Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

Genomic architecture and standing variation can play a key role in ecological adaptation, and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behaviour in regional analyses. However, the degree of parallelism , the extent of independent inheritance, and functional distinctiveness of these rearrangements remains poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangement with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing m...