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The very first sentence of the abstract of this article is:

"In finite populations subject to selection, genetic drift generates negative linkage disequilibrium, on average, even if selection acts independently (i.e., multiplicatively) upon all loci."

Question

Why does genetic drift generate negative linkage disequilibrium?

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Genetic drift is the change of allele frequencies in a population due to random sampling during reproduction. This can cause some allele combinations to become more or less common than would be expected without drift, thus creating a disequilibrium. However, it's the combination of genetic drift AND selection that generates negative (instead of positive) disequilibria. From the discussion of the article you linked to:

Selection eliminates positive disequilibria more efficiently than it eliminates negative disequilibria, because negative disequilibrium reduces the genetic variance upon which selection acts. Consequently, the average disequilibrium over loci ... becomes negative over time.

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Drift can cause negative or positive disequilibria, not just negative, by changing allele frequencies through random sampling error. Since selection acts on variance and negative equilibria correlate with low variance, they are not affected by selection as much as positive disequilibria. Thus genetic drift favours a negative linkage disequilibrium only in the presence of selection. Does that make it clearer? Perhaps I'm not understanding what you're asking (wouldn't be the first time today). –  canadianer Apr 25 '14 at 18:12

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