| Summary: | Many cod stocks have been described as metapopulations, each containing multiple semi-discrete spawning groups with limited connectivity between them. Reproductive isolation leads to independent and asynchronous demographics among sub-populations adapted to different habitats, which offers stability and resilience to the overall metapopulation (i.e., the "portfolio effect"). Ignoring this population structure can eventually lead to depletion and loss of unique spawning groups, jeopardizing the stability and persistence of the stock. A variety of other factors also serve to create spatiotemporal heterogeneity in fish size and abundance - including ontogeny, habitat preference, and schooling behavior. When combined with spatiotemporal patterns in fishing effort, the apparent trends in the overall population may differ substantially from what is predicted by models that rely on assumptions of homogeneity. Using the Gulf of Maine stock of Atlantic cod as an example, this dissertation explores several ways in which spatiotemporal heterogeneity, driven by metapopulation structure, habitat complexity, and spatial fishing patterns, prevent an accurate portrayal of the population dynamics using current approaches to stock assessment and fishery management. Each chapter relies on the unique perspective provided by a relatively new bottom trawl survey (the Industry-Based Survey or IBS), which was specifically designed to deliver an objective and comprehensive view of the Gulf of Maine cod stock. Genetic studies demonstrated that the Gulf of Maine cod stock is comprised almost entirely of two distinct sub-populations whose spawning grounds overlap in space, but not season. Lack of a practical tool for discriminating between these spring and winter spawners has prevented accounting for metapopulation structure in stock assessments and fishery management plans. To address this issue, Chapter 1 presents a simple approach to discriminate between the sympatric sub-populations that relies on internal otolith structures. Using a ...
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