Date of Award


Level of Access Assigned by Author

Campus-Only Thesis

Degree Name

Doctor of Philosophy (PhD)


Marine Biology


Yong Chen & James A. Wilson

Second Committee Member

David W. Townsend

Third Committee Member

Lisa Kerr

Additional Committee Members

Timothy Waring


Habitat plays a critical role in regulating spatial distribution of fish population. Many fish populations have been considered as metapopulations inhabiting spatially heterogeneously with complex hierarchical structures (i.e., subpopulations, spawning components and schools of individual fish). Unfortunately, population structure and spatial variation in habitat quality have often been ignored in fisheries stock assessment and management, which might result in biased assessment estimates and a high probability of local depletion.

This study developed modeling framework to assess impacts of habitat and stock structure on fish population dynamics, using Atlantic cod (Gadus morhua) in the Gulf of Maine (GOM) as a case study. Data used included calibrated abundance indices and related spatial information from the Northeast Fisheries Science Center spring and fall bottom trawl surveys over the period of 1982 - 2013 and key physical environmental variables including depth, bottom temperature, bottom salinity and sediment types.

In Chapter 2, season-specific Habitat Suitability Index (HSI) models were developed to quantify spatio-temporal variation in the habitat suitability of GOM cod and evaluate the potential influence of such variation on the stock recruitment and spatial dynamics. Significant declines were found in the average HSI across the study area in the springs of early 2000s and 2010s. These low average HSI values coincide with reduced age-1 recruitment of GOM cod stock after the mid-1990s. Moreover, the western coastal areas of the GOM generally exhibited higher average HSI values than the eastern coastal areas, whereas the offshore areas always had the lowest average HSI. Relatively higher cod survey catch rates in the western GOM may imply positive influences of environmental controls on the distribution of GOM cod.

In chapter 3, season-specific distribution of GOM cod was hindcasted by year to quantify temporal variations in the spatial dynamics of the stock, using a geostatistical delta-generalized linear mixed model. Subsequently, evaluation of stock structure influence on the spatial dynamics was conducted via testing impacts of climate changes and density-dependent effects on the distribution and density of GOM cod. Results showed that the rapid southwestward shift in the stock distribution after the late 1990s was not a simple result of decreasing stock abundance or increasing temperature, but likely resulted from variations in the stock structure.

In chapter 4, we constructed a generalized agent-based metapopulation model to evaluate the influence of spatial variation and connectivity in recruitment among spawning components on the dynamics of a metapopulation and potential implications on ecology and management. Results show that increased recruitment connectivity among components tends to increase metapopulation productivity and stability at local and systematic scales, and reduce the proportion of depleted components due to overfishing. Additionally, depletion of less productive components may occur without a substantial reduction in metapopulation biomass and recruitment.

This research provides modeling frameworks for evaluating influence of habitat and stock structure on fish population dynamics, and can contribute to sustainable management of fisheries stocks with complex structure.