Extensive linkage disequilibrium in the achaete-scute complex of Drosophila melanogaster.

Abstract We have analyzed the level of gametic association between restriction map variants in a sample of 44 X chromosomes from a natural population of Drosophila melanogaster. Of 21 pairwise tests involving 7 restriction map polymorphisms in the yellow-achaete-scute complex, 17 were found to be significant, including some between restriction sites over 80 kb apart. Three-way linkage disequilibria and their variances were also estimated for all 35 three-way comparisons between these loci. Twelve such tests were found to be significant, again spanning distances of up to 80 kb on the restriction map. Only 9 of a possible 128 haplotypes were represented in the sample and 8 of these could be linked together by changes at a single site. The strength of these associations at y-ac-sc is unusual by comparison with studies on other regions of the genome of D. melanogaster, and is consistent with the very low level of recombination which has been reported for the complex. However, our estimate of nucleotide diversity in the region is not significantly different from those made for some other loci in this species.

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Analysis of linkage disequilibria between allozyme loci in natural populations of Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672300018711 ◽

1978 ◽

Vol 32 (3) ◽

pp. 215-229 ◽

Cited By ~ 19

Author(s):

Charles H. Langley ◽

Diana B. Smith ◽

F. M. Johnson

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Natural Population ◽

Analysis Of Variance ◽

Natural Populations ◽

Correlation Coefficients ◽

Absolute Value ◽

Linkage Disequilibria ◽

Enzyme Loci ◽

Allozyme Loci

SUMMARYLinkage disequilibria between pairs of 8 polymorphic enzyme loci (αGpdh, Mdh, Adh, Est-6, Pgm, Odh, Est-C and Acph) in some 100 natural population samples of Drosophila melanogaster were examined. The estimates of linkage disequilibrium were made from zygotic frequencies. The magnitude of linkage disequilibria are small and similar to those in previous reports. Variation in linkage disequilibrium among related subpopulations was analysed by analysis of variance of the correlation coefficients. Despite the small absolute value of linkage disequilibrium there is a suggestion of a correlation among related subpopulations. The magnitude of linkage disequilibrium was observed to be positively correlated with linkage. Two cage populations were observed to demonstrate large amounts of linkage disequilibrium between closely linked loci in contrast to the situation in natural populations. This is attributable to the finite sizes of these cage populations.

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Molecular and phenotypic variation of the white locus region in Drosophila melanogaster.

Genetics ◽

10.1093/genetics/120.1.199 ◽

1988 ◽

Vol 120 (1) ◽

pp. 199-212

Author(s):

N Miyashita ◽

C H Langley

Keyword(s):

Drosophila Melanogaster ◽

X Chromosome ◽

Restriction Site ◽

Restriction Enzymes ◽

Transcriptional Unit ◽

X Chromosomes ◽

Linkage Disequilibria ◽

Restriction Sites ◽

White Locus ◽

Shock Locus

Abstract Restriction site and insertion/deletion polymorphism in a 45-kb region of the white locus on the X chromosome in Drosophila melanogaster was investigated for 64 X chromosome lines with six 6-cutter and ten 4-cutter restriction enzymes. A total of 109 polymorphisms were detected (54 restriction sites and 55 insertions/deletions). Estimated heterozygosity per nucleotide for this region (0.004-0.008) was similar to those of the Adh and 87A heat-shock locus regions located on the autosomes in D. melanogaster. This is contrary to a simple prediction based on the theory of mutation selection-balance of partially recessive deleterious mutants which predicts less variation on X chromosomes. Large linkage disequilibria between pairs of polymorphisms (including insertions and deletions) within the transcriptional unit (especially the 3' end of the 1st intron) were observed. As expected from population genetics theory, linkage disequilibria between these polymorphisms were greater for those pairs that are physically closer on the restriction map. Linkage equilibrium was typically observed when the pairs of sites were separated by 2 kb or more. Although significant between-line variation in eye pigment was observed (P less than 0.05), there is little evidence for strong associations between this phenotype and the polymorphisms at the DNA level.

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Naturally occurring variation in the restriction map of the amy region of Drosophila melanogaster.

