Estimating recombination fraction separately for males and females: a counterintuitive result

In the course of performing a linkage analysis on rats bred from inbred doubly heterozygous parents, we observed the following counterintuitive finding: the lod scores more strongly supported the hypothesis that all the recombinations occurred in one sex (without specifying which sex), rather than that some recombinations occurred in each sex. In this brief paper we explain how this apparent anomaly can arise. We point out that very different values of the recombination fraction vector theta = (theta Male, theta Female) can give rise to likelihoods that do not differ by much. We suggest that caution be exercised when investigators interpret results of linkage analyses in which estimates of theta Male and theta Female differ widely.