Fig. S1 Seventeen MHC alleles in lake whitefish including nucleotide and amino acid sequences.

Fig. 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).

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

Fig. S4 Results of the omegaMap analysis mapped onto our 3D protein structure prediction of allele 1.

Fig. S5 Posterior probability for the rho parameter for the MHCIIβ sequences generated with omegaMap.

Fig. S6 Spineplot representing the infection status vs. within individual MHCIIβ diversity.

Fig. S7 Spineplot representing the infection status vs. number of MHCIIβ alleles within an individual.

mec12358-sup-0002-TableS1.pdfapplication/PDF45KTable S1 454 multiplex primers.

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