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The drivers of recruitment of selected Baltic sprat (Sprattus sprattus) and herring (Clupea harengus) stocks were investigated. Data on the interaction dynamics among fish species, the biological characteristics of the stocks, the biomass of the main predators, and the hydroclimatic environmental factors (Baltic Sea Index and sea surface temperature) were used in the analysis. The combination of random forest (Boruta algorithm) and "sliding window" approaches was tested on the simulated data and then used for the selection of relevant predictors and the optimal time window for real environmental variables. Sea surface temperature had a significant positive effect on the recruitment processes. Moreover, contrasting effects were observed in the mean Baltic Sea Index from two different time windows. The same environmental variable generated contrasting short-term and long-term effects on fish recruitment. This paper highlights the potential benefits of random forest and data mining applications for the incorporation of environmental factors in the assessment of stocks. The proposed analytical approach may be valuable for the investigations of complex environmental impacts in a broad range of ecological studies. [ABSTRACT FROM AUTHOR]

Commercial fishing fleets play a critical role in the population dynamics of exploited stocks. Understanding the spatial distribution of fleets allows managers to anticipate how fishing pressure on exploited stocks changes in response to fishing regulations or to large-scale perturbations. By anticipating how fishing pressure changes, managers can develop proactive responses to better protect stocks that are vulnerable to overfishing. Modern fisheries monitoring techniques, including vessel monitoring systems (VMS), have advanced this endeavor. This paper presents a framework for using VMS data to develop spatial distributions of catch, fishing effort, and catch per unit of effort (CPUE) as well as associated estimates of uncertainty in a vertical line fishery. VMS data are classified as fishing using a random forest (RF) model. Uncertainty is calculated using a two-step approach to account for uncertainty arising from the RF modeling process and the classification accuracy of the model. This framework is applied to investigate changes in the Gulf of Mexico reef fish fishery during a period of 6 years, including the 2010 Deepwater Horizon oil spill. [ABSTRACT FROM AUTHOR]

Multispecies modeling is being increasingly accepted in stock assessment, especially in the context of an ecosystem approach to fisheries management (EAF). To achieve a future implementation of an EAF in the Flemish Cap, we present a multispecies model developed in Gadget, which covers the main commercial stocks over the period 1988-2012: cod ( Gadus morhua), redfish ( Sebastes spp.), and northern shrimp ( Pandalus borealis). The model highlights the interdependent dynamic of these stocks and reveals strong interactions among recruitment, fishing, and predation (including cannibalism). These drivers have shown marked changes in their relative importance by species, age, and length over time, producing a transition from a traditional redfish- and cod-dominated system in the early 1990s to an intermediate shrimp and other fish species state by the late 1990s and in turn back to something close to the initial state by the late 2000s. The multispecies model developed in this paper shows that disregarding the species interactions would lead to serious underestimates of natural mortality and overestimations of the exploitable biomass and highlights the need to move beyond single-species management in this highly coupled ecosystem. [ABSTRACT FROM AUTHOR]

Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine migrations and residents that complete their life cycle in fresh water. Many populations' anadromous components are threatened or endangered, prompting interest in understanding ecological and evolutionary processes underlying anadromy and residency. In this paper, we synthesize information to better understand genetic and environmental influences on O. mykiss life histories, identify critical knowledge gaps, and suggest next steps. Anadromy and residency appear to reflect interactions among genetics, individual condition, and environmental influences. First, an increasing body of literature suggests that anadromous and resident individuals differ in the expression of genes related to growth, smoltification, and metabolism. Second, the literature supports the conditional strategy theory, where individuals adopt a life history pattern based on their conditional status relative to genetic thresholds along with ultimate effects of size and age at maturation and iteroparity. However, except for a generally positive association between residency and high lipid content plus a large attainable size in fresh water, the effects of body size and growth are inconsistent. Thus, individuals can exhibit plasticity in variable environments. Finally, patterns in anadromy and residency among and within populations suggested a wide range of possible environmental influences at different life stages, from freshwater temperature to marine survival. Although we document a number of interesting correlations, direct tests of mechanisms are scarce and little data exist on the extent of residency and anadromy. Consequently, we identified as many data gaps as conclusions, leaving ample room for future research. [ABSTRACT FROM AUTHOR]

