Anmina Murielle Djiguemde

Dimitri Dubois

Mabel Tidball

Alexandre Sauquet

Murielle Djiguemde

Dynamic games applied to common resources: modeling and experimentation

come   L'archive ouverte pluridisciplinaire

Objectives

Study the exploitation behavior of a renewable groundwater table by 2 identical and symmetrical farmers ⇒ optimal control and game the continuous time problem :

max w i (t) ∞ 0 e -rt     aw i (t) - b 2 w i (t) 2 Gross profit - Unitary cost c t (H(t)) w i (t) Total cost     dt (1) st        Ḣ (t) = R -αw i (t) : the optimal control Ḣ (t) = R -α w i (t) : the game w i (t) ≥ 0 H(t) ≥ 0 H(0) = H 0 ,
max w i n ∞ n=0 (1 -rτ ) n β n aw i n - b 2 w 2 i n -c n (H n )w i n τ (2) st        H n+1 = H n + τ (R -αw i n ) : the optimal control H n+1 = H n + τ (R -α w i n ) :

  Clarify some ambiguities between discrete and continuous time, and the time horizon chosen for lab experiments What type of behavior will the experimental subjects exhibit : feedback, myopic, open-loop or social optimum ? Continuous time can be approched by discrete time ⇒ confront theory with Rubio & Casino (2003) ⇒ continuous time, infinite horizon Lab experiment : Janssen & al. (2010) ⇒ spatial aspect Theoretical with lab experiment : Herr & al. (1997) ⇒ discrete time, finite horizon Oprea & al. (2014) ⇒ compares continuous and discrete time Tasneem & al. (2017) ⇒ continuous time, infinite horizon MD, DD, MT and AS (ISDG

  and H 0 given

F-

  The game : feedback, myopic, open-loop and social optimum Model the discrete time problem :

  the game w i (t) ≥ 0 H(t) ≥ 0 H(0) = H 0 , and H 0 given Continuous & discrete time : availabilty of all formulas for the optimal control and the game

MD, DD, MT and AS (ISDG) Dynamic games and experimentation July 2018

Model

Calibration : a = 2.5; b = 1.8; α = 1; R = 0.56; c 0 = 2; c 1 = 0.1; r = 0.005; H 0 = 15 The unitary cost is such that :


Keywords: Fertilisation, manure management enteric fermentation by ruminants, rice fields CO 2 : Respiration soil plant animal, fermentation processes

Agriculture acounts for : 84% of N 2 O emitted in France 80% of CH 4 3% of CO 2 21,2% of GHG in France French breeding accounts for 10% of GHG Contribution of agriculture to global GHG emissions in France A.-I.

The greenhouse effect is a natural phenomenon and has positive impact on the Earth's surface that would be -18°C otherwise Half of incoming solar radiation passes through the atmosphere then is absorbed by the Earth's surface and warms it 1/3 is reflected to space by the atmosphere and the Earth, the remaining part is absorbed by the atmosphere To compensate for this incoming energy, the Earth emits infrared radiation (IR) Some gases in the atmosphere called greenhouse gases aborb most of this IR and reemit it in all directions, warming the Earth's surface : This is the greenhouse effect  What is expected ?

• ↗ temperature whatever the scenario  The climate change impacts that could be simulated

•

•

Environmental conditions for grass growth (climate, soil, management)

•

Grassland growth, standing biomass and yield (quantity and digestibility)

A•

  Lifetime and GWP of GHGs • GHG are assigned a global warming potential (GWP)= cumulated radiative forcing (ability to warm the climate system) over a specific time horizon • It is expressed relatively to the GWP of CO 2 (fixed to 1) • It is computed for different time horizons (20-yr, 100-yr or 500-yr), and accounts for the lifetime of each GHG En comparaison des prairies, les grandes cultures sont une source faible ou forte de C selon l'état initial du sol. Le C s'y constitue lentement mais s'y vide rapidement (labour) Les prairies temporaires à rotation rapide sont un modèle comparable Le stockage du C réduit les émissions de CO 2 donc l'implication de l'élevage dans le CC Chez les prairies, le stockage se fait dans le sol, lentement mais en très grande , Tallec, Guix & Soussana GCB 2011  Maintien de la fonction puits de C au cours du temps (2t C ha -1 an -1 )  Le stockage de C est supérieur en gestion extensive (non significatif) sauf en année sèche (2003, 2005) où la tendance s'inverse Bilan de carbone sur 6 années (SOERE-ACBB, Site Laqueuille) PUITS SOURCE INTENSIF : 1 UGB ha -1 210 kg N ha -1 EXTENSIF : 0.5 UGB ha -1 pas de fertilisation Grassland C sequestration is influenced by climate and management A.-I. Graux / Modelling climate change impacts on grasslandsexample of the ModVege model .012 Context and objective • launched during COP21 in December 2015 and supported by almost 150 signatories (countries, regions, international agencies, private sectors and NGOs) • ↗ global soil organic matter stocks by 0.4 % per year as a compensation for the global emissions of GHG by anthropogenic sources The per mille or 4 per 1000 initiative Source: Minasny et al. 2017 A.-I. Graux / Modelling climate change impacts on grasslandsexample of the ModVege model .013 The per mille or 4 per 1000 initiative Sources: https://www.4p1000.org/ https://www.youtube.com/watch?v=AY9YVwJZDvw https://www.youtube.com/watch?v=ORncZnlKOZg A.-I. Graux / Modelling climate change impacts on grasslands journées et les nuits froides ont diminué tandis que les journées et nuits chaudes ont augmenté, la fréquence des vagues de chaleur s'est accentuée Evolution des températures moyennes annuelles en France métropolitaine Le réchauffement du système climatique (continents, océans) est sans équivoque 12 des années de 1995-2006 figurent parmi les plus chaudes depuis 1850, date à laquelle ont commencé les relevés instrumentaux Variabilité s'accompagne de : Une élévation du niveau de la mer et de la réduction du manteau neigeux et des calottes glaciaires Une acidification des océans liée à la dissolution du CO 2 Une baisse graduelle de la circulation thermohaline ('Gulf Stream') Une augmentation des épisodes de fortes pluies dans la plupart des régions Une augmentation de l'activité cyclonique tropicale dans l'Atlantique Nord Climate change is not limited to global warming Source: IPCC 2007 narrative storylines : A1, A2, B1 and B2 to describe the relationships between emissions and their driving forces : the demographic, social, economic, technological, and environmental developments  Scenarios = alternative images of how the future might unfold. All the scenarios based on the same storyline constitute a scenario "family"; The corresponding climate is simulated by different global climate models Very heterogeneous world ; increasing global population ; regionally-oriented economic development ; more fragmented and slower economic growth and technological changes A1B (medium) Global population increases until 2050 then decreases; Very rapid economic growth with rapid introduction of new and more efficient technologies; convergence among regions B1 (optimist) convergent world; global population increases until 2050 then decreases; development of service and information economy and of clean and resource-The expected increase of temperature in 2100 is between +1.

•

  Faster warming in the South of Bretagne and in the Loire Valley • Higher ↗ in summer than in winter, higher summer increase in the Loire Valley and the region Centre Source: Météo-France (2010) influencing factors could we account for with this model? 2. Which impacts could we simulate with this model? Availability of soil ressources (water holding capacity, nutrition index) • Cutting management frequency and intensity (number of cutting events, cutting height) • Grassland type (A, B, C, D)

Net biome productivity (g m -2 ) 2002

Water reserves

What is the assumption about the nature of interactions between fT, fW and fPAR ?

.036

Environmental conditions for grass growth


••

  Huge diversity between the models mimicking the GI tract of the adult (E/S, pH…)  Impossible to compare results from one study to another -Need for harmonization Updated version accepted for publication Nature Protocols Simulated Gastric Fluid of 63:37 Enzymes : Pepsin (268 U/mL) and Lipase (21 U/mL) from Rabbit Gastric Extract 60 min of digestion at pH 51962) Human milk or infant formula (Cavell, 1983) Infant formula (Armand et al., 1996) Similac formula (Armand et al., 1996) SMA formula (Armand et al., 1996) Human milk (Mitchell et al., 2001) Human milk (Omari et al., 2003) Human milk or infant formula (Roman et al., 2007) Pregallia formula (Malagelada ,1976) Meal, adultGastric acidification curve• In vivo data are crucial to set up simulators and be relevant: data needed to adjust parameters)• Flow of enzymes and transit•More expensive than static models • Too « large » to use pure enzymes (gastric lipase) • Few instruments available • No nervous or hormonal control/feedback  Difficult to mimic the complexity of the GI tract in a test tube!!! (no transit, no secretion flows..) Bohn et al. 2017 Crit Rev Food Sci Nutr Dupont et al. 2018 Crit Rev Food Sci Nutr  Standardisation of the experimental conditions • Good reproducibility and repeatability • Low cost, less time consuming • Usefull for screening different foods best model to mimic the upper part of the human GI tract Gnotobiotic animals (« humanized » mice) are of interest to study the effect of food on the microbiota Pigs Piglets Mini-pigs Multi-canulated and catheterized pigs Pretty good model of the upper GI tract Canulas and catheters allow to collect effluent and plasma throughout digestion (kinetics)


Oliver Kaltz

Michael E Hochberg

Brian P Lazzaro

Francis Jiggins

Kate Howell

Darren Obbard

INTRODUCTORY WORDS

This document was written in April 2017, shortly after the publication of the first article of Antoine Rombaut, my first PhD student. This was, to my eyes, a necessary condition to submitting an HDR thesis. Four years after being hired by INRA, the research dynamics I hoped for has now began to bear fruit. This thesis is organized in three main sections. The first one is boring and in French, it closely matches the what is expected by our Ecole Doctorale. The second one contains a description of my work within the broad field of Evolutionary Ecology. The third one is a reflection on the meaning of my efforts with respect to science and society. This, in my view is the bulk of the synthesis and perspective that writing an HDR thesis implies.

