Kell, L. T., Mosqueira, I., Grosjean, P., Fromentin, J-M., Garcia, D., Hillary, R., Jardim, E., Mardle, S., Pastoors, M. A., Poos, J. J., Scott, F., and Scott, R. D. 2007. FLR: an open-source framework for the evaluation and development of management strategies. – ICES Journal of Marine Science, 64: 640–646. The FLR framework (Fisheries Library for R) is a development effort directed towards the evaluation of fisheries management strategies. The overall goal is to develop a common framework to facilitate collaboration within and across disciplines (e.g. biological, ecological, statistical, mathematical, economic, and social) and, in particular, to ensure that new modelling methods and software are more easily validated and evaluated, as well as becoming widely available once developed. Specifically, the framework details how to implement and link a variety of fishery, biological, and economic software packages so that alternative management strategies and procedures can be evaluated for their robustness to uncertainty before implementation. The design of the framework, including the adoption of object-orientated programming, its feasibility to be extended to new processes, and its application to new management approaches (e.g. ecosystem affects of fishing), is discussed. The importance of open source for promoting transparency and allowing technology transfer between disciplines and researchers is stressed.

Fishery managers must often reconcile conflicting estimates of population status and trend. Superensemble models, commonly used in climate and weather forecasting, may provide an effective solution. This approach uses predictions from multiple models as covariates in an additional “superensemble” model fitted to known data. We evaluated the potential for ensemble averages and superensemble models (ensemble methods) to improve estimates of population status and trend for fisheries. We fit four widely applicable data‐limited models that estimate stock biomass relative to equilibrium biomass at maximum sustainable yield (B/BMSY). We combined these estimates of recent fishery status and trends in B/BMSY with four ensemble methods: an ensemble average and three superensembles (a linear model, a random forest and a boosted regression tree). We trained our superensembles on 5,760 simulated stocks and tested them with cross‐validation and against a global database of 249 stock assessments. Ensemble methods substantially improved estimates of population status and trend. Random forest and boosted regression trees performed the best at estimating population status: inaccuracy (median absolute proportional error) decreased from 0.42 – 0.56 to 0.32 – 0.33, rank‐order correlation between predicted and true status improved from 0.02 – 0.32 to 0.44 – 0.48 and bias (median proportional error) declined from −0.22 – 0.31 to −0.12 – 0.03. We found similar improvements when predicting trend and when applying the simulation‐trained superensembles to catch data for global fish stocks. Superensembles can optimally leverage multiple model predictions; however, they must be tested, formed from a diverse set of accurate models and built on a data set representative of the populations to which they are applied.

Tunas and their relatives dominate the world's largest ecosystems and sustain some of the most valuable fisheries. The impacts of fishing on these species have been debated intensively over the past decade, giving rise to divergent views on the scale and extent of the impacts of fisheries on pelagic ecosystems. We use all available age-structured stock assessments to evaluate the adult biomass trajectories and exploitation status of 26 populations of tunas and their relatives (17 tunas, 5 mackerels, and 4 Spanish mackerels) from 1954 to 2006. Overall, populations have declined, on average, by 60% over the past half century, but the decline in the total adult biomass is lower (52%), driven by a few abundant populations. The trajectories of individual populations depend on the interaction between life histories, ecology, and fishing pressure. The steepest declines are exhibited by two distinct groups: the largest, longest lived, highest value temperate tunas and the smaller, short-lived mackerels, both with most of their populations being overexploited. The remaining populations, mostly tropical tunas, have been fished down to approximately maximum sustainable yield levels, preventing further expansion of catches in these fisheries. Fishing mortality has increased steadily to the point where around 12.5% of the tunas and their relatives are caught each year globally. Overcapacity of these fisheries is jeopardizing their longterm sustainability. To guarantee higher catches, stabilize profits, and reduce collateral impacts on marine ecosystems requires the rebuilding of overexploited populations and stricter management measures to reduce overcapacity and regulate threatening trade.

