How demography shapes linkage disequilibrium with or without recombination
Kerdoncuff, E.; Lambert, A.; Achaz, G.
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Linkage Disequilibrium (LD) is a measure of the statistical association, within a population, between alleles present at different loci. We first briefly explain how LD, and in particular its decay as a function of the genetic distance between the two loci, is expected to be affected by mutation, recombination, selection, drift and demography. We then focus on three specific, widely used measures of LD: D, |D'|, and r2, in three different contexts: absence of recombination, a single recombination event, and an infinite amount of recombination events. We produce detailed characterizations of these three statistics under different demographic scenarios, with simulations, and with analytic results for D. We classify recombination events into four types and rank them according to their respective frequencies and effects. Finally, we provide recommendations for the uses of the different statistics and suggest applications of LD measures in the absence of recombination.
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