scholarly journals A study of ten families of transposable elements on X chromosomes from a population of Drosophila melanogaster

1989 ◽  
Vol 54 (2) ◽  
pp. 113-125 ◽  
Author(s):  
Brian Charlesworth ◽  
Angela Lapid
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Copy Number ◽  
Distal Part ◽  
Polytene Chromosomes ◽  
Chromosome Band ◽  
X Chromosomes ◽  
High Frequencies ◽  
Chromosome Element

SummaryData were collected on the distribution of ten families of transposable elements among fourteen X chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization to polytene chromosomes. It was found that, with the exception of roo, the copy number per chromosome followed a Poisson distribution. There was no evidence for linkage disequilibrium, either within or between families. Some pairs of families of elements were correlated with respect to the identity of the sites that were occupied in the sample, although there was no evidence for a correlation with respect to the sites at which elements attained relatively high frequencies. Elements appeared to be distributed randomly along the distal part of the X chromosome. There was, however, a strong tendency for elements to accumulate at the base of the chromosome. Element frequencies per chromosome band were generally low, except at the base of the chromosome where bands in subdivisions 19E and 20A sometimes had high frequencies of occupation. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The accumulation of elements at the base of the chromosome is consistent with the idea that unequal exchange between elements at non-homologous sites is such a force, although other possibilities cannot be excluded at present. The data suggest that the rate of transposition per element per generation is of the order of 10−4, for the elements included in this study.

scholarly journals The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution

1992 ◽  
Vol 60 (2) ◽  
pp. 103-114 ◽  
Author(s):  
Brian Charlesworth ◽  
Angela Lapid ◽  
Darlene Canada
Keyword(s):  
Population Dynamics ◽  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Transposable Elements ◽  
Copy Number ◽  
Polytene Chromosomes ◽  
Chromosome Band ◽  
High Frequencies ◽  
Copy Numbers

SummaryData were collected on the distribution of nine families of transposable elements among second and third chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of element probes to polytene chromosomes. It was found that the copy numbers per chromosome in the distal sections of the chromosome arms followed a Poisson distribution. Elements appeared to be distributed randomly along the distal sections of the chromosome arms. There was no evidence for linkage disequilibrium in the distal sections of the chromosomes, but some significant disequilibrium was detected in proximal regions. There were many significant correlations between different element families with respect to the identity of the sites that were occupied in the sample. There were also significant correlations between families with respect to sites at which elements achieved relatively high frequencies. Element frequencies per chromosome band were generally low in the distal sections, but were higher proximally. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The data suggest that the rate of transposition perelement per generation is of the order of 10−4, for the elements included in this study.

scholarly journals The distribution of transposable elements on X chromosomes from a natural population of Drosophila simulans

1995 ◽  
Vol 66 (2) ◽  
pp. 159-166 ◽  
Author(s):  
Sergey V. Nuzhdin
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Population ◽  
Copy Number ◽  
Polytene Chromosomes ◽  
Distal Region ◽  
Drosophila Simulans ◽  
Chromosome Band ◽  
X Chromosomes

SummaryThe distribution of 13 transposable element families along 15 X chromosomes from an African natural population of Drosophila simulans was determined by in situ hybridization to polytene chromosomes. The transposable elements cloned from Drosophila melanogaster all hybridized with Drosophila simulans chromosomes. The number of copies per family was 3·5 times lower in the latter species and correlated with the copy number per family in Drosophila melanogaster. With the exception of 297, the copy number per chromosome followed a Poisson distribution. Element frequencies per chromosome band were generally low. However, several sites of the distal region and the base of the X chromosome had high frequencies of occupation. Elements had higher abundance at the base of the chromosome compared to distal regions. Overall, the distribution of transposable elements in Drosophila simulans is similar to that found in Drosophila melanogaster. These data provide evidence for the operation of a force (or forces) opposing transpositional increase in copy number, and that this force is weaker at the bases of chromosomes, consistent with the idea that recombination between elements at non-homologous sites contains TE copy number. The reduction in copy number of all TE families in Drosophila simulans compared to Drosophila melanogaster can be explained by stronger selection against transposable element multiplication and/or lower rates of transposition in Drosophila simulans.

scholarly journals Population dynamics of the copia, mdg1, mdg3, gypsy, and P transposable elements in a natural population of Drosophila melanogaster

1994 ◽  
Vol 63 (3) ◽  
pp. 197-212 ◽  
Author(s):  
C. Biémont ◽  
F. Lemeunier ◽  
M. P. Garcia Guerreiro ◽  
J. F. Brookfield ◽  
C. Gautier ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Natural Population ◽  
Copy Number ◽  
Population Biology ◽  
Insertion Site ◽  
Polytene Chromosomes ◽  
Sharp Decrease ◽  
Theoretical Models ◽  
X Chromosomes

