What is the cause of "imbalanced" linkage disequilibrium? With perfect linkage disequilibrium ($D' = 1, R^2 = 1$), you might have the following table of counts for the alleles: B b A 100 0 a 0 100 With "partial" linkage disequilibrium ($D' < 1, R^2 < 1$), you'll see something like this: B b A 100 25 a 25 100 But I've sometimes seen the following "imbalanced" linkage disequilibrium ($D' = 1, R^2 < 1$): B b A 100 0 a 50 100 What gives rise to this sort of situation, where _aB_ occurs, but _Ab_ never does? Is there a name for this phenomenon? Which is a better measure of linkage disequilibrium in this case, the normalized LD coefficient $D'$, or the squared-correlation $R^2$?

This can occur if the **Ab** genotype is lethal, i.e. you won't observe individuals with a **Ab** genotype.

Allele lethality is a common mechanisms that can explain non-mendelian inheritance of a trait.

For the question of which LD metric to use, this is tricky. Under the assumption that allele lethality is indeed at play, you observed perfect haplotypes, so _D'=1_ wouldn't be incorrect. Yet the correlation coefficient is also correct in the sense that SNP A is not a perfect proxy for SNP B.