BackgroundThe degree of genetic differentiation among populations experiencing high levels of gene flow is expected to be low for neutral genomic sites, but substantial divergence can occur in sites subject to directional selection. Studies of highly mobile marine fish populations provide an opportunity to investigate this kind of heterogeneous genomic differentiation, but most studies to this effect have focused on a relatively low number of genetic markers and/or few populations. Hence, the patterns and extent of genomic divergence in high-gene-flow marine fish populations remain poorly understood.ResultsWe here investigated genome-wide patterns of genetic variability and differentiation in ten marine populations of three-spined stickleback (Gasterosteus aculeatus) distributed across a steep salinity and temperature gradient in the Baltic Sea, by utilizing >30,000 single nucleotide polymorphisms obtained with a pooled RAD-seq approach. We found that genetic diversity and differentiation varied widely across the genome, and identified numerous fairly narrow genomic regions exhibiting signatures of both divergent and balancing selection. Evidence was uncovered for substantial genetic differentiation associated with both salinity and temperature gradients, and many candidate genes associated with local adaptation in the Baltic Sea were identified.ConclusionsThe patterns of genetic diversity and differentiation, as well as candidate genes associated with adaptation, in Baltic Sea sticklebacks were similar to those observed in earlier comparisons between marine and freshwater populations, suggesting that similar processes may be driving adaptation to brackish and freshwater environments. Taken together, our results provide strong evidence for heterogenic genomic divergence driven by local adaptation in the face of gene flow along an environmental gradient in the post-glacially formed Baltic Sea.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0130-8) contains supplementary material, which is available to authorized users.

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Graphical AbstractHighlights d Laterally acquired genes rapidly spread among established populations of a grass d Subsequent genomic erosion created neutral gene presenceabsence polymorphisms d One of these neutral genes was secondarily swept into a population d Lateral gene transfers have both direct and delayed adaptive impacts

The flat periwinkles, Littorina fabalis and L. obtusata, are two intertidal gastropods that offer a promising system for local adaptation and ecological speciation studies. Taking advantage of 17 recently developed specific microsatellite loci, we performed the first comprehensive genetic characterization of these sister species in the Iberian Peninsula. Special attention was given to L. fabalis by sampling populations representing the three morphotypes/ecotypes described from the region, which mainly differ in the habitat they are confined to (i.e. algae/seagrass 'host' species and level of wave exposure). Our analysis revealed, for the first time, the existence of hybrids between L. fabalis and L. obtusata in a natural population, which suggests that despite their strong genetic differentiation, reproductive isolation is not complete. Furthermore, the differentiation between L. fabalis ecotypes is lower than between these and L. obtusata; and their population genetic structure appears to be mainly governed by geography. However, ecological and demographic factors seem to have also played an important role, as suggested by the higher population differentiation in one of the ecotypes. Altogether, this work provides an important baseline for further studies on flat periwinkles as a model to explore how reproductive barriers evolve and interact with each other across a speciation continuum.