Genetic Data Reveal Nonlocal Juvenile Recruitment and Variable Seasonal Movement of a Highly Mobile Marine Fish Across Alaska

Movement patterns of marine fish are often difficult to accurately define given seasonal variation, ontogenetic shifts, and changing environmental conditions. However, outlining movement is crucial for understanding population dynamics, as well as for conservation and management efforts. Here, we evaluate seasonal adult movement and juvenile spatial distribution of Pacific cod (<i>Gadus macrocephalus</i>), a highly mobile and commercially important species, by developing and applying a genotyping-in-thousands by sequencing (GT-seq) panel. This panel identifies four genetically distinct stocks within Alaska waters with high confidence in assignment (97% average accuracy across stocks). The application of this panel to adult, summer-caught Pacific cod identified limited seasonal movement within and between populations, with the exception of those in the Northern Bering Sea (NBS). Two stocks occupied this region during the summer, non-spawning season, and mixed at variable proportions in a west-to-east gradient potentially tied to the directionality of sea-ice retreat in the NBS. Juvenile results indicated that although a predominant westward advection of larvae was prevalent in the Gulf of Alaska (GOA), two major deviations from this overall trend were apparent: (i) an eastward advection of a western GOA stock into the eastern GOA that varied interannually and (ii) a consistently high proportion of eastern GOA individuals in a western GOA narrow strait. These two deviating patterns suggest that mesoscale oceanographic processes play an important role in transport dynamics in the GOA that may be contrary to patterns expected based on the prevailing current. Taken together, our study provides novel insights into the movement dynamics of Pacific cod that can be leveraged by managers to help guide decision-making for the species. Additionally, this inexpensive genetic panel can continue to be applied to further explore important questions about the ecology of Pacific cod in Alaska waters.