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This work was supported by funding from the International Whaling Commission's Pollution 2000+Program, the U.S. NOAA/NFMS Health and Stranding Response Program and the UK's Natural Environment Research Council (Grant Code SMRU 10001). The potential impact of exposure to polychlorinated biphenyls (PCBs) on the health and survival of cetaceans continues to be an issue for conservation and management, yet few quantitative approaches for estimating population level effects have been developed. An individual based model (IBM) for assessing effects on both calf survival and immunity was developed and tested. Three case study species (bottlenose dolphin, humpback whale and killer whale) in four populations were taken as examples and the impact of varying levels of PCB uptake on achievable population growth was assessed. The unique aspect of the model is its ability to evaluate likely effects of immunosuppression in addition to calf survival, enabling consequences of PCB exposure on immune function on all age-classes to be explored. By incorporating quantitative tissue concentration-response functions from laboratory animal model species into an IBM framework, population trajectories were generated. Model outputs included estimated concentrations of PCBs in the blubber of females by age, which were then compared to published empirical data. Achievable population growth rates were more affected by the inclusion of effects of PCBs on immunity than on calf survival, but the magnitude depended on the virulence of any subsequent encounter with a pathogen and the proportion of the population exposed. Since the starting population parameters were from historic studies, which may already be impacted by PCBs, the results should be interpreted on a relative rather than an absolute basis. The framework will assist in providing quantitative risk assessments for populations of concern. Postprint Postprint

International audience; In response to climate warming, a southward shift in productive frontal systems serving as the main foraging sites for many top predator species is likely to occur in Subantarctic areas. Central place foragers, such as seabirds and pinnipeds, are thus likely to cope with an increase in the distance between foraging locations and their land-based breeding colonies. Understanding how central place foragers should modify their foraging behavior in response to changes in prey accessibility appears crucial. A spatially explicit individual-based simulation model (Marine Central Place Forager Simulator (MarCPFS)), including bio-energetic components, was built to evaluate effects of possible changes in prey resources accessibility on individual performances and breeding success. The study was calibrated on a particular example: the Antarctic fur seal (Arctocephalus gazella), which alternates between oceanic areas in which females feed and the land-based colony in which they suckle their young over a 120 days rearing period. Our model shows the importance of the distance covered to feed and prey aggregation which appeared to be key factors to which animals are highly sensitive. Memorization and learning abilities also appear to be essential breeding success traits. Females were found to be most successful for intermediate levels of prey aggregation and short distance to the resource, resulting in optimal female body length. Increased distance to resources due to climate warming should hinder pups' growth and survival while female body length should increase.

The understanding of the interactions between plants within heterogeneous crops could allow for a more efficient use of wheat varietal mixtures, as there is a gap of knowledge on the complementarity, synergy and competition that develop among varieties within these systems. Our study is focused on competition for light, and its impact on the above ground architecture of wheat, coupling experimental analysis and model development. We first characterized the plasticity of the aerial architecture in response to different sowing densities, for 20 contrasting genotypes of winter wheat. The number of axes per plant was shown to be the most plastic trait for all genotypes. We developed an individual-based model representing wheat growth, from the sowing to flowering. The model is composed of two parts: a descriptive part of the foliar development based on the ADEL-wheat model and a mechanistic part which accounts for the regulation of tillering by light. Tillering is regulated by two simple hypotheses: (1) tillering stops when a critical value of local Green Area Index (GAI) is reached, (2) a tiller dies if the amount of intercepted light falls below a critical threshold. A realistic tillering dynamics was simulated by our model over a wide range of sowing densities, with a good fit with experimental data. We also experimentally characterized the plasticity of plant architecture for eight wheat genotypes observed in various two-components varietal mixtures. Contrasted plastic responses were observed when compared to those expressed in pure stands, underlining the specificity of certain plant-plant interactions. These experiments confirmed that the cultivar mixtures generally contribute to an overyielding, particularly in low-input agriculture . Finally, our results revealed that variety mixtures including genotypes with different heights may provide an advantage to the taller genotype with limited tradeoff on the short genotype. This work contributed to the development of a simplified formalism for tillering process, allowing to explore and optimize complementarities / competitions between plants within variety mixtures. Ultimately, the model could be coupled with a genetic model, in order to better describe the impact of plant-to-plant interactions in the selective value of individuals in heterogeneous populations., L’étude des interactions entre les plantes au sein de couverts hétérogènes pourrait permettre une meilleure utilisation des associations variétales de blé, car nous manquons de connaissances sur la manière dont les complémentarités, synergies et compétitions entre variétés affectent leurs performances dans ces conditions. Notre étude s'est focalisée sur la compréhension de l'impact de la compétition pour la lumière sur l'architecture aérienne du blé, en couplant une analyse expérimentale et une approche par modélisation. Nous avons dans un premier temps, caractérisé la plasticité de l’architecture aérienne en réponse à la modification de la densité de semis, pour 20 génotypes contrastés de blé tendre. Ainsi, nous avons déterminé que le nombre d’axes par plante était le trait le plus plastique pour tous les génotypes. Nous avons ensuite développé un modèle individu-centré représentant le développement du blé du semis à la floraison. Ce modèle est composé de deux parties : une partie descriptive du développement foliaire basée sur un modèle existant (ADEL-blé) et une partie plus mécaniste où nous avons intégré une régulation du tallage par la ressource lumineuse. Cette régulation du tallage se fait selon deux hypothèses simples : (1) la plante arrête d'émettre des talles dès que le Green Area Index (GAI) de son voisinage atteint une valeur seuil et (2) une talle meurt si la quantité de lumière qu'elle intercepte est inférieure à un seuil critique. La dynamique de tallage simulée par le modèle sur une large gamme de densité de semis est proche de la dynamique de tallage observée expérimentalement. Nous avons également caractérisé expérimentalement la plasticité de l’architecture aérienne de huit génotypes de blé en réponse à la compétition dans différentes associations variétales binaires. Ces analyses ont révélé des réponses assez différentes de celles mesurées en culture pure, soulignant la spécificité de certaines interactions entre plantes de génotypes différents. Ces essais ont confirmé que les associations contribuaient généralement à une augmentation de la production, en particulier dans des itinéraires techniques économes en intrants. Nous avons montré que des associations variétales comprenant des génotypes avec des hauteurs différentes permettaient d’avantager fortement le génotype haut sans trop pénaliser le génotype court. Ce travail a permis de développer un formalisme simplifié des processus régulant le tallage, qui va permettre d'explorer et optimiser les complémentarités/compétitions entre variétés dans des peuplements multi-variétaux. A terme le modèle pourra être couplé à des modèles génétiques pour mieux décrire l'impact de l'interaction plate-plante dans la valeur sélective des individus dans des populations hétérogènes.

