Supplementary Material for: On the Uses and Applications of the Most Commonly Used Measures of Linkage Disequilibrium from the Comparative Analysis of Their Statistical Properties

Background/Objective: The analysis of linkage disequilibrium is relevant for the exploration of the structure and evolution of genomes and for the gene mapping of quantitative characters and human diseases. The strength of linkage disequilibrium between diallelic loci is commonly measured by the coefficients D′ and r. Recent studies suggest that r is more useful than D′ as a general measure of the strength of disequilibrium because it provides much more precise (lower sampling variance) and accurate (lower bias) estimates of disequilibrium. We compared for the first time the statistical properties of D′ and r taking into account their differences in range. Methods: The sampling properties of D′ and r were evaluated by simulation under a variety of realistic population conditions and varying sample sizes using standardised statistics that allow for comparisons of the precision, accuracy and efficiency of estimates with different ranges. Results: Simulations revealed that estimates of r do not tend to be significantly more precise, accurate or efficient than those of D′ when compared by means of standardised statistics. Conclusion: The supposed advantage of r over D′ based on direct comparisons of their sampling distributions is more apparent than real. The obtained results are useful to assess the uses and applications of these widely used disequilibrium measures.