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Equation S1 Landscape resistance as a function of elevation; inverse Gaussian function.

Equation S2 Landscape resistance as a function of aspect; modified heat load index.

Equation S3 Landscape resistance as a function of topographic complexity.

Table S1 Details for each microsatellite locus, including original source.

Table S2 Final multivariate models from the optimization with partial Mantel correlation after partialling out the IBD model for (1) PCA and (2) Bray–Curtis per cent dissimilarity genetic distance metrics.

Fig. S1 Map of the analysis frame within Crater Lake National Park showing surface relief ratio, a measure of topographic complexity.

Fig. S2 Map of the analysis frame within Crater Lake National Park showing the location of streams and simulated pikas.

Fig. S3 Map of Crater Lake National Park showing land cover categories from the 2006 National Land Cover Dataset.

Fig. S4 Resistance values for each land cover category ranked according to cover, with lowest rank assigned to land cover types that provide greater cover.

Fig. S5 Population genetic structure of pikas at Crater Lake National Park.

Fig. S6 Correlation between genetic distance and geographical distance (open circle, solid line), resistance distance (solid circle, dotted line) and resistance distance after partialling out geographical distance (solid triangle, dashed line), averaged across all ten MC replicates.

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