inter-population polymorphism we analyzed the inter-population helena copy number polymorphism by southern blot, using a restriction enzyme that does not cut inside the element. this method detects both heterochromatic and euchromatic sequences. as shown in figure d. melanogaster had to bands per population, and several bands were shared by different populations. these copies could correspond to ancient and fixed heterochromatic copies in the d. melanogaster genome. d. simulans populations contained numerous helena copies with a high level of insertion polymorphism. since the enzyme used for the southern blot did not cut inside the element, all bands over kb could correspond to a complete element. because both species harbored bands over kb, they could have full-length helena copies. pcr screening three sets of primers were used to amplify the whole orf and two fragments of the orf no bands corresponding to the orf were observed in any of the d. melanogaster natural populations in agreement with the absence of this orf in the sequenced genome. there was a high level of size polymorphism for the d. melanogaster orf corresponding to the different internal deletions already analyzed by petrov et al.. in contrast, d. simulans displayed low size polymorphism for helena orf and orf indeed, only one population out of twenty had two sets of orf. all d. simulans populations had two to three sets of orf analysis of helena copies in d. simulans populations pcr fragments obtained from the d. simulans population screening mentioned above were cloned and sequenced. surprisingly several common indels were detected at the same positions in different sequences from all the populations analyzed. phylogenetic reconstructions based on the orf and orf showed that the sequences that displayed the same indels are grouped in the tree. this suggests that the deletion or insertion events were produced before the amplification of these sequences. some copies had only a few insertions, and might be inactive since their reading frames were not preserved. however, the amplification of some of these copies could have been promoted in trans. we did not find any population that had both complete orfs. nevertheless, some orfs had no internal stop codons in their sequence, suggesting that copies bearing them could be active despite the deletions. the percentage identity between the reference copy and orf ranges between 96% and 99%, meaning that these copies have not diverged much. no relationship was detected between the size and location of the deletions, and the percentage identity. for the orf we found copies with a percentage identity of more than 93% that reached 100% for some copies. a common 401-bp deletion was found in copies with 93% identity with the complete helena copy, but no correlation was observed with the percentage identity for the other deletions or insertions. based on the age estimation of each copy, we found that most of the oldest orf fragments had the 401-bp deletion. several young copies of both orf and orf displayed major internal deletions, showing that the mechanism leading to these deletions is much more powerful than copy divergence in inactivating them. transcript analysis in d. simulans to test the transcriptional potential of helena in d. simulans, we performed northern blot and rt-pcr in various populations. since the sequenced genome was obtained from strains from north america, we added three populations from this continent. no transcripts were found by northern blot in any of the populations. however, the rt-pcr method detected transcripts of both orf and orf in the valence population, an extremely low signal for orf and orf in three of the american populations, and orf transcripts in the amieu population. none of the other populations had any transcript for helena, implying that this element is extinct in these populations. since the northern blot technique is less sensitive than rt-pcr, these findings suggest that helena is transcribed at extremely low levels in the populations in which some transcripts were detected by rt-pcr. discussion our in silico and experimental analyses of the d. melanogaster genome show that helena copies are mostly doa, devoid of orf and therefore unable to transpose autonomously. all these features have been associated with elements that are in the process of inactivation. the scenario for the helena copies in d. simulans is quite different. analysis of the sequenced genome of this species allowed us to identify a full-length copy of helena with the structures required for an active element: two intact orfs, a poly-a tail, and regulatory regions. the high level of insertion polymorphism detected in the natural populations suggests that helena is an active element or has been active recently. however, sequence analysis of the two orfs of helena in the natural populations revealed two main points: first, both orfs are intact in only very few populations; second, even though the sequences of helena are very similar at the nucleotide level, their deletion features differ. the first point was strengthened by the almost total absence of helena transcripts in all natural populations of d. simulans, which means that very few copies were involved in transcription. because a single master copy is enough to maintain te transposition, the putative activity of helena in this species could reside in the full-length copy probably present in some populations such as valence, where we did observe transcripts. hence, we would expect sequences that are still similar at nucleotide level to differ only in the 5' end truncation size, as usually observed for line-like elements. however, as mentioned in the second point, we actually observed many other kinds of internal deletions that occurred throughout the length of the element. intriguingly this deletion-promoting process appears to be quite powerful in inactivating the elements, and could be even more powerful than other mutation processes such as point mutations. this means that a real-time loss of helena is ongoing in all d. simulans populations. the nature of the mechanisms leading to internally deleted copies is still unknown. in humans, line elements can be spliced, a process that creates internal deletions. we used bioinformatic analyses, but were unable to find splice sites in the full-length helena sequence. also, although recombination between mrnas can produce internal deletions, helena sequences are not sufficiently divergent to allow us to infer the origin of a single copy. helena appears to be extinct in d. melanogaster, and this recalls the i element, which also disappeared from the d. melanogaster genome in the past, and reinvaded it only recently. the i and helena elements are both line-like elements, leading us to wonder whether amplification/loss of copies could be a characteristic of this type of element. waves of amplification/loss have been observed in humans, where only the youngest l subfamily is active, perhaps as a result of competition between different l subfamilies. our data show that helena has been almost entirely removed from the d. melanogaster genome, and was not subjected to the recent wave of transpositions reported for other elements. in d. simulans, we did observe an insertion site polymorphism of helena, but this corresponds to copies that are being internally deleted by an efficient mechanism. this may be generalized on the basis of data on the ltr retrotransposons and tirant, which have also internal deletions. we still do not clearly understand which mechanisms lead to a low copy number in the d. simulans genome, but a mechanism promoting internal deletions could be a major force at work.  tes are major players in genome evolution, and the way they are controlled by the host genome is one of the most fundamental questions in evolutionary genomics. here we show that two closely related species of drosophila have a te family at different stages in its life cycle. the mechanism by which this is achieved in d. simulans implies that a very efficient internal deletion mechanism is acting on tes, which is more powerful than the simple neutral evolution of non-active elements. the difference in the amount of tes between d. melanogaster and d. simulans could be explained by such a process, that doesn't seem to be very active in d. melanogaster present populations. 
in situ hybridization experiments revealed that helena is absent from the chromosome arms of d. melanogaster, while it is present in the chromosome arms of d. simulans, which is an unusual feature for a te in these species. taking advantage of differences in the amount and distribution of the long interspersed nuclear element, helena in drosophila melanogaster and d. simulans, we analyzed the dna sequences of copies of this element in samples of various natural populations of these two species. transposable elements are major players in evolution. natural populations of d. simulans have several copies, a few of them full-length, but most of them internally deleted. molecular analyses showed that the helena sequences detected in d. melanogaster were all deleted copies, which diverged from the canonical element. overall, our data suggest that a mechanism that induces internal deletions in the helena sequences is active in the d. simulans genome.
 transposable elements are major players in evolution. we know that they play an essential role in genome size determination, but we still have an incomplete understanding of the processes involved in their amplification and elimination from genomes and populations. taking advantage of differences in the amount and distribution of the long interspersed nuclear element, helena in drosophila melanogaster and d. simulans, we analyzed the dna sequences of copies of this element in samples of various natural populations of these two species.  in situ hybridization experiments revealed that helena is absent from the chromosome arms of d. melanogaster, while it is present in the chromosome arms of d. simulans, which is an unusual feature for a te in these species. molecular analyses showed that the helena sequences detected in d. melanogaster were all deleted copies, which diverged from the canonical element. natural populations of d. simulans have several copies, a few of them full-length, but most of them internally deleted.  overall, our data suggest that a mechanism that induces internal deletions in the helena sequences is active in the d. simulans genome. 