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

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malate dehydrogenase-1 (Mdh-1), alcohol dehydrogenase (Adh), and hexokinase-C (Hex-C, tentative name, F. M. Johnson, unpublished; position determined by the present authors to be 2-74.5) were assayed for 617 second chromosomes, and esterase-C (Est-C) and octanol dehydrogenase (Odh) were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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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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Linkage disequilibrium in the white locus region of Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672300031694 ◽

1993 ◽

Vol 62 (2) ◽

pp. 101-109 ◽

Cited By ~ 19

Author(s):

Naohiko T. Miyashita ◽

Montserrat Aguadé ◽

Charles H. Langley

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Natural Populations ◽

Restriction Enzymes ◽

Transcriptional Unit ◽

Similar Degree ◽

Significant Linkage Disequilibrium ◽

White Locus ◽

Different Populations ◽

Significant Linkage

SummaryLinkage disequilibrium between molecular polymorphisms in a 10 kb region in the white locus of Drosophila melanogaster, revealed with a battery of four-cutter restriction enzymes, was investigated in 266 lines sampled from seven natural populations around the world. A total of 73 (35 restriction site, 37 insertion/deletion and 1 inversion) polymorphisms were detected, of which 55 non-unique polymorphisms were analysed for linkage disequilibrium. Clustering of significant linkage disequilibrium was observed in the transcriptional unit of the white locus as in Miyashita & Langley (1988). It was shown that about two thirds of the 2-locus combinations showing significant linkage disequilibrium have similar degree and direction of association over different populations. Despite lower divergence in allelic frequencies of molecular polymorphisms among populations, an increase in the proportion of 2-locus pairs showing significant linkage disequilibrium is observed in the transcriptional unit. Large values of Ohta's D measure ratio (1982 a, b) cluster in the transcriptional unit, and correspond to significant linkage disequilibria. Although the exact molecular mechanism is not clear, these results suggest that epistatic selection is responsible for significant linkage disequilibrium in the transcriptional unit of this locus

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LINKAGE DISEQUILIBRIUM IN NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽

10.1093/genetics/78.3.921 ◽

1974 ◽

Vol 78 (3) ◽

pp. 921-936

Author(s):

Charles H Langley ◽

Yoshiko N Tobari ◽

Ken-Ichi Kojima

Keyword(s):

Drosophila Melanogaster ◽

Genetic Variation ◽

Linkage Disequilibrium ◽

Natural Populations ◽

Chromosomal Gene ◽

Gene Frequencies ◽

Linkage Disequilibria ◽

Allozyme Loci ◽

Two Populations ◽

Stable Populations

ABSTRACT Two large, stable populations (Texas and Japan) of Drosophila melanogaster were surveyed at 21 allozyme loci on the second and third chromosomes and for chromosomal gene arrangements on those two chromosomes. Over 220 independent gametes were sampled from each population. The types and frequencies of the surveyed genetic variation are similar to those observed previously and suggest only slight differentiation among geographically distant populations. Linkage disequilibrium among linked allozymes loci is only slightly, if at all, detectable with these sample sizes. Linkage disequilibrium between linked inversions and allozymes loci is common especially when located in the same arm. These disequilibria appear to be in the same direction for most comparisons in the two population samples. This result is interpreted as evidence of similar selective environments (ecological and genetic) in the two populations. It is also noted that the direction of these linkage disequilibria appears to be oriented with respect to the gene frequencies at the component loci.

