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The study of spatiotemporal dynamics of fish populations is important for both stock assessment and fishery management. I explored the impacts of environmental and anthropogenic factors on spatiotemporal patterns of fish populations, and contributed to stock assessment and management by incorporating the inherent spatial structure. Hierarchical models were developed to specify spatial and temporal variations, and Bayesian methods were adopted to fit the models. Yellow perch (Perca flavescens) is one of the most important commercial and recreational fisheries in Lake Erie, which is currently managed using four management units (MUs), with each assessed by a spatially-independent stock-specific assessment model. The current spatially-independent stock-specific assessment assumes that movement of yellow perch among MUs in Lake Erie is statistically negligible and biologically insignificant. I investigated whether the assumption is violated and the effect this assumption has on assessment. I first explored the spatiotemporal patterns of yellow perch abundance in Lake Erie based on data from a 27-year gillnet survey, and analyzed the impacts of environmental factors on spatiotemporal dynamics of the population. I found that yellow perch relative biomass index displayed clear temporal variation and spatial heterogeneity, however the two middle MUs displayed spatial similarities. I then developed a state-space model based on a 7-year tag-recovery data to explore movements of yellow perch among MUs, and performed a simulation analysis to evaluate the impacts of sample size on movement estimates. The results suggested substantial movement between the two stocks in the central basin, and the accuracy and precision of movement estimates increased with increasing sample size. These results demonstrate that the assumption on movements among MUs is violated, and it is necessary to incorporate regional connectivity into stock assessment. I thus developed a tag-integrated multi-region model to incorporate movements into a spatial stock assessment by integrating the tag-recovery data with 45-years of fisheries data. I then compared population projections such as recruitment and abundance derived from the tag-integrated multi-region model and the current spatial-independent stock-specific assessment model to detect the influence of hypotheses on with/without movements among MUs. Differences between the population projections from the two models suggested that the integration of regional stock dynamics has significant influence on stock estimates. American Shad (Alosa sapidissima), Hickory Shad (A. mediocris) and river herrings, including Alewife (A. pseudoharengus) and Blueback Herring (A. aestivalis), are anadromous pelagic fishes that spend most of the annual cycle at sea and enter coastal rivers in spring to spawn. Alosa fisheries were once one of the most valuable along the Atlantic coast, but have declined in recent decades due to pollution, overfishing and dam construction. Management actions have been implemented to restore the populations, and stocks in different river systems have displayed different recovery trends. I developed a Bayesian hierarchical spatiotemporal model to identify the population trends of these species among rivers in the Chesapeake Bay basin and to identify environmental and anthropogenic factors influencing their distribution and abundance. The results demonstrated river-specific heterogeneity of the spatiotemporal dynamics of these species and indicated the river-specific impacts of multiple factors including water temperature, river flow, chlorophyll a concentration and total phosphorus concentration on their population dynamics. Given the importance of these two case studies, analyses to diagnose the factors influencing population dynamics and to develop models to consider spatial complexity are highly valuable to practical fisheries management. Models incorporating spatiotemporal variation describe population dynamics more accurately, improve the accuracy of stock assessments, and would provide better recommendations for management purposes. / Doctor of Philosophy / Many fish populations exhibit complex spatial structure, but the spatial patterns have been incorporated into stock assessment only in few cases. A full understanding of spatial structure of fish populations is needed to better manage the populations. Stock assessment and management strategies should depend on the inherent spatial structure of the target fish population. There have been many approaches developed to analyze spatial structure of fish populations. In this dissertation, I developed quantitative models to analyze fish demographic data and tagging data to explore spatial structure of fish populations. Yellow perch (Perca flavescens) in Lake Erie and Alosa group including American Shad (Alosa sapidissima), Hickory Shad (A. mediocris) and river herrings (Alewife A. pseudoharengus and Blueback Herring A. aestivalis) in selected tributaries of the Chesapeake Bay were taken as examples. Fishery-independent data for yellow perch displayed spatial similarities in the central basin of Lake Erie. Distinct temporal trends were observed in relative abundance data for Alosa sp. in different tributaries of the Chesapeake Bay. Substantial yellow perch movement among the central basin of the Lake was observed in tagging data. Ignoring the inherent spatial structure may cause fish to be overfished in some regions and underfished in others. To maximize the effectiveness of management in all regions for fish populations, I highly recommend incorporating spatial structure into stock assessment and management such as the ones developed in this dissertation.

