Appendix S1GenBank accessions numbers, MHC II and microsatellite genotypes.

Appendix S2Alignment of MHC II alleles.

Table S1 Sampling localities.

Table S2 The average rates of nonsynonymous substitutions per nonsynonymous site (dN) and synonymous substitutions per synonymous sites (dS) with standard errors obtained through 1000 bootstrap replicates in parentheses, and the results of the Z-test of neutrality.

Table S3 Evaluation of the goodness of fit for different models of codon evolution and estimated parameter values.

Table S4 Summary of MHC class II variation in populations.

Table S5 The results of amovas for the minusS dataset, in which northern L.  vulgaris, southern L.  vulgaris and L.  montandoni were used as the highest level of hierarchical grouping of populations, and two groups were analyzed at a time.

Table S6 Parwise FST values for the dataset minusS, computed for binary encoded data.

Table S7 Comparison of cDNA and gDNA MHC alleles for three individuals with coverage sufficient for genotyping.

Table S8 Parwise FST values for the dataset plusS, computed for binary encoded data.

Table S9 Number of microsatellite alleles (Na) and null allele frequencies (Pnull) for each population.

Fig. S1 Schematic representation of the location of primers used to amplify 2nd exon of MHC class II (A) and the structure of amplicons generated with fusion primers (B).

Fig. S2 Allelic richness and number of private alleles (dark blue, range 0–8) in populations of L.  vulgaris (red, range 5.8–19.3) and L.  montandoni (light blue, range 7.8–21.0) for data set minusS.

Fig. S3 Genetic structure of L.  vulgaris and L.  montandoni populations in MHC II inferred by Structure analysis for = 10 (data set minusS). Assignment of populations to particular clusters is shown on the map.

Fig. S4 Nonmetric two-dimensional scaling of the pairwise FST matrix computed for binary-encoded MHC class II data; stress = 0.203 (data set minusS). The names of populations corresponding to numbers are given in Tables 5 and S1, Supporting information.

Fig. S5 Distribution of the number of alleles per individual in L.  vulgaris and L.  montandoni in data set plusS (A, B) and in data set minusS (C, D).

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