Linkage disequilibrium due to random genetic drift in finite subdivided populations

In order to clarify the mechanisms responsible for the observed linkage disequilibrium, such as that found between markers in the major histocompatibility complex of man and mouse, linkage disequilibrium between two linked loci was studied for a finite population with a subdivided structure. The infinite allele model was used. In analogy with the subdivision of the inbreeding coefficient, the linkage disequilibrium coefficient was subdivided, and various variance components of disequilibrium were defined. It was found that the disequilibrium components may get very large when migration is limited if the correlation of alleles at the two loci within a colony is taken relative to that of the entire population. In other words, with limited migration, random genetic drift of gamete types prevails in each colony. A possible test in which the variance components of disequilibrium are compared is suggested; the test discriminates between epistatic natural selection and limited migration, showing the former as the main cause of the observed linkage disequilibrium. It is pointed out that the major histocompatibility complex polymorphism is in accord with the population genetics model of multigene families that incorporate gene conversion or double unequal crossing-over between the loci in the supergene family.