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Data are currently being used, and reused, in ecological research at an unprecedented rate. To ensure appropriate reuse however, we need to ask the question: "Are aggregated databases currently providing the right information to enable effective and unbiased reuse?" We investigate this question, with a focus on designs that purposefully favor the selection of sampling locations (upweighting the probability of selection of some locations). These designs are common and examples are those designs that have uneven inclusion probabilities or are stratified. We perform a simulation experiment by creating data sets with progressively more uneven inclusion probabilities and examine the resulting estimates of the average number of individuals per unit area (density). The effect of ignoring the survey design can be profound, with biases of up to 250% in density estimates when naive analytical methods are used. This density estimation bias is not reduced by adding more data. Fortunately, the estimation bias can be mitigated by using an appropriate estimator or an appropriate model that incorporates the design information. These are only available however, when essential information about the survey design is available: the sample location selection process (e.g., inclusion probabilities), and/or covariates used in their specification. The results suggest that such information must be stored and served with the data to support meaningful inference and data reuse. [ABSTRACT FROM AUTHOR]

Sex‐determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex‐determination systems and corresponding statistical methods for identifying sex‐linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex‐linked SNPs and minor allele frequency. The application of three methods was made here: (a) identification of heterozygote excess in one sex, (b) FST outlier analysis between the two sexes and (c) neuronal net modelling. These methods were applied to a large SNP data set (4604 SNPs) for 1680 thornback rays (Raja clavata). Using method (a), nineteen putative sex‐linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata) indicated that all 19 SNPs are probably located on the same chromosome. These results suggest that thornback ray has a XX/XY sex‐determination system. Method (b) identified eight SNPs probably located on different chromosomes. Method (a) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males). [ABSTRACT FROM AUTHOR]

Effective population size (Ne) is a key parameter of population genetics. However, Ne remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient FIS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Neestimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies. [ABSTRACT FROM AUTHOR]

Sustainable fisheries management requires assessment of exploited populations and communities. Traditional fisheries stock assessment methods need species‐specific input data, which for skates have only recently become available in Europe. To overcome this limitation, a Bayesian multispecies biomass production model was developed. In addition to aggregated landings, input data are short time series with species‐specific information (landings and biomass indices). Applying the approach to four main skate species and a group of two skate species, all managed together in the Bay of Biscay (Northeast Atlantic), long‐term changes in the skate assemblage composition were identified. Since the 1990s, Leucoraja naevus became increasingly dominant, while the contributions of the other three species (Raja brachyura, Raja clavata and Raja montagui) declined. The abundance of the grouped Leucoraja fullonica and L. circularis has also strongly decreased, suggesting long‐term overexploitation. All species except this species group are expected to increase over the next decade under current harvest rates. Currently, the species considered here are managed under a single fishing quota making it unlikely that the group of the two most depleted species will recover soon. The multispecies modelling approach bears promise for other harvested assemblages for which only grouped harvest information is available for certain periods. [ABSTRACT FROM AUTHOR]

Sustainable exploitation of marine populations is a challenging task relying on information about their current and past abundance. Fisheries‐related data can be scarce and unreliable making them unsuitable for quantitative modelling. One fishery independent method that has attracted attention in this context consists in estimating the effective population size (Ne), a concept founded in population genetics. We reviewed recent empirical studies on Ne and carried out a simulation study to evaluate the feasibility of estimating Ne in large fish populations with the currently available methods. The detailed review of 26 studies found that published empirical Ne values were very similar despite differences in species and total population sizes (N). Genetic simulations for an age‐structured fish population were carried out for a range of population and samples sizes, and Ne was estimated using the Linkage Disequilibrium method. The results showed that already for medium‐sized populations (1 million individuals) and common sample sizes (50 individuals), negative estimates were likely to occur which for real applications is commonly interpreted as indicating very large (infinite) Ne. Moreover, on average, Ne estimates were negatively biased. The simulations further indicated that around 1% of the total number of individuals might have to be sampled to ensure sufficiently precise estimates of Ne. For large marine populations, this implies rather large samples (several thousands to millions of individuals). If however such large samples were to be collected, many more population parameters than only Ne could be estimated. [ABSTRACT FROM AUTHOR]