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THE GENETIC STRUCTURE OF NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER. XII. LINKAGE DISEQUILIBRIUM IN A LARGE LOCAL POPULATION

Genetics ◽

10.1093/genetics/77.4.771 ◽

1974 ◽

Vol 77 (4) ◽

pp. 771-793

Author(s):

Terumi Muki ◽

Takao K Watanabe ◽

Osamu Yamaguchi

Keyword(s):

Drosophila Melanogaster ◽

Local Population ◽

Natural Populations ◽

Large Cage ◽

Linkage Disequilibria ◽

Esterase 6 ◽

Relative Viability ◽

Carolina Population ◽

Isozyme Loci ◽

Glycerol 3 Phosphate Dehydrogenase

ABSTRACT Seven hundred and three second chromosomes were extracted from a Raleigh, North Carolina population of Drosophila melanogaster in 1970. Additionally, four hundred and eighty-nine third chromosomes were extracted from a large cage population founded from the flies in the 1970 Raleigh collection. The α glycerol-3-phosphate dehydrogenase-1, malate dehydrogenase-1, alcohol dehydrogenase, and α amylase loci were studied from the second chromosomes, and the esterase-6, esterase-C, and octanol dehydrogenase loci were analyzed from the third chromosomes. Inversions, relative viability and fecundity were studied for both classes of chromosomes. The following significant findings were obtained: (1) All loci examined were polymorphic or had at least two alleles at appreciable frequencies. Analysis of the combined data from this experiment with that of Mukai, Mettler and Chigusa (1971) revealed that the frequencies of the genes in the second chromosomes collected in early August were approximately the same over three years. (2) Linkage disequilibria between and among isozyme genes inter se were not detected except in a few cases which can be considered due to non-random sampling. (3) Linkage disequilibria between isozyme genes and polymorphic inversions were detected when the recombination values between the breakage points of the inversions and the genes in question were small. In only a few cases, were second and third order linkage disequilibria including polymorphic inversions detected. (4) Evidence for either variation among genotypes within loci or cumulative effects of heterozygosity was found for viability and fecundity. As a result of these findings, it was tentatively concluded that although selection might be perceptibly operating on some polymorphic isozyme loci, most of the polymorphic isozyme genes are selectively neutral or near-neutral in the populations studied.

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Joint Linkage and Linkage Disequilibrium Mapping in Natural Populations

Genetics ◽

10.1093/genetics/157.2.899 ◽

2001 ◽

Vol 157 (2) ◽

pp. 899-909

Author(s):

Rongling Wu ◽

Zhao-Bang Zeng

Keyword(s):

Linkage Disequilibrium ◽

Complex Traits ◽

Positional Cloning ◽

Genome Structure ◽

Natural Populations ◽

Linkage Disequilibrium Mapping ◽

Linkage Disequilibria ◽

Time Simulation ◽

New Strategy ◽

Fisher Scoring Algorithm

Abstract A new strategy for studying the genome structure and organization of natural populations is proposed on the basis of a combined analysis of linkage and linkage disequilibrium using known polymorphic markers. This strategy exploits a random sample drawn from a panmictic natural population and the open-pollinated progeny of the sample. It is established on the principle of gene transmission from the parental to progeny generation during which the linkage between different markers is broken down due to meiotic recombination. The strategy has power to simultaneously capture the information about the linkage of the markers (as measured by recombination fraction) and the degree of their linkage disequilibrium created at a historic time. Simulation studies indicate that the statistical method implemented by the Fisher-scoring algorithm can provide accurate and precise estimates for the allele frequencies, recombination fractions, and linkage disequilibria between different markers. The strategy has great implications for constructing a dense linkage disequilibrium map that can facilitate the identification and positional cloning of the genes underlying both simple and complex traits.

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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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A COMPUTER MODEL ALLOWING MAINTENANCE OF LARGE AMOUNTS OF GENETIC VARIABILITY IN MENDELIAN POPULATIONS. II. THE BALANCE OF FORCES BETWEEN LINKAGE AND RANDOM ASSORTMENT

Genetics ◽

10.1093/genetics/82.2.377 ◽

1976 ◽

Vol 82 (2) ◽

pp. 377-399

Author(s):

Christopher Wills ◽

Charles Miller

Keyword(s):

