Data from: Putative chromosomal rearrangements are associated primarily with ecotype divergence rather than geographic separation in an intertidal, poorly-dispersing snail

Littorina saxatilis is becoming a model system for understanding the
genomic basis of ecological speciation. The parallel formation of
crab-adapted ecotypes that exhibit partial reproductive isolation from
wave-adapted ecotypes has enabled genomic investigation of conspicuous
shell traits. Recent genomic studies suggest that chromosomal
rearrangements may enable ecotype divergence by reducing gene flow.
However, the genomic architecture of traits that are divergent between
ecotypes remains poorly understood. Here, we use 11,504 single nucleotide
polymorphism (SNP) markers called using the recently-released L. saxatilis
genome to genotype 462 crab ecotype, wave ecotype, and
phenotypically-intermediate L. saxatilis individuals with scored
phenotypes. We used redundancy analysis to study the genetic architecture
of loci associated with shell shape, shape corrected for size, shell size,
and shell ornamentation, and to compare levels of co-association among
different traits. We discovered 341 SNPs associated with shell traits.
Loci associated with trait divergence between ecotypes were often located
inside putative chromosomal rearrangements recently characterized in
Swedish L. saxatilis. In contrast, we found that shell shape corrected for
size varied primarily by site rather than by ecotype and showed little
association with these putative rearrangements. Together, these results
reveal that genomic regions of elevated divergence with putative
rearrangements are associated with divergence along steep environmental
axes in L. saxatilis ecotypes, consistent with models of adaptation with
gene flow, but these regions are distinct from genomic architecture
associated with site-specific variation. Our findings here further support
predictions from models indicating the importance of genomic regions of
reduced recombination allowing co-association of loci during ecological
speciation with ongoing gene flow.