Data from: Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq

Understanding the genomic basis of adaptive divergence in the presence of
gene flow remains a major challenge in evolutionary biology. In prickly
sculpin (Cottus asper), an abundant euryhaline fish in northwestern North
America, high genetic connectivity among brackish-water (estuarine) and
freshwater (tributary) habitats of coastal rivers does not preclude the
build-up of neutral genetic differentiation and emergence of different
life history strategies. Because these two habitats present different
osmotic niches, we predicted high genetic differentiation at known teleost
candidate genes underlying salinity tolerance and osmoregulation. We
applied whole-genome sequencing of pooled DNA samples (Pool-Seq) to
explore adaptive divergence between two estuarine and two tributary
habitats. Paired-end sequence reads were mapped against genomic contigs of
European Cottus, and the gene content of candidate regions was explored
based on comparisons with the threespine stickleback genome. Genes showing
signals of repeated differentiation among brackish-water and freshwater
habitats included functions such as ion transport and structural
permeability in freshwater gills, which suggests that local adaptation to
different osmotic niches might contribute to genomic divergence among
habitats. Overall, the presence of both repeated and unique signatures of
differentiation across many loci scattered throughout the genome is
consistent with polygenic adaptation from standing genetic variation and
locally variable selection pressures in the early stages of life history
divergence.