Table S1 List of populations sampled for the spatial survey and their characteristics.

Table S2 Quantitative assessment of fish predation, land use intensity and parasite infection in the populations from the spatial survey.

Table S3 Collinear variation of environmental stressors tested with Mantel test.

Table S4 Details on the microsatellite markers used in the genome scan analysis.

Table S5 Outlier analysis conducted with microsatellite markers.

Table S6 Outlier analysis conducted with SNP markers.

Table S7 GO annotation of the outlier loci and of candidate genes putatively liked to them.

Table S8 Pairwise Fst values in the set of populations analyzed.

Table S9 Summary statistics of assembly and scaffolding for D.   magna.

Fig. S1 Population genetic structure based on neutral microsatellites.

Fig. S2 Candidate genes linked to specific and general stress response.

Fig. S3 LD analysis.

Fig. S4 Allele frequency at neutral and selected loci in the spatial survey.

Fig. S5 Allele frequency at selected loci in the temporal survey.

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