Search

Annual run size and timing of Atlantic salmon smolt migration was estimated using Bayesian model framework and data from six years of a video monitoring survey. The model has a modular structure. It separates sub-processes of departing, traveling and observing, of which the first two together define the arrival distribution. The sub-processes utilize biological background and expert knowledge about the migratory behavior of smolts and about the probability to observe them from the video footage under varying environmental conditions. Daily mean temperature and discharge were used as environmental covariates. The model framework does not require assuming a simple distributional shape for the arrival dynamics and thus also allows for multimodal arrival distributions. Results indicate that 20% - 43% of smolts passed the Utsjoki monitoring site unobserved during the years of study. Predictive studies were made to estimate daily run size in cases with missing counts either at the beginning or in the middle of the run, indicating good predictive performance.

Many studies underscore the importance of incorporating the effect of environmental data within a life-history-stage–specific framework for determining the recruitment and survival of small pelagic fish. The recruitment of anchovy (Engraulis encrasicolus) in the Gulf of Cádiz (NE Atlantic) is sensitive to the effect of intense easterlies, stratification of the water column, and discharges from the Guadalquivir River on early life stages. As a proof of concept, we have developed the basis for a new Bayesian model with a dual time step resolution: monthly for juveniles and adults, and weekly for earlier life stages. This dual time step resolution resolves environmental effects on prerecruits while simulating the effect of fishing on recruits. Our estimates for juvenile abundances are validated with field data. The Bayesian framework accounts for the uncertainty, thus providing consistent length-frequency estimates and a plausible environmentally driven stock-recruitment relationship., The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under grant agreement 244706/ ECOKNOWS project and M. Rincón was funded by P09-RNM-5358 of the Junta de Andalucía.

A participatory Bayesian approach was used to investigate how the views of stakeholders could be utilized to develop models to help understand the Central Baltic herring fishery. In task one, we applied the Bayesian belief network methodology to elicit the causal assumptions of six stakeholders on factors that influence natural mortality, growth, and egg survival of the herring stock in probabilistic terms. We also integrated the expressed views into a meta-model using the Bayesian model averaging (BMA) method. In task two, we used influence diagrams to study qualitatively how the stakeholders frame the management problem of the herring fishery and elucidate what kind of causalities the different views involve. The paper combines these two tasks to assess the suitability of the methodological choices to participatory modeling in terms of both a modeling tool and participation mode. The paper also assesses the potential of the study to contribute to the development of participatory modeling practices. It is concluded that the subjective perspective to knowledge, that is fundamental in Bayesian theory, suits participatory modeling better than a positivist paradigm that seeks the objective truth. The methodology provides a flexible tool that can be adapted to different kinds of needs and challenges of participatory modeling. The ability of the approach to deal with small data sets makes it cost-effective in participatory contexts. However, the BMA methodology used in modeling the biological uncertainties is so complex that it needs further development before it can be introduced to wider use in participatory contexts.

Despite their name, hierarchical stock–recruit meta-analyses are often parameterized in terms of steepness, which depends not only on the assumed stock–recruitment relationship but also on the recruit–spawner relationship. This parameterization requires assumptions about the reproductive potential of the recruit that are not desirable if the focus of the study is limited to the spawning–recruitment phase instead of the full life cycle. Thus, usage of steepness should be avoided in studies that aim to produce informative priors for the stock–recruit relationship for use in studies of other salmon stocks. An alternative key parameter for stock–recruit models is the maximum survival of eggs, which is the slope at the origin of the stock–recruitment curve when spawning stock size is defined in terms of the number of eggs. Furthermore, the current widely used practices in stock–recruit modeling could be improved by taking into account the stock-specific model uncertainty. We use the method of Bayesian model averaging to build a hierarchical stock–recruit model that allows stock-specific model structures with Beverton–Holt, Ricker, and hockey stick models as alternatives, all of which can be parameterized with the maximum survival of eggs. We illustrate our approach by analyzing nine previously published datasets for Atlantic salmon (Salmo salar).

Excessively high rates of fishing mortality have led to rapid declines of several commercially important fish stocks. To harvest fish stocks sustainably, fisheries management requires accurate information about population dynamics, but the generation of this information, known as fisheries stock assessment, traditionally relies on conservative and rather narrowly data-driven modelling approaches. To improve the information available for fisheries management, there is a demand to increase the biological realism of stock-assessment practices and to better incorporate the available biological knowledge and theory. Here, we explore the development of fisheries stock-assessment models with an aim to increasing their biological realism, and focus particular attention on the possibilities provided by the hierarchical Bayesian modelling framework and ways to develop this approach as a means of efficiently incorporating different sources of information to construct more biologically realistic stock-assessment models. The main message emerging from our review is that to be able to efficiently improve the biological realism of stock-assessment models, fisheries scientists must go beyond the traditional stock-assessment data and explore the resources available in other fields of biological research, such as ecology, life-history theory and evolutionary biology, in addition to utilizing data available from other stocks of the same or comparable species. The hierarchical Bayesian framework provides a way of formally integrating these sources of knowledge into the stock-assessment protocol and to accumulate information from multiple sources and over time.