Beacham and Withler (2010. Can. J. Fish. Aquat. Sci. 67: 202-205) raise concerns about the experimental design and interpretation of data in the analysis of temporal genetic variation of Chinook salmon (Oncorhynchus tshawytscha) from the Upper Fraser River, Canada (Walter et al. 2009. Can. J. Fish. Aquat. Sci. 66: 167-176). They note that for the sampled populations, spatial genetic variance should far exceed temporal variance components based on previously published work and suggest that limited sample sizes biased our results by confounding sampling error with temporal variation. Here, we perform a rarefaction analysis by randomly removing up to 50% of the individuals from sample sites, yet the pattern of temporal versus spatial variation is similar to that reported in our original paper. We reiterate that caution should be applied to the interpretation of migration rates estimated from assignment tests, yet the absolute magnitude of our migration estimates was not central to the goals of the original paper. Although Beacham and Withler raise important points on the validation of genetic stock identification analyses, our analyses of temporal variation in genetic population structure in the Upper Fraser River population likely differ due to demographic differences between the timing of sampling of their earlier work versus our analyses. [ABSTRACT FROM AUTHOR]

This paper introduces a semiqualitative approach to analyse the joint dynamics of fleets and stocks in a multispecies, multifleet fishery. We ask whether changes in fleets affect resource dynamics and whether trends in resource influence fleet dynamics more than external drivers do. External drivers include vessel buyback, fuel price, and fish prices, as well as environmental fluctuations. Resource status is measured by abundance and length metrics; fleet capacity is measured by total horse power, and economic metrics such as profitability and earnings are examined as well. A maximum likelihood approach is used to identify the combined metric trends with the largest support in the data. The approach is applied to the French Bay of Biscay fisheries in 2000-2007. Combined-metric time trends suggest that decreases in fleet capacity did not result in decreasing fishing impacts; trends in stocks and fish prices were not the major drivers of changes in fleets either. Rather, the vessel buyback program might have been the main factor determining fleet dynamics over that period. [ABSTRACT FROM AUTHOR]

Studies suggest anglers allocate fishing effort across lakes districts based on fishing quality and travel time resulting in high effort near urban areas, which declines with distance. This results in quality fisheries in remote areas and poorer quality near population centres. In this paper we explore the effectiveness of harvest and effort regulations to counter this tendency for overfishing and stock collapse for a rainbow trout ( Oncorhynchus mykiss) fishery from a lake district in British Columbia, Canada. Our results suggest that daily bag limits can improve fishing quality if the effort is not too high, but fail to prevent collapse close to population centres. The ability of complete catch-and-release regulations to maintain quality fisheries is inversely related to the rate of release mortality. Catch-and-release fisheries with low mortality can maintain quality close to large cities, whereas higher release mortality does not prevent collapse. Direct fishing effort limitation can maintain quality fisheries, but a high proportional reduction in effort is required to maintain quality near population centres. Explicit consideration of the location of fisheries within lake districts is necessary to design effective management approaches and will likely require a mixed strategy with substantial spatial variation in harvest control. [ABSTRACT FROM AUTHOR]

Different age classes do not generally experience the same rates of fishing mortality. The processes resulting in age- (or length-) selection operate at several scales. At the broadest scale, population-selection measures the age-specific probability of capture, while at the finest scale contact-selection describes the vulnerability of fish that encounter the fishing gear. Population-selectivity is the process most relevant to fish population dynamics and stock assessment, but it has received far less attention than processes operating at gear-specific scales. Despite wide recognition of the diverse shapes possible for population-selectivity, the processes determining these shapes are poorly understood. This paper develops a reasonably simple model of population-selectivity from a set of survival equations, coupled to allow movement between subpopulations, and explores the conditions necessary to produce different shaped population-selection curves. Important factors influencing the population-selectivity model are the gear-specific selection characteristics of the fleets, their effort levels relative to one another, the spatial distribution of fishing mortality, and the movement of fish between subpopulations. The model can generate quite complicated curves and has surprising properties. For example, under a wide variety of conditions, even though the same asymptotic gear-selectivity applies in all subpopulations, the overall population-selectivity will be dome-shaped unless fishing mortality is uniform across all subpopulations. [ABSTRACT FROM AUTHOR]

