An attempt to measure the patchwork pattern observed among alleles at major histocompatibility complex loci

By means of simulations and DNA sequence analyses, standardized identity excess (a measure of linkage disequilibrium) between segregating nucleotide sites was studied as an effort to quantify the patchwork pattern among alleles of the major histocompatibility complex loci. It was found that the pattern under selective neutrality, and/or no intralocus recombination does not fit the observed pattern based on DNA sequences. However, the intensity and type of selection and the rate of recombination are difficult to estimate by comparing simulation results with the observed pattern.