International audience; During routine monitoring of commercial purse seine catches in 2011, 87 fingerling specimens of scombrids were collected in the southern Adriatic Sea. Sequencing of the mitochondrial DNA control region locus inferred that specimens belonged to the Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758) (N = 29), bullet tuna, Auxis rochei (Risso, 1810) (N = 30) and little tunny, Euthynnus alletteratus, Rafinesque, 1810 (N = 28). According to previously published growth parameters, the age of the collected specimens was estimated at approximately 30–40 days, suggesting they might have been spawned in the Adriatic Sea, contrary to the current knowledge. A coupled modelling system with hydrodynamic (ROMS) and individual based model (IBM—Ichthyop) was set up to determine the location of the spawning event. Numerical simulations with the IBM model, both backward and forward in time, indicate commercial tuna cages in the middle Adriatic coastal area as possible spawning location. The two other non-commercial species likely opportunistically use the positive environmental (abiotic and biotic) conditions to spawn in the same area.

arXiv:1304.6623, Savannas are characterized by a discontinuous tree layer superimposed on a continuous layer of grass. Identifying the mechanisms that facilitate this tree-grass coexistence has remained a persistent challenge in ecology and is known as the "savanna problem". In this work, we propose a model that combines a previous savanna model Calabrese et al., 2010, which includes competitive interactions among trees and dispersal, with the Drossel-Schwabl forest fire model, therefore representing fire in a spatially explicit manner. The model is used to explore how the pattern of fire-spread, coupled with an explicit, fire-vulnerable tree life stage, affects tree density and spatial pattern. Tree density depends strongly on both fire frequency and tree-tree competition although the fire frequency, which induces indirect interactions between trees and between trees and grass, appears to be the crucial factor controlling the tree-extinction transition in which the savanna becomes grassland. Depending on parameters, adult trees may arrange in different regular or clumped patterns, the later of two different types (compact or open). Cluster-size distributions have fat tails but clean power-law behavior is only attained in specific cases. © 2013 Elsevier B.V., F.S.B. and E.H.-G. acknowledge financial support from Spanish MINECO and FEDER through project FISICOS (FIS2007-60327). J.M.C acknowledges the support of the European Union project PATRES (Pattern Re-silience; project NEST 43268). F.S.B. acknowledges a grant from the Balearic Government.

Anchovy and sardine belong to the guild of small pelagic fish and are of peculiar importance at the scales of ecosystems and fisheries. Both species are worldwide spread and commonly occur in the same ecosystems. They display large interannual variability in biomass with markedly different trends or even asynchronous. A growing literature suggests that those dynamics are due to respective sensibility to environmental conditions driven by different biological traits. A priori both species are very similar but show slightly distinct feeding behaviours and reproductive strategies. Understanding divergences in both species biology and life history strategies is thus crucial to understand and predict past and future dynamics of these stocks. The aim of this PHD is to assess how both species diverge in terms of biological and life history traits on a physiological basis. Owing to the complexity of biological traits, potential interactions among these traits and ontogenetic evolutions, to answer this question an integrative approach based on a bioenergetics model of the whole life cycle is requested. First the study focus on a condition index: the energy density (energy content per unit of mass). Energy density integrates historic of numerous physiological processes, both gain from food and diverse metabolic expenses. This analysis shows effects on the bioenergetics cycle of the fish, namely species, size, season and geographic area. Linked with bioenergetics data, a full life cycle model has been parametrised for both species in the Bay of Biscay, in order to get an integrative, predictive and exploratory tool. This model is based on the “Dynamic Energy Budget” theory. This theory aims at predicting the life cycle of an organism, using environmental forcing, by simulating energy fluxes inside the organism. This modelling approach underlines the particularly significant feature of reproductive strategies on the bioenergetics annual cycle of both species., L’anchois et la sardine appartiennent à la guilde des petits poissons pélagiques, qui tiennent une place considérable à l’échelle des écosystèmes et des pêcheries. Ces deux espèces sont très largement répandues dans les mers et océans du globe et souvent occupent les mêmes écosystèmes. Leurs populations montrent d’importantes fluctuations interannuelles de biomasses, dont les tendances ne suivent pas les mêmes schémas, voire sont parfois déphasées. Une littérature croissante suggère que ces dynamiques sont dues à des sensibilités relatives aux conditions environnementales différentes induites par des traits biologiques distincts. Bien que de prime abord anchois et sardines semblent très similaires, ils montrent notamment des stratégies alimentaires et reproductives quelque peu différentes. Comprendre ces divergences biologiques et de stratégies d’histoire de vie apparait donc essentiel pour appréhender les dynamiques passées et éventuellement anticiper les évolutions futures de ces stocks. L’objectif de cette thèse est de déterminer en quoi se démarquent ces deux espèces en termes de traits biologiques et d’histoire de vie sur une base physiologique. En effet, du fait de la complexité de potentielles interactions entre les traits biologiques et de leurs évolutions ontogéniques, il convient, pour répondre à cette question, de mettre en œuvre une approche intégratrice via la modélisation bioénergétique à l’échelle du cycle de vie. Dans un premier temps l’étude a été dédiée à un indice de condition : la densité énergétique (contenu énergétique par unité de masse). La densité énergétique résulte de nombreux processus physiologiques, intégrant ainsi l’historique des dépenses énergétiques diverses face aux gains acquis via l’alimentation. L’analyse de cet indice a notamment permis d’identifier divers effets sur la condition énergétique du poisson : l’espèce, la taille, la saison et la zone géographique. En lien avec l’énergie observée, un modèle du cycle de vie a été paramétré pour les deux espèces dans le golfe de Gascogne, afin de disposer d’un outil intégrateur, exploratoire et prédictif. Il s’agit d’un modèle bioénergétique basé sur la théorie du « Dynamic Energy Budget » (DEB). Ce cadre vise à prédire le cycle de vie d’un organisme, en fonction de forçages environnementaux, en simulant la résultante des différents flux d’énergies qui s’y produisent. Cette approche a notamment permis de souligner le caractère particulièrement structurant des stratégies reproductives sur le cycle bioénergétique annuel des deux espèces.