Mäntyniemi, S., Romakkaniemi, A., Dannewitz, J., Palm, S., Pakarinen, T., Pulkkinen, H., Gårdmark, A., and Karlsson, O. 2012. Both predation and feeding opportunities may explain changes in survival of Baltic salmon post-smolts. – ICES Journal of Marine Science, 69: 1574–1579. The survival of wild and hatchery-reared post-smolts of salmon (Salmo salar) in the Baltic Sea has declined since the 1990s. Direct observations of the processes affecting survival are, however, lacking. Here, the importance of food availability and predation in regulating post-smolt survival is analysed. Based on previous studies, the following explanatory variables were selected: (i) availability of herring (Clupea harengus membras) recruits in the Gulf of Bothnia (Bothnian Sea, Bothnian Bay) in the northern Baltic Sea; (ii) sprat (Sprattus sprattus balticus) and herring abundance in the southern Baltic Sea; and (iii) abundance of grey seal (Halichoerus grypus) along the post-smolt migration route. Bayesian analysis was used to estimate the relative probability of each of the 32 combinations of these variables and revealed that the model including grey seal abundance and herring recruits per post-smolt had the highest posterior probability and a high coefficient of determination. The results suggest that the declining trend in post-smolt survival is explained by the increased number of grey seals, whereas the annual variation in survival coincides with variation in the recruitment of Bothnian Sea herring. However, it remains uncertain whether the observed correlations arise from direct causalities or other mechanisms.

Juntunen, T., Vanhatalo, J., Peltonen, H., and Mäntyniemi, S. 2012. Bayesian spatial multispecies modelling to assess pelagic fish stocks from acoustic- and trawl-survey data. – ICES Journal of Marine Science, 69: 95–104. A Bayesian spatial model was constructed to estimate the abundance of multiple fish species in a pelagic environment. Acoustic- and trawl-survey data were combined with environmental data to predict the spatial distribution of (i) the acoustic backscattering of fish, (ii) the relative proportion of each species, and (iii) their mean length in the Gulf of Finland in the northeastern Baltic Sea. By combining the three spatial model layers, the spatial distribution of the biomass of each species was estimated. The model consists of a linear predictor on environmental variables and a spatial random effect given by a Gaussian process. A Bayesian approach is a natural choice for the task because it provides a theoretically justified means of summarizing the uncertainties from various model layers. In the study area, three species dominate pelagic waters: sprat (Sprattus sprattus), herring (Clupea harengus), and three-spined stickleback (Gasterosteus aculeatus). Results are presented for each model layer and for estimated total biomass for each species in 2 × 2 km lattices. The posterior mean and central 95% credible intervals of total biomass were sprat 45.7 kt (27.7–71.6), herring 24.6 kt (9.7–41.3), and three-spined stickleback 1.9 kt (0.9–3.2).

In fisheries stock assessment, the amount of information available from a specific stock is often limited, and the resources to gather new data can be insufficient. This is especially the case when management advice is required for by-catch species which are not always well monitored. However, information is often available from other stocks of the same or closely related species. Also, potential correlations between the life history parameters may contain information which is not usually taken into account in stock assessments. Utilizing all available information can be a cost-efficient way to diminish the amount of uncertainty about key parameters for a case with limited data or when constructing an informative prior for a new case study. In hierarchical modeling, different hierarchical levels can be used to connect closely related and more distant stocks. For example, a lower level of hierarchy can link the stocks within the same species, and a higher level, stocks of related species. We use length-weight and length-fecundity datasets from the FishBase database. Using these datasets, we demonstrate how Bayesian hierarchical correla- tion analysis can improve understanding of fecundity and formalize available knowledge about length-weight and length-fecundity relationships in terms of informative priors for future analysis.

A Poisson process is a commonly used starting point for modeling stochastic variation of ecological count data around a theoretical expectation. However, data typically show more variation than implied by the Poisson distribution. Such overdispersion is often accounted for by using models with different assumptions about how the variance changes with the expectation. The choice of these assumptions can naturally have apparent consequences for statistical inference. We propose a parameterization of the negative binomial distribution, where two overdispersion parameters are introduced to allow for various quadratic mean-variance relationships, including the ones assumed in the most commonly used approaches. Using bird migration as an example, we present hypothetical scenarios on how overdispersion can arise due to sampling, flocking behavior or aggregation, environmental variability, or combinations of these factors. For all considered scenarios, mean-variance relationships can be appropriately described by the negative binomial distribution with two overdispersion parameters. To illustrate, we apply the model to empirical migration data with a high level of overdispersion, gaining clearly different model fits with different assumptions about mean-variance relationships. The proposed framework can be a useful approximation for modeling marginal distributions of independent count data in likelihood-based analyses.

