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Appendix S1 Supplementary methods and results.

Table S1 List of environmental variables used in the correlation analysis with temporal outlier loci in 4T.

Table S2 Estimates of generation length, generations sampled in the study, and the effective population size (Ne) and its 95% confidence interval (CI) for each population.

Table S3 List of gene models located within 10 kb up- or downstream of each outlier SNP.

Table S4 Ranked list of the MGI GOslim2 summary categories represented in the GO-terms associated with gene models located within 10 kb up- or downstream from outlier loci (listed in Table S3).

Table S5 Pairwise differentiation between samples based on all loci (n = 160).

Table S6 Pairwise differentiation between samples based on non-outlier loci (n = 101).

Table S7 Pairwise differentiation between pooled samples (all years) for each population based on non-outlier loci (n = 101).

Fig. S1 Observed allele frequencies at significant 3NO temporal outliers (left panel) and significant 4T temporal outliers (right panel) in samples from different years in 3NO (a and b), 3Ps (c and d), 4T (e and f) and 4VsW (g and h).

Fig. S2 Results from the spatial outlier tests in the 1960s (a), the 1980s–1990s (b), and the 2000s (c).

Fig. S3 Results from the spatial BayeScan outlier tests on samples from the 1960s (a), 1980s–1990s (b), and 2000s (c).

Fig. S4 Results from the Lositan spatial outlier tests in the 1960s (a) and 2000s (b) excluding the 4VsW sample.

Fig. S5 LD patterns among the total set of 1960–2010 temporal and spatial outlier loci in samples from 3NO (a), 3Ps (b), 4T (c), and 4VsW (d).

Fig. S6 Heatmap showing the absolute value of Pearson's correlation coefficients (r; see scale on plot) between temporal patterns in allele frequencies at outlier loci and the selected explanatory variables in the 4T population.

Fig. S7 Heatmaps showing the maximum number of temporal outliers (regardless of locus identity) obtained in simulations of various combinations of local Ne and migration rates from the other populations for focal population 3NO (a), 3Ps (b), 4T (c), and 4VsW (d).

Fig. S8 Heatmaps showing the number of observed temporal outlier loci (in the real data) that also became temporal outliers in simulations of various combinations of local Ne and migration rates from the other populations for focal population 3NO (a) and 4T (b).

Fig. S9 Harmonic mean sample size (excluding missing data) and temporal differentiation (FGT) for each locus in the 4T 1960–2002 (five time points; a) and the 4T 1928–2008 (two time points; b) comparisons

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