•Both seasonal and inter-annual variability in body condition strongly depend on age.•The period 2007-2011 is the critical phase of decrease in sardine body condition.•Changes in temperature and ...chlorophyll-a may explain the decrease in body condition.•High levels of Chl-a during the critical phase suggest more complex trohic responses.
In the Bay of Biscay, mean body length and weight of sardines (Sardina pilchardus) have been decreasing since the early 2000s and could severely impact the fishing and seafood industry sector. These trends have no apparent link with fishing pressure, although the latter has been increasing since the late 2000s. As part of an effort to develop suitable assessment and management tools for this stock, we investigated the life-history traits of sardine and analyze its seasonal and inter-annual variations. Based on 14 years of morphometric data from both scientific surveys and professional samples, we analyzed the variability in sardine body condition and its responses to environmental changes. Generalized Additive Models revealed an age-sex specific decreasing trend in body length over the study period, with most of the variability explained by the age class. Linear Mixed Effect Models applied to the body condition evidenced its strong seasonality and an age class specific decreasing trend. Regardless of age class, maximal body condition is reached at the end summer, after the spawning and plankton productive periods. Overall, annual trends in body condition-at-age showed remarkable coherence, with a significant decrease since 2007 for all age classes, suggesting that factors influencing body condition operate at population level. The shift in sardine body condition towards lower values could be broken down into three periods, with a high dependence on surface Chlorophyll-a and sea surface temperature. However, this study highlights that the period supporting the main decrease in body condition is characterized by high Chlorophyll-a, the available proxy for food, which is counterintuitive. Such a result suggests more complex trophic responses involving secondary production, with potential shift in the timing of the production and/or the quality of the food. At the population level, those changes may have a long-term negative effect, with a decrease in body length and important changes in phenology (length at first maturity, reproductive phenology) and potential consequences on sardine population dynamics in the Bay of Biscay.
Abstract
The population of European anchovy of the Bay of Biscay collapsed at the beginning of the 21st century, causing the closure of its fishery between 2005 and 2010. In order to study both the ...human and environmental causes of the anchovy population dynamics, an approach coupling individual bioenergetics to an individual-based model was applied between 2000 and 2015. This modelling framework was forced with outputs from a physical–biogeochemical model. In addition to a base-case scenario with realistic forcing, alternative scenarios were run without inter-annual variability in either fishing mortality or environmental conditions. During the decrease in population biomass, a high fishing pressure coincided with a combination of environmental variables promoting the appearance of large individuals that could not survive severe winters because of their high energetic demands. The recovery of the population was favoured by a period of warm years with abundant food favouring the winter survival of age 1 individuals, in coincidence with the closure of the fishery. Our modelling approach also allows to test the consequences of a retrospective implementation of the current harvest control rule from 2000 which, according to our results, would have prevented the collapse of the population and avoided the fishery closure.
European sardine or pilchard is a planktonic small pelagic fish present from the North Sea in Europe to the coast of Senegal in the North of Africa, and across the Mediterranean sea to the Black Sea. ...Ecologically, sardines are an intermediary link in the trophic network, preying on plankton and being predated by larger fishes, marine mammals, and seabirds. This species is of great nutritional and economic value as a cheap but rich source of protein and fat. It is either consumed directly by humans or fed as fishmeal for aquaculture and farm animals. Despite its importance in the food basket, little is known about the molecular mechanisms involved in protein and lipid synthesis in this species. We collected nine tissues of Sardina pilchardus and reconstructed the transcriptome. In all, 198,597 transcripts were obtained, from which 68,031 are protein-coding. Quality assessment of the transcriptome was performed by back-mapping reads to the transcriptome and by searching for Single Copy Orthologs. Additionally, Gene Ontology and KEGG annotations were retrieved for most of the protein-coding genes. Finally, each library was quantified in terms of Transcripts per Million to disclose their expression patterns.
This paper presents a novel application of the geostatistical multivariate method known as min–max autocorrelation factors (MAFs) for analysing fisheries survey data in a space–time context. The ...method was used to map essential fish habitats and evaluate the variability in time of their occupancy. Research surveys at sea on marine fish stocks have been undertaken for several decades now. The data are time series of yearly maps of fish density, making it possible to analyse the space–time variability in fish spatial distributions. Space–time models are key to addressing conservation issues requiring the characterization of variability in habitat maps over time. Here, the variability in fisheries survey data series is decomposed in space and time to address these issues, using MAFs. MAFs were originally developed for noise removal in hyperspectral multivariate data and are obtained using a specific double principal components analysis. Here, MAFs were used to extract the most continuous spatial components that are consistent in time, together with the time series of their amplitudes. MAFs formed an empirical isofactorial model of the data, which served for kriging in each year using all available information across the data series. The approach was applied on the spawning distributions of sardine in the Bay of Biscay from 2000 to 2017. A multivariate approach for dealing with space–time data was adapted here, because the evolution in time was highly variable. Maps were classified using the amplitudes of the MAFs, and groups of typical distributions were identified, which showed different occurrence probabilities in different periods.
