The Role of Chromosomal Fusions in Genetic Divergence of a Keystone Arctic Species ( Boreogadus saida )

ABSTRACT Local adaptation in species with high gene flow can be facilitated through different genomic mechanisms. For example, multiple studies have demonstrated that chromosomal inversions (CIs) are important for adaptive divergence in systems with high gene flow because they help protect locally adaptive alleles from recombination. Although much focus has been given to the importance of CIs in harboring adaptive alleles, there are other mechanisms that can facilitate genetic divergence. Chromosomal fusions can also promote local adaptation in the face of high gene flow by bringing together previously unlinked loci. Herein, we utilized a newly available reference genome for Arctic cod ( Boreogadus saida ), together with whole‐genome sequence data from locations spanning a large portion of the Canadian Arctic, to describe the genomic architecture in this circumpolar fish. The Arctic cod genome contains many CIs and five chromosomes that appear to have undergone lineage‐specific chromosomal fusions. Consistent with previous studies, we documented both high gene flow and signals of non‐neutral divergence at a relatively small subset of loci that are driving local population structure. However, our analyses illustrate that most non‐neutral loci are found on fused chromosomes, suggesting chromosomal fusions might be important for local adaptation in this species. This result is especially notable given the localization of divergence in the fused chromosomes when the Arctic cod genome has numerous CIs that are infrequently utilized for divergence across the locations sampled in this study. Our study strongly suggests that non‐neutral loci are concentrated on chromosomal fusions, which may facilitate localized adaptation despite high levels of gene flow in a non‐model species.