An equal-tempered measure of linkage disequilibrium

Mark M. Tanaka

Theoretical Population Biology, 2025, vol. 166, issue C, 36-43

Abstract: Linkage disequilibrium (LD), the association of alleles at two loci, is defined in multiple ways. Because LD measures depend on allele frequencies, it is difficult to compare LD values between populations or loci with different allele frequencies. Here, I consider a geometric interpretation of a commonly used LD measure r2 which suggests a modification that is frequency-independent in the sense that equal evolutionary forces lead to the same effect at different frequencies. This new measure is a very simple expression that is known elsewhere as the Hamann coefficient and the G index of agreement; it is a linear transformation of the simple matching coefficient. I explore properties of this quantity in comparison with D and r2, and discuss its interpretation, advantages and disadvantages.

Keywords: Genetic association; Linkage disequilibrium; Frequency-dependence; Hamann; Correlation coefficient; Cosine similarity; Zeta (search for similar items in EconPapers)
Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:166:y:2025:i:c:p:36-43

DOI: 10.1016/j.tpb.2025.09.002

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