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As the oceans absorb anthropogenic CO2 they become more acidic, a problem termed ocean acidification (OA). Since this increase in CO2 is occurring rapidly, OA may have profound implications for marine ecosystems. In the temperate northeast Pacific, fisheries play key economic and cultural roles and provide significant employment, especially in rural areas. In British Columbia (BC), sport (recreational) fishing generates more income than commercial fishing (including the expanding aquaculture industry). Salmon (fished recreationally and farmed) and Pacific Halibut are responsible for the majority of fishery-related income. This region naturally has relatively acidic (low pH) waters due to ocean circulation, and so may be particularly vulnerable to OA. We have analyzed available data to provide a current description of the marine ecosystem, focusing on vertical distributions of commercially harvested groups in BC in the context of local carbon and pH conditions. We then evaluated the potential impact of OA on this temperate marine system using currently available studies. Our results highlight significant knowledge gaps. Above trophic levels 2-3 (where most local fishery-income is generated), little is known about the direct impact of OA, and more importantly about the combined impact of multi-stressors, like temperature, that are also changing as our climate changes. There is evidence that OA may have indirect negative impacts on finfish through changes at lower trophic levels and in habitats. In particular, OA may lead to increased fish-killing algal blooms that can affect the lucrative salmon aquaculture industry. On the other hand, some species of locally farmed shellfish have been well-studied and exhibit significant negative direct impacts associated with OA, especially at the larval stage. We summarize the direct and indirect impacts of OA on all groups of marine organisms in this region and provide conclusions, ordered by immediacy and certainty.

Empirical dynamic modelling (EDM) is becoming an increasingly popular method for understanding the dynamics of ecosystems. It has been applied to laboratory, terrestrial, freshwater and marine systems, used to forecast natural populations and has addressed fundamental ecological questions. Despite its increasing use, we have not found full explanations of EDM in the ecological literature, limiting understanding and reproducibility. Here we expand upon existing work by providing a detailed introduction to EDM. We use three progressively more complex approaches. A short verbal explanation of EDM is then explicitly demonstrated by graphically working through a simple example. We then introduce a full mathematical description of the steps involved. Conceptually, EDM translates a time series of data into a path through a multi‐dimensional space, whose axes are lagged values of the time series. A time step is chosen from which to make a prediction. The state of the system at that time step corresponds to a ‘focal point’ in the multi‐dimensional space. The set (called the library) of candidate nearest neighbours to the focal point is constructed, to determine the nearest neighbours that are then used to make the prediction. Our mathematical explanation explicitly documents which points in the multi‐dimensional space should not be considered as focal points. We suggest a new option for excluding points from the library that may be useful for short‐term time series that are often found in ecology. We focus on the core simplex and S‐map algorithms of EDM. Our new R package, pbsEDM, enhances understanding (by outputting intermediate calculations), reproduces our results and can be applied to new data. Our work improves the clarity of the inner workings of EDM, a prerequisite for EDM to reach its full potential in ecology and have wide uptake in the provision of advice to managers of natural resources. We provide a detailed introduction to empirical dynamic modelling (EDM), an increasingly popular method for understanding the dynamics of ecosystems. Our work provides greater clarity of the inner workings of EDM, a prerequisite for EDM to reach its full potential in ecology and have wide uptake in the provision of advice to managers of natural resources.

Quantifying the variability in the delivery of ecosystem services across the landscape can be used to set appropriate management targets, evaluate resilience and target conservation efforts. Ecosystem functions and services may exhibit portfolio‐type dynamics, whereby diversity within lower levels promotes stability at more aggregated levels. Portfolio theory provides a framework to characterize the relative performance among ecosystems and the processes that drive differences in performance. We assessed Pacific salmon Oncorhynchus spp. portfolio performance across their native latitudinal range focusing on the reliability of salmon returns as a metric with which to assess the function of salmon ecosystems and their services to humans. We used the Sharpe ratio (e.g. the size of the total salmon return to the portfolio relative to its variability (risk)) to evaluate the performance of Chinook and sockeye salmon portfolios across the west coast of North America. We evaluated the effects on portfolio performance from the variance of and covariance among salmon returns within each portfolio, and the association between portfolio performance and watershed attributes. We found a positive latitudinal trend in the risk‐adjusted performance of Chinook and sockeye salmon portfolios that also correlated negatively with anthropogenic impact on watersheds (e.g. dams and land‐use change). High‐latitude Chinook salmon portfolios were on average 2·5 times more reliable, and their portfolio risk was mainly due to low variance in the individual assets. Sockeye salmon portfolios were also more reliable at higher latitudes, but sources of risk varied among the highest performing portfolios. Synthesis and applications. Portfolio theory provides a straightforward method for characterizing the resilience of salmon ecosystems and their services. Natural variability in portfolio performance among undeveloped watersheds provides a benchmark for restoration efforts. Locally and regionally, assessing the sources of portfolio risk can guide actions to maintain existing resilience (protect habitat and disturbance regimes that maintain response diversity; employ harvest strategies sensitive to different portfolio components) or improve restoration activities. Improving our understanding of portfolio reliability may allow for management of natural resources that is robust to ongoing environmental change.

