Likelihood analysis of recombinational disequilibrium in multiple-locus gametic frequencies.

Likelihood methods are developed for the estimation and testing of multiple-locus gametic disequilibria, using log-linear models of parametric effects. The estimates of disquilibrium are related to Kimura's Z-measure, and may be extended to multiple alleles and multiple loci. Likelihood ratio test criteria are constructed, which are asymptotically distributed as chi(2). The analysis is partitioned into various components corresponding to two-locus, residual three-locus, and higher order disequilibria. A four-locus example from Hordeum vulgare L. is utilized to illustrate the analysis. Most of the multiple-locus disequilibrium is accounted for by two-locus effects, and closely linked loci show considerably more disequilibrium than unlinked loci. It is shown that all possible pairwise comparisons are not statistically independent.