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

Genetics ◽  
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.

scholarly journals Joint Linkage and Linkage Disequilibrium Mapping in Natural Populations

Genetics ◽  
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.

The variance of linkage disequilibrium between three loci in a finite population

1983 ◽  
Vol 25 (2) ◽  
pp. 139-145 ◽  
Author(s):  
C. Strobeck ◽  
G. B. Golding
Keyword(s):  
Linkage Disequilibrium ◽  
Finite Population ◽  
Intragenic Recombination ◽  
Random Drift ◽  
Third Order ◽  
Linkage Disequilibria ◽  
Order Of Magnitude ◽  
Infinite Alleles Model

The variance of three-locus linkage disequilibria for an equilibrium infinite alleles model is solved numerically on a computer, using identity coefficients. It is shown that the variance of three-locus linkage disequilibrium created by random drift, although smaller than the variance of two-locus linkage disequilibrium, is of the same order of magnitude. Hence third-order disequilibria are not necessarily good indications of selection. The formula for the variance of linkage disequilibrium is given when there is no recombination between the genes. This model can also be interpreted as intragenic recombination between three sites within a gene.

scholarly journals 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 ◽  
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.

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 Decay of linkage disequilibrium in a finite island model

1994 ◽  
Vol 64 (2) ◽  
pp. 137-144 ◽  
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.

scholarly journals THE GENETICS OF DROSOPHILA SUBOBSCURA POPULATIONS. IX. STUDIES ON LINKAGE DISEQUILIBRIUM IN FOUR NATURAL POPULATIONS

Genetics ◽  
1979 ◽  
Vol 93 (2) ◽  
pp. 497-523
Author(s):  
M Loukas ◽  
C B Krimbas ◽  
Y Vergini
Keyword(s):  
Linkage Disequilibrium ◽  
Geographical Variation ◽  
Natural Populations ◽  
Strong Linkage Disequilibrium ◽  
Linkage Equilibrium ◽  
Strong Linkage ◽  
Linkage Disequilibria ◽  
Break Points ◽  
Complex Locus ◽  
Two Populations

ABSTRACT Gametic frequencies were obtained in four natural populations of D. subobscura by extracting wild chromosomes and subsequently analyzing them for inversions and allozymes. The genes Lap and Pept-1, both located within the same inversions of chromosome 0, were found in striking nonrandom associations with them of the same kind and degree in all populations studied. On the contrary, the gene Acph, also located within the previously mentioned inversions, was found in linkage disequilibrium with them only in two populations and of opposite directions. This is also the case for the genes Est-9 and Hk, both located within chromosome E inversions. While the gene Est-9 was in strong linkage disequilibrium with the inversions, of the same kind and degree in all populations studied, Hk was found to be in linkage equilibrium. Allele frequencies for the 29 genes studied do not show geographical variation except for the genes Lap, Pept-1 and Est-9, the ones found in linkage disequilibria with the geographically varying gene arrangements. Although mechanical or historical explanations for these equilibria cannot be ruled out, these data cannot be explained satisfactorily by the "middle gene explanation," which states that loci displaying such linkage disequilibria are the ones located near the break points of inversions, while the ones displaying linkage equilibria with them are located in the middle of them. There is no evidence for consistent linkage disequilibria between pairs of loci, except for the closely linked genes of the complex locus, Est-9. This would imply, if it is not a peculiarity of the Est-9 complex, that the linkage disequilibria aye found only between very closely linked loci or that, far less closely linked genes, the associations are too weak to be detected by the usual samples sizes.

scholarly journals The detection of linkage disequilibrium in molecular sequence data.

