(a) Z-standardized composite PC loadings (zComposite PC) for each analyzed transcript across the genome highlighting transcripts with strong parallel marine-freshwater divergence in gene expression. Red lines correspond to the upper and lower 1% composite PC quantiles. Genes highlighted with red points have putative roles in ion transport and osmoregulation (kcnj1a.6, atp1a1a.2, pvalb4, trpm4b.2, slc12a1, slc12a10.3, slc9a3.2, trpm2, trpv6, cftr, ca2, CA-like, aqp3a), calcium homeostasis (FAM111A, ca_hom_mod6-like), respiration (HBB2), cold temperature adaptation (TypeII AFP), jaw, gill and skeletal morhpogenesis (caspa, FAM111a), and immune system function (IFSF5b, caspa, PRSS27, MHCclassI, GVINP1, IFI44L (x2), GIMAP8-like (x2), NLRC3-like (x2), siglec). (b) An example highlighting the proximity of parallel differentially expressed genes to adaptive loci is a novel transcript coding for a sialic-acid binding Ig-like lectin. This gene shows strong parallel expression divergence among freshwater and marine ecotypes from all four river-systems and overlaps a previously identified adaptive locus with a signature of parallel marine-freshwater genomic divergence (CSS FDR 0.05, Jones et al., 2012) (c) Across the genome, loci with strong parallel expression divergence (loci in the upper and lower 1% quantiles of composite PC, black line) are more proximal to adaptive loci identified in Jones et al. (2012) than randomly sampled ‘control’ loci (gray line). Gray shading shows 95% confidence intervals from 100 random samples of 586 transcripts. (d and e) In marine and freshwater fish from the Little Campbell River (LITC), loci with strong parallel expression divergence show molecular signatures of natural selection (d, increased genetic divergence FST; and e, decreased nucleotide diversity, Pi) centered around their transcription start sites (black points) compared to control loci (expressed loci showing non-parallel expression divergence). Points represent mean values of 1 kb sliding windows and gray shading shows the standard error of the mean.