Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?

Parallel patterns of adaptive divergence and speciation are cited as
powerful evidence for the role of selection driving these processes.
However, it is often not clear whether parallel phenotypic divergence is
underlain by parallel genetic changes. Here, we asked about the genetic
basis of parallel divergence in the marine snail Littorina saxatilis,
which has repeatedly evolved coexisting ecotypes adapted to either crab
predation or wave action. We sequenced the transcriptome of snails of both
ecotypes from three distant geographical locations (Spain, Sweden and
United Kingdom) and mapped the reads to the L. saxatilis reference genome.
We identified genomic regions potentially under divergent selection
between ecotypes within each country, using an outlier approach based on
FST values calculated per locus. In line with previous studies indicating
that gene reuse is generally common, we expected to find extensive sharing
of outlier loci due to recent shared ancestry and gene flow between at
least two of the locations in our study system. Contrary to our
expectations, we found that most outliers were country specific,
suggesting that much of the genetic basis of divergence is not shared
among locations. However, we did find that more outliers were shared than
expected by chance and that differentiation of shared outliers is often
generated by the same SNPs. We discuss two mechanisms potentially
explaining the limited amount of sharing we observed. First, a polygenic
basis of divergent traits might allow for multiple distinct molecular
mechanisms generating the same phenotypic patterns. Second, additional,
location-specific axes of selection that we did not focus on in this study
may produce distinct patterns of genetic divergence within each site.