It is no common in science writing to use "I" as often as I have in this document. It even feels wrong given the collaborative nature of our activity. In most, if not all, cases, the work presented here was the result of teamwork... "we" carried it out. The opinions, however, are strictly mine, no one else may be held responsible for my mistakes and too candid analyses.

Also, I wanted this HDR experience to be enjoyable both for its few spectators and me. As a consequence, the tone is in many instances a little more familiar than is customary of science writing. I hope freedom of speech won't get in the way of rigor and readability.

-I am impossible to control (as once stated by Nicolas, as he was -wisely -rejecting my application as postdoc in one of his ANR projects). I apologise to all of you who hired me and had to deal with the utter anarchist I am.

-I chose not to develop on friends and family in these pages. However, I must acknowledge the role of the first lab director who ever had to deal with my always-diversifying enthusiasm, my mother Béatrice. Without her patience and trust I would not have raised the thousands of odd animals and plants that populated my teenager's bedroom; I would have never become the experimental biologist I am now. Also, I wish to acknowledge the influence of two men, both left us already. The first one, Pierre Jauffret, an extra-ordinary man in all respects; a man who, hosting me in his hard fought for piece of Amazonian forest, infected me with the research virus in the summer of 2000... It feels his dream took life in my own life. The second, my father Armand, who taught me how to think, analyse and reason. He used to strike me with questions about evolution that 20 years later remain incredibly sharp to the eyes of the professional I have become. He is the one who brought home the book that changed everything "The redqueen-sex and the evolution of human nature" by Matt Ridley.

-Standing on the shoulders of giants. How could a sentence describe better the process of learning science?

I. CV ET AUTRES INFORMATIONS REQUISES (EN FRANÇAIS)

A. Résumé quantitatif TEACHING, MENTORING AND OTHER PROFESSIONAL ACTIVITIES

2005-2017 Mentoring

Supervision and co-supervision of 7 undergraduate and 11 masters students, of which 8 continued with a PhD.

Pour simplifier l'évaluation du dossier, les sections ci-dessous et leur ordre sont identiques à ceux recommandés dans la notice.

Toutes ces informations sont également disponibles dans le document principal en anglais.

Rapport sur les stages et collaborations

Postdoctorats:

2011-2012 Centre de Biologie et Gestion des Populations (CBGP), INRA, Montpellier. Supervision par Maria Navajas.

Dépôt de brevets

2015 Déclaration d'invention relative à Drosophila suzukii.

Direction d'étudiants

Supervision et co-supervision des stages de 9 étudiants de Master 2. Supervision en cours de 2 thèse de doctorat (HDR officielle Flavie Vanlerberghe).

Année Mes travaux se situent aujourd'hui à l'intersection entre science fondamentale1 et enjeux appliqués 2 (Fig. 9, ci-dessous, chapitre II.B.3).

Mon expérience en sciences de l'évolution m'a amené à réfléchir aux conditions nécessaires à la gestion durable de ravageurs de culture, notamment de la mouche envahissante Drosophila suzukii. Dans un premier temps seuls les processus évolutifs ont retenu mon attention. Ainsi, mes premières années à l'INRA sont marquées par le développent d'un projet sur l'évolution de la résistance d'insectes holométaboles au déploiement d'agent de lutte biologique (Postdoctorat de Julie Collet, Financements INRA SPE et Agreenskills).

Mais la découverte d'une possible nouvelle méthode de mitigation des dégâts induits par D. suzukii m'a ouvert les yeux sur les défis économiques et sociétaux de l'agroécologie. Il s'en est suivis la prise de conscience que des objectifs de durabilité ne sont atteignable qu'en intégrant un panel de disciplines scientifiques (écologie, évolution, économie, sociologie) et en prêtant attention aux différentes étapes de l'innovation, de l'idée originelle à la diffusion de la nouvelle solution auprès de son public, les agriculteurs dans notre cas. Pour résumer, le spectre de questions fondamentale pertinente est large, celui des questions appliquées tout autant, mais le temps comme l'argent sont limités. Travailler à l'interface entre connaissance et enjeux sociétaux permettra, je l'espère, d'être utile à la société aujourd'hui comme demain.

b. Discipline scientifique

Mes travaux se situent dans le champ large de l'écologie évolutive (Fig. 1). L'écologie -la science de l'habitat -est essentiellement une question d'interactions entre les organismes et leurs «facteurs» environnants (et facteurs internes, dans le cas des symbiotes). Souvent, ces facteurs sont d'autres organismes vivants. Ensemble, ils forment des communautés [START_REF] Vellend | Conceptual Synthesis in Community Ecology[END_REF]. La complexité intérieure des interactions multi-espèces nécessite de décomposer les réseaux d'interactions en plus petites parties, les modules [START_REF] Bascompte | Simple Trophic Modules For Complex Food Webs[END_REF]. Le plus simple d'entre eux contient 2 espèces. Dans la majorité des projets que j'ai mené, ces deux espèces étaient un hôte et un parasite.

L'interaction interspécifique, sous l'influence de facteurs environnementaux, détermine les phénotypes des espèces focales. Ces phénotypes sont le moteur des dynamiques écologique (i.e. dynamique des populations) et évolutives.

Au sein de ce cadre conceptuel, mes travaux portent sur 3 grands axes: (i) Communautés dans l'espace, (ii) écologie des interactions, (iii) rôle de la métamorphose. Le concept de symbiose est transversal à ces 3 grands axes. J'utilise essentiellement la méthode expérimentale au laboratoire.

(i). Communautés dans l'espace [voir section II.B.1 du document principal]

Les communautés d'organismes sont structurées dans l'espace. Chaque sous-ou métapopulation est liée aux autres par la dispersion et le succès de colonisation [START_REF] Clobert | Causes, mechanisms ad consequences of dispersal[END_REF][START_REF] Ronce | How Does It Feel to Be Like a Rolling Stone? Ten Questions About Dispersal Evolution[END_REF]. Les flux d'individus affectent non seulement les densités de population, mais aussi leur composition puisque les mouvements des animaux dépendent souvent de leur génotype et état physiologique. (e.g. [START_REF] Klaczko | Genetic variation for dispersal by Drosophila pseudoobscura and Drosophila persimilis[END_REF][START_REF] Dieckmann | The evolutionary ecology of dispersal[END_REF][START_REF] Snoeijs | A strong association between immune responsiveness and natal dispersal in a songbird[END_REF]. Ainsi, les flux de gène, qui dépendent en grande partie des taux de dispersion, affectent l'évolution puisque la variation génétique est le carburant de la sélection naturelle. L'étude de déplacement et de la capacité des organismes à s'installer dans de nouvelles localités [START_REF] Marshall | Phenotypeenvironment mismatches reduce connectivity in the sea[END_REF] participe ainsi à la compréhension de la dynamique globale des communautés dans l'espace et le temps [START_REF] Massol | Linking community and ecosystem dynamics through spatial ecology[END_REF].

Les facteurs qui influent sur les taux de dispersion ne sont pas toujours bien compris. On sait que la décision de quitter un site est souvent fonction des conditions externes [START_REF] Bowler | Causes and consequences of animal dispersal strategies: relating individual behaviour to spatial dynamics[END_REF][START_REF] Clobert | Informed dispersal, heterogeneity in animal dispersal syndromes and the dynamics of spatially structured populations[END_REF] et internes [START_REF] Clobert | Causes, mechanisms ad consequences of dispersal[END_REF][START_REF] Goodacre | Microbial modification of host long-distance dispersal capacity[END_REF][START_REF] Suhonen | Activation of the immune system promotes insect dispersal in the wild[END_REF]. Dans le cas des systèmes hôte-parasite, les mouvements parasites sont souvent passifs et déterminés par ceux de leurs hôtes obligés [START_REF] Prugnolle | Population genetics of complex lifecycle parasites: an illustration with trematodes[END_REF]. Il a notamment été suggéré que la dispersion de l'hôte peut être fonction de son état infectieux [START_REF] Heeb | Ectoparasite infestation and sex-biased local recruitment of hosts[END_REF]. Ainsi J'avais étudié en microcosmes la dispersion d'hôtes unicellulaires, des paramécies, infectés par des bactéries (Fellous et al. 2011), ou encore les stratégies de transmission d'un parasite de moustique selon les différentes opportunités qu'offrent les hôtes males et femelle (Fellous and Koella 2009a).