Age and size at maturation appear as key parameters governing the dynamics of a population as they affect growth rate, fecundity, and survival. The expression of such life history traits is ...determined by genetic make-up and modulated by environmental factors mainly through phenotypic plasticity. Moreover, fishing, besides decreasing population size and changing demographic composition can alter allelic frequencies through fisheries-induced evolution by selecting for some particular traits. In the Bay of Biscay, a decreasing trend in both sardine body condition and size-at-age has recently been pointed out at the population level. The Probabilistic Maturation Reaction Norm (PMRN) approach was applied to help disentangle phenotypic plasticity and genetic changes. Based on the analysis of sardine spawning seasonality, PMRN was estimated by considering body condition as additional life-history state variable to predict the onset of maturation. The resulting PMRN was then used to investigate temporal trends in reaction norm midpoints to test whether changes in length at maturation can be explained by plastic and/or evolutionary adaptive change. Overall, our results emphasize for the first time that including sardine body condition as explanatory variable improves predictions of maturation probability. We found that better individual condition increases maturation probability. The assessment of temporal changes in length at maturation confirms the low plasticity in this trait for a species maturing mostly at age-1 and advocates for the use of a monthly time scale when investigating PMRNs for this species. Beside environmental variables included in this analysis (water temperature, chlorophyll-
a
, and population biomass) that only show a weak correlation with PMRN midpoints, our results reveal no evidence for recent fisheries-induced evolution in the sardine stock of the Bay of Biscay. They suggest that the short-term variability in length at maturation is strongly dependent upon individual growth which is likely driven by environmental factors. For sardine fisheries management, our study highlights the need to consider both the length-composition data and the seasonality within a stock assessment model. Finally, we discuss the fact that considering individual growth trajectories should improve our understanding of the relationship between environmental variability and changes in maturation for sardine.
•A new calibration of a DEB model for anchovy and a first set of parameter estimates for sardine in the Bay of Biscay.•Using a robust method for parameter estimation, the evolution strategy, ...guaranteeing the uniqueness of the solution.•The sardine model is derived from the anchovy one through a scenario approach that successively tested the effect of distinctive traits (size, spawning, feeding).•Bioenergetics and reproduction strategy strongly interact.•Sardine displays a slower but more regular energy allocation to both growth and reproduction than anchovy.
Similar or very contrasted puzzling population dynamics between anchovy and sardine occur worldwide. Underlying factors are not well understood, but insights towards different biological traits are suggested, in particular trophic specialisation, leading to different responses to environmental conditions. Based on most striking differences in biological and life history traits, i.e. size, spawning and feeding, we calibrated a bioenergetics model, based on the Dynamic Energy Budget theory, for Engraulis encrasicolus and Sardina pilchardus in the Bay of Biscay. Starting from the anchovy model, differences in traits were successively integrated to build the sardine model through a novel exploratory approach by scenarios. We used a robust method for parameter estimation, the Evolution Strategies, with a large dataset of length and mass at age, as well as energy density, which is the first time in such a model calibration. Energy density data proved to be particularly well suited to assess the quality of DEB model predictions and parameter set estimates. Insights in respective physiology were drawn from analysis of parameter values and predictions of the model. We showed that anchovy and sardine have distinct strategies with respect to energy acquisition and especially to allocation to spawning. Anchovy are characterised by higher metabolic rates and requirements. This species is more likely to benefit from periods of high food availability to carry out both growth, spawning and reserve storage. Sardine have less demanding food requirements and metabolic costs. Sardine take advantage of larger reserves storage capacity to decouple spawning and prey blooms and to lengthen spawning period, and thus display a more capital breeding spawning behaviour. Overall, our model outputs distinguish between anchovy that tend towards an almost “all or nothing” energetic strategy, and sardine that tend to carry out lower metabolic activities but on a more regular basis. This first modelling demonstration of a bioenergetics difference between these two species, and the explanation it brings in the understanding of their respective reproduction strategies, opens new perspectives in the interpretation of their differential responses at the population scale to environment variability.
For many fishes, their early life stages are transported (passively) by currents between spawning areas and coastal nurseries, but also potential dispersal towards new habitats. Therefore, species ...have developed strategies to enhance the recruitment success, including the selection of appropriate spawning grounds. However, increased temperature due to climate change may lead to changes in hydrodynamics, shorter larval drifts, and earlier spawning, and consequently the location of the most suitable spawning grounds may change. We investigated whether the location of the most favourable spawning areas (allowing higher rates of larvae reaching coastal nurseries) was stable over time, and if differences could be found between environmentally contrasted years. We used a larval drift model taking into account hydrodynamics, larval characteristics and behaviour for three commercially exploited fish species (sole Solea solea, flounder Platichthys flesus and seabass Dicentrarchus labrax) in the Western Europe (encompassing the Bay of Biscay, the Celtic Sea and the English Channel). According to our model, we conclude that despite contrasting environmental conditions, the location of spawning grounds allowing the best chance of recruitment to nurseries for the offspring was fairly similar. However, even if the location of the main spawning grounds is stable over time, their relative effectiveness varies greatly between years. This would suggest that natural selection may favour the emergence of homing behaviour. This stability in this fish essential habitat location could facilitate protection measures. Going further, it could be interesting to study the variations occurring in spawning grounds (in terms of recruitment success, and retention/dispersion) during the course of a spawning season.
