A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut

Abstract Characterizing the nature of genetic differentiation among individuals and populations its distribution across genome is increasingly important to inform both conservation management exploited species. Atlantic Halibut (Hippoglossus hippoglossus) an ecologically commercially fish species, yet knowledge population structure genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing a chromosome-level assembly identify over 86 000 single nucleotide polymorphisms mapped 24 chromosome-sized scaffolds, genotyped 734 Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between Gulf St. Lawrence adjacent continental shelf. However, majority divergence with large putative chromosomal rearrangement (5.74 megabases) displaying high linkage disequilibrium, no evidence geographic variation. Demographic reconstructions suggest periods expansion coinciding glacial retreat, more recent declines Ne. This work highlights utility data multiple sources marine