On the analysis and application of measures of linkage disequilibrium

The maximum likelihood, jackknife and bootstrap estimators of linkage disequilibrium, a measure of association in population genetics, are derived and compared. It is found that for point estimation, the resampling methods generate almost identical mean square errors. The maximum likelihood estimator could have bigger or smaller mean square errors depending on the parameters of the underlying population. However the bootstrap confidence interval is superior to the other two as the length of the intervals is shorter or the probability that the 95% confidence intervals include the true parameter is closer to 0.95. Although the standardised measure of linkage disequilibrium has a range from ‐1 to 1 regardless of marginal frequencies, it is shown that the distribution of this standardised measure is still not allele frequency independent under the multinomial sampling scheme. Copyright © 1991 Wiley Blackwell. All rights reserved.