SummaryThe insertion site polymorphism of the copia, mdg1, mdg3, gypsy, and P transposable elements was analysed by in situ hybridization to the polytene chromosomes in genomes of males from a natural population of Drosophila melanogaster. Parameters of various theoretical models of the population biology of transposable elements were estimated from our data, and different hypotheses explaining TE copy number containment were tested. The copia, mdg1 and gypsy elements show evidence for a deficiency of insertions on the X chromosomes, a result consistent with selection against the mutational effects of insertions. On the contrary, mdg3 and P copy numbers fit a neutral model with a balance between regulated transposition and excisions. There is no strong evidence of a systematic accumulation of elements in the distal and proximal regions of the chromosomes where crossing over and ectopic exchanges are reduced. For all chromosome arms but 3L, however, the TE site density increases from the proximal to the distal parts of the chromosomes (the centromeric regions were excluded in this analysis) with sometimes a sharp decrease in density at the extreme tip, following in part the exchange coefficient. The way the copy number of TEs is contained in genomes depends thus on the element considered, and on various forces acting simultaneously, indicating that models of TE dynamics should include details of each element.

scholarly journals Rates of movement of transposable elements on the second chromosome of Drosophila melanogaster

2000 ◽  
Vol 75 (3) ◽  
pp. 275-284 ◽  
Author(s):  
XULIO MASIDE ◽  
STAVROULA ASSIMACOPOULOS ◽  
BRIAN CHARLESWORTH
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Polytene Chromosomes ◽  
Mutation Accumulation ◽  
Long Terminal Repeats ◽  
Significant Difference ◽  
Transposable Element Copy ◽  
Excision Rate

The rates of movement of 11 families of transposable elements of Drosophila melanogaster were studied by means of in situ hybridization of probes to polytene chromosomes of larvae from a long-term mutation accumulation experiment. Replicate mutation-accumulation lines carrying second chromosomes derived from a single common ancestral chromosome were maintained by backcrosses of single males heterozygous for a balancer chromosome and a wild-type chromosome, and were scored after 116 generations. Twenty-seven transpositions and 1 excision were detected using homozygous viable and fertile second chromosomes, for a total of 235056 potential sources of transposition events and a potential 252880 excision events. The overall transposition rate per element per generation was 1·15×10−4 and the excision rate was 3·95×10−6. The single excision (of a roo element) was due to recombination between the element's long terminal repeats. A survey of the five most active elements among nine homozygous lethal lines revealed no significant difference in the estimates of transposition and excision rates from those from viable lines. The excess of transposition over excision events is in agreement with the results of other in situ hybridization experiments, and supports the conclusion that replicative increase in transposable element copy number is opposed by selection. These conclusions are compared with those from other studies, and with the conclusions from population surveys of element frequencies.

scholarly journals TRANSPOSABLE ELEMENTS IN MENDELIAN POPULATIONS. II. DISTRIBUTION OF THREE COPIA-LIKE ELEMENTS IN A NATURAL POPULATION OF DROSOPHILA MELANOGASTER

Genetics ◽  
1983 ◽  
Vol 104 (3) ◽  
pp. 473-483
Author(s):  
Elizabeth A Montgomery ◽  
Charles H Langley
Keyword(s):  
Drosophila Melanogaster ◽  
In Situ Hybridization ◽  
Transposable Elements ◽  
Natural Population ◽  
High Frequency ◽  
X Chromosomes ◽  
Cytogenetic Location ◽  
Very High

ABSTRACT Twenty X chromosomes isolated from a natural population of Drosophila melanogaster were surveyed using in situ hybridization to determine the number and cytogenetic location of three families of transposable elements: copia, 412 and 297. We found no sites of insertions in high frequency; in fact, frequencies of specific sites for all three elements were so low that each insertion could be interpreted as being unique. This suggests that rates of transposition and deletion for these elements are very high. Our data also show a higher than expected rate of the co-occurrence of different elements at the same site on the same chromosome.

scholarly journals Rates of movement and distribution of transposable elements in Drosophila melanogaster: in situ hybridization vs Southern blotting data

2001 ◽  
Vol 78 (2) ◽  
pp. 121-136 ◽  
Author(s):  
XULIO MASIDE ◽  
CAROLINA BARTOLOMÉ ◽  
STAVROULA ASSIMACOPOULOS ◽  
BRIAN CHARLESWORTH
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Southern Blotting ◽  
Polytene Chromosomes ◽  
Element Abundance ◽  
Data Sets ◽  
Copy Numbers ◽  
Blotting Technique ◽  
Controlling Element

Genomic copy numbers and the rates of movement of nine families of transposable elements (TEs) of Drosophila melanogaster were estimated in two sets of mutation accumulation lines: Beltsville and Madrid. Southern blotting was used to screen a large number of samples from both genetic backgrounds for TEs. The Madrid lines were also screened by in situ hybridization of TEs to polytene chromosomes, in order to obtain more detailed information about the behaviour of TEs in the euchromatin. Southern blotting data provided evidence of insertions and excision events in both genetic backgrounds, occurring at rates of approximately 10−5 and 10−6 per element copy per generation, respectively. In contrast, in situ data from the Madrid background presented a completely different picture, with no evidence for excisions, and a significantly higher rate of transposition (1·01×10−4). Direct comparison of the two data sets suggests that the Southern blotting technique had serious deficiencies: (i) it underestimated element abundance; (ii) it revealed less than 30% of the new insertions detected by in situ hybridization; and (iii) changes in the size of restriction fragments from any source were spuriously identified as simultaneous insertion–excision events. Our in situ data are consistent with previous studies, and suggest that selection is the main force controlling element spread by transposition.