-> Cette ligne de recherche se poursuit maintenant au travers doctorat de Robin Guilhot (commencé en mars 2017). La première partie de son projet porte en effet sur l'acquisition et la transmission de symbiotes microbiens au cours du cycle de vie de mouches D. suzukii et D. melanogaster (voir ci-dessous). Dans ces espèces, l'identité du symbiont reflète l'environnement passé [START_REF] Chandler | Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host-Microbe Model System[END_REF]) et détermine la capacité de la mouche à exploiter les ressources nutritionnelles [START_REF] Storelli | Lactobacillus plantarum Promotes Drosophila Systemic Growth by Modulating Hormonal Signals through TOR-Dependent Nutrient Sensing[END_REF][START_REF] Becher | Yeast, not fruit volatiles mediate Drosophila melanogaster attraction, oviposition and development[END_REF] [START_REF] Atallah | The making of a pest: the evolution of a fruit-penetrating ovipositor in Drosophila suzukii and related species[END_REF]. Ceci est possible grâce à son grand ovipositeur qui permet de percer peau des fruits et de déposer ses oeufs dans la chair de fruits autrement non accessible.

En 2014, alors que nous étudions les interactions entre D. suzukii et D. melanogaster dans le laboratoire en collaboration avec Patricia Gibert (UMR LBBE, Lyon, France), de premiers dommages sur raison imputés à D. suzukii ont été signalés [START_REF] Ioriatti | Drosophila suzukii (Diptera: Drosophilidae) and its Potential Impact to Wine Grapes During Harvest in Two Cool Climate Wine Grape Production Regions[END_REF]. La mouche semblait causer une maladie des fruits, la pourriture acide, qui était normalement causée par D. melanogaster [START_REF] Barata | New Insights into the Ecological Interaction Between Grape Berry Microorganisms and Drosophila Flies During the Development of Sour Rot[END_REF] -Fin du document en français - The broad field of Ecology -the science of habitat -is by essence a matter of interactions between organisms and their surrounding "factors" (and inner factors, in the case of symbionts). Often, these factors are other living organisms. Together they form communities [START_REF] Vellend | Conceptual Synthesis in Community Ecology[END_REF]. The inherent complexity of multi-species interactions call for breaking down networks of interactions into smaller parts, coined modules [START_REF] Bascompte | Simple Trophic Modules For Complex Food Webs[END_REF]. The simplest of them contains 2 species. In the large majority of the work I conducted, these two species were a host and a parasite3 .

II. REPORT ON PAST, CURRENT AND FUTURE RESEARCH

A. One on one in one place

Bi-and tri-partite interactions 4

Mundane event of our daily lives illustrate important aspects of host-parasite interactions.

For example, a running nose, due to fairly avirulent5 virus, readily transforms into a bacterial infection that keeps us coughing for days or weeks. This shows how host infection by a first parasite can facilitate infection by a second one [START_REF] Pedersen | Emphasizing the ecology in parasite community ecology[END_REF]Fenton 2007, Rigaud et al. 2010). How parasites affect each other's traits, and those of the host, determine their epidemiology as well as their evolution. Numerous authors have investigated the influence of multiple infection on virulence evolution (e.g. [START_REF] Brown | Does multiple infection select for raised virulence?[END_REF][START_REF] Literature Alizon | Multiple infections and the evolution of virulence[END_REF]). It appears that the within host dynamics of parasite replication has a large influence on strain dynamics and therefore evolutionary trajectory [START_REF] Mideo | Linking within-and between-host dynamics in the evolutionary epidemiology of infectious diseases[END_REF]. Empirical investigations of parasite-parasite interactions are therefore needed to gain predictive ability on the consequences of multiple infections.

Interactions between coinfecting parasites was one of the topics of my PhD -supervised by Jacob Koella at UPMC, in Paris, and Imperial College London, in Silwood Park. I carried out experiments with 2 parasites of the mosquito Aedes aegypti [START_REF] Christophers | Aëdes aegypti (L.). The Yellow Fever Mosquito. Its Life History, Bionomics and Structure[END_REF], the microsporidium Vavraia culicis [START_REF] Wang | The pathobiology of the mosquito parasite: Vavraia culicis (Weiser)[END_REF] and the gregarine Ascogregarina culicis [START_REF] Chen | The life cycle of Ascogregarina taiwanensis (Apicomplexa:Lecudinidae)[END_REF]. I particularly focused on within host interactions between them.

Focus article 1:

(focus articles illustrate with some detail the main concepts discussed in the manuscript)

Fellous and Koella, 2009. Infectious dose affects the outcome of the within-host competition between parasites. The American Naturalist, (173) E177-84.

In this article we investigated the factors that may affect their transmission. In particular, we manipulated infectious dose6 of both parasites and the amount of resources available to the host. Our results showed that the number of propagules a parasite produces is function of both its own infectious dose and that of its competitor. As infectious dose is expected to increase with prevalence, these results suggest a positive feedback between prevalence and competitive ability. This may lead to the exclusion of one of the competitor, its identity depending on the initial conditions.

Other relevant articles: (article are cited only once, even when they would be relevant to other concepts discussed elsewhere in the manuscript)

Intraspecific genetic diversity

Testing the effect a given species has on another is making the assumption that all individuals from the same species are equivalent. But, all species harbour some degree of (non-neutral) genetic diversity 7 . This diversity has numerous effects on the functioning of communities [START_REF] Bolnick | Why intraspecific trait variation matters in community ecology[END_REF][START_REF] Violle | The return of the variance: intraspecific variability in community ecology[END_REF]). In the case of inter-specific interactions, complexity due to the diverse source of phenotypic variation scales up rapidly. Indeed, numerous articles from the literature on parasitology and mutualism show that phenotypes depend on so-called Genotype-by-Genotype interactions (or G*G interactions) (Lambrechts et al. 2006, Heath and[START_REF] Heath | Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies[END_REF]. These refer to situations where a phenotype depends of the combination of genotypes of each of two species in presence. The phenomenon is reminiscent of the extended phenotype concept advocated by Richard Dawkins [START_REF] Dawkins | The Extended Phenotype[END_REF].

Focus article 2:

Orsucci, Navajas* and Fellous*. 2017. Genotype-specific interactions between parasitic arthropods. Heredity 118:260-265. *shared last authorship

During my third postdoc -with Maria Navajas at CBGP in Montpellier -I studied the interactions between two species of parasitic arthropods, Tetranychus urticae [START_REF] Grbic | The genome of Tetranychus urticae reveals herbivorous pest adaptations[END_REF] and T. evansi [START_REF] Boubou | Recent emergence and worldwide spread of the red tomato spider mite, Tetranychus evansi: genetic variation and multiple cryptic invasions[END_REF]). These phytophagous spider-mites develop on numerous species of plants. T. urticae is native to Europe, whereas T. evansi has recently invaded Africa and Europe [START_REF] Boubou | Recent emergence and worldwide spread of the red tomato spider mite, Tetranychus evansi: genetic variation and multiple cryptic invasions[END_REF][START_REF] Boubou | Test of Colonisation Scenarios Reveals Complex Invasion History of the Red Tomato Spider Mite Tetranychus evansi[END_REF]). These two species meet in crop fields and in the wild were they are sometimes, but rarely, observed on the same plant. Published work shows T. evansi can rapidly outcompete T. urticae on tomato plants (Sarmento et al. 2011a, Sarmento et al. 2011b), which is mirrored by in-natura observations in Kenyan tomato fields (E. Deletré personal communication).

After studying T. urticae host range (Fellous et al. 2014) and at the light of population genetics data [START_REF] Tsagkarakou | Genetic Differentiation in Tetranychus Urticae (Acari: Tetranychidae) from greenhouses in France[END_REF][START_REF] Navajas | Genetic Differentiation in Tetranychus Urticae (Acari: Tetranychidae): polymorphism, host races or sibling species?[END_REF], Sauné et al. 2015), we concluded that single genotypes of this species can infest several plant species. As the European population of T. evansi is also dimorphic [START_REF] Boubou | Recent emergence and worldwide spread of the red tomato spider mite, Tetranychus evansi: genetic variation and multiple cryptic invasions[END_REF], we decided to investigate the combined influence of these two sources of phenotypic variation. We therefore set up an experiment on tomato where the competition between the two T. evansi phylotypes and four T. urticae populations from diverse host plants were tested in a fullfactorial fashion. The work conducted with then Master 2 student Marion Orsucci revealed that the influence each species had on the other depended on the combination of their genotypes. In the conditions of our assay, the two species had little influence on each other. But in several specific cases they facilitated the development of the other mite species, probably through interference with the plant immune system [START_REF] Kant | Intraspecific variation in a generalist herbivore accounts for differential induction and impact of host plant defences[END_REF], Sarmento et al. 2011a). This work was the first one to describe the influence of such G.parasite*G.parasite interaction on parasite multiplication.

