Admixture generates linkage disequilibrium between loci, even those that are unlinked (i.e. segregate independently or reside on different chromosomes). A lot of my PhD was spent thinking about admixture and admixture LD gave me some grief.
Motivation The effects of population structure in GWAS (genome-wide association studies) have been well-studied. It’s one of those problems that on a surface level is quite easy to grasp intuitively.
Motivation Ever wondered why the effect size of a tag variant is \(r\beta_{causal}\)? Here, \(r\) is the correlation (measure of LD) between the tag and causal variant, and \(\beta_{causal}\) is the effect size of the causal variant.