In this paper, we present two mathematical models related to different aspects and scales of cancer growth. The first model is a stochastic spatiotemporal model of both a synthetic gene regulatory network (the example of a three-gene repressilator is given) and an actual gene regulatory network, the NF- $$\upkappa $$ B pathway. The second model is a force-based individual-based model of the development of a solid avascular tumour with specific application to tumour cords, i.e. a mass of cancer cells growing around a central blood vessel. In each case, we compare our computational simulation results with experimental data. In the final discussion section, we outline how to take the work forward through the development of a multiscale model focussed at the cell level. This would incorporate key intracellular signalling pathways associated with cancer within each cell (e.g. p53–Mdm2, NF- $$\upkappa $$ B) and through the use of high-performance computing be capable of simulating up to $$10^9$$ cells, i.e. the tissue scale. In this way, mathematical models at multiple scales would be combined to formulate a multiscale computational model.

International audience; European sturgeon (Acipenser sturio) is an anadromous fish that breeds in rivers and which was previously found on most coasts of Europe. The last population of this species, nowadays listed as critically endangered, is reproducing in the Garonne basin near Bordeaux, south-west of France. In order to avoid extinction, the applied strategy since 1985 has been to release young fish into natural environment. These young individuals resulted from the assisted reproduction of wild and/or captive mature individuals. Recently recorded data in the Garonne basin show that in some sectors, where juveniles are likely to growth, summer temperatures have reached very high levels and water column has been hypoxic. Therefore, the combined influence of these factors on the young developmental stages needs to be assessed. The main goal of our project is to provide key information for improving the management of young fish release, especially age at release and release sites that maximize the fish survival. In this purpose, we will first calibrate a standard DEB model, based on the large dataset provided by the long term ex-situ stock breeding in our research institute. This model will firstly be used to evaluate the effect of temperature and oxygen on the survival rate of the first developmental stages. Other aspects of the life cycle will also be investigated, such as the link between maturity and the migration dynamics of the species and the impact of environmental conditions on eggs quality. The last part of our project will consist in the implementation of the standard DEB model within a pre-existing Individual Based Model (IBM) of the sturgeon population dynamics in the Garonne basin. This methodology will allow us to identify which individual traits are determinant in order to maximize the reinforcement of the sturgeon population in this basin.

The dynamics of coevolution is a spatio-temporal process that cannot be understood by mean field approximations, where populations are considered well mixed and interactions are random. This intrinsic characteristic makes comprehensive empirical studies difficult and computer simulations can help to understand the interplay between the many components of the interactions. Here we created an individual-based model to study the coevolution of sexually reproducing populations of prey and predators that engage in an arms race. The phenotype interface of the interaction is a defensive trait for the prey and a counter-defensive one for the predator, both having costs that decrease reproduction chances. The simulations captured several features of natural systems, such as oscillations of the phenotypes levels and abundances. More importantly, the simulations show that local depletion of prey by predators with high levels of counter-defenses followed by recolonization by less defensive prey is a key mechanism that regulates the arms race and the spatio-temporal distribution of phenotypes, creating mismatches similar to those observed in natural systems FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQ COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPES Fechado