Other relevant articles:

Lambrechts, Fellous & Koella, 2006. Coevolutionary interactions between host and parasite genotypes. Trends in Parasitology, [START_REF] Fellous | Combining experimental evolution and field population assays to study the evolution of host range breadth[END_REF] 12-16. Fellous, Duncan, Quillery, Vale & Kaltz, 2012. Genetic influence on parasite spread following arrival of infected carrier. Ecology Letters [START_REF] Duncan | Reverse evolution: Selection against costly resistance in disease-free microcosm populations[END_REF] 186-192.

Variable environments

If genetic identity can vary among members of a same species, numerous other environmental factors, many of them abiotic, can affect their phenotypes. This variation, rather than mere noise, can have large consequences on population dynamics and evolution [START_REF] Stearns | The evolution of life histories[END_REF]. The very structure of environmental variation, and how genotypes respond to these variations 8 , are then key to populations' trajectories [START_REF] Pigliucci | Phenotypic plasticity : beyond nature and nurture[END_REF].

Focus article 3:

Duncan, Fellous & Kaltz, 2011. Temporal variation in temperature determines disease spread and maintenance in Paramecium microcosm populations. Proceedings of the Royal Society Series B, (278) 3412-3420.

During my second postdoc -with Oliver Kaltz at ISEM in Montpellier -I worked with the ciliate host, Paramecium caudatum [START_REF] Wichterman | The biology of Paramecium[END_REF], and its bacterial parasite Holospora undulata [START_REF] Görtz | Life cycle and infectivity of Holospora elegans (Haffkine), a micronucleus-specific symbiont of Paramecium caudatum (Ehrenberg)[END_REF].

Together with postdoc Alison Duncan, now CNRS researcher at ISEM, we studied the influence of environmental variation on the population dynamics and epidemiology of these two species. We used microcoms where individuals reproduced and died freely, which we could monitor by regular sampling. The key feature of this experiment was the comparison of treatments with similar mean temperatures but some were kept in constant conditions while the other alternated between two extreme temperatures. In other word we played with the structure of abiotic environmental variation. The main finding of this study was that variable conditions reduced parasite prevalence compared to variable ones. Besides, parasite extinction in the microcosms was less frequent in constant conditions than when they were exposed to extreme conditions. This made sense at the light of the thermal sensitivity of the two species [START_REF] Fels | Temperature-dependent transmission and latency of Holospora undulata, a micronucleus-specific parasite of the ciliate Paramecium caudatum[END_REF]. More generally, it follows than the frequency of extreme events, such as observed with human-induced climate change, may have effects on communities that add to that of the variation of mean conditions. In practical terms, it also questions the validity of the degreeday metrics for the analysis of organism development and dynamics.

Other relevant articles:

B. Communities in space and time

Concepts and focus articles in this section are described in greater details than in the previous one as they correspond to the projects I currently conduct.

Communities of organisms are usually structured in space. Each sub-or meta-population is linked to the others through dispersal9 [START_REF] Clobert | Causes, mechanisms ad consequences of dispersal[END_REF][START_REF] Ronce | How Does It Feel to Be Like a Rolling Stone? Ten Questions About Dispersal Evolution[END_REF], in combination with colonization events when habitats are short-live or local populations go extinct (e.g. [START_REF] Harrison | Genetic and evolutionary consequences of metapopulation structure[END_REF]Hastings 1996, Mihaljevic 2012). These fluxes of individual not only affect population densities, but also their composition as dispersing immigrants may differ in genotype or condition (e.g. [START_REF] Klaczko | Genetic variation for dispersal by Drosophila pseudoobscura and Drosophila persimilis[END_REF][START_REF] Dieckmann | The evolutionary ecology of dispersal[END_REF][START_REF] Snoeijs | A strong association between immune responsiveness and natal dispersal in a songbird[END_REF]). Gene flow, which largely depends on dispersal rates, affects evolution as genetic variation is the fuel of natural selection. The study of organism displacement and the ability of organisms to settle into new localities [START_REF] Marshall | Phenotypeenvironment mismatches reduce connectivity in the sea[END_REF]) hence participates to the understanding of the global dynamics of communities in space and time [START_REF] Massol | Linking community and ecosystem dynamics through spatial ecology[END_REF]).

Space

The factors that influence dispersal rates are not always well understood. It is often argued that decision to leave a current site is function of surrounding [START_REF] Bowler | Causes and consequences of animal dispersal strategies: relating individual behaviour to spatial dynamics[END_REF]Benton 2005, Clobert et al. 2009) or internal condition [START_REF] Clobert | Causes, mechanisms ad consequences of dispersal[END_REF][START_REF] Goodacre | Microbial modification of host long-distance dispersal capacity[END_REF][START_REF] Suhonen | Activation of the immune system promotes insect dispersal in the wild[END_REF]). In the case of host-parasite systems, parasite movements are often passive and determined by those of their obligate hosts [START_REF] Prugnolle | Population genetics of complex lifecycle parasites: an illustration with trematodes[END_REF]. Host dispersal itself may be function of its infectious status [START_REF] Heeb | Ectoparasite infestation and sex-biased local recruitment of hosts[END_REF].

Focus article 4:

Fellous*, Quillery*, Duncan & Kaltz, 2011. Parasitic infection reduces dispersal of ciliate host. Biology Letters, [START_REF] Fellous | Infectious dose affects the outcome of the within-host competition between parasites[END_REF] 327-329. *Equal authorship With master 2 student Elsa Quillery -now a postdoc in Alnard University, in Sweden -we studied the effect of parasitic infection on host dispersal. We used the system Paramecium caudatum -Holospora undulata (see above) and compared the propensity of infected and uninfected hosts to move between interconnected microcosms. This work revealed greater dispersal of uninfected than infected hosts. It follows that host populations in patches of resources recently colonized are more likely to be free of parasites than long established populations; hence forming refuges possibly maintaining ecological and genetic diversity. Our results further suggest that host may be ahead in the co-evolutionary race with parasites as theory has shown that relative rates of gene flow are key to this process [START_REF] Gandon | Local adaptation and the geometry of host-parasite coevolution[END_REF][START_REF] Gandon | Local adaptation, evolutionary potential and hostparasite coevolution: interactions between migration, mutation, population size and generation time[END_REF].

This line of research now continues through the PhD of Robin Guilhot (started March 2017). The first part of his project indeed focuses on the acquisition and transmission of microbial symbionts along the life cycles of D. suzukii and D. melanogaster flies (see below). In these species, symbiont identity both reflect past environment [START_REF] Chandler | Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host-Microbe Model System[END_REF]) and determines the fly ability to exploit nutritional resources [START_REF] Storelli | Lactobacillus plantarum Promotes Drosophila Systemic Growth by Modulating Hormonal Signals through TOR-Dependent Nutrient Sensing[END_REF][START_REF] Becher | Yeast, not fruit volatiles mediate Drosophila melanogaster attraction, oviposition and development[END_REF]). Robin's work will permit to better understand host jumps by the fruit pest D. suzukii, and, therefore, how infestation of a given crop may spillover onto other neighbouring crops.

The relationship between evolution and range expansion10 is also the topic of an on-going collaboration with Elodie Vercken and Eric Lombaert (UMR ISA, Nice, France). This project, part of the Triptic ANR (a joint project between CBGP and ISA laboratories on Trichogramma parasitoids), also involves postdoc Aline Bertin. By manipulating the spatial structuring of microcosms [START_REF] Morel-Journel | The highs and lows of dispersal: how connectivity and initial population size jointly shape establishment dynamics in discrete landscapes[END_REF], we study the influence of local population dynamics on dispersal and the associated evolution of their phenotype.

Other relevant articles:

Communities and meta-communities

The experimental study of large communities represents a challenge as complexity increases exponentially with species number. But the need to discover generic processes, and the possible emergent properties due to having more than a handful of species [START_REF] Darley | Emergent phenomena and complexity[END_REF], has favoured approaches where species identity is secondary. Indeed, mathematical modelling and the analysis of species networks have permitted major advances in the field (e.g. Thébault and Fontaine 2010). In some cases, however, questions arise that concern specific organisms in given ecosystems. In that case empirical approaches are mandatory. Indeed, even well thought modelling can only provide relevant insight if its assumptions are right. These assumptions, or parameters, rely on empirical data.