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•Using a larval drift model, we located optimal spawning grounds of three species depending on environmental conditions.•Most favourable spawning ground location remained rather stable over years despite varying environmental conditions.•The recruitment success was highly sensitive to environmental conditions, likely due to different hydrodynamic conditions.
•Sensitivity analysis on a larval drift model through an orthogonal experimental design enabling the quantification of main effects and their first-order interactions.•Larvae thermal tolerance is a ...key factor when modelling species at the limit of their distribution area.•At a large scale, nychtemeral vertical migration does not affect much the overall recruitment success.•Local hydrodynamics and inter-annual variability are the most important source of variations for recruitment success.•We advise simulating over multiple years before exploring recruitment success and connectivity outputs.
Many marine fish species display a long larval drift between offshore spawning grounds and coastal nursery areas. This drift, whose efficiency drive the renewal of the population, critically depends on many environmental factors and on the spawning behaviour of species. Given the complexity to collect field data on fishes early life stages, modelling has proved to be one of the most valuable tool to explore such questions. However, these complex models require many parameters, many of which are uncertain, making a comprehensive sensitivity analysis a crucial step before drawing conclusions on the effects of environmental drivers. This study focused on the larval drift of five species archetypes mimicking five commercially important fish species with contrasted spawning strategies and larval ecology, in five different sub regions over Western Europe, from the Iberian coast to the North Sea. Using an hydrodynamic model (MARS3D) coupled with an individual-based model, and by building a simulation design suitable for such sensitivity analysis, we assessed the relative influence of extrinsic (years and region’s hydrodynamics) and intrinsic (spawning grounds’ depth, spawning period, vertical migration, developmental rate, daily mortality and tolerance to temperature) factors and their two-ways interactions on recruitment success to nurseries. The thermal tolerance of species was one of the leading factors, suggesting that this is a critical parameter, especially when modelling species recruitment success at the edge of their distribution range. On the other hand, other parameters such as the nycthemeral vertical migration, that are often discussed in such larval drift simulation exercise, have proved to have a more limited influence for an analysis at such a large spatial scale. Overall, when studying larval drift on a large scale, local hydrodynamics and inter-annual variations hold most of the explained variance in the recruitment success, confirming the importance of repeating simulations over multiple years before exploring the connectivity among spawning and nursery areas.
Monitoring and predicting the biogeochemical state of the ocean and marine ecosystems is an important application of operational oceanography that needs to be expanded. The accurate depiction of the ...ocean's physical environment enabled by Global Ocean Data Assimilation Experiment (GODAE) systems, in both real-time and reanalysis modes, is already valuable for various applications, such as the fishing industry and fisheries management. However, most of these applications require accurate estimates of both physical and biogeochemical ocean conditions over a wide range of spatial and temporal scales. In this paper, we discuss recent developments that enable coupling new biogeochemical models and assimilation components with the existing GODAE systems, and we examine the potential of such systems in several areas of interest: phytoplankton biomass monitoring in the open ocean, ocean carbon cycle monitoring and assessment, marine ecosystem management at seasonal and longer time scales, and downscaling in coastal areas. A number of key requirements and research priorities are then identified for the future. GODAE systems will need to improve their representation of physical variables that are not yet considered essential, such as upper-ocean vertical fluxes that are critically important to biological activity. Further, the observing systems will need to be expanded in terms of in situ platforms (with intensified deployments of sensors for O₂ and chlorophyll, and inclusion of new sensors for nutrients, zooplankton, micronekton biomass, and others), satellite missions (e.g., hyperspectral instruments for ocean color, lidar systems for mixed-layer depths, and wide-swath altimeters for coastal sea levels), and improved methods to assimilate these new measurements.
Although many oceanographic data products are now considered operational, continued dialogue between data producers and their user communities is still needed. The fisheries and environmental science ...communities have often been criticized for their lack of multidisciplinarity, and it is not clear whether recent developments in operational oceanographic products are addressing these needs. The International Council for the Exploration of the Sea (ICES) Working Group on Operational Oceanographic products for Fisheries and Environment (WGOOFE) identified a potential mismatch between user requirements and the perception of requirements by the providers. Through a questionnaire (98 respondents), WGOOFE identified some of these issues. Although products of physical variables were in higher demand, several biological parameters scored in the top 10 rankings. Users placed specific focus on historic time series products with monthly or annual resolution and updating on similar time scales. A significant percentage requested access to numerical data rather than graphical output. While the outcomes of this survey challenge our views of operational oceanography, several initiatives are already attempting to close the gap between user requirements and products available.
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