scholarly journals LINKAGE DISEQUILIBRIUM IN ISOLATED POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽  
1980 ◽  
Vol 96 (2) ◽  
pp. 507-522
Author(s):  
Osamu Yamaguchi ◽  
Motoshi Ichinose ◽  
Muneo Matsuda ◽  
Terumi Mukai
Keyword(s):  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Genetic Drift ◽  
Pacific Islands ◽  
Gene Action ◽  
Random Genetic Drift ◽  
Adjacent Region ◽  
Isolated Populations ◽  
Linkage Disequilibria ◽  
Northern District

ABSTRACT In order to test the interaction effect of overdominance and random genetic drift on the formation of linkage disequilibria under the condition of multiplicative gene action, linkage disequilibria between isozyme genes, inter se, and between polymorphic inversions and isozyme genes were tested for the second chromosomes of Drosophila melanogaster sampled from two isolated Pacific islands and one locality of the northern district of the mainlands of Japan. The effective sizes of these populations were known to be approximately 3,000 to 6,000 on the basis of the allelism rate of lethal chromosomes and their frequencies. The following results were obtained: (1) No linkage disequilibrium considered to be induced by epistasis, including the interaction between overdominance and random genetic drift, was detected. (2) Nonrandom association between polymorphic inversions and isozyme genes that are included in the inversions or located in the adjacent region outside the inversions was detected. (3) On the basis of the comparison of χ2 values, indicating the magnitudes of linkage disequilibrium, between the present isolated populations and the Raleigh, N. C., population (Mukai et al. 1974, 1977), the characteristics of the isolated populations and the nature of these linkage disequilibria are discussed.

Disequilibrium Pattern Analysis. I. Theory

Genetics ◽  
1987 ◽  
Vol 116 (4) ◽  
pp. 623-632
Author(s):  
Glenys Thomson ◽  
William Klitz
Keyword(s):  
Linkage Disequilibrium ◽  
Dna Sequencing ◽  
Genetic Drift ◽  
Pattern Analysis ◽  
Population Data ◽  
Distinct Pattern ◽  
Random Genetic Drift ◽  
A Value ◽  
Selection Event ◽  
Entire Array

ABSTRACT We have developed a method, disequilibrium pattern analysis, for examining the disequilibrium distribution of the entire array of two locus multiallelic haplotypes in a population. It is shown that a selected haplotype will produce a distinct pattern of linkage disequilibrium values for all generations while the selection is acting. This pattern will also presumably be maintained for many generations after the selection event, until the disequilibrium pattern is eventually broken down by genetic drift and recombination. Related haplotypes, sharing an allele with a selected haplotype, assume a value of linkage disequilibrium proportional to the frequency of the unshared allele and have a single negative value of the normalized linkage disequilibrium. The analysis assumes zero linkage disequilibrium for all allelic combinations initially. The same basic results continue to apply if the selection involves a new mutant, the occurrence of which creates linkage disequilibrium for some haplotypes. The disequilibrium pattern predicted under selection is robust with respect to the influence of migration and random genetic drift. This method is applicable to population data having linked polymorphic loci including that determined from protein or DNA sequencing.

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

1978 ◽  
Vol 32 (3) ◽  
pp. 215-229 ◽  
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.

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

Genetics ◽  
1990 ◽  
Vol 126 (1) ◽  
pp. 121-129
Author(s):  
J N Macpherson ◽  
B S Weir ◽  
A J Leigh Brown
Keyword(s):  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Natural Population ◽  
Nucleotide Diversity ◽  
Single Site ◽  
Restriction Map ◽  
X Chromosomes ◽  
Linkage Disequilibria ◽  
Restriction Sites ◽  
Gametic Association

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.

scholarly journals Linkage disequilibrium due to random genetic drift

1969 ◽  
Vol 13 (1) ◽  
pp. 47-55 ◽  
Author(s):  
Tomoko Ohta ◽  
Motoo Kimura
Keyword(s):  
Stochastic Process ◽  
Linkage Disequilibrium ◽  
Genetic Drift ◽  
Recombination Fraction ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Finite Populations ◽  
Population Number ◽  
Backward Equation ◽  
Expected Values

The behaviour of linkage disequilibrium between two segregating loci in finite populations has been studied as a continuous stochastic process for different intensity of linkage, assuming no selection. By the method of the Kolmogorov backward equation, the expected values of the square of linkage disequilibrium z2, and other two quantities, xy(1 − x) (1 − y) and z(1 − 2x) (1 − 2y), were obtained in terms of T, the time measured in Ne as unit, and R, the product of recombination fraction (c) and effective population number (Ne). The rate of decrease of the simultaneous heterozygosity at two loci and also the asymptotic rate of decrease of the probability for the coexistence of four gamete types within a population were determined. The eigenvalues λ1, λ2 and λ3 related to the stochastic process are tabulated for various values of R = Nec.

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

Genetics ◽  
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.

scholarly journals Disequilibrium Pattern Analysis. II. Application to Danish HLA A and B Locus Data

Genetics ◽  
1987 ◽  
Vol 116 (4) ◽  
pp. 633-643
Author(s):  
William Klitz ◽  
Glenys Thomson
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Drift ◽  
Pattern Analysis ◽  
Human Leukocyte ◽  
Population Admixture ◽  
Random Genetic Drift ◽  
Leukocyte Antigen ◽  
Antigen System ◽  
Hla Haplotypes ◽  
General Method

ABSTRACT Disequilibrium pattern analysis, a general method for analyzing evolutionary events acting on pairs of tightly linked polymorphic loci, is applied to a large sample of Danish individuals typed for A and B loci of the HLA (human leukocyte antigen) system. Cases of selection on particular haplotypes are revealed from patterns of linkage disequilibrium among the HLA haplotypes. These patterns cannot be explained by either population admixture or random genetic drift. Six haplotypes out of the total array of 273 haplotypes have been identified which show in varying extents the patterns indicating selection.

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