Figure S1: Seventeen MHC alleles in lake whitefish including nucleotide and amino acid sequences. Putative peptide binding region (PBR) sites are indicated with the grey arrow annotations (Brown et al. 1993). Amino acid residues found to be under balancing selection from the omegaMap results are indicated by the maroon arrow annotations. To create this figure, we used Geneious version 6.0.0beta created by Biomatters. Available from http://www.geneious.com/

Figure S2: NeighborNet haplotype network of the overlapping translated 16 alleles (nonfunctional allele 10 excluded) observed in lake whitefish together with 20 alleles from European whitefish (as indicated with “EW”) (Binz et al. 2001). The scale is uncorrected P ML distance. Alleles EW18-20 share the insertion also present in lake whitefish, while all others have the deletion.

Figure S3: Histograms of alleles per individual in dwarf and normal lake whitefish for all five lakes.

Figure S4: Results of the omegaMap analysis mapped onto our 3D protein structure prediction of allele 1. Red residues are both putative peptide binding region (PBR) based on alignment with human HLA and >95% posterior probability for balancing selection in the majority of lakes. Dark blue represents putative PBR residues that did not have a >95% posterior probability for balancing selection. Orange residues represent non-putative PBR residues that have a >95% posterior probability for balancing selection in this study. Light blue represents non-putative PBR residues that did not have a signal of balancing selection in the studied populations.

Fig. S4: Posterior probability for the rho parameter for the MHCIIβ sequences generated with omegaMap. The black line is the point estimate and the grey field is the 95% credibility interval.

Figure S6: Spineplot representing the infection status vs. within individual MHCIIβ diversity. The spineplot fuction in R makes the π continuous variable discreetclusters. The width of the bars represent the number of individuals in the cluster.

Figure S7: Spineplot representing the infection status vs. number of MHCIIβ alleles within an individual. . The width of the bars represent the number of individuals with that number of alleles.