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 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.

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 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.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

CYTO-NUCLEAR EPISTASIS: TWO-LOCUS RANDOM GENETIC DRIFT IN HERMAPHRODITIC AND DIOECIOUS SPECIES

Evolution ◽  
2006 ◽  
Vol 60 (4) ◽  
pp. 643 ◽  
Author(s):  
Michael J. Wade ◽  
Charles J. Goodnight
Keyword(s):  
Genetic Drift ◽  
Random Genetic Drift ◽  
Dioecious Species
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