Large-scale atmospheric conditions in the Northeast Pacific Ocean affect both the freshwater environment in the Columbia River Basin and marine conditions along the coasts of Oregon, Washington, and British Columbia, resulting in correlated conditions in the two environments. For migrating species, such as salmonids that move through multiple habitats, these correlations can amplify the impact of good or poor physical conditions on growth and survival, as movements among habitats may not alleviate effects of anomalous conditions. Unfortunately, identifying the mechanistic drivers of salmon survival in space and time is hindered by these cross-habitat correlations. To address this issue, we modeled the marine survival of Snake River spring/summer Chinook salmon with multiple indices of the marine environment and an explicit treatment of the effect of arrival timing from freshwater to the ocean, and found that both habitats contribute to marine survival rates. We show how this particular carryover effect of freshwater conditions on marine survival varies by year and rearing type (hatchery or wild), with a larger effect for wild fish. As environmental conditions change, incorporating effects from both freshwater and marine habitats into salmon survival models will become more important, and has the additional benefit of highlighting how management actions that affect arrival timing may improve marine survival.

Population diversity can reduce temporal variability in aggregate population abundances in a process known as the portfolio effect. Portfolio effects may weaken, however, due to greater synchrony among component populations. While weakened portfolio effects have been previously documented, the consequences of reduced stability on meeting conservation goals for population aggregates that are harvested (e.g., stock aggregates in fisheries) are rarely quantified. Here, we demonstrate how changes in variability within components, synchrony among components, and population productivity interact to influence the probability of achieving an array of management objectives for Fraser River sockeye salmon: a stock aggregate of high economic, ecological, and cultural value. We first present evidence that component variability and synchrony have increased over the last two decades, consistent with a weakening portfolio effect. We then parameterize a stochastic, closed-loop model that simulates the population dynamics of each stock, the fishery that harvests the stock aggregate, and the management framework used to establish mixed-stock exploitation rates. We find that while median aggregate abundance and catch through time were relatively insensitive to greater aggregate variability, catch stability and performance metrics associated with achieving management targets generally declined as component variability and synchrony increased. A notable exception we observed is that harvest control means that scale exploitation rates based on aggregate abundance may be more effective as synchrony increases. Reductions in productivity led to broad declines in performance, but also moderated the impacts of component variability and synchrony on the proportion of component stocks above management targets and catch stability. Our results suggest that even precautionary management strategies that account for declines in productivity may underestimate risk, particularly to socioeconomic objectives, if they fail to consider changes in aggregate variability. Adequately incorporating changes in portfolio effect strength may be particularly relevant when developing recovery strategies that are robust to climate change, which is likely to increase synchrony and component variability.

