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Small pelagic fish (SPF) species are heavily exploited in the four main eastern boundary upwelling systems (EBUS), including both Atlantic African ones, as their transformation are increasingly used in the world food chain. Management rely on regular monitoring, but there is a lack of model for population traits emergence and evolution according to the variability of the environment. We attempt to extract some general rules based on the analysis of a life cycle biophysical individual based model applied to the round sardinella (Sardinella aurita, Clupeidae) population off North West Africa. Our analysis focused on the processes responsible for seasonal migrations, spatio-temporal body-length distribution, and inter-annual biomass fluctuations. These patterns were found at individual level in the dynamic change of preferred habitat, and variability in exploration capacities. The former resulted from complex interactions between natal homing behavior and environmental variability, while the last was determined by individual swimming capacities, the mesoscale structure of the habitat and the horizontal currents. Observed spatio-temporal abundance variability emerged from a superposition of numerous distinct individual life histories. This work also suggested an alongshore pattern in size distributions confirmed by in situ surveys. New insights about population structure are provided, with a focal area in Mauritania and mainly two migrating sub-populations centered at 18°N and 21°N, respectively. Inter-annual biomass fluctuations were linked to variability in Sahara Bank's fish recruitment, itself depending on southward current intensity. The identified processes constitute an analytical frame that can be transposed to study Small pelagic fish in all eastern boundary upwelling systems and used to study potential effect of regional climate change.

International audience; Overview of the DEBSe@ course project

International audience; Estimating age and growth of fish larvae is often required in connectivity and recruitment studies. When validated, daily growth increment formation in fish larvae otoliths allows such estimations of larval age and growth. However, several experimental studies showed that otolith distinguishable increments are not always formed at a daily scale, which biases age and growth reconstruction. Here, to better understand the factors controlling the formation of a fish larvae otolith, we propose to further develop a bioenergetics-modeling framework previously applied to the seasonal formation of fish otoliths. This model couples both the growth of an otolith and its opacity to the metabolism of the organism. The model relies on well-tested properties of the Dynamic Energy Budget (DEB) theory, which predicts individual growth, development and maintenance as a function of food density and temperature conditions. We apply the model to sagittae of Atlanto-Iberian sardine larvae Sardina pilchardus. Data on otolith diameter and growth increment numbers, together with individual known age and total length, from larvae reared in laboratory under four different food conditions (high, intermediate, low and starvation conditions, see Ferreira S. et al. abstract) showed that increment deposition was significantly less than one per day. We use data at two different food levels (high and low) to calibrate the otolith module. We first test the ability of the model to reproduce the otolith and fish size for the two other food conditions (intermediate and starvation). We then test the assumption that individuals do not deposit sufficient material of contrasted opacity for an increment to be formed at low food levels. Different opacity functions linked to feeding timings and photoperiod are tested to simulate opacity variation of the deposited otolith material. We discuss the use of this model to reconstruct growth and feeding conditions when increments widths are measured.

Sardinella aurita, or round sardinella, has been the main small pelagic fish species harvested off Senegal and Mauritania coasts over the last 4 decades and plays a central role for sub-regional food security and economic incomes. The landings of this species have strongly declined recently. Intense exploitation and climate change are acting together but population’s dynamics are too poorly understood to disantangle the different drivers and to clearly evaluate the current state of S. aurita’s population. In the present study, we developed a bio-physical, individual based model for S. aurita population off North-West Africa. The hydrodynamic environment was simulated by a regional model ("ROMS") configuration covering the area 5°-40°N and 5°-30°W, with a 8km resolution and 32 sigma-levels in our area of interest. The biogeochemical compartments were simulated using the PISCES model coupled with ROMS. Fish schools of S. aurita were represented by active lagrangian markers affected with ad hoc larval, juvenile and adult fish swimming behavior. Individual’s physiology was described following the local temperature and food availability by the Dynamic Energy Budget model "DEB". The extended kinesis algorithm ruled the horizontal fish movement and depends on food research, individual temperature preference and spawning migration, whereas fish vertical position in the water column was set for each stage according to scientific knowledge. We investigate the predicted seasonal migrations pattern of S. aurita off West Africa over the period 1980-2006. Then we also evaluate the fluctuations of fish biomass available for coastal fisheries (h