Genetics ◽

10.1093/genetics/119.3.619 ◽

1988 ◽

Vol 119 (3) ◽

pp. 619-629

Author(s):

C H Langley ◽

A E Shrimpton ◽

T Yamazaki ◽

N Miyashita ◽

Y Matsuo ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Restriction Site ◽

Natural Populations ◽

Alpha Amylase ◽

Low Frequencies ◽

Linkage Disequilibria ◽

Restriction Sites ◽

Site Variation ◽

Transcriptional Units ◽

Polymorphic Restriction

Abstract The restriction maps of 85 alleles of the Amy region of Drosophila melanogaster from natural populations were surveyed. A subset of these were also scored for allozyme phenotype and adult enzyme activity of alpha-amylase. Large insertions were found in 12% of the alleles in a 15-kb region surrounding the two transcriptional units of the duplicated Amy locus. The low frequencies at which each of these large insertions were found are consistent with earlier reports of variation in other loci. Four small deletions were found in the region 5' to the Amy genes. Each was also rare in the population. Restriction site variation provided an estimate of per nucleotide heterozygosity of 0.006. Several statistically significant linkage disequilibria were observed between four polymorphic restriction sites and the allozymes. Adult alpha-amylase activity was correlated with the allozymes and with the polymorphism at one restriction site close to the transcriptional units.

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Transposition of the I element and copia in a natural population of Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672300026914 ◽

1987 ◽

Vol 49 (2) ◽

pp. 121-128 ◽

Cited By ~ 36

Author(s):

Andrew J. Leigh Brown ◽

Julie E. Moss

Keyword(s):

Drosophila Melanogaster ◽

Natural Population ◽

Copy Number ◽

Evolutionary Dynamics ◽

Data Sets ◽

X Chromosomes ◽

Genetic Elements ◽

Population Structuring ◽

Transposable Genetic Elements

SummaryIn order to increase our understanding of the evolutionary dynamics of transposable genetic elements we have studied the chromosal location of copies of 2 element families in 20 X chromosomes extracted from a natural population of Drosophila melanogaster from Spain. The I element was localized at a total of 64 chromosomal sites and copia at 45 sites in this sample with a mean copy number of 3·2 and 2·3 elements/chromosome respectively. Both elements were highly variable in location, with no site reaching a higher frequency than 4/20 in either case. Comparisons with other data sets suggest that insertion frequencies can be used to detect population structuring.

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

Genetics ◽

10.1093/genetics/104.3.473 ◽

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.

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LINKAGE DISEQUILIBRIUM IN NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER. SEASONAL VARIATION

Genetics ◽

10.1093/genetics/86.2.447 ◽

1977 ◽

Vol 86 (2) ◽

pp. 447-454

Author(s):

Charles H Langley ◽

Kazuko Ito ◽

Robert A Voelker

Keyword(s):

Drosophila Melanogaster ◽

Seasonal Variation ◽

Linkage Disequilibrium ◽

Natural Population ◽

Natural Populations ◽

The Other ◽

Allozyme Loci

ABSTRACT Linkage disequilibrium among ten polymorphic allozyme loci and polymorphic inversions on chromosomes 2 and 3 in a natural population of Drosophila melanogaster was examined early and late in the annual season. Similar to previous studies, little linkage disequilibrium was observed among allozymes. The two significant cases that were observed in the first sample behaved in a contradictory way. One declined much more rapidly than expected due simply to recombination; the other declined slowly as expected. There was little change in allozyme or inversion frequencies during the season.

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A CONTRIBUTION TO THE STUDY OF LINKAGE DISEQUILIBRIUM IN DROSOPHILA MELANOGASTER

Canadian Journal of Genetics and Cytology ◽

10.1139/g76-087 ◽

1976 ◽

Vol 18 (4) ◽

pp. 739-745 ◽

Cited By ~ 12

Author(s):

S. Alahiotis ◽

M. Pelecanos ◽

A. Zacharopoulou

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Natural Population ◽

Environmental Conditions ◽

Gene Pool ◽

Ecological Factors ◽

Random Drift ◽

Different Populations ◽

Food Medium

Linkage disequilibrium was detected in 12 out of 30 cases involving gene alleles and inversions in three cage populations and in a natural population of Drosophila melanogaster from Greece. The cage populations possessed practically the same gene pool at their origin and were maintained simultaneously under the effects of the ecological factors "food medium" and "humidity". It is discussed that the correlation of the same direction found between the frequencies of nonallelic elements of Adh locus and In(2L)22D-34A or In(2R)52A-56F in such different populations as American, Japanese (Mukai et al., 1971, 1974; Langley et al., 1974) and Greek, as well as cage populations under different environmental conditions, could be attributed to the effect of epistatic selection. Moreover, it seems that the In(2L)22D-34A has a tendency to interact genetically with the α-Gpdh locus, particularly when the populations are maintained under crowding conditions. However, further data are needed to assess whether other cases of the observed nonrandom associations can be better explained as transient associations generated by random drift, or as the result of epistatic selection.

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Evidence for balanced linkage of X chromosome polygenes in a natural population of Drosophila.