Since I started working on fruit-flies at INRA (January 2013), my main species of interest has been Drosophila suzukii [START_REF] Cini | A review of the invasion of Drosophila suzukii in Europe and a draft research agenda for integrated pest management[END_REF]. This close relative of D. melanogaster originates in mainland Asia (China mostly) and has recently invaded North, South America and Europe. It is the only species in its clade to preferentially oviposit in ripe but undamaged fruit [START_REF] Atallah | The making of a pest: the evolution of a fruit-penetrating ovipositor in Drosophila suzukii and related species[END_REF]. This is possible thanks to its large ovipositor that permits sawing through fruit skin and laying eggs in otherwise non-accessible fruit flesh.

In 2014, as we were studying interactions between D. suzukii and D. melanogaster in the lab in a collaboration with Patricia Gibert (UMR LBBE, Lyon, France). Reports of heavy D.

suzukii damages on grape arrived [START_REF] Ioriatti | Drosophila suzukii (Diptera: Drosophilidae) and its Potential Impact to Wine Grapes During Harvest in Two Cool Climate Wine Grape Production Regions[END_REF]. It seemed to cause a fruit disease, sour rot, that was normally caused by D. melanogaster [START_REF] Barata | New Insights into the Ecological Interaction Between Grape Berry Microorganisms and Drosophila Flies During the Development of Sour Rot[END_REF]). However, despite the presence of numerous D. suzukii adults in vineyards and the unusual prevalence of the rot, infected berries collected in the field contained D. melanogaster rather than D. suzukii larvae.

Focus article 5:

Rombaut, Guilhot, Xuéreb, Benoit, Chapuis, Gibert and Fellous. 2017. Invasive Drosophila suzukii facilitates Drosophila melanogaster infestation and sour rot outbreaks in vineyards.

Royal Society Open Science. 4:170117

Sour rot, is a disease of grape berries caused by the joint development of yeast and acetic acid bacteria [START_REF] Barata | New Insights into the Ecological Interaction Between Grape Berry Microorganisms and Drosophila Flies During the Development of Sour Rot[END_REF]. In Europe, until recently, several simultaneous factors were necessary for its appearance: damages to fruit skin due to climatic events or large animal bites and infestation by D. melanogaster or D. simulans larvae. We combined field observations with laboratory assays to disentangle the relative roles of both Drosophila species in disease development. Our results revealed invasive D. suzukii indeed oviposits in undamaged berries, which initiates the development of sour rot. In the following days, the volatiles emitted by the microbes attract D. melanogaster females that lay numerous eggs. As Drosophila larval activity accelerate yeast population growth [START_REF] Stamps | Drosophila Regulate Yeast Density and Increase Yeast Community Similarity in a Natural Substrate[END_REF] this series of events lead to intense rot. The study hence shows how biological invasion can benefit local species and favour the spread of microbial diseases.

These advances, of particular significance to wine makers, were possible thanks to the combination of different methods: study of field infestations, meta-barcoding (i.e. genomics), behavioural assays and microbiology. Each of this technique was acquired at a different stage of my career as PhD student or postdoc or through collaboration within CBGP (i.e. meta-barcoding).

These results correspond to the first publication of PhD student Antoine Rombaut (started October 2015), co-supervised by Patricia Gibert from LBBE, Lyon. His following projects aim at deepening our understanding of the interactions between D. suzukii and D. melanogaster. We believe the success of D. suzukii as an invader is linked to its ability to carve an ecological niche into new ecosystems, which would be restricted by interactions with resident species.

Other relevant articles:

Parrain

Animals with metamorphosis connect communities

The previous study exemplifies how the movements and choices of an adult stage determine the conditions in which larval stages develop. The ecology of flies is typical of that of complex life cycle animals11 : different life stages usually belong to different ecosystems or communities (Moran 1994, Stoks and[START_REF] Stoks | Evolutionary Ecology of Odonata: A Complex Life Cycle Perspective[END_REF]. As conditions experienced during a given stage cascade onto other stages -at least through numerical [START_REF] Miller | Thinking inside the box: community-level consequences of stage-structured populations[END_REF] and developmental effects [START_REF] Pechenik | Larval experience and latent effects: metamorphosis is not a new beginning[END_REF]) -animals metamorphosis establish links between otherwise independent communities.

During my first postdoc -with Brian Lazzaro at Cornell University, USA -I studied plastic and genetic constrains between different life stages of D. melanogaster. This work focused on insect immune system as this organ is a prime determinant of the interaction between the host and the community of microorganisms it lives with.

Focus article 6:

Fellous & Lazzaro, 2011. Potential for evolutionary coupling and decoupling of larval and adult immune gene expression. Molecular Ecology, (20) 1558-1567. Evolutionary coupling between the traits of a single organisms but expressed in different life stages, each belonging to different communities, could induce a form of coevolution between species of different communities. This scenario, where the evolutionary trajectory of pairwise interactions in a given community depend on those experienced by the same organisms in a different stage and community, relies on genetic constraints between traits across the life cycle. We investigated the existence of such constrains in D. melanogaster using quantitative genetics methods (80 crosses between inbred lines) and molecular assays of immune system activity (i.e. qPCR of transcripts coding for antimicrobial peptides) This line of research now continues through the postdoc of Julie Collet (started September 2016). Using quantitative genetics (i.e. 50 DGRP lines) and transcriptomics (i.e. genome wide transcription analysis) she aims at correlating gene function (i.e. ontology) with the nature and magnitude of genetic constraints between life stages. This is a first step towards a predictive framework for evolutionary coupling between traits separated by metamorphosis. By paying particular attention to immune related function, this project should help identify the best bio-control agents: those that are not fought by immune components that exhibit positive genetic correlation between host life stages. Indeed, positive correlation would imply that increased defence against biocontrol agent would cascade onto resistance to other natural enemies specific to other life stages, hence creating a form of benefit of resistance.

Other relevant articles:

Fellous & de Roos. Beyond numbers: how plasticity, evolution and symbiosis affect the community ecology of animals with metamorphosis. Under review at Trends in Ecology and Evolution.

Collet & Fellous. Evolutionary constraints on traits separated by metamorphosis. In prep.

Fellous & Lazzaro, 2010. Larval food quality affects adult (but not larval) immune gene expression independent of effects on general condition. Molecular Ecology, [START_REF] Chevin | Phenotypic plasticity in evolutionary rescue experiments[END_REF] 1462-1468.

Symbiosis

One thing that doing experiments with microbial parasites teaches is that their effects on hosts are always changing [START_REF] Thomas | Understanding parasite strategies: a state-dependent approach?[END_REF]. So much so that virulent parasites often become costless when host resources increase (Bedhomme et al. 2004, Fellous and[START_REF] Fellous | Cost of co-infection controlled by infectious dose combinations and food availability[END_REF]. The literature is indeed rich with cases of so-called parasites being actually beneficial is some environments. The distinction between parasites and mutualists blurs as we get free from the prism of parasitology [START_REF] Neuhauser | A mutualism-parasitism continuum model and its application to plant-mycorrhizae interactions[END_REF]. In other words, microbes are symbionts 12 ; as such they have effects on phenotypic traits of their hosts.

Sometimes, what is detrimental in one environment (e.g. the early flowering of an infected host plant) is beneficial in another (e.g. if winter is coming) [START_REF] Salvaudon | Arabidopsis thaliana and the Robin Hood parasite: a chivalrous oomycete that steals fitness from fecund hosts and benefits the poorest one?[END_REF].

During my PhD, I soon realized that the odd observation -a beneficial "parasitic infection"was in fact the norm. The concept had obviously been discussed many times before (e.g. [START_REF] Michalakis | Pleiotropic action of parasites: How to be good for the host[END_REF], sometimes with excessive enthusiasm (Smith 1968) 13 . It appears the idea has largely spread since 2008 with the discovery that Wolbachia "parasites" protect insect hosts against RNA viruses [START_REF] Teixeira | The Bacterial Symbiont Wolbachia Induces Resistance to RNA Viral Infections in Drosophila melanogaster[END_REF]. It is now well established that microbes are a source of evolutionary novelty, a concept that late Linn Margulis defended for many years against the wide scepticism she had to face [START_REF] Margulis | Symbiosis as a source of evolutionary innovation: speciation and morphogenesis[END_REF].

I have published a few articles on this topic. Now, that my students and I investigate the symbiosis between fruit flies and microbes, we try, as much as possible, to avoid prejudice regarding the nature of their interactions.

Relevant articles:

Fellous

III. SCIENCE, SOCIETY AND ME

A. Methodology

Looking back at my research activity so far leaves no doubt, I am an experimental biologist.