Successful exotic plant invasions are likely to be caused by multiple, non-mutually exclusive mechanisms, and it is exceptionally difficult to weight the relative importance of these mechanisms identified in different experiments. To this end we used individual-based models to explore how integrating empirical results from experiments might help to elucidate the relative importance of seed origin, biogeographic differences in competitive outcomes, and disturbance in exotic plant invasion. We integrated results from (1) competition experiments between Centaurea solstitialis derived from populations in the non-native range (California), the native range (Spain), and co-occurring native species from both ranges, (2) seed production by Centaurea plants from the different ranges grown in a common-garden environment, and (3) responses to disturbance experiments with plants from different native and non-native ranges. Californian C. solstitialis reached slightly higher abundances than its Spanish counterparts in every scenario, mainly due to higher seed production of Californians than their Spanish conspecifics, indicating the potential importance of evolutionary changes in the non-native range. In the absence of disturbance, grass species native to Europe showed stronger competitive effects on C. solstitialis than grass species native to North America, suggesting that release from competition in the native range may have some explanatory power for successful C. solstitialis invasion. However, the intensity of competition depended on the disturbance regime used in models. When intense disturbance was incorporated into the model, C. solstitialis was favored, with plants from Californian seed sources reaching higher densities than plants from Spanish seed sources. Our results are consistent with the idea that disproportional positive responses to disturbance in California, relative to those in the invader's native range of Spain, may be an important factor in the dominance of C. solstitialis in its non-native ranges. It is not clear why disturbance would have more beneficial effects on the invader in its non-native range, but the powerful effects of disturbance appear to interact in subtle ways with biogeographic differences in evolutionary trends, competitive intensities, life histories, and reproductive rates., DM was funded by the Spanish Micinn (2008-0662), by the Portuguese FCT (PCT/BIA-PLA/3389/2012 and IF-00066-2013), and by the European Commission (FP7-PEOPLE-MC-CIG-321909); FCT is partially funded by the EU via QREN, COMPETE and FEDER. SX thanks the State Key Program of the National Natural Science of China (31230014, 41430749), the Program for New Century Excellent Talents in University (NCET-13-0265), the Central University Special Fund (lzujbky-2014-k09, lzujbky-2014-200), the National Key Technology R&D Program (No. 2014BAC05B02), and the National Natural Science Foundation of China (31470492).

Three new emergy computational methods are developed with identical outcomes to substantiate and in some cases improve the conventional emergy algebra, particularly with regard to the computations associated with system cycling. The power series, the algebraic method, and the individual-based methods are derived and presented by example. Considering energy flow and its accumulation from an individual quanta or energy particle perspective, the discrete individual-based approach that we present is constructed from a single, reasonably simple, agent-based rule of interaction. As such, emergy calculations are the result of a simulated agent-based method where discrete packets of available energy are labeled and tracked in time as they flow through system processes. To quantify energy memory, each particle has a transformity attribute derived from process inefficiencies. This agent- (or individual-) based method provides a way to compute emergy for complex multiple input, output, or even cycling systems, without assuming additional rules. We compare the outcomes from the power series, the algebraic, and the agent-based methods with the current algebra rules of conventional emergy computation. We also point out that the conventional emergy algebra, the power series, the algebraic, and the individual-based methods all need additional research and corresponding reconciliation with regard to the emergy of by-products.

The functional-trait approach to communities focuses on the distribution of traits and on their variations in communities along environmental gradients. We devised a pattern-oriented demarche to predict specific leaf area (SLA) distribution in three plant communities located along an environmental gradient governed by soil fertility and nutrient stress in subalpine gypsic dolines. An individual-based model incorporating physiological mechanisms simulated the growth of thirty functional groups varying in leaf traits (SLA and correlated leaf life-span) and nitrogen (N) stress tolerance which competed with their neighbours for access to light and nitrogen. The SLAs of these groups encompassed the range of SLAs measured in the sites. Leaf traits governed the daily temperature-dependent processes involved in capturing resources (N and light), biomass synthesis and loss, and the value of the parameter Nc governed the decrease in growth rate of organisms according to a decline in N supply. Biomass drove the competitive ability of each plant in its neighbourhood. A soil sub-model described the amount of available nitrogen in the soil. Simulations yielded performances of functional groups according to the availability of nitrogen in the soil. An integration function, which simulated the effects of the dominance process according to the performances of the groups, yielded the frequency distribution of the groups at the community scale. The SLAs patterns were deduced from this distribution. Comparison of simulated and measured distribution of SLA frequency (Kendall tests) showed the model’s ability to reproduce realistically SLA distributions along a nutrient gradient; measured SLA community patterns at lower, medium and higher fertility levels matched simulated SLA distribution with respectively 5 to 30, 82, and 154 kg N ha−1 year−1. These results demonstrate the efficacy of a strategy based on a pattern-oriented approach and the use of functional traits and trade-offs to predict the distributions of traits and their variations in communities along an environmental gradient.

Harmful algal blooms are a recurrent, expensive and at times fatal problem plaguing the Philippines. In particular, Sorsogon Bay in the Bicol region has experienced prolonged shellfish bans due to blooms by the Paralytic Shellfish Poisoning causative species Pyrodinium bahamense var. compressum (Pbc). In order to help explore and understand the population dynamics of Pbc in Sorsogon Bay in relation to environmental factors, an individual-based model has been developed. This model accounts for key life history processes (reproduction, mortality, encystment, excystment) in a spatially-explicit setting. Vegetative cells and resting cysts are separately represented. Movement is due to advection rates from a 3D hydrodynamic model, as well as sinking rates. Asexual reproduction (population growth) occurs in response to light, temperature, salinity and nutrient conditions where the cells are spatially situated. Encystment and excystment processes are also spatially-explicit based on intrinsic factors, and environmental factors. Grazing effects on blooms are also being explored in the model. Results from field studies in the past years indicate that Pbc blooms develop a few months after the onset of rains, relatively lower temperature, and stratification of the water column. Pronounced blooms are observed at a particular time of the year and in certain areas of the Bay. Bloom formation patterns in the model are compared with these field results. This model will be used to further investigate the conditions leading to blooms and their decline, specifically the roles of transport, stratification, nutrients, cyst dynamics, and grazing on Pbc blooms in Sorsogon Bay.

