The evolution of genomic structural variation in Atlantic cod populations
Genomic structural variants (SVs) can have profound evolutionary consequences in a species through gains, losses and rearrangement of DNA. In Atlantic cod four large chromosomal inversions have been identified and shown to act as supergenes linked to differences in migratory behavior and physiology between co-occurring populations. However, it is unknown to which extent structural variation in general facilitates local adaptation in Atlantic cod. To answer this question, we have sequenced the whole genome of 885 individuals from across the range of this species and characterized SVs, including inversions, duplications and deletions. We demonstrate extensive structural variation in Atlantic cod, including complex nested SV loci. By scanning the genome for differentiated SVs between populations we identify several candidate SVs linked to local adaptation. Furthermore, we have investigated how SVs shape the evolution of different genomic regions, from coding sequences to putative regulatory regions. This brings us closer to reveal how structural variation underpins genome evolution in the enigmatic Atlantic cod.