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 discreet
clusters. 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.