Raw nucleotide counts for clinal Misty Lake and stream stickleback samples

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 in 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 a distance of just a
few hundred meters. This strong polygenic adaptive divergence must
constitute a genome-wide barrier to gene flow because a steep cline in
allele frequencies is observed across the entire genome, and because the
cline center co-localizes with the habitat transition. Simulations confirm
that such strong divergence can be maintained by polygenic selection
despite high dispersal and small per-locus selection coefficients.
Finally, comparing samples from near the habitat transition before and
after an unusual ecological perturbation 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.