Atlantic cod ( Gadus morhua ) populations in the Gulf of Maine (GoM) are at a fraction of their historical abundance, creating economic hardships for fishermen and putting at risk the genetic diversity of the remaining populations. An understanding of the biocomplexity among GoM populations will allow for adaptive genetic diversity to be conserved to maximize the evolutionary potential and resilience of the fishery in a rapidly changing environment. We used restriction-site-associated DNA sequencing (RADseq) to characterize the population structure and adaptive genetic diversity of five spawning aggregations from the western GoM and Georges Bank. We also analyzed cod caught in the eastern GoM, an under-sampled area where spawning aggregations have been extirpated. Using 3,128 single nucleotide polymorphisms (SNPs), we confirmed the existence of three genetically separable spawning groups: (1) winter spawning cod from the western GoM, (2) spring spawning cod, also from the western GoM, and (3) Georges Bank cod. Non-spawning cod from the eastern GoM could not be decisively linked to either of the three spawning groups and may represent a unique component of the resource, a mixed sample, or cod from other unsampled source populations. The genetic differentiation among the three major spawning groups was primarily driven by loci putatively under selection, particularly loci in regions known to contain genomic inversions on linkage groups (LG) 7 and 12. These LGs have been found to be linked to thermal regime in cod across the Atlantic, and so it is possible that variation in timing of spawning in western GoM cod has resulted in temperature-driven adaptive divergence. This complex population structure and adaptive genetic differentiation could be crucial to ensuring the long-term productivity and resilience of the cod fishery, and so it should be considered in future management plans.

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Alewife Alosa pseudoharengus is an anadromous clupeid fish of long-standing ecological and socioeconomic importance along the Atlantic coast of North America. Since the 1970s, Alewife populations have been declining throughout the species' range. A number of hypotheses have been proposed to explain the decline, but a lack of basic information on population demographics inhibits hypothesis testing. In this study, we evaluated the use of morphometric analysis to discriminate among spawning stocks of Alewives collected from 24 sites in Maine and one site in Massachusetts. We first identified 10 morphometric measurements that were not influenced by the freezing-thawing process, and then used principal component and discriminant function analyses to develop stock-structure classification models from these 10 measurements. Classification models were able to discriminate Alewives to be from Maine or the single Massachusetts site 100% of the time. In addition, classification models correctly classified pooled sampling sites from the extreme western and eastern parts of Maine with 64% accuracy. Morphometric analysis may therefore provide an easily accessible, comparatively fast, and inexpensive method to discriminate marine-captured Alewives spawned in areas separated by major biogeographic regions, large geographic distances (100s of kilometers), or both, and thus help inform questions about stock composition at these spatial scales for assessment surveys and bycatch events.