Gametic Disequilibrium Measures: Proceed With Caution

Gametic Disequilibrium Measures: Proceed With Caution

October, 1987 | Philip W. Hedrick
The article discusses various measures of gametic disequilibrium and their properties. Five commonly used measures and a new one based on R. C. Lewontin's D' are compared. All measures, except the one based on D', are highly dependent on allelic frequencies. Some measures, such as those suggested by Brown, Feldman, and Nevo, and Ohta, can have negative values when there is maximum disequilibrium and have rates of decay in infinite populations that depend on the initial gametic array. The variances of all measures are large in samples from populations at equilibrium under neutrality, with the D' measure having the lowest variance. Three of the measures are highly correlated, including D², D* (equal to the correlation coefficient when there are two alleles at each locus), and X(2) of Brown et al. Using frequency-dependent measures may lead to mistaken conclusions, as illustrated by studies inferring recombinational hot spots and the effects of population bottlenecks from disequilibrium values. The article examines six different measures of two-locus gametic disequilibrium, focusing on their allelic frequency dependence and rate of decay from recombination. It also compares the distributions of these measures and calculates their correlation coefficients for randomly obtained samples. The measures include D', D², D*, Q*, F', and X(2). The D' measure is frequency-independent and has the same range for all allelic frequencies. Other measures, such as D*, Q*, and F', are highly frequency-dependent and can have negative values. The rate of decay of disequilibrium depends on the initial gametic array and recombination rate. The article concludes that frequency-independent measures like D' should be used to ensure confidence in conclusions based on statistical associations of alleles at two or more loci. The use of frequency-dependent measures may lead to incorrect conclusions, as demonstrated by studies on recombinational hot spots and population bottlenecks. The article also discusses the statistical properties of these measures, including their variances, skewness, and kurtosis, and their correlations with each other. The study emphasizes the importance of using appropriate measures to accurately interpret gametic disequilibrium data.The article discusses various measures of gametic disequilibrium and their properties. Five commonly used measures and a new one based on R. C. Lewontin's D' are compared. All measures, except the one based on D', are highly dependent on allelic frequencies. Some measures, such as those suggested by Brown, Feldman, and Nevo, and Ohta, can have negative values when there is maximum disequilibrium and have rates of decay in infinite populations that depend on the initial gametic array. The variances of all measures are large in samples from populations at equilibrium under neutrality, with the D' measure having the lowest variance. Three of the measures are highly correlated, including D², D* (equal to the correlation coefficient when there are two alleles at each locus), and X(2) of Brown et al. Using frequency-dependent measures may lead to mistaken conclusions, as illustrated by studies inferring recombinational hot spots and the effects of population bottlenecks from disequilibrium values. The article examines six different measures of two-locus gametic disequilibrium, focusing on their allelic frequency dependence and rate of decay from recombination. It also compares the distributions of these measures and calculates their correlation coefficients for randomly obtained samples. The measures include D', D², D*, Q*, F', and X(2). The D' measure is frequency-independent and has the same range for all allelic frequencies. Other measures, such as D*, Q*, and F', are highly frequency-dependent and can have negative values. The rate of decay of disequilibrium depends on the initial gametic array and recombination rate. The article concludes that frequency-independent measures like D' should be used to ensure confidence in conclusions based on statistical associations of alleles at two or more loci. The use of frequency-dependent measures may lead to incorrect conclusions, as demonstrated by studies on recombinational hot spots and population bottlenecks. The article also discusses the statistical properties of these measures, including their variances, skewness, and kurtosis, and their correlations with each other. The study emphasizes the importance of using appropriate measures to accurately interpret gametic disequilibrium data.
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