Genetics ◽  
1995 ◽  
Vol 140 (1) ◽  
pp. 377-388 ◽  
Author(s):  
R C Lewontin
Keyword(s):  
Linkage Disequilibrium ◽  
Sequence Data ◽  
Natural Populations ◽  
Total Work ◽  
Molecular Sequence Data ◽  
Exact Test ◽  
Molecular Sequence ◽  
Linkage Disequilibria ◽  
Tests Of Association ◽  
A Site

Abstract Studies of genetic variation in natural populations at the sequence level usually show that most polymorphic sites are very asymmetrical in allele frequencies, with the rarer allele at a site near fixation. When the rarer allele at a site is present only a few times in the sample, say below five representatives, it becomes very difficult to detect linkage disequilibrium between sites from tests of association. This is a consequence of the numerical properties of even the most powerful test of association, Fisher's exact test. Sites with fewer than five representatives in the sample should be excluded from association tests, but this generally leaves few site pairs eligible for testing. A test for overall linkage disequilibrium, based on the sign of the observed linkage disequilibria, is derived which can use all the data. It is shown that more power can be achieved by increasing the length of sequence determined than by increasing the number of genomes sampled for the same total work.

Absence of linkage disequilibria between chromosomal arrangements and mtDNA haplotypes in natural populations of Drosophila subobscura from the Balkan Peninsula

Genome ◽  
2012 ◽  
Vol 55 (3) ◽  
pp. 214-221 ◽  
Author(s):  
Mihailo Jelić ◽  
José A. Castro ◽  
Zorana Kurbalija Novičić ◽  
Bojan Kenig ◽  
Danica Dimitrijević ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Linkage Disequilibrium ◽  
Natural Populations ◽  
Balkan Peninsula ◽  
Drosophila Subobscura ◽  
Mitochondrial Haplotypes ◽  
Linkage Disequilibria ◽  
Mtdna Haplotypes ◽  
Mitochondrial Dna Variability

The genetic structure of Drosophila subobscura from the Balkan Peninsula was studied with respect to restriction site polymorphism of mitochondrial DNA in populations from the Derventa River Gorge and Sicevo Gorge (Serbia). To investigate the role of cytonuclear interactions in shaping mitochondrial DNA variability in natural populations of this species, the study was complemented with the analysis of linkage disequilibria between mitochondrial haplotypes and chromosomal inversion arrangements. Similar to other populations of D. subobscura, two main haplotypes (I and II) were found, as well as a series of less common ones. The frequencies of haplotypes I and II accounted for 25.8% and 71.0%, respectively, in the population from the Derventa River Gorge, and for 32.4% and 58.1%, respectively, in the population from Sicevo Gorge. One of the haplotypes harbored a large insertion (2.7 kb) in the A+T rich region. The frequency distribution of both haplotypes did not depart from neutrality. Contrary to prior studies, we did not detect any significant linkage disequilibrium between the two most frequent mtDNA haplotypes and any of the chromosomal arrangements in either of the populations. We conclude that linkage disequilibrium is not a general occurrence in natural populations of D. subobscura, and we discuss how transient coadaptations, ecologically specific selective pressures, and demographics could contribute to population-specific patterns of linkage disequilibrium.

scholarly journals EXPECTED LINKAGE DISEQUILIBRIUM FOR A NEUTRAL LOCUS LINKED TO A CHROMOSOMAL ARRANGEMENT

Genetics ◽  
1983 ◽  
Vol 103 (3) ◽  
pp. 545-555
Author(s):  
Curtis Strobeck
Keyword(s):  
Linkage Disequilibrium ◽  
Balancing Selection ◽  
Natural Populations ◽  
Transient Behavior ◽  
Random Drift ◽  
Strong Linkage ◽  
Linkage Disequilibria ◽  
Chromosomal Arrangement ◽  
Neutral Locus ◽  
Selection For

ABSTRACT The expected value of the squared linkage disequilibrium is derived for a neutral locus associated with a chromosomal arrangement that is maintained in the population by strong balancing selection. For a given value of recombination, the expected squared linkage disequilibrium is shown to decrease as the intensity of selection maintaining the arrangement increases. The transient behavior of the expected square linkage disequilibrium is also derived. This theory applies to loci that are closely linked to inversions in Drosophila species and to loci closely linked to the differential segments of the translocation complexes in ring-forming species of Oenothera. In both cases the strong linkage disequilibria that have been observed in natural populations can be explained by random drift.

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.

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