•The evidence for respectively top-down control and bottom-up control of the ecosystem features of the Eastern Scotian Shelf off Atlantic Canada from the 1970s to the present is evaluated.•There is limited evidence in support of the fisheries induced trophic cascade hypothesis.•Stratification/nutrient/plankton trends are generally consistent with climate variability hypothesis.•It is concluded that a combination of concurrent top-down forcing by grey seals and bottom forcing due to climate variability is consistent with the aggregate observations on the ecosystem decadal trends.

Uncertainty in assessments has historically taken a backseat to the point estimates. Managers and industry seem to want "the number" without all the qualifiers and caveats. Recently measurement error and process error have been more commonly reported, but both of these are predicated by models. However, the uncertainty in model choice is much more difficult to quantity. Inter-model comparisons have been done in the past (e.g., Several ICES Methods Working Groups of the 1980s or National Research Council 1998) with the goal of picking the best model, mine versus Yours. The determination of model uncertainty requires a different paradigm, the simultaneous contemplation of mine and yours. Consequently, quantifying model uncertainty requires some replication of work. A fundamental problem in quantifying model uncertainty is determining the universe of plausible models. This approach means that multiple and divergent runs are routinely required. using multiple models on a single stock is resonant to Rosen's definition of a complex system (Rosen 1985, p 322): "Namely, we are going to define a system to be complex to the extent that we can observe it in non-equivalent ways." Our challenge is to navigate the way through the complexity of resource assessment and develop, utilize, review, and communicate the resultant uncertainty from the consideration of multiple models.

The continental shelf ecosystem on the Eastern Scotian Shelf (ESS) has experienced drastic changes. Once common top predators are a small fraction of their historical abundance, and much of the current community structure is now dominated by pelagic fishes and invertebrates. Embedded within this food web, Atlantic cod and gray seal populations have recently exhibited nearly opposite trends. Since 1984, cod populations have decreased exponentially at a rate averaging 17% per year, whereas gray seals have continued to increase exponentially at a rate of 12%. We reexamined the impact of gray seals on Atlantic cod dynamics using more than 30 years of data on the population trends of cod and gray seals while incorporating new information on seal diet and seasonal distribution. The closure of the cod fishery over 10 years ago allowed for a better estimation of natural mortality rates. We quantified the impact of seals on ESS cod by (1) estimating trends in seal and cod abundance, (2) estimating the total energy needed for seal growth and maintenance from an energetics model, (3) using estimates of the percentage of cod in the total diet derived from quantitative fatty acid signature analysis (QFASA) and of the size-specific selectivity of cod consumed (derived from otoliths collected from fecal samples), and (4) assuming a gray seal functional response. Uncertainties of the model estimates Were calculated using the Hessian approximation of the variance-covariance matrix. Between 1993 and 2000, cod comprised, on average, < 5% of a gray seal's diet. Our model shows that, since the closure of the fishery, gray seals have imposed a significant level of instantaneous mortality (0.21), and along with other unknown sources of natural mortality (0.62), are contributing to the failure of this cod stock to recover.

Excessive and unsustainable fishing mortality was the predominant factor in the depletion of Northwest Atlantic cod (Gadus morhua) stocks. However, despite imposition of severe catch restrictions for over a decade, stocks have mostly failed to recover at predicted rates. A number of explanations have been considered. Our analysis of demographic characteristics of 12 of these stocks indicates that recent productivity over the northern portion of the range is much lower than 20 years previous when several stocks recovered from less severe declines. Main contributing factors are, in rank order, increased natural mortality, decreased body growth, and in a few cases, reduced recruitment rates. Continued fishing in directed and bycatch fisheries is also an important factor. Under current conditions, we estimate negative or very low (< 2% per year) average growth rates in eight stocks. If fishing ceases, growth rates of > 5% would be expected in six stocks, with > 10% in four of these. Although productivity is low, we conclude that fishing mortality is further delaying recovery.