There are pros and cons to carrying out experiments compared to modelling, or the description of patterns from the wild (e.g. phylogeny, population genetics...). Combining methods, as we timidly tried in Rombaut et al. (2017), is obviously best. In this matter, I wish I learned more from Jacob Koella, my PhD supervisor, who fed his experiments with his wide knowledge of modelling. However, like Isabelle Olivieri often claimed, "I am a theoretician, even if I don't do mathematical models".

My personal history -a teenager who reared hundreds of creatures in jars of all size -is however a source of inspiration to design new protocols or troubleshoot faulty ones.

Performing experiments is in many ways similar to DYI home improvement 14 : there is always a solution; the fun is in looking for it.

In the pure Evolutionary Ecology tradition, I was taught to carry out the biggest experiments I was able to deal with. One experiment amounted to one paper, at least. I did follow this path until working at Cornell University. The Entomology and Genetics departments had strong bonds; I was exposed to work by evolutionary geneticists. These people combined dozens of reasonably scaled experiments to build their reasoning. Each result led to the next experiment; each experiment confirmed previous observations and opened new perspectives. Obviously, all questions may not be tackled in this way, but when relevant, it is what I now try teaching my students. The method seems beneficial for two reasons. First, published results are not based on single observations anymore. It follows that spurious discoveries should be fewer, and repeatability improved. Second, whole projects do not depend on the success and results of single big endeavours. Whenever an experiment fails for technical reasons, it is not excessively disappointing, as we only have invested a few days or weeks in it. This makes life in the lab much nicer and keeps everyone's mood high. Besides, I suspect we do not analyse datasets the same way: since data flows regularly, we are less prone to go fishing for unexpected patterns. Once again, this methodology should reduce the publication of spurious results.

B. Personal Evo-devo

Early life-stages

When I joined Jacob's lab, some 15 years ago, life-history theory seemed in every mind. People tested model predictions with their pet biological system. Finding a trade-off was the Holy Grail for us, students fascinated by the predictive power of evolutionary theory.

I did study the Trade-off model of parasite virulence [START_REF] Anderson | Infectious diseases of humans: dynamics and control[END_REF]May 1992, Lenski and[START_REF] Lenski | The Evolution of Virulence in Parasites and Pathogens -Reconciliation between 2 Competing Hypotheses[END_REF] and its numerous spin-offs. Coevolutionary models of host-parasite attack and defence were so sexy. So I followed the pack, encouraged by Jacob, himself a student of Steve Stearns [START_REF] Stearns | The evolution of life histories[END_REF]. I even tried to build models with fellow modellers 15 . Nevertheless, in the end, my stubborn, anarchist nature always dragged me back to looking at what (I thought) others had not studied yet (e.g. Fellous andKoella 2009b, a, Fellous and[START_REF] Fellous | Cost of co-infection controlled by infectious dose combinations and food availability[END_REF]. As Jacob said in a number of occasions, "There is no point in testing model predictions: if the modelling is correct, the predictions are right; testing models' assumptions, this is what we really need". It was a little reassuring to think my investigations were not completely detached from theory... I simply was testing (new) assumptions.

In the end, my work added complexity to our understanding of the world. This is what I did too when working with Brian Lazzaro on plastic and evolutionary links between the different stages of a holometabolous insect (Fellous andLazzaro 2010, 2011). My tooshallow knowledge of the literature led me to think very few had studied these constraints, which was somewhat true in the case of immune defence.

Later, when I joined Oliver Kaltz at ISEM in 2009, I was still in the mood for adding complexity to prevailing theories. These have been fruitful years. Together with Alison Duncan and Oliver we published several nice papers with Oliver's biological system, a ciliate and its bacterial parasite. Most of them focused on pairwise interactions (i.e. hostparasite) and described new ways things could be different (e.g. Duncan et al. 2011, Fellous et al. 2011, Fellous et al. 2012). After a few months I started collaborating with Michael Hochberg and his PhD student Johan Ramsayer, working with the bacterium Pseudomonas fluorescens and its bacteriophages. Since Paramecium fed on bacteria, I initially wanted to add this extra trophic level. Little of this work was ever published 16 , even though we carried out interesting work on the constraints between adaptation to various abiotic and biotic factors (i.e. competition, infection, combined stresses, richness in resources).

Then, when ANR money ran out I had to move on to another lab. I worked with Maria Navajas on phytophagous spider mites at CBGP. Even if the project theme was fairly fundamental -specialisation to host plant species -we had to go to the field and meet colleagues from the agricultural world whose aim was to get rid of mites. This is when I realized evolutionary theory could be used to predict agricultural pest evolution.

Metamorphosis

My application to an INRA "open position" in 2012 was another important step in the evolution of my scientific objectives. To prepare and write the project 17 had taken me a full year. This time was necessary to understand what the merging of science and impact meant. It seemed possible to design "evolution proof" methods of pest control, something reminiscent of Andrew Read's claimed objectives against malaria a few years earlier. To be honest, I was still mostly interested in fundamental questions, quite distant from the possible requests of farmers, but the target application was now in sight.

Metamorphosis advanced further when first reports of D. suzukii damages on grape arrived. We18 had been studying D. suzukii oviposition behaviour, finding the basis of a potential repellent 19 . It was obvious this line of research may be translated into something useful to farmers. With Patricia Gibert we then started scooting for collaboration with the wine industry. A year of phone calls and hopeful emails later, we signed a joint project with the Bureau Interprofessionnel des Vins de Bourgogne (BIVB), the Comité Interprofessionel de Vins de Champagne (CIVC) and the Agropolis foundation. This grant now supports Antoine Rombaut's PhD.

In the process, I had talked with INRA's lawyers and partnership advisors. They insisted it was important that findings that predated the beginning of our collaboration with BIVB and CIVC be identified and intellectual property correctly shared. This was a shock. I hoped our discoveries may one day be implemented in the field, but I had never realized the conditions for success. This is when emerged numerous questions that have found no answer to date: should we patent our findings to ensure industry invests in them? Or should we publish, make them freely available and hope for the best? How can we anticipate downstream obstacles between discovery and implementation? And, the hardest of all, without being proponents of the current economic system, would working with the crop protection industry be a turncoat?

Now and next

One thing that evolutionary thinking teaches is that reliable predictions necessitate anticipating future conditions and identifying the most influential factors. Designing evolution-proof solutions for the agricultural world necessitates a thorough analysis of the many steps between discovery in the lab and adoption in the farm. In other words, one must pay attention to the complexity of our world. Sustainability is by essence multidisciplinary: by overlooking the distant by-products of our actions we may miss their real cost [START_REF] Bourguet | The hidden and external costs of pesticide use[END_REF].

For the last two years, I have tried to develop collaborations with various players of the agronomic and academic world, all involved in the fight of insect pests. Together with CIRAD researchers Anais Chailleux and Emilie Deletré, respectively based in Senegal and Kenya, we organized in September 2016 a workshop on the theme "Sustainable Fruit Fly Control" (Fig. 8). Drosophilids like Tephritids20 flies were the subject of our discussions: the ecology of flies from these two clades is very similar, but the economic context of the damages they cause is very different. Besides, researchers from tropical and temperate regions can both learn from each other. We now ambition to maintain the contact between the three dozens of actors who responded to our call. This may be through a network facilitating cooperation and the building of joint, multidisciplinary projects. As I am writing these lines, I am in Kenya where I spent a week meeting with local researchers from the International Centre for Insect Physiology and Ecology (ICIPE) -for whom fundamental research is not an option -, visiting field sites and even a factory of biocontrol agents (Real IPM, Nairobi, Kenya) whose representative has participated in our workshop.

I did not expected however how little colleagues from the pest control world have, in general, thought about sustainability. Often, non-chemical solutions are assumed environment-friendly, which is sufficient to most people. Besides, the incentive for greener solutions often comes from consumers rather than a personal analysis. Crop production is a business, as such; it is managed with profit in mind. Therefore, we need to approach this industry with realistic business models (e.g. identify who will buy and use our solutions, and at what cost), leaving the advocacy for green solutions to others.

A personal aim is now to develop relationships with those who represent farmers' interests, fight to protect them and, importantly, advise them. These people, the syndicates, know the challenges met by farmers, how crops are really produced and understand the business model upon which crop protection is based. It is them to whom we need to show that alternative solutions work and can be economically profitable. I believe it is our role, as researchers and public servants, to make sure the solutions we propose are green and sustainable, but this does not need to be the aspect we advertise most. In brief, my goal now as a researcher is to work at the intersection between basic and applied research (Figure 9). Research questions in both fields are numerous, but time and money are limiting. Obviously, all experiments, or articles will not meet both requirements. Nevertheless, the way I understand diriger des recherches is to make sure that, in the long run, our work meets its objectives.

