ABSTRACT Aim Climate change is threatening aquatic populations with rapid changes in habitat salinity and temperature. Locally adapted alleles along environmental gradients, along with low but sufficient gene flow, could provide crucial genetic variation to adapt to future climate change and rescue populations from extinction. Thus, we explored whether planktonic populations exhibit genomic signatures of selection and gene flow across salinity and temperature gradients in the Baltic Sea and North Sea region. Location Baltic Sea, North Sea region. Methods We performed whole‐genome sequencing of 11 populations of the copepod Eurytemora affinis proper along salinity and temperature gradients. We determined signatures of population structure, admixture, and natural selection by analysing single nucleotide polymorphism (SNP) frequencies across populations using TreeMix, PoPoolation2, poolfstat, and BayPass. Results We found significant population genomic signatures of selection associated with salinity and temperature gradients using BayPass X T X and environmental association tests, consistent with local adaptation. Several ion transport functional categories (GO terms) were significantly associated with the salinity gradient across all populations, whereas only one GO term, ‘prostaglandin biosynthetic process’, was significantly associated with the temperature gradient in the North Sea region. We found clear population structure with PoPoolation2 and TreeMix. We also found signals of admixture between populations with poolfstat and TreeMix, consistent with the presence of gene flow. Site‐frequency spectra (SFS) of candidate SNPs tested against simulated SFS distributions revealed an excess of intermediate frequency alleles within a few populations. Main Conclusions The interplay between local adaptation and gene flow had not been fully explored in passive holoplankton dispersers. Many of the same ion transporter genes showed signatures of selection as in our prior studies, but in this case across a metapopulation of E. affinis spanning a broad geographic range. The presence of locally adapted alleles along with gene flow across environmental gradients could provide genetic substrate for natural selection, enabling populations to adapt to future climate change.
Diaz et al. (Fri,) studied this question.