In Figure 3, we give posterior intervals along with posterior medians and MLEs for each of the fixation indices. The posterior medians are all pulled toward 1, relative to the MLEs, due to the prior, see Figure 1a. We see that the fixation index associated with the A1A4 combination is furthest from zero and negative, and most responsible for the negative estimate of f in the single inbreeding coefficient model. The heterogeneity of the fixation indices explains why the data are slightly more consistent with the saturated model than the single f model. It is interesting to observe that the A1A4 combination was not noteworthy in these data using the method implemented in Thomson et al. (1986). However, they comment that in the German population that they also examined (and in a Caucasian population investigated in Winnearls et al., 1984) there was an excess of A1A4 individuals, which is consistent with the posterior interval observed in Figure 3.
