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 disequilibrium between a pair of genetic markers. Under a model of reciprocal recombination, the decay rate of linkage disequilibrium depends on the distance between the two markers, while under conversion the decay rate is independent of this distance, provided that conversion tracts are short. A population genetic three-locus model provides a function Q of two-locus linkage disequilibria. Viewed as a random variable, Q is the basis for a test of the relative impact of conversion and recombination. This test requires haplotype frequency data of a sufficiently variable three-locus system. One of the few examples 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 stretches of DNA, whereas reciprocal recombination may have played a greater role over longer stretches of DNA. However, in order to draw firm conclusions more independent data are necessary.