Worldwide, many commercial fish stocks have experienced dramatic declines due to overfishing. Such fisheries-induced population reductions could potentially erode the genetic diversity of marine fish populations. Based on analyses of DNA extracted from archived and contemporary samples, this paper compares the genetic variability at nine microsatellite loci in a Canadian population of Atlantic cod (Gadus morhua) over 80 years, spanning from before the fishery intensified to now when the population is at historically low abundance. Extensively validated genetic data from the temporally spaced samples were used to estimate the effective population size. Over the period, we observed no loss of either heterozygosity or allelic diversity. Several of the estimation methods applied could not distinguish the effective population size from infinity, and the lower 95% confidence limit on estimates was generally >500, suggesting that the effective population size is probably considerably larger than this. Hence, it appears that the southern Gulf of St. Lawrence cod stock has maintained genetic variability to sustain future evolution despite a dramatic population decline. [ABSTRACT FROM AUTHOR]

Fisheries analysts often rely on relative abundance indices for assessing stock status. However, trends in abundance can be difficult to discern when there are multiple indices or when correlation among indices is weak or negative. In this paper, I present a hierarchical framework for analyzing multiple, noisy indices with the goal of estimating a single time series of relative abundance. An implicit assumption is that each index is measuring the same quantity (relative abundance) but that each is subject to process error (attributable to variation in catchability, spatial distribution, etc.) in addition to an estimable level of within-survey variance (i.e., sampling error). I use simulation to explore estimator performance under a number of scenarios, including several that violate underlying assumptions. In general, the hierarchical approach produced estimators with reasonable properties. I illustrate the method with an analysis of seven fishery-dependent catch-per-unit-effort indices of Spanish mackerel (Scomberomorus maculatus) off the US Atlantic coast and provide several suggestions for how this approach can be used in practice. [ABSTRACT FROM AUTHOR]

The effective sampling volume of trawl and acoustics is an important parameter in fish abundance estimation surveys. This paper presents a method to compute the probability of a fish being available to the bottom trawl and the probability of it being seen on the echo sounder, given its initial position relative to the vessel path. These probabilities are then related to the calculation of the effective observational volume for trawl and acoustics, the two main tools of measuring abundance of Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus). As an example, the computation is carried out for a typical vertical distribution in the Barents Sea. Our model is based on an Ornstein–Uhlenbeck model for the fish swimming trajectories, and its parameters are estimated using observations of swimming trajectories for individual fish, recorded by a split-beam echo sounder. The model itself constitutes a general method to translate observations on behaviour of individual fish to probability maps. The results indicate a typical fishing height of 20 m for the bottom trawl, but it is also shown that there is a relatively low probability of catching by the trawl what you see on the echo sounder, even for fish positioned directly in the trawl path. This is because of strong lateral movements of the fish. [ABSTRACT FROM AUTHOR]

In this paper, we describe a discrete-time formalism for describing the dynamics of the size-at-age distribution of a cohort of individuals exhibiting irreversible von Bertalanffy growth in a statistically uniform random environment. This formalism yields a highly efficient numerical implementation, which is particularly suited to automatic optimization. In the special case where mortality is sufficiently size-independent not to vary substantially across the bulk of the size distribution at any given age, we can further increase this efficiency by deriving compact update rules for the mean and coefficient of variation of size-at-age. In this case, we also demonstrate that the depensatory effect of random growth variability and the compensatory effect of deterministic von Bertalanffy growth balance to yield an attracting (initial condition independent) trajectory of mean length and length coefficient of variation against age. We demonstrate the applicability and extensibility of this formalism by two exemplary applications - juvenile salmonids and demersal cod. [ABSTRACT FROM AUTHOR]

This paper validates a new length-based model of the dynamics of fish stocks or crustaceans by hierarchically testing statistical hypotheses and thereby investigating model complexity. The approach is based entirely on scientific survey data and on determination of the statistical distributions of the number of fish caught per haul in each length class. In our example, the negative binomial distribution is statistically accepted and linked to the population level through the new length-based model. The model is derived from the characteristics of continuous recruitment, individually based growth, and continuous, length-dependent mortality rates. Continuous recruitment with annually varying recruitment peaks and individually based growth was crucial for obtaining a model that could be statistically accepted. Natural mortality was estimated as well by the model. The model was applied to survey data for Atlantic cod (Gadus morhua) in the Baltic. Its simple generic nature, as well as the validation procedure, is useful in studying and understanding life history and stock dynamics. [ABSTRACT FROM AUTHOR]

