Data from: Disentangling structural genomic and behavioral barriers in a sea of connectivity

Genetic divergence among populations arises through natural selection or
drift and is counteracted by connectivity and gene flow. In sympatric
populations, isolating mechanisms are thus needed to limit the
homogenizing effects of gene flow to allow for adaptation and speciation.
Chromosomal inversions act as an important mechanism maintaining isolating
barriers, yet their role in sympatric populations and divergence with gene
flow is not entirely understood. Here, we revisit the question whether
inversions play a role in the divergence of connected populations of the
marine fish Atlantic cod, by exploring a unique dataset combining
whole-genome sequencing data and behavioral data obtained with acoustic
telemetry. Within a confined fjord environment, we find three genetically
differentiated Atlantic cod types belonging to the oceanic North Sea
population, the western Baltic population, and a local fjord-type cod.
Continuous behavioral tracking over four years revealed temporally stable
sympatry of these types within the fjord. Despite overall weak genetic
differentiation consistent with high levels of gene flow, we detected
significant frequency shifts of three previously identified inversions,
indicative for an adaptive barrier to gene flow. In addition, behavioral
data indicated that North Sea cod and individuals homozygous for the LG12
inversion had lower fitness in the fjord environment. However, North Sea
and fjord-type cod also occupy different depths, possibly contributing to
prezygotic reproductive isolation and representing a behavioral barrier to
gene flow. Our results provide the first insights into a complex interplay
of genomic and behavioral isolating barriers in Atlantic cod and establish
a new model system towards an understanding of the role of genomic
structural variants in adaptation and diversification.