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Meta-analyses of published data for 19 marine reserves reveal that marine protected areas enhance species richness consistently, but their effect on fish abundance is more variable. Overall, there was a slight (11%) but significant increase in fish species number inside marine reserves, with all reserves sharing a common effect. There was a substantial but non-significant increase in overall fish abundance inside marine reserves compared to adjacent, non-reserve areas. When only species that are the target of fisheries were considered, fish abundance was significantly higher (by 28%) within reserve boundaries. Marine reserves vary significantly in the extent and direction of their response. This variability in relative abundance was not attributable to differences in survey methodology among studies, nor correlated with reserve characteristics such as reserve area, years since protection, latitude nor species diversity. The effectiveness of marine reserves in enhancing fish abundance may be largely related to the intensity of exploitation outside reserve boundaries and to the composition of the fish community within boundaries. It is recommended that studies of marine reserve effectiveness should routinely report fishing intensity, effectiveness of enforcement and habitat characteristics. 2001 The Fisheries Society of the British Isles

Reference points based on fishing mortality (F) and spawning stock biomass (SSB) are a requirement of many fisheries management frameworks. SSB is assumed to be a proxy for stock reproductive potential (SRP). Limit reference points based on SSB are used to indicate the level of biomass below which productivity is affected. SSB fails to account for changes in fecundity, egg viability and sex ratio, and it has been argued that total egg production (TEP) provides a better reflection of SRP. We explore how accounting for TEP impacts limit reference points and evidence for a relationship between stock and recruit. Time series of SSB and TEP are compared for three North Sea stocks: cod (Gadus morhua), herring (Clupea harengus) and plaice (Pleuronectes platessa). Dynamics based on TEP are different from those based on SSB for cod and plaice, but the stock–recruit relationships were not ‘improved’ using TEP. Shifts in productivity (spawner per recruit) occur in all three time series and SSB underestimated uncertainty. Yet again, it was shown that assumptions of stationarity about fish population productivity are incorrect. We argue that the use of TEP does improve the realism in our understanding of stock dynamics, and demographically, more complex management strategy evaluation is required to develop management procedures that are robust to uncertainty and integrate F and the demographic health of a stock. Empirical feedback control systems based on fisheries independent indices including surveys of eggs, larvae, recruits, juveniles or spawning adults should be evaluated and compared to traditional approaches.

The exploitation status of marine fisheries stocks worldwide is of critical importance for food security, ecosystem conservation, and fishery sustainability. Applying a suite of data-limited methods to global catch data, combined through an ensemble modeling approach, we provide quantitative estimates of exploitation status for 785 fish stocks. Fifty-three percent (414 stocks) are below B MSY and of these, 265 are estimated to be below 80% of the B MSY level. While the 149 stocks above 80% of B MSY are conventionally considered "fully exploited," stocks staying at this level for many years, forego substantial yield. Our results enable managers to consider more detailed information than simply a categorization of stocks as "fully" or "over" exploited. Our approach is reproducible, allows consistent application to a broad range of stocks, and can be easily updated as new data become available. Applied on an ongoing basis, this approach can provide critical, more detailed information for resource management for more exploited fish stocks than currently available.

Larger-bodied species in a wide range of taxonomic groups including mammals, fishes and birds tend to decline more steeply and are at greater risk of extinction. Yet, the diversity in life histories is governed not only by body size, but also by time-related traits. A key question is whether this size-dependency of vulnerability also holds, not just locally, but globally across a wider range of environments. We test the relative importance of size-and time-related life-history traits and fishing mortality in determining population declines and current exploitation status in tunas and their relatives. We use high-quality datasets of half a century of population trajectories combined with population-level fishing mortalities and life-history traits. Time-related traits (e.g. growth rate), rather than size-related traits (e.g. maximum size), better explain the extent and rate of declines and current exploitation status across tuna assemblages, after controlling for fishing mortality. Consequently, there is strong geographical patterning in population declines, such that populations with slower life histories (found at higher cooler latitudes) have declined most and more steeply and have a higher probability of being overfished than populations with faster life histories (found at tropical latitudes). Hence, the strong, temperature-driven, latitudinal gradients in life-history traits may underlie the global patterning of population declines, fisheries collapses and local extinctions.