The effect of subdivision on variation at multi-allelic loci under balancing selection

Simulations are used to investigate the expected pattern of variation at lo ci under different forms of multi-allelic balancing selection in a finite i sland model of a subdivided population. The objective is to evaluate the ef fect of restricted migration among demes on the distribution of polymorphis m at the selected loci at equilibrium and to compare the results with those expected for a neutral locus. The results show that the expected number of alleles maintained, and numbers of nucleotide differences between alleles, are relatively insensitive to the migration rate, and differentiation rema ins low even under very restricted migration. However, nucleotide divergenc e between copies of functionally identical alleles increases sharply when m igration decreases. These results are discussed in relation to published su rveys of allelic diversity in MHC and plant self-incompatibility systems, a nd to the possibility of inferring ancient population genetic events and pr ocesses. In addition, it is shown that, for sporophytic self-incompatibilit y systems, it is not necessarily true in a subdivided population that reces sive alleles are more frequent than dominant ones.