SNPs linkage disequilibrium

Linkage disequilbrium is a widely used measure of association between two polymorphic loci. Classical population genetics theory suggests that for two loci with recombinaton any amount of linkage disequilibrium will be eliminated after sufficient number of generations. This result is sometimes misinterpreted particularly when equilibrium is observed. I will discuss the properties of linkage disequilibrium between two segregating sites (or single nucleotide polymorphism [SNPs]) in a sample, utilizing coalescent theory.