The linkage disequilibrium which measures the association between linked genes is a temporary phenomenon in a population because of crossing over. But such associations persist in HLA system. These persistent linkage disequilibria may be due to the very small fraction of recombinaison between the loci but other explanations are possible: selection or migration. A linkage disequilibrium produces a phenotypic correlation in a population. A phenotypic correlation may be due to pleiotropic effect of a gene, or epistasie of two genes, or population stratification... On the same hand, if a correlation appears in an inter population study, it may be due to a migration or a subdivided population. In medical genetics the research of such association intra or inter population studies may permit to point out a defect gene. In particular, HLA system study has proved that many susceptibility genes of various diseases are linked to B or D alleles.
Female Genetic Linkage