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

"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 do genetic drift generates 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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Thanks for your answer. I still don't really understand. I understand that negative disequilibrium is synonymous to low additive genetic variance in fitness. Your citation seems to say that selection tends somehow (I don't understand how) to cause a negative linkage. Why does genetic drift causes linkage disequilibrium to be negative? I don't feel that this question has been addressed in your answer but I might misunderstand something. –  Remi.b Apr 25 at 17:18
    
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 at 18:12
    
I suddenly made a big jump toward understanding $\ddot \smile$. Thanks a lot. In order to make sure I really understand this process, I've asked there for a mathematical model demonstrating this process. Please let me know whether you think my new post is correctly phrased! –  Remi.b Apr 26 at 16:19
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