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Table S1 Red spruce populations sampled, their geographic locations, and the site classes.

Table S2 EST loci (RPRS) annotations and number of SNPs assayed in Picea rubens.

Table S3 Flanking sequences of targeted SNPs in red spruce.

Table S4 Microsatellite primers sequences, amplification conditions, amplicon size range, and number of alleles in Picea rubens.

Table S5 Genetic diversity parameters in three age classes in polluted (TN, WV, NY) and control (NB, NS) populations.

Table S6 Multilocus variance components with regard to pollution class for red spruce populations.

Fig. S1 Loadings on the first principal component (PC) from a principal components analysis (PCA) of 19 bioclimatic variables obtained for each of the five sampled populations.

Fig. S2 Patterns of pairwise linkage disequilibrium (LD) as measured by the sqaured allelic correlation coefficient (r2) within age classes and populations of red spruce for 33 SNPs.

Fig. S3 Results from the program STRUCTURE with regard to the number of genetic clusters (K).

Fig. S4 Simulation-based estimates (= 1000 sets of 33 SNPs) of the false positive rate associated with the modified logistic regression method of Joost et al. (2007).

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