b2. Frequency-dependent selection: are allele effects inconsistent across lakes?
If stickleback and their parasites engage in a Red Queen race style co-evolution, the efficacy of any single allele will shift through time. For hosts and parasites with limited dispersal, physically disconnected sites are unlikely to be in the same phase of the arms race. As a result, a given MHC allele may have different effects on a given parasite from one site to the next: effective against defense in some places/times, ineffective or susceptible at others. Alternatively, if the same allele has similar effects on the same parasite across different lakes (without gene flow), such fluctuating frequency-dependent selection is unlikely. To test these alternatives, we first identified the moderately prevalent MHC-parasite combinations that were present in more than one site. For each qualified combination, we used a generalized linear model with negative binomial distribution to examine if the infection intensity of the parasite is influenced by the MHC allele, sampling site, and the interaction between site and MHC allele (this differs from the GLMs described in b1, which were done separately for each sample site). We corrected p values for multiple-comparison with BH method. We used the anova function in R to perform an analysis of deviance for each regression model. It reported the reductions in the residual deviance as each term of the formula was added in turn. We evaluated whether, across many parasite-allele combinations, more variation was explained by the focal allele’s main effect (implying consistent protection across populations), or allele × population interactions (inconsistent protection). Parasites transmitted by birds could spread in a larger spatial scale, so they are less likely to be engaged in evolutionary arms race. We did a Chi-squared test to test whether the parasite taxa, which have birds as final hosts, were more likely to be found in the models with significant main effect than in the models with significant allele x population effect.