Linkage Disequilibrium ◽

Genetic Variability ◽

Natural Populations ◽

Bimodal Distribution ◽

Average Heterozygosity ◽

Epistatic Interactions ◽

Selective Sampling ◽

Two Factors ◽

Random Assortment ◽

Balance Of Forces

ABSTRACT It is shown, through theory and computer simulations of outbreeding Mendelian populations, that there may be conditions under which a balance is struck between two factors. The first is the advantage of random assortment, which will, when multilocus selection is for intermediate equilibrium values, lead to higher average heterozygosity than when linkage is introduced. There is some indication that random assortment is also advantageous when selection is toward a uniform distribution of equilibrium values. The second factor is the advantage of linkage between loci having positive epistatic interactions. When multilocus selection is for a bimodal distribution of equilibrium values, an early advantage of random assortment is replaced by a later disadvantage. Linkage disequilibrium, which in finite populations is increased only by random or selective sampling, may hinder the movement of alleles to their selective equilibria, thus leading to the advantage of random assortment.—Some consequences of this approach to the structure of natural populations are discussed.

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THE EFFECT OF COMBINING ALLELES INTO ELECTROPHORETIC CLASSES ON DETECTING LINKAGE DISEQUILIBRIUM

Genetics ◽

10.1093/genetics/85.3.543 ◽

1977 ◽

Vol 85 (3) ◽

pp. 543-556

Author(s):

E Zouros ◽

G B Golding ◽

Trudy F C MacKay

Keyword(s):

Linkage Disequilibrium ◽

Sample Size ◽

Natural Populations ◽

Epistatic Interactions ◽

Detection Power ◽

Linkage Disequilibria ◽

Allelic Distribution ◽

Order Of Magnitude ◽

Actual Degree

ABSTRACT When alleles are combined into few detectable classes, linkage correlations are underestimated most of the time. The probability that the linkage correlation will be underestimated is a function of the actual degree of correlation and the evenness of the allelic distribution, but is mainly determined by the distribution of alleles into distinguishable classes. With only two alleles per class this probability will usually be higher than 0.7. Also, the consistency in the sign of the linkage disequilibrium over many populations may escape detection. An increase of sample size by one order of magnitude or more may be required to compensate for the loss in detection power. It follows that the available electrophoretic studies of linkage correlations, although negative in their majority, do not suggest that epistatic interactions and linkage disequilibria are rare in natural populations.

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Linkage disequilibrium in French natural populations of Drosophila melanogaster

Genetics Selection Evolution ◽

10.1186/1297-9686-21-1-33 ◽

1989 ◽

Vol 21 (1) ◽

pp. 33 ◽

Cited By ~ 3

Author(s):

J Sanchez Prado ◽

L Charles-Palabost ◽

M Katz ◽

A Merçot

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Natural Populations

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Decay of linkage disequilibrium in a finite island model

Genetics Research ◽

10.1017/s0016672300032742 ◽

1994 ◽

Vol 64 (2) ◽

pp. 137-144 ◽

Cited By ~ 2

Author(s):

Hidenori Tachida

Keyword(s):

Linkage Disequilibrium ◽

Migration Rate ◽

Natural Populations ◽

Decay Rates ◽

Island Model ◽

The Past ◽

Linkage Disequilibria ◽

Subdivided Populations ◽

Time Dependent Behaviour ◽

Dependent Behaviour

SummaryTime-dependent behaviour of linkage disequilibrium when there was initial linkage disequilibrium is studied in a finite island model assuming neutrality. Explicit expressions for linkage disequilibrium parameters are obtained. From these expressions, the initial and the ultimate decay rates of linkage disequilibrium parameters are found to be increased and decreased, respectively, by finiteness of the population when recombination rate, migration rate and inverse of subpopulation size are of comparable order. Thus, linkage disequilibrium created in the past may persist longerin smaller subdivided populations. Also, differentiation of the gametic parameter of linkage disequilibrium among subpopulations is found to diminish quickly compared tothe linkage disequilibrium in the whole population. Implications of these results for the interpretation of linkage disequilibria in natural populations are discussed.

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