My doctoral thesis challenges the traditional paradigm of phosphorus (P) limitation of phytoplankton communities in freshwaters by suggesting colimitation of P, nitrogen (N), and iron (Fe) in Great Lakes. Oceanographers have recognized Fe, N and P colimitation, and biomass response to Fe is documented in freshwater lakes. I studied African and North American Great Lakes that are similar to large inland oceans. I discovered that Fe is a key nutrient that is often limiting in the offshore, and may explain the dominance of cyanobacteria in nutrient enriched lakes. I also discovered that the nearshore and offshore areas of these large lakes are very different, particularly when invasive dreissenid mussels are impacting the nearshore, as seen in the eastern basin of Lake Erie. As a result of the dreissenids, chlorophyll a (chla) concentrations are significantly lower in the nearshore of Lake Erie, but higher in the nearshore in the three African Great Lakes, as well as pre-dreissenid Lake Erie. The objective of my thesis was to determine the limiting nutrient(s) to the phytoplankton of the Great Lakes Erie, Malawi, Tanganyika, and Victoria in both the nearshore and offshore by measuring the physiological status of the phytoplankton. I also examined how dreissenids affect the distribution of seston and nutrient concentrations between the nearshore and offshore of the eastern basin of Lake Erie. My study design included temporal and spatial surveys in the nearshore and offshore of the four lakes, in which I used a variety of nutrient limitation indicators for P (C:P, N:P, P debt, APA, Fv/Fm), N (C:N, NH4 debt, NO3 debt, Fv/Fm), and Fe (Fv/Fm), as well as photosynthetic efficiency (Fv/Fm) experiments. Nutrient enrichment experiments were also conducted in the nearshore and offshore of the eastern basin of Lake Erie which involved the addition and removal of Fe alone, as well as in combination with P and/or N. Lake Erie nutrient enrichment experiments provided evidence for P, N and Fe colimitation where the addition of Fe with P relieved Fe and P limitation and allowed nitrate (NO3-) assimilation, alleviating N limitation. However, the offshore experiments indicated stronger Fe limitation than the nearshore experiment. Lower chla concentrations in the post-dreissenid nearshore of the eastern basin of Lake Erie may not be due entirely to lower phytoplankton biomass, as photoacclimation of the phytoplankton may also be occurring. Dreissenid grazing effects can be seen in the distribution of dissolved nutrient concentrations between the nearshore and offshore of post-dreissenid Erie. The African Great Lakes are threatened by expanding human populations, resulting in increased nutrient runoff; the consequences of which will depend on the limiting nutrient(s). I found that the nearshore regions of Lakes Malawi and Tanganyika were colimited by N and P, while the offshore regions were colimited by N, P and Fe. The nearshore of Lake Victoria was colimited by light and N, while the offshore was colimited by N, P and Fe. Fe limitation only occurs in the offshore, and positive, significant relationships were found between total dissolved Fe concentrations and cyanobacteria. Continued P and Fe loading to the lakes will create a higher N demand that will result in a shift to N2-fixing cyanobacteria, which has serious consequences to human and ecosystem health as they are a poor nutritive food source and some are potentially toxigenic. The majority of studies conducted on Great Lakes involve offshore sampling, however, the less understood nearshore is where human impacts and activities are concentrated. I discovered there are significant differences between the nearshore and offshore, which has implications for water quality monitoring.