International audience; Limited empirical studies have elucidated the daily egg production and associated reproductive processes of egg bearing copepod. Herein, we present an individual-based model which constitutes a realistic representation of the reproduction in egg bearing copepods. The model has been parameterized using an extensive set of experimental data obtained from the literature and from the laboratory and field experiments on the estuarine copepod Eurytemora affinis. The proposed model takes into account the adult female longevity, the clutch size and interclutch duration, which is a function of egg maturation time and latency time required by the female after egg hatching to produce a new clutch. The embryonic development time and hatching success are also taken into account. The effect of temperature on the means and variances of above-mentioned reproductive parameters has been also incorporated. A multi agent system based generic platform "Mobidyc" has been used to generate and calibrate the model. The model demonstrates the reproductive parameters of females of E. affinis which is validated through individual based experiments. Temperature specific simulations provide a dynamical explanation of temperature effect on the cumulative egg production. The daily survival principally affects the number of clutches produced per female during its life span. The results obtained in the present study by combining temperature and survival effects reveal the relatively greater importance of the first factor on the daily egg production of egg-carrying copepods. The present model is generic and hence easily applicable to other animals with comparable reproductive strategy.

We carried out simulations of various scenarios for bioterrorist attacks using smallpox occurring in a virtual area set up on the basis of the census of Okayama-city, Japan, which predict the effect of control strategies against bioterrorism and the loss scale. On simulating a smallpox epidemic, we followed the method of the Individual Based Model stochastically, which can treat the population in the virtual area as individuals. Individuals have personal information, behavior patterns, and interactions among social groups. We took into consideration the influence of residual immunity due to past vaccination. We considered Traced Vaccination (TV) and Mass Vaccination (MV) strategies against bioterrorism. We investigated the effect of TV and MV strategies on the suppression of smallpox epidemics. Consequently, the TV strategy was found to have higher effectiveness than the MV strategy.

International audience; In this paper we address the problem of modelling fish population movements. We first consider a description of movements at the level of individuals. An individual-based model is formulated as a biased random walk model in which the velocity of each fish has both a deterministic and a stochastic component. These components are function of a habitat suitability index, $h$, and its spatial gradient $\gh$. We derive an advection-diffusion partial differential equation which approximates this individual-based model. The approximation process enables us to obtain a mechanistic representation of the advection and diffusion coefficients which improves the heuristic approaches of former studies. Advection and diffusion are linked and exhibit antagonistic behaviors: strong advection goes with weak diffusion leading to a directed movement of fish. On the contrary weak advection goes with strong diffusion corresponding to a searching behavior. Simulations are conducted for both models which are compared by computing spatial statistics. It is shown that the partial differential equation model is a good approximation to the individual-based model.

One hypothesis about the origins and evolution of coordinated animal movements is that they may serve as a defensive mechanism against predation. Earlier studies of the possible evolution of coordinated movement in prey concentrated on predators with simple attack tactics. Numerous studies, however, suggest that to overcome the apparent defensive mechanisms which grouping and coordinated movement may provide to prey, predators in nature appear to use elaborate target selection and pursuit/hunting tactics. We here study predators that use composite tactics, (a) predators that in successive attacks based on probability choose one of several simple attack tactics, (b) predators that first disperse prey and then pick off isolated individuals. We develop an individual based model of a group of prey that is attacked by a solitary predator agent. By using genetic algorithms, we enable the predator agent to adapt (a) the probability that a specific tactic will be selected in the next attack, (b) the distance at which it stops dispersing the prey and the radius within which it searches for the most isolated prey. With a direct competition of the evolved predator agents we examine which is the better tactic against a group of prey moving in a polarized cohesive manner in three different settings. Our results suggest that, (a) a delayed response is an efficient advanced prey defence tactic, (b) predator confusion plays an important role in the evolution of composite tactics, and (c) when confusion is at play, the dispersing predator is a much better hunter, capable of at least partially diminishing the effectiveness of the prey's delayed response. (C) 2015 Elsevier B.V. All rights reserved.

Plasmids drive genomic diversity in bacteria via horizontal gene transfer [1, 2]; nevertheless, explaining their survival in bacterial populations is challenging [3]. Theory predicts that irrespective of their net fitness effects, plasmids should be lost: when parasitic (costs outweigh benefits), plasmids should decline due to purifying selection [4-6], yet under mutualism (benefits outweigh costs), selection favors the capture of beneficial accessory genes by the chromosome and loss of the costly plasmid backbone [4]. While compensatory evolution can enhance plasmid stability within populations [7-15], the propensity for this to occur across the parasitism-mutualism continuum is unknown. We experimentally evolved Pseudomonas fluorescens and its mercury resistance mega-plasmid, pQBR103 [16], across an environment-mediated parasitism-mutualism continuum. Compensatory evolution stabilized plasmids by rapidly ameliorating the cost of plasmid carriage in all environments. Genomic analysis revealed that, in both parasitic and mutualistic treatments, evolution repeatedly targeted the gacA/gacS bacterial two-component global regulatory system while leaving the plasmid sequence intact. Deletion of either gacA or gacS was sufficient to completely ameliorate the cost of plasmid carriage. Mutation of gacA/gacS downregulated the expression of ∼17% of chromosomal and plasmid genes and appears to have relieved the translational demand imposed by the plasmid. Chromosomal capture of mercury resistance accompanied by plasmid loss occurred throughout the experiment but very rarely invaded to high frequency, suggesting that rapid compensatory evolution can limit this process. Compensatory evolution can explain the widespread occurrence of plasmids and allows bacteria to retain horizontally acquired plasmids even in environments where their accessory genes are not immediately useful.