scholarly journals The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. II. Inferences on the nature of selection against elements

1992 ◽  
Vol 60 (2) ◽  
pp. 115-130 ◽  
Author(s):  
Brian Charlesworth ◽  
Angela Lapid ◽  
Darlene Canada
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Polytene Chromosomes ◽  
Element Abundance ◽  
General Tendency ◽  
Fourth Chromosome ◽  
Considerable Heterogeneity ◽  
Fitness Consequences ◽  
Random Expectation

SummaryData were collected on the distribution of nine families of transposable elements among a sample of autosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of biotinylated probes to polytene chromosomes. There is no general tendency for elements to accumulate at the tips of chromosomes. Elements tend to be present in excess of random expectation in the euchromatin proximal to the centromeres of the major autosomes, and on chromosome four. There is considerable heterogeneity between different families in the extent of this excess. The overall abundance of element families is inversely related to the extent to which they accumulate proximally. The level of proximal accumulation for the major autosomes is similar to that on the fourth chromosome, but less than that for the X chromosome. There is an overall deficiency of elements in the mid-section of the X compared with the mid-sections of the major autosomes, with considerable heterogeneity between families. The magnitude of this deficiency is positively related to the extent to which elements accumulate proximally. No such deficiency is seen if the proximal regions of the X and autosomes are compared. There is a small and non-significant excess of elements in third chromosomes carrying inversions. There is some between-year heterogeneity in element abundance. The implications of these findings are discussed, and it is concluded that they generally support the hypothesis that transposable element abundance is regulated primarily by the deleterious fitness consequences of meiotic ectopic exchange between elements. If this is the case, such exchange must be very infrequent in the proximal euchromatin, and the elements detected in population surveys of this kind must be inserted into sites where they have negligible mutational effects on fitness.

scholarly journals The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. III. Element abundances in heterochromatin

1994 ◽  
Vol 64 (3) ◽  
pp. 183-197 ◽  
Author(s):  
Brian Charlesworth ◽  
Philippe Jarne ◽  
Stavroula Assimacopoulos
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Natural Population ◽  
Polytene Chromosomes ◽  
Control Element ◽  
Element Abundances ◽  
Evolutionary Forces ◽  
Isogenic Lines ◽  
Copy Numbers

SummaryThe total genomic copy numbers of ten families of transposable elements of Drosophila melanogaster in a set of ten isogenic lines derived from a natural population were estimated by slot-blotting. The numbers of euchromatic copies of members of each family were determined for each line by in situ hybridization of element probes to polytene chromosomes. Heterochromatic numbers were estimated by subtraction of the euchromatic counts from the total numbers. There was considerable variation between element families and lines in heterochromatic abundances, and the variance between lines for many elements was much greater for the heterochromatin than for the euchromatin. The data are consistent with the view that much of the β-heterochromatin consists of sequences derived from transposable elements. They are also consistent with the hypothesis that similar evolutionary forces control element abundances in both the euchromatin and heterochromatin, although amplification of inert sequences derived from transposable elements may be in part responsible for their accumulation in heterochromatin.

scholarly journals Chromosomal Distribution of Transposable Elements in Drosophila melanogaster Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 197-204
Author(s):  
Christine Hoogland ◽  
Christian Biémont
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Dna Content ◽  
Recombination Rate ◽  
Alternative Hypothesis ◽  
Insertion Site ◽  
Polytene Chromosomes ◽  
Negative Relationship ◽  
Site Occupancy ◽  
Site Number

Abstract 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.

scholarly journals Direct determination of retrotransposon transposition rates in Drosophila melanogaster

1994 ◽  
Vol 63 (2) ◽  
pp. 139-144 ◽  
Author(s):  
Sergey V. Nuzhdin ◽  
Trudy F. C. Mackay
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Inbred Line ◽  
Copy Number ◽  
Direct Determination ◽  
Hybridization Analysis ◽  
Spontaneous Mutations ◽  
Insertion Sites

SummaryRates of transposition and excision of the Drosophila melanogaster retrotransposon elements mdg3, 297, Doc, roo and copia were estimated directly, by in situ hybridization analysis of their cytological insertion sites in 31 replicates of a highly inbred line that had accumulated spontaneous mutations for approximately 160generations. Estimated transposition rates of Doc, roo and copia were, respectively, 4·2 × 10−5, 3·1 × 10−3 and 1·3 − 10−3; no transpositions of 297 nor mdg3 were observed. Rates of transposition of copia varied significantly among sublines. Excisions were only observed for roo elements, at a rate of 9·0 × 10−6 per element per generation. Copy number averaged over these element families increased 5·9 %; therefore, in these lines the magnitude of the forces opposing transposable element multiplication were weaker than transposition rates.

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