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Figure S1. Expression patterns for genes with responses during the time-course of acclimation to hyperosmotic challenge that are conserved between species (significant time-course effect, but no significant species-by-time-course interaction).

Figure S2. Correlation between Fst calculated in pooled samples and Fst calculated using individual genotypes (Infinium SNP bead chip data).

Table S1. Gene expression during the hyperosmotic challenge.

Table S2. GO term enrichment for outlier contigs between species (Lucania goodei vs. Lucania parva).

Table S3. GO term enrichment for outlier contigs between Lucania goodei populations.

Table S4. GO term enrichment for outlier contigs between most distant Lucania parva saltwater populations (Florida Atlantic salt and Texas Gulf salt).

Table S5. GO term enrichment for outlier contigs between freshwater and saltwater Lucania parva drainages (at least one drainage; saltwater–saltwater shared contigs removed).

Table S6. GO term enrichment for outlier contigs present two of more freshwater–saltwater L. parva drainages (only those categories with a count greater than one reported).

Table S7. Outlier loci shared between multiple freshwater and saltwater drainages in L. parva and between species.

Table S8. GO term enrichment for outlier contigs present between species in using genomic DNA and Infinium genotyping.

Table S9. GO term enrichment for outlier contigs present between all freshwater and saltwater Lucania parva using genomic DNA and Infinium genotyping.

Table S10. Genes with species-dependent expression differences and sequence divergence in freshwater–saltwater populations.

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