Genomic Islands of Adaptive Divergence and Their Consequences for the Resolution of Spatial Population Structure in a Marine Fish

Heterogeneous genomic divergence may be the culmination of the homogenizing influences of gene flow as well as the impact of localized selection and divergence. As populations diverge regions of the genome associated with local adaptation are expected to display elevated differentiation contrasting neutral regions. The factors determining the distribution and number of these islands of elevated differentiation remain unexamined in many species.  We explored the genomic and geographic distribution genomic regions identified as potentially experiencing directional selection and the impact of adaptive variation on the resolution of spatial population structure in Atlantic cod.  Spatial variation at 1441 SNPs was examined using 24 samples from the east and western Atlantic.  Bayesian tests for outliers were used to examine the presence of SNPs displaying signatures of directional selection and linkage maps were used to place outliers across the cod genome. Outliers clustered into several linkage groups, often at the same location.  Outliers displayed significant linkage even across several mapped linkage groups and in several instances were clustered in association previously identified QTLs.  Bayesian clustering and Principle Coordinate Analysis were used to evaluate the scale of population structure resolved.  Neutral loci displayed isolation by distance and divergence associated with barriers to gene flow.  Overall, fine scale geographic differentiation in Atlantic cod is driven by a small number of discrete islands of genomic divergence which are associated with environmental and physiological linkages.