In this paper, I argue that we have at hand what is needed to provide scientific advice for ecosystem-based management of small pelagics and other species groups now. The ingredients for this advice are (i) large marine ecosystems as spatial management units; (ii) maintaining ecosystem productivity and exploiting at multispecies maximum yield as overarching management objectives; (iii) assessment of ecosystems by evaluating changes in primary productivity; (iv) an operational management procedure in which single-species catch proposals are adjusted to ecosystem productivity using a set of control rules. Inspection of historic landings for small pelagics and other small species in the Northeast Atlantic (ICES area) reveals that most likely fisheries exploitation does not, and never did, exceed system productivity in most LMEs and is therefore overall sustainable, although not necessarily for individual stocks. [ABSTRACT FROM AUTHOR]

We present a framework for evaluating fisheries management plans comprehensively, both rebuilding plans and others. The framework includes a first rapid appraisal of the likelihood that the plan will result in management meeting its objectives, and guides subsequent quantitative analyses of potential weaknesses in the proposed plan. The framework includes four steps: (i) evaluating if a set of management objectives, if achieved, would result in a sustainable fishery, (ii) using qualitative analysis of a bio-economic model to evaluate whether the set of stock management tactics might be capable of achieving the specified fisheries objectives, (iii) using empirical criteria derived from the literature to evaluate if other management measures in the plan related to the ecological, social or economic context of the fishery actually contribute to sustainability, and (iv) carrying out quantitative simulations to compare alternative implementation options. Generally, several management measures have to be combined to increase stock size without sacrificing the economic benefits to the fishers remaining in the fishery. We demonstrate application of the framework for evaluating the stock rebuilding plan for plaice ( Pleuronectes platessa) and sole ( Solea solea) in the North Sea and, the management measures currently in place for the roundnose grenadier ( Coryphaenoides rupestris) stock exploited to the west of the British Isles. [ABSTRACT FROM AUTHOR]

Fishery catch data offer a rich potential source of information for management, if modelling can separate out the effects of fishing effort, species behaviour and population abundance. Here, we model catch data from the blue ling fishery off the northwest coast of Scotland, using generalised additive mixed models with a space time interaction represented via a novel tensor product of a soap film smooth of space with a penalized regression spline of time. The use of soap film smoothers avoids imposing correspondences between spatially adjacent areas that are in fact separated by the stock boundary. The comparison of the performance of the soap film smooth for space-time with that of a thin plate regression spline based on root mean squared prediction errors and k-means cross-validation suggests that in this application, the former is better overall and in particular for modelling local changes. Further, a model with continuous space-year interaction performed better compared with one with an additive space-year effect. After model selection, checking and validation, there is evidence for increasing blue ling abundance from 2000-2010 in some spatial locations. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The article presents a study which aims to investigate the abundance-occupancy (A-O) patterns for the Georges Bank shellfish and finfish community. The study analyzed 32 species that represent the shellfish and finfish aggregation from 1963 to 2006, with the use of the annual survey data of the National Marine Fisheries Service. Results show that A-O relationships' strengths and slopes dropped significantly over time series duration, which is associated to groundfish landings.

1. Metrics have become a standard way for summarizing environmental monitoring results. Different metrics react differently to natural variations and human-induced stressors. We suggest that combined analysis of time trends in selected biological metrics allows identification of biological processes (e.g. individual growth, mortality or recruitment) that have changed (increased or decreased) persistently. Alternatively, time trends in the abundance of sensitive species could indicate changes in environmental stressors. 2. We calculate the joint likelihood of time trends in three metrics and use it to evaluate the evidence in the data for different combinations of metric time trends. A simulation study provides guidelines for interpreting log-likelihood differences. 3. We illustrate the approach for identifying biological process changes for three North Sea fish stocks (cod Gadus morhua, lesser-spotted dogfish Scyliorhinus canicula and whiting Merlangius merlangius) using metrics derived from international bottom-trawl survey data for the period 1997–2008. Over the period, a decrease in recruitment and several simultaneous process changes were most likely for cod, while a recruitment increase, mortality decrease and several process changes were most likely for lesser-spotted dogfish. No significant persistent process changes were found for whiting. 4. Synthesis and applications. The likelihood approach offers a way of combining monotonic time trends in multiple metrics for identifying persistent changes in exploited populations or environmental stressors, given suitable metric time series and tables for interpreting joint time trends. For data rich fish populations, the proposed method can supplement analytical stock assessments. For many other populations with no fisheries-dependent data, it offers a way to identify population changes, which will be crucial for implementing the ecosystem approach to fisheries management and the European marine strategy framework directive. [ABSTRACT FROM AUTHOR]

