Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

Abstract How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over distance of just few hundred meters. This polygenic adaptive must constitute genome-wide barrier gene flow because steep cline allele frequencies is observed across entire genome, center closely matches habitat transition. Simulations confirm that such can be maintained by selection despite high dispersal small per-locus coefficients. Finally, comparing samples from near transition before after an unusual perturbation demonstrates fragility balance selection. Overall, our highlights efficacy divergent maintaining without physical isolation, analytical power studying speciation fine eco-geographic scale.