In this paper, we use dynamic factor and intervention analysis to identify and quantify the effect of human encroachments on anadromous salmonid catches in 22 Norwegian rivers over a 128-year period. In particular, we address effects of hydropower development, gravel removal, and stock enhancement (fish ladder construction and stocking). The methods allow for quantification of perturbation effects in the river environment on the annual catch, after removing long-term temporal trends at the appropriate spatial scale. The estimated effects of the encroachments differed among rivers, indicating that the mechanisms differ among rivers even for the same type of encroachment. In three rivers where hydropower development and stock enhancement had occurred, a significant increase of 0.8–9.8 tonnes (t) (34%–44%) was estimated, whereas a significant reduction of 11.2 t (38%) was estimated for the river where gravel removal had taken place. For rivers with additional biological information available, we find support for our estimated effects. In general, removal of gravel significantly reduced catch and there were positive effects of fish ladder constructions and variable effects of hydropower development and stocking (both positive and negative coefficients). [ABSTRACT FROM AUTHOR]

In this paper, we demonstrate how information from broodstocks can be combined with lab information on alevins to obtain annual stock-specific mortality estimates from early mortality syndromes (EMS) using a probabilistic approach, how a hierarchical model structure can be used to predict these mortality rates for related, partly sampled, or unsampled stocks, and why these estimates should be used to remove the effect of this mortality on stock–recruit estimates. The approach has been illustrated for Atlantic salmon (Salmo salar) stocks in the Baltic Sea affected by the M74 syndrome. Results indicate that data on the proportion of M74-affected females, commonly used to approximate M74 mortality, overestimate actual M74-related mortality because of a declining trend in mortality among offspring of these females. The stock-specific M74 mortality estimates are used to account for nonstationarity in the stock–recruitment relationship caused by this fluctuating mortality. Because hierarchical meta-analyses assume exchangeability, the effect of M74 mortality is removed before including these stocks within hierarchical stock–recruit analyses of Atlantic salmon stocks, which are commonly unaffected by M74 mortality. Failure to remove the effect of M74 mortality on the stock–recruit data results in underestimation of the stock's productivity and resilience to exploitation, especially in the case of stocks with steep stock–recruit curves. [ABSTRACT FROM AUTHOR]

This paper presents preliminary results of a study to evaluate the potential utility of supplementation of natural origin coho salmon (Oncorhynchus kisutch) on the Clearwater River, a tributary of the Queets River in western Washington. The study, initiated in 1984, involves the collection of natural origin brood stock, rearing in a combination of hatchery and natural environments, and volitional releases, combined with marking and sampling of natural origin fish. Primary findings relative to five essential research questions of this study concluded that (i) smolts from supplementation returned at a lower rate than natural smolts; (ii) the reproductive efficiency (spawner to spawner) of fish taken for supplementation was higher than that for fish allowed to spawn naturally; (iii) supplemental fish successfully reproduced and the combined supplemental–natural spawning population had a high productivity; (iv) supplementation did not appear to have affected the overall reproductive performance of the population for the duration of the project; and (v) supplementation increased the overall spawner return on the Clearwater River and is required to maximize adult production, unless conditions in both freshwater and ocean environments are optimal. [ABSTRACT FROM AUTHOR]

The important decline of Atlantic salmon (Salmo salar) across its range during the past three decades, despite numerous management and conservation programmes, is an alarming index of the vulnerability of this species. The following series of papers was produced to summarize current knowledge on specific interactions between biotic and abiotic variables that may contribute to determine the survival of Atlantic salmon. Evaluation of the challenges encountered in spawning grounds (siltation, oxygenation), nursery habitats (substrate, trophic interactions), overwintering habitats (flow conditions, winter feeding opportunities), and coastal and oceanic environments (water temperature, predators, parasites) suggest that all habitats required by Atlantic salmon and all processes that occur in each habitat represent a critical link that allows this species to persist. Management practices employed during artificial fish selection, incubation, and stocking also affect the success of restoration efforts. Because limiting factors may change in time and because our ability to intervene in specific habitats may be minimal, the only strategy within our reach may be to continue gathering information about processes that determine the fragility of Atlantic salmon and, in the light of our findings, to implement scientifically sound actions where and when possible. [ABSTRACT FROM AUTHOR]