Understanding the recruitment variability of fish populations is a major challenge in fishery sciences. In the present work, we explore a new approach to study the potential factors that determine this recruitment in the context of biophysical modelling. The adult spawning pattern might influence the survival of the larvae as it determines the environmental conditions they experience during this critical period. We apply our study to the Bay of Biscay anchovy Engraulis encrasicolus, which is a multiple-batch spawner. The objective of the study is to understand the effect of the environmental conditions experienced by an individual i) on the energy available for reproduction and ii) on the temporal distribution of the spawning events and its consequences on larval growth, development and survival. To study these processes, the Dynamic Energy Budget (DEB) theory is particularly suitable. This theory allows us to identify the common processes and the specificities of each life stage. First, we actualise the growth curve of Bay of Biscay anchovy. Juvenile growth is reproduced by taking into account they experience in average a higher temperature during this stage than the adults thereafter. Larval growth in fish typically deviates from later juvenile and adult growth. We suggest to consider how food intake depends on body length to explain the observed growth patterns. Second, the present work allows us to better understand and quantify the effect of environmental conditions experienced by an individual on the length of its spawning season. These conditions determine on one hand the length of the individual and thus its reproduction potential, and on the other hand the amount of energy that it can actually store for reproduction. In limiting conditions, this energy can be mobilised for survival. Hence, the length structure of the population and the limiting conditions encountered by the individuals are determinant factors of the spawning windows. Third, we are able to identify the food conditions that allow survival until the juvenile stage for larvae issued from different spawning windows. We obtain this result from the selection of environmental scenarios that reproduce the observed age and otolith radius at metamorphosis according to first feeding date. The link between fish metabolism and otolith formation (a complex crystal in the inner ear of the fish) is explicitly modelled. We show the potential of the model to reconstruct individual life history from the observed variations of opacity in the otolith. The approach we used is a deterministic approach of the link between the environment and the individual, through bioenergetic processes. It allows us to formulate original mechanisms underlying classical observations in fishery sciences. As a better understanding of fish life cycles requires the study of individual behavior and strategies in response to environmental variations, we suggest the present work can be used as a basis for such studies., Comprendre la variabilité du recrutement est une problématique majeure en halieutique. Dans ce travail, nous explorons une nouvelle approche pour étudier les facteurs qui déterminent le recrutement, dans le cadre de la modélisation biophysique. Le schéma de ponte des adultes peut influencer la survie des larves car il détermine les conditions environnementales qu'elles rencontrent pendant cette période critique. Notre cas d'étude est l'anchois du golfe de Gascogne Engraulis encrasicolus, qui est une espèce à pontes multiples. L'objectif de la thèse est de comprendre l'effet de l'environnement vécu par un individu i) sur l'énergie disponible pour la reproduction et ii) sur l'étalement des pontes et ses conséquences sur la croissance, le développement et la survie des larves. Pour appréhender les processus métaboliques en jeu, la théorie Dynamic Energy Budget est un outil particulièrement adapté. Cette théorie permet d'identifier les processus communs et les spécificités de chaque stade. Nous apportons tout d'abord une révision de la courbe de croissance de l'anchois du golfe de Gascogne. Nous reproduisons la croissance des juvéniles en tenant compte du fait qu'ils expérimentent en moyenne une température plus élevée durant cette phase que celle vécue ensuite par les adultes. La croissance larvaire diffère de la croissance des juvéniles et des adultes. Nous proposons de considérer la relation entre prise de nourriture et longueur de l'individu pour expliquer cette croissance. Ce travail nous permet ensuite de mieux comprendre et de quantifier l'effet des conditions environnementales vécues par un individu sur la durée de sa saison de reproduction. Ces conditions déterminent d'une part la taille de l'individu donc son potentiel reproducteur et d'autre part la quantité d'énergie qu'il peut effectivement mettre en réserve pour la reproduction. En conditions limitantes de nourriture, cette énergie peut en effet être mobilisée pour sa survie. Ainsi la structure en taille de la population et les conditions limitantes rencontrées par les individus sont des facteurs déterminants des fenêtres de ponte. La thèse permet enfin d'identifier les conditions de nourriture nécessaires à la survie jusqu'au stade juvénile, pour des larves issues de fenêtres de pontes différentes. Nous obtenons ce résultat à partir de la sélection des scénarios environnementaux qui reproduisent l'âge et la taille de l'otolithe à la métamorphose en fonction de la date d'ouverture de la bouche. Le lien entre métabolisme du poisson et formation de l'otolithe (une pièce calcifiée de l'oreille interne) est explicitement modélisé. Nous démontrons le potentiel du modèle pour la reconstruction de la quantité d'énergie assimilée par un individu au cours de sa vie à partir des variations observées de l'opacité dans l'otolithe. L'approche développée dans ce travail est une approche déterministe du lien environnement – individu, au travers des processus bioénergétiques. Cette approche nous permet de proposer des mécanismes originaux sous-jacents à certaines observations classiques en halieutique telles que le découplage entre la croissance de l'otolithe et la croissance en longueur du poisson et la phase exponentielle de la croissance pendant le stade larvaire. Une meilleure compréhension des cycles de vie requiert également la prise en compte du comportement et des stratégies individuelles. Ce travail peut constituer la base sur laquelle de telles études pourront à l'avenir s'appuyer.