Genetics ◽

10.1093/genetics/127.1.117 ◽

1991 ◽

Vol 127 (1) ◽

pp. 117-123

Author(s):

J N Thompson ◽

J J Hellack ◽

R R Tucker

Keyword(s):

Drosophila Melanogaster ◽

Natural Population ◽

X Chromosome ◽

X Chromosomes ◽

Bristle Number ◽

Internal Balance ◽

Chromosome Regions ◽

Polygenic Variation

Abstract Extensive levels of polygenic variation can be maintained in a population without creating a severe segregational load. One way to account for this is that the alleles are arranged on a chromosome so that different regions balance each other phenotypically. To test whether this occurs in a natural population, we isolated ten Drosophila melanogaster X chromosomes and mapped regions of polygenic activity affecting sternopleural bristle number. The chromosomes fell into a small number of groups based upon the similarity of their distributions of polygenic activity. The results are consistent with a model in which a large proportion of the variation can be attributed to a small number of segregating chromosome regions and in which the chromosomes show internal balance.

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THE GENETIC STRUCTURE OF NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER XIII. FURTHER STUDIES ON LINKAGE DISEQUILIBRIUM

Genetics ◽

10.1093/genetics/86.1.175 ◽

1977 ◽

Vol 86 (1) ◽

pp. 175-185

Author(s):

Terumi Mukai ◽

Robert A Voelker

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Natural Populations ◽

Linkage Disequilibria ◽

Two Factors ◽

Carolina Population ◽

Recombination Value ◽

Significant Linkage ◽

Octanol Dehydrogenase ◽

Double Crossovers

ABSTRACT The Raleigh, North Carolina, population of Drosophila melanogaster was examined for linkage disequilibrium in 1974, several years after previous analyses in 1968, 1969, and 1970. αglycerol-3-phosphate dehydrogenase-1 (αGpdh-1), malate dehydrogenase-1 (Mdh-1), alcohol dehydrogenase (Adh), and hexokinase-C (Hex-C, tentative name, F. M. Johnson, unpublished; position determined by the present authors to be 2-74.5) were assayed for 617 second chromosomes, and esterase-C (Est-C) and octanol dehydrogenase (Odh) were assayed for 526 third chromosomes. In addition, two polymorphic inversions in the second chromosomes [In(2L)t and In(2R)NS] were examined, and the following findings were obtained: (1) No linkage disequilibrium between isozyme genes was detected. Significant linkage disequilibria were found only between the polymorphic inversions and isozyme genes [In(2L)t vs. Adh, and In(2R)NS vs. Hex-C]. Significant disequilibrium was not detected between In(2L)t and αGpdh-1, which is included in the inversion, but a tendency toward disequilibrium was consistently found from 1968 to 1974. The frequency of two-strand double crossovers within inversion In(2L)t involving a single crossover on each side of αGpdh-1 was estimated to be 0.00022. Thus, the consistent but not significant linkage disequilibrium between the two factors can be explained by recombination after the inversion occurred. (2) Previously existing linkage disequilibrium between Adh and In(2R)NS (the distance is about 30 cM, but the effective recombination value is about 1.75%) was found to have disappeared. (3) No higher-order linkage disequilibrium was detected. (4) Linkage disequilibrium between Odh and Est-C (the distance of which was estimated to be 0.0058 ± 0.002) could not be detected (χ2 df=1 = 0.9).—From the above results, it was concluded that linkage disequilibria among isozyme genes are very rare in D. melanogaster, so that the Franklin-Lewontin model (Franklin and Lewontin 1970) is not applicable to these genes. The linkage disequilibria between some isozyme genes and polymorphic inversions may be explained by founder effect.

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Restriction map variation at the adh locus of Drosophila melanogaster in inverted and noninverted chromosomes.

Genetics ◽

10.1093/genetics/119.1.135 ◽

1988 ◽

Vol 119 (1) ◽

pp. 135-140

Author(s):

M Aguade

Keyword(s):

Drosophila Melanogaster ◽

Natural Population ◽

Evolutionary History ◽

Restriction Site ◽

Restriction Enzymes ◽

Restriction Map ◽

Allozyme Polymorphism ◽

Length Polymorphisms ◽

History Of ◽

Restriction Site Polymorphisms

Abstract Restriction map variation among 39 Standard and 40 In(2L)t chromosomes extracted from a Spanish natural population of Drosophila melanogaster was investigated for a 2.7-kb region encompassing the Adh locus with ten four-cutter restriction enzymes. A total of 20 polymorphisms were detected, representing 15 restriction site polymorphisms, 4 length polymorphisms and the allozyme polymorphism. Variation at the DNA level was compared among St-Adh(F), St-Adh(S) and t-Adh(S) chromosomes. t-Adh(S) chromosomes show a higher level of variation than St-Adh(F) chromosomes. This suggests that In(2L)t arose before the fast/slow allozyme divergence in the evolutionary history of D. melanogaster.

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