Relative efficiencies of chi 2 models of recombination for exclusion mapping and gene ordering

In multilocus linkage analysis, it is common to assume chiasma interference is absent. While this assumption provides mathematical tractability, there is substantial biological evidence contradicting it, particularly when the loci are closely spaced. The chi 2 class of recombination models, recently described by Foss et al. (Genetics 133: 681-691, 1993), has a plausible biological basis and provides a dramatically improved fit over virtually all other models currently in use. Here, a simulation study is performed to assess the relative efficiency of a no interference model analysis to an analysis with a chi 2 model which allows for interference. The results presented show that analysis with the no interference model is inefficient in the presence of interference.