Appendix S1 Univariate divergence in four morphological traits within each lake–stream system.

Appendix S2 Strategy adopted to eliminate uninformative polymorphisms from the marker data sets.

Appendix S3 Summary statistics on library size, read coverage, alignment success and marker numbers.

Appendix S4 Recombination rate along stickleback chromosomes.

Appendix S5 Resampling approach used to determine significance thresholds FST for outlier regions.

Appendix S6 Genome-wide sliding window profile of lake–stream divergence within the Boot system (both rawFST and residual FST).

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