Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow

Adaptive divergence and speciation may happen despite opposition by gene
flow. Identifying the genomic basis underlying divergence with gene flow
is a major task in evolutionary genomics. Most approaches (e.g. outlier
scans) focus on genomic regions of high differentiation. However, not all
genomic architectures potentially underlying divergence are expected to
show extreme differentiation. Here, we develop an approach that combines
hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency
change) with system-specific simulations to identify loci inconsistent
with neutral evolution. We apply this to a genome-wide SNP set from an
ideally-suited study organism, the intertidal snail Littorina saxatilis,
which shows primary divergence between ecotypes associated with different
shore habitats. We detect many SNPs with clinal patterns, most of which
are consistent with neutrality. Among non-neutral SNPs, most are located
within three large putative inversions differentiating ecotypes. Many
non-neutral SNPs show relatively low levels of differentiation. We discuss
potential reasons for this pattern, including loose linkage to selected
variants, polygenic adaptation and a component of balancing selection
within populations (which may be expected for inversions). Our work is in
line with theory predicting a role for inversions in divergence, and
emphasises that genomic regions contributing to divergence may not always
be accessible with methods purely based on allele frequency differences.
These conclusions call for approaches that take spatial patterns of allele
frequency change into account in other systems.