Globally, economies and marine ecosystems are increasingly dependent on sustainable fisheries management (SFM) to balance social, economic, and conservation needs. The overarching objectives of SFM are to maximize both conservation and socio-economic benefits, while minimizing short-term socio-economic costs. A number of tools have been developed to achieve SFM objectives, ranging from fishery specific to ecosystem-based strategies. Closures are a common SFM tool used to balance the trade-off between socio-economic and conservation considerations; they vary in scope from small-scale temporary closures to large-scale permanent networks. Unfortunately, closures are frequently implemented without a plan for monitoring or assessing whether SFM objectives are met. In situations in which a monitoring plan is not in place we propose that commonly available fishery data can often be used to evaluate whether management tools are effective in meeting SFM objectives. Here, we present a case study of closures on Georges Bank that shows how fishery data can be analyzed to perform such an assessment. Since 2006, on the Canadian side of Georges Bank, seasonal scallop fishery closures have been implemented with the aim of reducing by-catch of Atlantic cod (Gadus morhua) and yellowtail flounder (Pleuronectes ferruginea) during spawning. In lieu of data from a dedicated monitoring program, we analyzed data from Vessel Monitoring Systems (VMS), fishery logbooks, and a scallop survey to assess the impact of these closures on the scallop fishery, and use observer data (i.e. by-catch) to assess the effectiveness of these closures in meeting their conservation objective. While compliance for these time-area closures was high, the closures did not significantly displace fishing activity and overall there was limited evidence of an impact on the scallop fishery. Further, the discard rates for both cod and yellowtail were above average when their respective closures were active. These results suggest that improvements to the closures design and/or other measures may be required to achieve the desired SFM objectives.

While the physical and ecological importance of the spring transition in the California Current System (CCS) is well recognized, there is no widely agreed upon metric for tracking the phenomenon. Most metrics reflect oceanographic events of the northern CCS; few pertain to southern regions. Our goal was to compare 2 commonly used methods for identifying spring transition in the CCS that use data on wind-driven upwelling and coastal sea levels to 2 newly developed methods that use data on sea levels as well as satellite-derived sea-surface temperatures (SSTs). More specifically, we assessed whether methods typically used in northern regions of the CCS could be applied to other regions. To demonstrate the biological implications of those methods, we evaluated relationships between timing of spring transition and recruitment of 2 groundfish species, Pacific ocean perchSebastes alutusand sablefishAnoplopoma fimbria. Our results suggest that while dramatic changes in wind-derived upwelling and coastal sea levels consistently indicate spring transition in the northern CCS, this is not the case for central and southern regions. In those regions, spring transition may be better represented by the rate of change in sea levels and/or changes in spatial patterns of SSTs. Only metrics based on wind-driven upwelling and sea levels were related to groundfish recruitment; when transitions in upwelling winds and sea levels were delayed, recruitment tended to be poor. We advise caution when identifying dates of spring transition and applying them to analyses of ecological phenomena; a combination of several methods may be required to reveal the multidimensional physical and biological changes that occur during that transition.

For fisheries with multiple, competing objectives, identifying and applying reference points for management can present difficult trade-offs between long-term biological and shorter-term socioeconomic considerations. The term biological benchmarks is proposed to demarcate zones of population status based on conservation and production considerations. These scientifically derived benchmarks contrast with management reference points that generally require additional shorter-term socioeconomic information best obtained through public consultations. This paper illustrates the distinction between biological benchmarks and management reference points with a case study on Pacific salmon (Oncorhynchus spp.). In Canada, the management and assessment of wild Pacific salmon are guided by a major 2005 conservation policy, which calls for the identification of biological benchmarks to categorize status of demographically isolated populations, and decision-support tools, such as management reference points, to integrate biological information with appropriate social and economic information. In the Fraser River (British Columbia, Canada), the selection of management reference points for sockeye salmon (O. nerka) fisheries explicitly considered trade-offs between the probability of meeting long-term biological objectives on component populations and harvest objectives on population aggregates. Decisions about reference points were made in a consultative process that included extensive stakeholder engagement. Other agencies are urged to distinguish biological benchmarks from management reference points to ensure transparency in the relative influence of biological versus socioeconomic information in decision making.

In sockeye salmon (Oncorhynchus nerka) fisheries, management targets are rarely achieved exactly, thereby creating uncertainties about outcomes from implementing fishing regulations. Although this type of uncertainty may be large, it is seldom incorporated into simulation models that evaluate management options. One objective of this study was to quantify the deviations that occur between realized and target mortality rates (i.e., the target fraction of adult recruits that die each year during return migration, mostly due to harvesting) in fisheries for sockeye salmon from the Fraser River, British Columbia. We found that for some sockeye stocks, realized mortality rates were higher than targets when recruitment was low (resulting in conservation concerns) and lower than targets when recruitment was high (resulting in foregone catch). Scientists and managers can at least partially account for effects of such deviations between realized and target mortality rates (outcome uncertainties) by choosing target harvest rules that reflect typical patterns in those deviations. We derived a method to permit modelers to incorporate those patterns into analyses of management options.