The relevance of laboratory observations to in natura processes

Applied research means conditions and methods employed must match the real world. This is an aspiration that pre-dates committing to agricultural challenges. Those who read my PhD thesis21 might recall a section where I discussed the likely disconnection between my work in the lab and in natura dynamics. I feared the processes I had discovered did not happen out there, or were buried under so many more phenomena that their influence was neglectable.

A largely overlooked benefit of working with fruit flies, such as Drosophilids, is the possibility to observe them in the field, replicate their natural habitat in microcosms and nevertheless benefit from the arsenal of laboratory tools developed during decades of work on this model organism.

My attention to fruit-fly ecology has led to fruitful collaborations with colleagues who study them for different reasons. The first of such projects that arrived to completion was about epigenetics. Giacomo Cavalli, from Institut de Genetique Humaine (IGH), Montpellier and his then PhD student Filippo Ciabrelli, had discovered a new mechanism of epigenetic regulation of transcriptional activity in D. melanogaster. Epialleles seemed to transmit for several generations in test tubes with transgenic lines. But the wanted to ensure the relevance of their observations to in natura processes. We therefore tested the resilience of their epialleles under a variety of environmental conditions. In the most interesting experiment we set up microcosms with real fruit and live plants, a diversity of micro-and macro-organisms as well as realistic climatic conditions. This was carried out at the ECOTRON facility in Montpellier, with the help of their efficient and dedicated team. This work has recently been published and is, to my knowledge the first to combine hard-core genetics with microcosm methods (Ciabrelli et al. 2017). Another collaboration involved Ted Morrow from University of Sussex, UK, and his then postdoc Allan Debelle. They wanted to study whether intra-locus sexual antagonisms, as revealed by the study of D. melanogaster hemiclonal lines, was maintained in field conditions. Over two years we helped Allan set up microcosms in which to assay fly sexual performance. These were specifically designed to take into account specific sexual behaviour of D. melanogaster (e.g. spatial structuring of reproduction sites, possible competition for resources between conspecifics). They were installed at CBGP, in outdoor cages. Results showed enormous G*E interactions. There was literally no relationship between line performance in the lab and that in cages with natural food and environmental complexity. Manuscripts describing these results are in preparation.

Note that Allan has since joined the "intersection between applied and fundamental research" squad at CBGP. We are currently putting together a project where his knowledge on sexual selection may improve Sterile Insect Technique 22 . This was first envisioned during the workshop on "Sustainable Fruit Fly Control" where he met with farmers' representatives 23 and had the idea to use experimental evolution in order to improve the performance of released males.

Another SIT-related project should start soon in association with my group at CBGP (but based at CEFE in Patrice David's group). Julie Collet, who currently works with me on genetic constraints between life stages, will begin a Marie Sklodowska-Curie fellowship in February 2018. Her project aims at investigating the evolutionary sustainability of SIT with D. suzukii.

B. Management of research

1.About mentorship and collaborative work

Metrics

Over the years I supervised the research project of 11 students in their first or second year of masters degree. The majority of them continued with a PhD, meaning I had not managed to disgust them from science. I also published articles with 4 of them 24 .

These good results probably reflect the quality of the lab where I have worked and the dedication of students to their career. 25 . I am usually surprised by the time it takes to gain scientific independence 26 . Friendship is also an important factor. "Old style management" advises to not be friend with colleagues and students with whom one has hierarchical relationships. This is simply impossible. These people are human beings, pretending not to care would be ridiculous.

Now that I directly supervise the PhD projects of 2 students new challenges arise. Among them, how to encourage reasoning and innovation is an important one. I believe it goes through self-confidence. In that respect, the similarities between mentorship and parenthood are sometimes disturbing. The co-supervision of Antoine's thesis by Patricia Gibert makes a big difference. She is the one with experience, her input is invaluable.

Postdocs and technicians

Regarding postdocs, my experience is short.

Animation of science and related tasks

Meeting and exchanging views with fellow researchers (or science practitioners, such as crop protection professional) is essential to the advancement of our ideas. I take, and have taken part, in this task in several ways:

Reseau Ecologie des Interactions Durables 28

Initiated in 1993, this (mostly) French-speaking network organizes yearly meetings and facilitates the activity of sub-groups dedicated to specific questions (e.g. virus evolution, ticks, fungal diseases of plants...). Depending on context, sub-groups meet separately or together with the rest of the REID members. General REID meetings attract students and researchers of various backgrounds, from theoreticians to physiologists, plant biologists to vets. Participants belong to INRA, CNRS, IRD, CIRAD, Universities, Grandes Ecoles, and often university from neighbouring country such as Belgium or Switzerland. A particular feature of the REID is to welcome the participation of early career scientists who get the opportunity to present their on-going work in a friendly environment, with less pressure than in a big international meeting.

Since 2014, I co-animate the network with Christine Chevillon (CNRS). Among other things, I am in charge of the interface with INRA, the, until recently, main funder of the network.

Recent meetings have seen a surge of participant numbers followed by a relative step back: Montpellier (2014) 200 participants; Lyon (2015) 165 participants; Poitier (2016) 80 participants; Toulouse (2017) 90 participants. As our sources of funding have run out (both INRA and CNRS have stopped supporting the network), we are currently thinking of new directions for the REID 29 .

Sustainable Fruit Fly Control group

As described above, this recent (2016) initiative aims at creating links between researchers from ecology, evolution, social sciences and plant protection professionals; all involved in the mitigation of crop damages due to Drosophilid and Tephritid fruit flies30 . Our idea is that sustainability can only be achieved if the various dimensions of pest control solutions are considered simultaneously: horizontally, through the different scientific fields, and vertically, from method inception to the production of control agents and their adoption by farmers and/or governmental agencies.

After a first meeting in September 2016 funded by the Agropolis Foundation, we (Anais Chailleux, CIRAD Senegal, Emilie Deletré, CIRAD Kenya, and myself) have created a database synthesizing the skills and interests of the participants. It is meant to facilitate the emergence of new collaborations. We are also working on a review article about the challenges of sustainability.

Environment and parasite ecology meeting, Paris, 2007

As a satellite to our PhD defences, Lucie Salvaudon and myself -with the participation of Oliver Kaltz -organized a one-day workshop in December 2007. This event brought together researchers from Europe and the USA, working on a variety of microbial, animal and plant systems, to discuss the role of the environment on the evolutionary ecology of host-parasite interactions. The workshop was followed by the publication of a report article (Vale et al. 2008).

FFECE

With the recent growth of the group of colleagues I supervise, it was time to give our group an identity. The name FFECE (Fruit Fly Evolution and Community Ecology) was elected, rejecting FFECES (Fruit Fly Evolution, Community Ecology and Symbiosis) for obvious reasons.

The functioning of our working group is analogous to the Anglo-Saxon system. This sometimes create misunderstanding as, despite the official lack of équipes in our lab, young researcher are often managed by older Directeurs de Recherche. I was hired as CR1 on a new project and new biological model, it hence seemed natural to follow an independent research track rather than follow the steps of well-established colleagues. It took almost four years to get things started; it felt like a very long time. The poor success rates of call proposal were a first obstacle; learning the tricks of the trade takes times. But this allowed me to build a network of colleagues in France and abroad with whom working is fun and rewarding.

SEEM

I am also involved in the organizational committee for the Seminars in Ecology and Evolution of Montpellier (SEEM). My role is marginal and, if not for comprehensivness, this task would not deserve being listed here.

Administrative tasks

If there is one thing that may curb my enthusiasm and, possibly one day, push me out of science, it is the administrative jail we work in.

-How is it possible we, French researchers, cannot pass orders from November to March? 31

-How can we accept to have to spend hard earned funds before we even know what we will need?

-Why do we have to fill excel sheets (that will be printed out and manually copied!) and give work to already overwhelmed administrative assistants to purchase 10€ items?

-Why is it so complicated to pay anything? Especially when we find it twice cheaper somewhere than on the dedicated "marché public"?

-Why do we need to warn weeks in advance of our every move?

-Who are the burocrates so disconnected from the reality of our activity they request reports of when researchers are and are not working on the projects their agencies funded?

-Unfortunately the list goes on and on... each time diverting our creativity from science to tricking out-dated rules.

Being involved in the management of the REID and SFFC networks, not being protected by a team structure within CBGP, looking for finance outside of the traditional ANR scheme, all this seems to have exposed me to the reality of French administration a little too early, and a little too much.

Of course, some tasks are useful and I don't regret committing to the Conseil d'Unité 32 of CBGP for two years. I also campaigned, together with colleague Elodie Vercken (UMR ISA, Nice), to be elected as the representative of our INRA Department, Santé des Plantes et Environement, in Conseil National de l'INRA 33 . We finished second. This would have been a great experience, and hopefully, one useful to both fellow scientists and citizens 34 .

31 These are retorical questions, their technical answers are well known. But the very reason these ridiculous constraints are still in place either reflects political choices or poor management by research instituts' CEOs.

