Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns

Deterministic theory suggests that reciprocal recombination and intragenic, interallelic conversion have different effects on the linkage disequilibri um between a pair of genetic markers. Under a model of reciprocal recombina tion, the decay rate of linkage disequilibrium depends on the distance betw een the two markers, while under conversion the decay rate is independent o f this distance, provided that conversion tracts are short. A population ge netic three-locus model provides a function Q of two-locus linkage disequil ibria. Viewed as a random variable, Q is the basis for a test of the relati ve impact of conversion and recombination. This test requires haplotype fre quency data of a sufficiently variable three-locus system. One of the few e xamples currently available is data from the Human Leukocyte Antigen (HLA) class I genes of three Amerindian populations. We find that conversion may have played a dominant role in shaping haplotype patterns over short stretc hes of DNA, whereas reciprocal recombination may have played a greater role over longer stretches of DNA. However, in order to draw firm conclusions m ore independent data are necessary.