Data from: Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside

Gene regulatory divergence is thought to play an important role in
adaptation, yet its extent and underlying mechanisms remain largely
elusive for local adaptation with gene flow. Local adaptation is
widespread in marine species despite generally high connectivity and is
often associated with tightly linked genomic architectures, such as
chromosomal inversions. To investigate gene regulatory evolution under
gene flow and the role of inversions associated with local adaptation to a
steep thermal gradient, we generated RNA-seq data from Atlantic
silversides (Menidia menidia) from two locally adapted populations and
their F1 hybrids, reared under two temperatures. We found substantial
divergence in gene expression and thermal plasticity between populations,
with up to 31% of genes being differentially expressed. Reduced thermal
plasticity, temperature-dependent gene misexpression and the disruption of
co-expression networks in hybrids point towards a role of regulatory
incompatibilities in local adaptation, particularly under colder
temperatures. Chromosomal inversions show an accumulation of regulatory
incompatibilities but are not consistently enriched for differentially
expressed genes. Together, these results suggest that gene regulation can
diverge substantially among populations despite gene flow, partly due to
the accumulation of temperature-dependent regulatory incompatibilities
within inversions.