Data from: Population genomic evidence for adaptive differentiation in the Baltic Sea herring

Detecting and estimating the degree of genetic differentiation among
populations of highly mobile marine fish having pelagic larval stages is
challenging because their effective population sizes can be large, and
thus, little genetic drift and differentiation is expected in neutral
genomic sites. However, genomic sites subject to directional selection
stemming from variation in local environmental conditions can still show
substantial genetic differentiation, yet these signatures can be hard to
detect with low-throughput approaches. Using a pooled RAD-seq approach, we
investigated genomewide patterns of genetic variability and
differentiation within and among 20 populations of Atlantic herring in the
Baltic Sea (and adjacent Atlantic sites), where previous low-throughput
studies and/or studies based on few populations have found limited
evidence for genetic differentiation. Stringent quality control was
applied in the filtering of 1 791 254 SNPs, resulting in a final data set
of 68 182 polymorphic loci. Clear differentiation was identified between
Atlantic and Baltic populations in many genomic sites, while
differentiation within the Baltic Sea area was weaker and geographically
less structured. However, outlier analyses – whether including all
populations or only those within the Baltic Sea – uncovered hundreds of
directionally selected loci in which variability was associated with
either salinity, temperature or both. Hence, our results support the view
that although the degree of genetic differentiation among Baltic Sea
herring populations is low, there are many genomic regions showing
elevated divergence, apparently as a response to temperature- and
salinity-related natural selection. As such, the results add to the
increasing evidence of local adaptation in highly mobile marine organisms,
and those in the young Baltic Sea in particular.