Genomic data reveal a lack of range-wide genetic structure for a broadly distributed ommastrephid, Northern shortfin squid ( <i>Illex illecebrosus</i> ), in the Northwest Atlantic Ocean

Abstract The resolution of population structure is central to accurate stock assessments and sustainable management of exploited marine species, especially with regards to the persistence of intraspecific diversity and species stability. Northern shortfin squid (Illex illecebrosus) has a subannual lifespan and a broad latitudinal distribution in the Northwest Atlantic Ocean facilitated by wide Gulf Stream dispersal of its early-life stages combined with long-distance adult migrations. As a result, this transboundary resource supports multiple fisheries managed by different entities. However, little is known regarding connectivity and genetic structure. Here, we provide the first genomic evaluation of intraspecific diversity in this species using whole genome sequencing to explore the geographic scale of differentiation and to reconstruct recent and historical trends in effective population size. Our genomic dataset encompassed 338 948 SNPs (9× coverage) for 540 specimens collected during 2022–2023 at &amp;gt;40 sites located throughout the species’ core geographic range from Newfoundland, Canada to Cape Hatteras, North Carolina, USA. Despite extensive genomic coverage, our results suggested a lack of significant genetic structure across this geographic range; a distance &amp;gt;2500 km. Biomass indices indicate periods of high and low productivity from 1967 to 2023. In contrast, our genomic-based reconstructed trends in effective population size-based on a linkage disequilibrium-based approach suggests general stability with a possible decline around 2018. Our results provide one of the most comprehensive genomic evaluations of intraspecific diversity in wide-ranging marine invertebrates to date, and the lack of genetic structuring across the species’ range confirms that the population should be managed as a single population. Our results also suggest that sequencing depth-based bias requires careful evaluation in future genomic analyses of intraspecific diversity in wide-ranging, weakly structured marine species.