Climate induced species range shifts might create novel interactions among species that may outweigh direct climatic effects. In an agricultural context, climate change might alter the intensity of competition or facilitation interactions among pests with, potentially, negative consequences on the levels of damage to crop. This could threaten the productivity of agricultural systems and have negative impacts on food security, but has yet been poorly considered in studies. In this contribution, we constructed and evaluated process-based species distribution models for three invasive potato pests in the Tropical Andean Region. These three species have been found to co-occur and interact within the same potato tuber, causing different levels of damage to crop. Our models allowed us to predict the current and future distribution of the species and therefore, to assess how damage to crop might change in the future due to novel interactions. In general, our study revealed the main challenges related to distribution modeling of invasive pests in highly heterogeneous regions. It yielded different results for the three species, both in terms of accuracy and distribution, with one species surviving best at lower altitudes and the other two performing better at higher altitudes. As to future distributions our results suggested that the three species will show different responses to climate change, with one of them expanding to higher altitudes, another contracting its range and the other shifting its distribution to higher altitudes. These changes will result in novel areas of co-occurrence and hence, interactions of the pests, which will cause different levels of damage to crop. Combining population dynamics and species distribution models that incorporate interspecific trade-off relationships in different environments revealed a powerful approach to provide predictions about the response of an assemblage of interacting species to future environmental changes and their impact on process rates.

Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers.

We integrated field and laboratory data with modeling to determine the extent to which the temporal patterns in population abundance of a copepod species as observed at sea may be explained by differences in production and mortality rates due to diet. A Lagrangian individual-based model utilizing birth and mortality rates whose values and variance were derived from the effects of dietary composition was implemented to simulate the growth of the multi-staged population of Temora stylifera. The four diets considered were represented by unialgal cultures of the dinoflagellate Prorocentrum minimum or the diatom Thalassiosira rotula, a mixture of the two species, and natural particle assemblages

We consider a continuous time stochastic individual based model for a population structured only by an inherited vector trait and with logistic interactions. We consider its limit in a context from adaptive dynamics: the population is large, the mutations are rare and we view the process in the timescale of mutations. Using averaging techniques due to Kurtz (1992), we give a new proof of the convergence of the individual based model to the trait substitution sequence of Metz et al. (1992) first worked out by Dieckman and Law (1996) and rigorously proved by Champagnat (2006): rigging the model such that "invasion implies substitution", we obtain in the limit a process that jumps from one population equilibrium to another when mutations occur and invade the population., Comment: 23 pages

In this paper we extend PALPS, a process calculus proposed for the spatially-explicit, individual-based modeling of ecological systems, with a synchronous parallel operator. The semantics of the resulting calculus, S-PALPS, is defined at the level of populations as opposed to the level of individuals as was the case with PALPS, thus, allowing a considerable reduction in a system’s state space. Furthermore, we provide a translation of the calculus into the model checker PRISM for simulation and analysis. We apply our framework to model and study the population dynamics of the Eleonora’s falcon in the Mediterranean sea. © Springer International Publishing Switzerland 2014. 8687 424 441 Cited By :4

A simple “first generation” multi-scale computational model of the formation of activated sludge flocs at micro-scale and reactor performance at macro-scale is proposed. The model couples mass balances for substrates and biomass at reactor scale with an individual-based approach for the floc morphology, shape and micro-colony development. Among the novel model processes included are the group attachment/detachment of micro-flocs to the core structure and the clustering of nitrifiers. Simulation results qualitatively describe the formation of micro-colonies of ammonia and nitrite oxidizers and the extracellular polymeric substance produced by heterotrophic microorganisms, as typically observed in fluorescence in situ hybridization images. These results are the first step towards realistic multi-scale multispecies models of the activated sludge wastewater treatment systems and a generic modelling strategy that could be extended to other engineered biological systems.

International audience; In this paper, we present a two-species Vicsek model, that describes alignment interactions of self-propelled particles which can either move or not. The model consists in two populations with distinct Vicsek dynamics that interact only via the passage of the particles from one population to the other. The derivation of a macroscopic description of this model is performed using the methodology used for the Vicsek model: we find out a regime where alignment in the whole population occurs. We obtain a new macroscopic model for the densities of each populations and the common mean direction of the particles. The treatment of the non-conservativity of the interactions requires a detail study of the linearised interaction operator.

In this paper, we present a two-species Vicsek model, that describes alignment interactions of self-propelled particles which can either move or not. The model consists in two populations with distinct Vicsek dynamics that interact only via the passage of the particles from one population to the other. The derivation of a macroscopic description of this model is performed using the methodology used for the Vicsek model: we find out a regime where alignment in the whole population occurs. We obtain a new macroscopic model for the densities of each populations and the common mean direction of the particles. The treatment of the non-conservativity of the interactions requires a detail study of the linearised interaction operator.

Special issue Egg Production Methods in Marine Fisheries.-- 10 pages, 7 figures, 1 table, Small pelagic fish populations exhibit reproductive strategies resulting from past natural selection pressure, by which certain traits become more or less common in a population, allowing them to adapt and become better suited to certain habitats. One such adaptation is the buoyancy of eggs, which is observed as density changes during development. This is an important issue in fisheries and modeling science, as it affects the vertical distribution of eggs and, therefore, egg transport. Recently, individual-based models for anchovies in the Mediterranean have focused on developing adequate biological algorithms to simulate realistic spatial variations of eggs and larvae. Some models that include movements of particles according to Stokes’ law also assume a constant value of egg density during egg development. However, field observations show differences in the vertical distribution of eggs when egg density during development is considered. We address the problem of egg density and its vertical distribution within a biological context. In Mediterranean waters, the incubation time for anchovy eggs during peak spawning is approximately 48–70 h; during these first hours, egg density has an influence on the horizontal and vertical trajectories of eggs, as well as their routes and hatching zones. In this study, we introduce an algorithm describing the egg density of European anchovy eggs throughout development. Egg density measurements were carried out in a density gradient column (DGC). We fitted a polynomial model that estimated egg density, as a function of time from fertilization and that was dependent on temperature. Simulations to study the vertical transport of eggs in the Mediterranean were carried out using ICHTHYOP/MARS3D. The vertical distribution of pelagic eggs was determined by a set of interacting biological and physical parameters related to eggs (density, diameter) and ambient seawater (density, viscosity, turbulence), respectively. The egg buoyancy model introduced here was validated and will provide insight for the design of anchovy egg surveys, as the vertical position of the eggs in the water column during development can be inferred by the hydrographic structure of seawater, This research was conducted within the European project SARDONE (FP6 – 44294). Egg samples were obtained from the MPOCAT-DEPM surveys financed by Generalitat de Catalunya. A. Ospina-Alvarez benefited from a PhD grant of the JAE program (CSIC). We are indebted with AZTI-Tecnalia for providing us with the Density Gradient Column used to conduct our experiments. Thanks to Anne Elizabeth Mohan for proofreading the English. We are grateful to P. Garreau and A. Nicolle for their support with MARS-3D hydrodynamic model outputs, as well as to P. Verley for his assistance in ICHTHYOP code. Finally, the authors gratefully acknowledge the assistance of the captain and crew of the RV Garcia del Cid for their help during the cruise

