The genomic consequences of fisheries collapse in a marine fish

Abstract The loss of genetic diversity during a population collapse may have important implications for fisheries management and conservation. However, the identification of the underlying changes to genetic diversity can be challenging. The 1990s collapse of the Atlantic cod (Gadus morhua) fishery in the northwest Atlantic, which included the largest population complex known as Northern Cod, raised questions regarding the potential biological consequences for the stock’s genetic diversity. Using low-coverage whole genome sequencing (lcWGS) on collections from the 1990s and 2010s, we detected a decline in genetic diversity of Atlantic cod in the Canadian portion of the species range. A comparison between 1990s and 2010s collections showed less variation in the 2010s, fewer distinguishable genetic clusters, and a significantly lower genetic diversity in the contemporary populations. Our results demonstrate a loss in genetic diversity at the population and individual levels following the fishery collapse and indicate that genetic diversity can be lost even in numerically large populations.