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Long-term ecological surveys (LTES) often exhibit strong variability among sampling dates. The use and interpretation of such interannual variability is challenging due to the combination of multiple processes involved and sampling uncertainty. Here, we analysed the interannual variability in ∼30 years of 150 species density (fish and invertebrate) and environmental observation time series in four aquatic systems (stream, river, estuary, and marine continental shelf) with different sampling efforts to identify the information provided by this variability. We tested, using two empirical methods, whether we could observe simultaneous fluctuation between detrended time series corresponding to widely acknowledged assumptions about aquatic population dynamics: spatial effects, cohort effects, and environmental effects. We found a low number of significant results (36%, 9%, and 0% for spatial, cohort, and environmental effects, respectively), suggesting that sampling uncertainty overrode the effects of biological processes. Our study does not question the relevance of LTES for detecting important trends, but clearly indicates that the statistical power to interpret interannual variations in aquatic species densities is low, especially in large systems where the degree of sampling effort is always limited. [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]

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The thornback ray (Raja clavata) in the Bay of Biscay is presumed to have declined during the 20th Century. To evaluate this decline and estimate biomass trajectories, a hypothetical catch time series was created for the period 1903-2013. A Bayesian state-space biomass production model with a Schaefer production function was fitted to the hypothetical catch time series and to a shorter research vessel Catch Per Unit Eeffort (CPUE) time series (1973-2013, with missing years). A censored likelihood made it possible to obtain biomass estimates without a CPUE time series or only with an estimate of biomass depletion. A simulation-estimation approach showed a high sensitivity of results to the prior for the intrinsic growth rate. The model provided biomass trajectories which corroborated and quantified the decline of the Bay of Biscay population. The estimated biomass corresponding to the maximum sustainable yield, BMSY, was 32 000 tonnes, which is 17 times higher than the estimated biomass in 2014. The biomass estimates obtained without a CPUE time series were highly uncertain. Adding a current biomass depletion observation improved precision, though the biomass time trend was sensitive to this value. Results should be interpreted carefully as several assumptions were necessary to create the long catch time series and to define informative priors, notably for the intrinsic growth rate. Despite this, the results confirm the depleted state of the thornback ray in the Bay of Biscay with the estimated biomass in 2014 being around 3% of carrying capacity. [ABSTRACT FROM AUTHOR]

Catch curves are widely used to estimate total mortality for exploited marine populations. The usual population dynamics model assumes constant recruitment across years and constant total mortality. We extend this to include annual recruitment and annual total mortality. Recruitment is treated as an uncorrelated random effect, while total mortality is modelled by a random walk. Data requirements are minimal as only proportions-at-age and total catches are needed. We obtain the effective sample size for aggregated proportion-at-age data based on fitting Dirichlet-multinomial distributions to the raw sampling data. Parameter estimation is carried out by approximate likelihood. We use simulations to study parameter estimability and estimation bias of four model versions, including models treating mortality as fixed effects and misspecified models. All model versions were, in general, estimable, though for certain parameter values or replicate runs they were not. Relative estimation bias of final year total mortalities and depletion rates were lower for the proposed random effects model compared with the fixed effects version for total mortality. The model is demonstrated for the case of blue ling ( Molva dypterygia) to the west of the British Isles for the period 1988 to 2011. [ABSTRACT FROM AUTHOR]

• We developed a generic qualitative model to capture depredation impacts on fisheries. • We assessed responses of depredation-impacted fisheries to long-term perturbations. • Responses of depredation-impacted systems can be classified into 4 categories. • We illustrate the 4 types of depredation-impacted fisheries with documented examples • We identify several conditions for the viability of depredation-impacted fisheries. Depredation can broadly affect marine socio-ecological systems, yet it has been little studied via modelling approaches. Here we used qualitative mathematical modelling of system feedback (Puccia and Levins' loop analysis) and a system of ordinary differential equations to represent major interactions between a fishery, an exploited stock and a depredating species. We then assess response of depredation-impacted fisheries to three scenarios of sustained changes: i) increased fishing effort, ii) increased abundance of depredating species and iii) increased abundance of the exploited stock. Persistence of depredation-impacted fisheries depends on (1) the fishers' success in retrieving fish onboard being relatively greater than the ability of depredating species to remove the catch from the gear and (2) sustainable management of the exploited and depredated stock. Moreover, predicted responses of depredation-impacted systems can be summarised according to four broad categories, which partially depend on (1) the population dynamics of the stock and its exploitation status, and (2) the ecology of the depredating species and the magnitude of its competition with fishers. In all categories, an increase in the rate of growth of the depredating species reduces fishery yield, which is likely to intensify fishing effort as fishers try and compensate for losses. However, such an increase in effort is only sustainable for well-managed stocks harvested by a fishery that is sufficiently profitable to support extra costs. We identify several processes that determine the co-existence of fishers, exploited stocks and depredating species and propose a suite of recommendations to better represent depredation in marine ecosystem and fisheries models. [ABSTRACT FROM AUTHOR]