International audience; Individual Based Models are emergent modeling approaches that are developed on the behavior of interacting individuals to study ecosystems properties. Their relevance resides in the validity of the interaction rules between individuals defined in the model. Competitive interactions between plant individuals can be implemented from the combination of four main attributes: (i) the zone of interaction of the target plant, (ii) the intensity of competition, (iii) the effect of competition, and (iv) the target plant response. This study aims at determining the effects of the method used for modeling competition on the performance and individual architecture of two species. We simulated the growth of a guerilla and of a phalanx species either in monoculture or in mixture using 61 methods for modeling competition derived from the published literature and implemented in an Individual Based Model. We showed that (i) the performance and individual architecture of the two species varies with the modeling method, (ii) the effect of the modeling method on the model outputs depends on the species and on the assemblage considered. We subsequently emphasized the importance of accurately calibrating models in particular with experimental data. We finally proposed basic rules supported by literature to evaluate the relevance of the different methods tested.

The modelling of contact processes between hosts is of key importance in epidemiology. Current studies have mainly focused on networks with stationary structures, although we know these structures to be dynamic with continuous appearance and disappearance of links over time. In the case of moving individuals, the contact network cannot be established. Individual-based models (IBMs) can simulate the individual behaviours involved in the contact process. However, with very large populations, they can be hard to simulate and study due to the computational costs. We use the moment approximation (MA) method to approximate a stochastic IBM with an aggregated deterministic model. We illustrate the method with an application in animal epidemiology: the spread of the highly pathogenic virus H5N1 of avian influenza in a poultry flock. The MA method is explained in a didactic way so that it can be reused and extended. We compare the simulation results of three models: 1. an IBM, 2. a MA, and 3. a mean-field (MF). The results show a close agreement between the MA model and the IBM. They highlight the importance for the models to capture the displacement behaviours and the contact processes in the study of disease spread. We also illustrate an original way of using different models of the same system to learn more about the system itself, and about the representation we build of it.

Experimental ecosystems such as mesocosms have been developed to improve the ecological relevance of ecotoxicity test. However, in mesocosm studies, the number of replicates is limited by practical and financial constraints. In addition, high levels of biological organization are characterized by a high variability of descriptive variables. This variability and the poor number of replicates have been recognized as a major drawback for detecting significant effects of chemicals in mesocosm studies. In this context, a tool able to predict precisely control mesocosms outputs, to which endpoints in mesocosms exposed to chemicals could be compared should constitute a substantial improvement. We evaluated here a solution which consists in stochastic modelling of the control fish populations to assess the probabilistic distributions of population endpoints. An individual-based approach was selected, because it generates realistic fish length distributions and accounts for both individual and environmental sources of variability. This strategy was applied to mosquitofish (Gambusia holbrooki) populations monitored in lentic mesocosms. We chose the number of founders as a so-called "stressor" because subsequent consequences at the population level could be expected. Using this strategy, we were able to detect more significant and biologically relevant perturbations than using classical methods. We conclude that designing an individual-based model is very promising for improving mesocosm data analysis. This methodology is currently being applied to ecotoxicological issues.

29th Conference of the French-Speaking-Society-for-Theoretical-Biology, St Flour, FRANCE, jun4-17, 2009; International audience; Dusky groupers (Epinephelus marginatus) are characterized by a complex sex allocation strategies and overexploitation of bigger individuals. We developed an individual based model to investigate the long-term effects of density dependence on grouper population dynamics and to analyze the variabilities of extinction probabilities as a result of interacting mortalities at different life stages. We conduct several simulations with different forms of sex allocation functions and different combinations of mortality rates. The model was parametrized using data on dusky grouper populations from the literature. The most important insights produced by this simulation study are that density dependence of sex allocation is an evolutionarily stable strategy, increases the population biomass, mitigates the effect of the removal of large male and indicates a need for protection of females and flexible stages.

