Genomic divergence between Misty lake and stream stickleback fish. MistyHybridZone

How ecological divergence can maintain strong reproductive isolation between populations in geographic contact remains poorly understood at the genomic level, but is here studied in a stickleback population pair adapted to ecologically different lake and stream habitat in direct physical contact in the Misty lake watershed (Vancouver Island, Canada). Whole-genome pooled sequence data from eleven sites across the habitat transition reveal numerous regions fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must coincide with a genome-wide barrier to gene flow, because a steep cline in allele frequencies is also observed across the entire genome. The center of this cline co-localizes with the major lake-stream habitat transition, indicating that reproductive isolation is tied to natural selection. Simulating parapatric divergence in a stepping stone model confirms that the strong reproductive isolation observed can be maintained by selection despite high dispersal and small per-locus selection coefficients. Comparing samples from the cline center before and after an unusual ecological event (flood) finally demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.