Mäntyniemi, S., Kuikka, S., Rahikainen, M., Kell, L. T., and Kaitala, V. 2009. The value of information in fisheries management: North Sea herring as an example. – ICES Journal of Marine Science, 66: 2278–2283. We take a decision theoretical approach to fisheries management, using a Bayesian approach to integrate the uncertainty about stock dynamics and current stock status, and express management objectives in the form of a utility function. The value of new information, potentially resulting in new control measures, is high if the information is expected to help in differentiating between the expected consequences of alternative management actions. Conversely, the value of new information is low if there is already great certainty about the state and dynamics of the stock and/or if there is only a small difference between the utility attached to different potential outcomes of the alternative management action. The approach can, therefore, help when deciding on the allocation of resources between obtaining new information and improving management actions. In our example, we evaluate the value of obtaining hypothetically perfect knowledge of the type of stock–recruitment function of the North Sea herring (Clupea harengus) population.

We review a success story regarding Bayesian inference in fisheries management in the Baltic Sea. The management of salmon fisheries is currently based on the results of a complex Bayesian population dynamic model, and managers and stakeholders use the probabilities in their discussions. We also discuss the technical and human challenges in using Bayesian modeling to give practical advice to the public and to government officials and suggest future areas in which it can be applied. In particular, large databases in fisheries science offer flexible ways to use hierarchical models to learn the population dynamics parameters for those by-catch species that do not have similar large stock-specific data sets like those that exist for many target species. This information is required if we are to understand the future ecosystem risks of fisheries., Published in at http://dx.doi.org/10.1214/13-STS431 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org)

We present a method by which the knowledge of stakeholders can be taken into account in stock assessment. The approach consists of a structured interview process followed by quantitative modelling of the answers. The outcome is a set of probability models, each describing the views of different stakeholders. Individual models are then merged to a large model by applying the techniques of Bayesian model averaging, and this model is conditioned on stock assessment data. As a result, the views of interviewed stakeholders have been taken into account and weighed based on how well their views are supported by the observed data. We applied this method to the Baltic Sea herring (Clupea harengus) stock assessment by interviewing six stakeholders and conditioning the resulting models on stock assessment data provided by the International Council for the Exploration of the Sea.

Comprehensive problem framing that includes different perspectives is essential for holistic understanding of complex problems and as the first step in building models. We involved five stakeholders to frame the management problem of the Central Baltic herring fishery. By using the Bayesian belief networks (BBNs) approach, the views of the stakeholders were built into graphical influence diagrams representing variables and their dependencies. The views of the scientists involved concentrated on biological concerns, whereas the fisher, the manager, and the representative of an environmental nongovernmental organization included markets and fishing industry influences. Management measures were considered to have a relatively small impact on the development of the herring stock; their impact on socioeconomic objectives was greater. Overall, the framings by these stakeholders propose a focus on socioeconomic issues in research and management and explicitly define management objectives, not only in biological but also in social and economic terms. We find the approach an illustrative tool to structure complex issues systematically. Such a tool can be used as a forum for discussion and for decision support that explicitly includes the views of different stakeholder groups. It enables the examination of social and biological factors in one framework and facilitates bridging the gap between social and natural sciences. A benefit of the BBN approach is that the graphical model structures can be transformed into a quantitative form by inserting probabilistic information.

How can uncertain fisheries science be linked with good governance processes, thereby increasing fisheries management legitimacy and effectiveness? Reducing the uncertainties around scientific models has long been perceived as the cure of the fisheries management problem. There is however increasing recognition that uncertainty in the numbers will remain. A lack of transparency with respect to these uncertainties can damage the credibility of science. The EU Commission’s proposal for a reformed Common Fisheries Policy calls for more self-management for the fishing industry by increasing fishers’ involvement in the planning and execution of policies and boosting the role of fishers’ organisations. One way of higher transparency and improved participation is to include stakeholders in the modelling process itself. The JAKFISH project (Judgment And Knowledge in Fisheries Involving StakeHolders) invited fisheries stakeholders to participate in the process of framing the management problem, and to give input and evaluate the scientific models that are used to provide fisheries management advice. JAKFISH investigated various tools to assess and communicate uncer- tainty around fish stock assessments and fisheries management. Here, a synthesis is presented of the participatory work carried out in four European fishery case studies (Western Baltic herring, North Sea Nephrops, Central Baltic Herring and Mediterranean swordfish), focussing on the uncertainty tools used, the stakeholders’ responses to these, and the lessons learnt. It is concluded that participatory modelling has the potential to facilitate and structure discussions between scientists and stakeholders about uncertainties and the quality of the knowledge base. It can also contribute to collective learning, increase legitimacy, and advance scientific understanding. However, when approaching real-life situations, modelling should not be seen as the priority objective. Rather, the crucial step in a science–stakeholder collaboration is the joint problem framing in an open, transparent way.