This PhD thesis is devoted to mathematical modelling of haematopoiesis and blood diseases. We investigate several models, which deal with different and complementary aspects of haematopoiesis.The first part of the thesis concerns a multi-scale model of erythropoiesis where intracellular regulatory networks, which determine cell choice between self-renewal, differentiation and apoptosis, are coupled with dynamics of cell populations. Using experimental data on anemia in mice, we evaluate the roles of different feedback mechanisms in response to stress situations. At the next stage of modelling, spatial cell distribution in the bone marrow is taken into account, the question which has not been studied before. We describe normal haematopoiesis with a system of reaction-diffusion-convection equations and prove existence of a stationary cell distribution. We then introduce malignant cells into the model. For some parameter values the disease free solution becomes unstable and another one, which corresponds to leukaemia, appears. This leads to the formation of tumour which spreads in the bone marrow as a travelling wave. The speed of its propagation is studied analytically and numerically. Bone marrow cells exchange different signals that regulate cell behaviour. We study, next, an integro-differential equation which describes cell communication and prove the existence of travelling wave solutions using topological degree and the Leray-Schauder method. Individual based approach is used to study distribution of different cell types in the bone marrow. Finally, we investigate a Physiologically Based Pharmacokinetics-Pharmacodynamics model of leukaemia treatment with AraC drug. AraC acts as chemotherapy, inducing apoptosis of all proliferating cells, normal and malignant. Pharmacokinetics provides the evolution of intracellular AraC. This, in turn, determines cell population dynamics and, consequently, efficacy of treatment with different protocols., Cette thèse est consacrée à la modélisation mathématique de l'hématopoïèse et des maladies sanguines. Plusieurs modèles traitant d'aspects différents et complémentaires de l'hématopoïèse y sont étudiés.Tout d'abord, un modèle multi-échelle de l'érythropoïèse est analysé, dans lequel sont décrits à la fois le réseau intracellulaire, qui détermine le comportement individuel des cellules, et la dynamique des populations de cellules. En utilisant des données expérimentales sur les souris, nous évaluons les rôles des divers mécanismes de retro-contrôle en réponse aux situations de stress.Ensuite, nous tenons compte de la distribution spatiale des cellules dans la moelle osseuse, question qui n'avait pas été étudiée auparavant. Nous décrivons l'hématopoïèse normale à l'aide d'un système d'équations de réaction-diffusion-convection et nous démontrons l'existence d'une distribution stationnaire des cellules. Puis, nous introduisons dans le modèle les cellules malignes. Pour certaines valeurs des paramètres, la solution "disease-free" devient instable et une autre solution, qui correspond à la leucémie, apparaît. Cela mène à la formation d'une tumeur qui se propage dans la moelle osseuse comme une onde progressive. La vitesse de cette propagation est étudiée analytiquement et numériquement. Les cellules de la moelle osseuse échangent des signaux qui régulent le comportement cellulaire. Nous étudions ensuite une équation integro-différentielle qui décrit la communication cellulaire et nous prouvons l'existence d'une solution du type onde progressive en utilisant la théorie du degré topologique et la méthode de Leray et Schauder. L'approche multi-agent est utilisée afin d'étudier la distribution des différents types de cellules dans la moelle osseuse.Finalement, nous étudions un modèle de type "Physiologically Based Pharmacokinetics-Pharmacodynamics" du traitement de la leucémie par l'AraC. L'AraC agit comme chimiothérapie et induit l'apoptose de toutes les cellules proliférantes, saines et malignes. La pharmacocinétique donne accès à la concentration intracellulaire d'AraC. Cette dernière, à son tour, détermine la dynamique des populations cellulaires et, par conséquent, l'efficacité de différents protocoles de traitement.

Eastern boundaries upwelling systems are very productive and sustain the largest fisheries in the world. Biomass in these systems is dominated by small pelagic fish, mainly sardine and anchovy species. Their population dynamics displays a very high abundance variability related to the upwelling physical variability. Understanding the linkage between the environmental fluctuations and the small pelagic fish recruitment in upwelling systems is a key issue for fisheries sciences. In this context, an individual-based model (IBM) approach is proposed to study the early life history of small pelagic fish. Hydrodynamics simulations are used as input in the IBM to represent the environmental conditions experienced by fish eggs and larvae. The results give information about ichthyoplankton survival rates as a function of spawning date and area. The effects of lethal temperature, egg buoyancy and vertical larval migration are also assessed. Finally, an evolutionary IBM was also developed in order to explore the hydrodynamic selective constraints that may influence the spatio-temporal spawning patterns, in the framework of a natal homing hypothesis. For a comparative purpose, these methods are applied to both the Humboldt current system (HCS), which sustains the world largest anchovy stock, and to the Canary current system (CCS), where primary production is higher. The comparison suggests different seasons for optimal ichthyoplankton retention over the shelf and food abundance in the CCS. In contrast, optimal retention and food abundance occur at the same time in the HCS. This could explain why the HCS sustains the largest small pelagic fish stock., Les écosystèmes d'upwelling de bord est des océans sont des zones très productives et soutiennent les pêches les plus abondantes du monde. Les petits poissons pélagiques y sont dominants en biomasse, principalement des espèces de sardines et anchois, dont la dynamique des populations est liée à la très forte variabilité physique de l'upwelling. La compréhension des mécanismes liant les fluctuations environnementales au recrutement de ces espèces est un des défis majeurs de l'halieutique dans ces régions. Dans le cadre de cette problématique, il est proposé ici une approche de modélisation individu-centrée des premiers stades de vie des petits pélagiques. L'évolution des individus dans leur environnement est étudiée grâce au couplage avec un modèle hydrodynamique. Les résultats obtenus renseignent sur le taux de survie de l'ichthyoplancton en fonction des lieux et dates de ponte. L'impact de la migration verticale des larves est également évalué. Un modèle individu-centré « évolutionnaire » a également été développé pour explorer les contraintes sélectives façonnant la distribution spatio-temporelle de la ponte. Dans une optique comparative, cette méthode est appliquée à la fois dans le courant de Humboldt, qui abrite le plus grand stock d'anchois au monde, et dans celui des Canaries, ou la production primaire est la plus forte. La comparaison suggère un antagonisme entre l'optimisation de la rétention de l'ichthyoplancton sur le plateau continental et l'optimisation de la nourriture disponible dans le courant des Canaries. Au contraire, dans le Humboldt une bonne adéquation entre ces deux contraintes pourrait être responsable du plus grand stock de petits pélagiques.