b1. Frequency-dependent selection: is there a rare allele advantage
Although we found many MHC-parasite associations, we found no tendency for alleles to be protective when rare, or vulnerable to infection when common. That is, the Z value of a given allele’s effect on a given parasite in a given site was independent of that alleles’ prevalence in that focal site. Across all sites, there were a total of 5623 MHC-parasite combinations that were moderately frequent and so included in the analysis. After excluding the models heavily influenced by outlier values with high leverage, we obtained 4130 linear regression models (see Fig. 3A for an example of this result from one population). 45 models had significant negative MHC-parasite associations and 45 models had significant positive MHC-parasite associations (see Fig. 3B for an example). Some MHC alleles, and parasites, are repeated across multiple regression models from different populations. None of the models were significant after we corrected for multiple-comparison with BH method. A mixed effect linear model showed that the impact of allele prevalence on Z values was not significant (coefficient = 0.09, t = 1.14, p = 0.27) (Fig. 3C). Therefore, this result did not provide evidence for rare allele advantage of MHC alleles on parasite infection intensities.