Data from: The role of a dominant predator in shaping biodiversity over space and time in a marine ecosystem

1. Exploitation of living marine resources has resulted in major changes to populations of targeted species and functional groups of large-bodied species in the ocean. However, the effects of overfishing and collapse of large top predators on the broad-scale biodiversity of oceanic ecosystems remain largely unexplored. 2. Populations of the Atlantic cod (Gadus morhua) were overfished and several collapsed in the early 1990s across Atlantic Canada, providing a unique opportunity to study potential ecosystem-level effects of the reduction of a dominant predator on fish biodiversity, and to identify how such effects might interact with other environmental factors, such as changes in climate, over time. 3. We combined causal modelling with model selection and multimodel inference to analyse 41 years of fishery-independent survey data (1970–2010) and quantify ecosystem-level effects of overfishing and climate variation on the biodiversity of fishes across a broad area (172 000 km2) of the Scotian Shelf. 4. We found that alpha and beta diversity increased with decreases in cod occurrence; fish communities were less homogeneous and more variable in systems where cod no longer dominated. These effects were most pronounced in the colder north-eastern parts of the Scotian Shelf. 5. Our results provide strong evidence that intensive harvesting (and collapse) of marine apex predators can have large impacts on biodiversity, with far-reaching consequences for ecological stability across an entire ecosystem.