Table S1. Genome level FST(μ) for pairs of populations.

Table S2. Number of loci that were classified as statistical FST outliers (q ≥ 0.95) in at least n (column names) out of N pairwise population analyses.

Figure S1. Plots depict hypothetical genomic clines.

Figure S2. Goodness of fit for NMDS.

Figure S3. Ordination-based summary of genetic differentiation in Lycaeides based on nonmetric multidimensional scaling (NMDS).

Figure S4. Statistical summary of morphological variation in Lycaeides based on male genitalic morphology PC1 and wing pattern PC1.

Figure S5. Estimated distribution of hybrid index in Jackson Hole Lycaeides (0 = L. melissa, 1 = L. idas).

Figure S6. Scatterplot depicting genetic divergence (measured by Neis GST) between L. idas, L. melissa, and Jackson Hole Lycaeides.

Figure S7. Estimated distribution of genomic cline parameters α and β in Jackson Hole Lycaeides.

Figure S8. Correlation between FST and the absolute value of α for simulated datasets.

Figure S9. Scatterplot depicting the relationship between GST between L. idas and L. melissa and genomic cline parameter α.

Figure S10. Histogram of expected admixture linkage disequilibrium (LD).

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