Hitchhiking and linkage disequilibrium between hemoglobin S and nearby restriction sites

The association of the hemoglobin S mutation with an unusual 13 kb Hpa I restriction fragment has been reexamined using new data and a stochastic model for linkage disequilibrium. In agreement with earlier analyses with deterministic models, the present-day association of the beta S allele with the 13 kb fragment is lower than would be expected if all beta S alleles carried by American blacks were derived from a unique mutation that occurred in the ancestral Bantu population. However, from the stochastic model, if the effective population size was small for an appreciable period during the time that selection has been operating on HbS, then the confidence limits on the allelic association are very large and a unique West African beta S mutation cannot be ruled out from the two locus data alone.