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.