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An equal-tempered measure of linkage disequilibrium

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  • Tanaka, Mark M.

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.

Suggested Citation

  • Tanaka, Mark M., 2025. "An equal-tempered measure of linkage disequilibrium," Theoretical Population Biology, Elsevier, vol. 166(C), pages 36-43.
    • Handle: RePEc:eee:thpobi:v:166:y:2025:i:c:p:36-43
    DOI: 10.1016/j.tpb.2025.09.002
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    References listed on IDEAS

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    1. VanLiere, Jenna M. & Rosenberg, Noah A., 2008. "Mathematical properties of the r2 measure of linkage disequilibrium," Theoretical Population Biology, Elsevier, vol. 74(1), pages 130-137.
    2. Matthijs Warrens, 2008. "On Association Coefficients for 2×2 Tables and Properties That Do Not Depend on the Marginal Distributions," Psychometrika, Springer;The Psychometric Society, vol. 73(4), pages 777-789, December.
    3. Uyenoyama, Marcy K., 2024. "Joint identity among loci under mutation and regular inbreeding," Theoretical Population Biology, Elsevier, vol. 159(C), pages 74-90.
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