1. The development of ecosystem approaches to environmental management implies the need to account for multiple pressures on ecosystems. Trends in multiple metrics that respond differently to changes in major environmental pressures need to be combined to evaluate the impacts of fishing and environmental changes on fish communities. 2. An exploited fish community is viewed as a three-level food chain in which the two upper levels, or functional groups, are targeted by fishing fleets, while the lowest level is subject to environmental variation. Qualitative modelling is used to predict changes at the two upper levels, that is, top-down vs. bottom-up perturbations. Abundance and length metrics are calculated from survey data for 14 Mediterranean and East-Atlantic groundfish shelf communities at both population and functional group levels. The joint likelihood of time trends in metrics is used to evaluate the evidence for different causes of changes. 3. A wide diversity of impacts is found to have equal evidence at the population level within each community. Consistency between the impacts identified and changes in pressures known from independent information is found at the functional group and community level. The results suggest that there is some compensation between species within functional groups. 4. Synthesis and applications. The method can be used to conduct an integrated assessment of community dynamics subject to multiple pressures. Joint trends in metrics provide evidence of which known pressures are having an impact on the community, and thus, which management actions should be taken to mitigate these changes. [ABSTRACT FROM AUTHOR]

Implementing ecosystem-based fisheries management requires indicators and models that address the impacts of fishing across entire ecological communities. However, the complexity of many ecosystems presents a challenge to analysis, especially if reliant on quantification because of the onerous task of precisely measuring or estimating numerous parameters. We present qualitative modelling as a complementary approach to quantitative methods. Qualitative modelling clarifies how community structure alone affects dynamics, here of exploited populations. We build an array of models that describe different ecosystems with different harvesting practices, and analyse them to predict responses to various perturbations. This approach demonstrates the utility of qualitative modelling as a means to identify and interpret community-level indicators for systems that are at or near equilibrium, and for those that are frequently perturbed away from equilibrium. Examining the interaction of ecological and socio-economic variables associated with commercial fisheries provides an understanding of the main feedbacks that drive and regulate exploited ecosystems. The method is particularly useful for systems where the basic relationships between variables are understood but where precise or detailed data are lacking. [ABSTRACT FROM AUTHOR]

According to the Ideal Free Distribution theory, individual fish are distributed where environmental conditions are optimal, and the occupied area may vary with population abundance. Thus, observed distributions are a combination of habitat suitability and density-dependent effects. Data from an annual bottom trawl survey taking place in autumn were used to assess associations between the distributions of eight demersal fish species, separately for juveniles and adults, and habitat characteristics (depth, temperature and salinity) in the Bay of Biscay and Celtic Sea. Cumulative distribution functions were used to describe the general frequency distributions of environmental variables and their relationships with fish density. During the period 1992–2006, observed bottom temperatures fluctuated with no time trend (ΔT = 8°C in the first 80 m) and population abundances varied significantly. Juvenile hake, poor cod, blue whiting, adult red gurnard, adult megrim, and lesser-spotted dogfish were found to be significantly associated with specific depth ranges. Associations with bottom temperature and salinity were weaker. For some species, preferred environmental conditions changed over time, independently of variations in environmental conditions. In general, most species seemed to be able to cope with the experienced range of conditions. Habitat associations were not influenced by abundance variations. Fluctuating abundances had an impact on spatial occupation only for red gurnard adults, lesser-spotted dogfish and blue whiting juveniles, independent of absolute densities. [ABSTRACT FROM AUTHOR]