Connectivity during early life stages of pelagic fish, defined here by survival probability between spawning and early juvenile habitats, depends on a combination of sufficient food availability and low predator encounter along drift trajectories. For anchovy in the Bay of Biscay, larval transport experiments throughout the spawning season suggest accumulation of early juveniles in the offshore area of the southern Bay, as well as retention over the mid-shelf at mid-latitude. However, late summer-early autumn surveys suggest presence of juveniles only in the former region. From this observation, we set up a bioenergetic individual based model to test for the effect of food availability on survival patterns. The model couples a Lagrangian transport module to the hydrodynamic model MARS-3D, as well as a DEB (Dynamic Energy Budget) model for estimation of larval growth and mortality under starvation. Temperature is provided either from CTD casts or the hydrodynamic model, whereas food is provided by observation of size structured zooplankton biomass, from both in-situ LOPC (Laser Optical Plankton Counter) and Zooscan processing of net haul samples from the Pelgas survey in May. Results suggest that for early spawning season, most of the mortality from starvation occurs at early larval stage, mostly for eggs spawned in the deepest on-shelf and off-shelf areas. The southern bay of Biscay is more suitable for growth and survival than the north at that time of the year for both temperature and food limitations reasons. The offshore occurence of late larvae in the south is consistent with observations in the area, but our model is not able to simulate a general drift of the whole distribution, that would be consistent with late larvae mostly found over the slope and off-shelf. Further simulations should investigate whether this comes from interannual and seasonal patterns explanations, or whether our model lacks an important process such as spatially explicit predation.

Tesis (Maestro en Ciencias del Mar). Universidad Peruana Cayetano Heredia. Aplicamos la teoría del Balance Energético Dinámico (DEB) a dos especies de pequeños pelágicos: la anchoveta (Engraulis ringens) y la sardina (Sardinops sagax) del Sistema Norte de la Corriente de Humboldt (NHCS) frente a Perú. El modelo DEB fue forzado por factores ambientales obtenidos de la Clorofila-a Superficial del Mar a partir del satélite MODIS y la Temperatura Superficial del Mar del modelo NOAA-NCDC en el periodo 2003-2014. Se extendió el modelo DEB estándar para comparar la respuesta bioenergética de la anchoveta y la sardina a variaciones ambientales estacionales. Se encontró que: (i) el alimento fue directamente restrictivo sobre la longitud asintótica en ambas especies, mientras que la temperatura afectó la velocidad de los procesos y tasas metabólicas; (ii) las larvas de sardina sobrevivieron más tiempo en condiciones de inanición respecto de las larvas de anchoveta; la temporada de desove influyó de manera directa y significativa (p