Figure 1 :

 1 Figure 1: a schematic depiction of the field of evolutionary ecology. Phenotypic traits are determined by interactions between species (red arrow) within communities and under the influence of the environment. Traits affect population and evolutionary dynamics. Communities are connected in space and time through dispersal and colonization.

Figure 2 :

 2 Figure 2: Infectious dose of a first parasite affects transmission of its coinfecting competitor. (a) Increased Vavraia culicis dose reduced the proportion of successful Ascogregarina infections when host food was low. Symbols indicate means, error-bars indicate confidence intervals; (b) Increased Ascogregarina culicis dose reduced the rate of Vavraia culicis spore production.

Fellous. 2009 .

 2009 Positive correlation between haemosporidian parasitemia and likelihood of PCR detection in co-infected birds. The Journal of Parasitology, (95) 472-473. Fellous and Koella, 2010. Cost of co-infection controlled by infectious dose combinations and food availability. Oecologia, (162) 935-940. Ramsayer*, Fellous*, Cohen and Hochberg, 2012. Taylor's law holds in experimental bacterial populations but competition does not influence the slope. Biology Letters, (8) 316-319. *Equal authorship

Figure :

 : Figure: Genotype-by-genotype interaction between two coinfecting mites. Number of T. evansi offspring 18 days after inoculation of detached tomato leaves. A similar G*G interactions was observed for reproductive output. Symbols indicate means, error-bars indicate standard errors.

Figure 4 :

 4 Figure 4: Effect of mean temperature and its temporal variations on (a) parasite prevalence and (b) parasite extinction rates from microcosms. Variable temperatures were obtained by alternating test tubes between chambers at 23°C and 35°C. Symbols indicate means, error-bars indicate standard errors.

Figure 5 :

 5 Figure 5: Effect of bacterial infection on the dispersal of ciliate host between interconnected microcosms. Regression lines show density-dispersal relationship for infected (full line) and uninfected populations (dashed line). Open circles, uninfected populations and crosses, infected populations.

Figure 6 :

 6 Figure 6: aetiology of D. suzukii induced sour rot on grape berries. In absence of D. suzukii, fruit skin integrity must be compromised for D. melanogaster to reach fruit flesh. Invasion by D. suzukii has therefore expanded the range of conditions for sour rot outbreaks and facilitate D. melanogaster populations by opening new ecological niches.

Figure 7 :

 7 Figure 7 : Genetic correlation between larval and adult constitutive transcription of two antimicrobial peptides, (a) Diptericin and (b) Drosomycin in Drosophila melanogaster. Each point corresponds to one of 80 crosses between 5 paternal lines and 16 maternal lines.

Figure 8 :

 8 Figure 8: conceptual diagram on the role and multi-disciplinary nature of sustainability in crop protection. We used this figure in the grant application to the Agropolis Foundation who initially funded the "Sustainable Fruit Fly Control" network.

Figure 9 :

 9 Figure 9: conceptual articulation between fundamental and applied research. Applied research is driven by requests from society, fundamental research follows its own path, guided by new discoveries and prevailing theories. It is possible to meet both objectives, as long as we accept to sometimes divert in a direction or another.

Figure 10 :

 10 Figure 10: Microcosm experiment testing the resilience and inheritance of D. melanogaster epialleles in semi-natural conditions. This part of the project, led by G. Cavalli and F. Ciabrelli (IGH), was run at the Ecotron facility in Montpellier. Note (a) replicated microcosms in climatecontrol chambers, (b) adult flies feeding and ovipositing on fruits produced by caged plants, (c) the presence of natural predators of flies (here centipedes) and the pupation of larvae in soil.

Résumé du projet de recherche en français

	4.
	Nom	Niveau Sujet et encadrement		Thèse ?	Publication
	2005 Joël Meunier M2	Parasite manipulation of	oui	non
			behavior
			Supervision principale J.
			Koella
	2005 Lideric	M2	G*G		interactions.	non	non
	Aubert		Supervision principale J.
			Koella
	2010 Elsa Quillery M2	Spatial	dynamics	of	oui	oui,
			infection.					3 articles
			co-supervision O. Kaltz
	2011 Elodie	M2	Evolution in community	oui	non,
	Parrain		context.					1 article in
			co-supervision O. Kaltz			prep
	2011 Jonas Durand M2	Resistance	to	abiotic	oui	non,
			stress and infection.			1 article in
									prep
			co-supervision O. Kaltz
	2012 Marion	M2	Interactions	between	oui	oui,
	Orsucci		mites						2 articles
			co-supervision M. Navajas
	2014 Haithem Haji M2	Effect of nutrition accross	non	non
			metamorphosis.
	2015 Antoine	M2	D.	suzukii	-		D.	oui, sous ma	oui,
	Rombaut		melanogaster interactions	supervision	1 article
			co-supervision P. Gibert
	2016 Robin Guilhot M2	Symbiosis between flies	oui, sous ma	oui,
			and bacteria.				supervision	1 article

a. Positionnement scientifique: Science fondamentale et Impact sociétal

  ). Le travail de Robin permettra de mieux comprendre les sauts d'hôte par le ravageur de fruits D. suzukii et, par conséquent, comment l'infestation d'une culture donnée peut se répandre sur d'autres cultures avoisinantes. -> La relation entre évolution et invasion est également le sujet d'une collaboration en cours avec Elodie Vercken et Eric Lombaert (UMR ISA, Nice, France). Ce projet, qui fait partie de l'ANR Triptic (un projet commun entre les laboratoires CBGP et ISA sur les parasitoïdes Trichogramma), implique également la postdoc Aline Bertin. En manipulant la structuration spatiale des microcosmes (Morel-Journel et al. 2015), nous étudions l'influence de la dynamique de la population locale sur la dispersion et l'évolution de leur phénotype.

	des
	processus génériques et les propriétés émergentes liées à la diversité (Darley, 1994) ont
	favorisé des approches négligeant l'identité des espèces. Par exemple, la modélisation
	mathématique et l'analyse des réseaux trophiques ont permis des avancées majeures dans
	le domaine (e.g. Thébault et Fontaine 2010). Dans certains cas, cependant, des questions se
	posent qui concernent des organismes spécifiques dans des écosystèmes donnés. Dans ces
	cas, les approches empiriques deviennent obligatoires. En effet, même une modélisation
	bien pensée ne peut être pertinente que si ses hypothèses sont correctes. Ces hypothèses,
	ou paramètres, s'appuient sur les données empiriques.
	Depuis que j'ai commencé à travailler sur les mouches des fruits à l'INRA (janvier 2013),
	mes travaux ont principalement porté sur Drosophila suzukii (Cini et al., 2012). Ce parent
	proche de D. melanogaster est originaire d'Asie continentale (Chine principalement) et a
	récemment envahit les Amériques et l'Europe. C'est la seule espèce de son clade à pondre
	préférentiellement dans des fruits mûrs mais non endommagés

(ii) Ecologie des interactions [voir section II.B.2 du document principal]

L'étude expérimentale des grandes communautés représente un défi car la complexité augmente exponentiellement avec le nombre d'espèces. Mais la nécessité de découvrir

  Fraimout, Debat, Fellous, Hufbauer, Foucaud, Pudlo, Marin, Price, Cattel, Chen, Deprá, Duyck, Guedot, Loeb, Kenis, Kimura, Martinez, Pascual, Richmond, Shearer, Singh, Tamura, Xuéreb, Zhang, Loiseau, and Estoup, 2017. Deciphering the routes of invasion of Drosophila suzukii by means of ABC random forest. Molecular biology and evolution. Fraimout, Loiseau, Price, Xuéreb, Martin, Vitalis, Fellous*, Debat* & Estoup*, 2015. New set of microsatellite markers for the spotted-wing Drosophila suzukii (Diptera: Drosophilidae): A promising molecular tool for inferring the invasion history of this major insect pest. European Journal of Entomology. 112(4). *Equal last authorship Sauné, Auger, Migeon, Longueville, Fellous, Navajas, 2015. Isolation, characterization and PCR multiplexing of microsatellite loci for a mite crop pest, Tetranychus urticae (Acari:

Tetranychidae). BMC Research Notes. 8(1):247. Azandémè-Hounmalon, Fellous, Kreiter, Fiaboe, Subramanian, Kungu & Martin, 2014. Dispersal Behaviour of Tetranychus evansi and T. urticae on Tomato at Several Spatial Scales and Densities: Implications for Integrated Pest Management. PloS ONE. 9(4) e95071 Fellous, Duncan, Coulon & Kaltz, 2012. Quorum sensing and density-dependent dispersal in an aquatic model organism. PLoS ONE. 7(11): e48436. Fellous & Koella, 2009. Different transmission strategies of a parasite in male and female hosts. The Journal of Evolutionary Biology, (22) 582-588.

  ,[START_REF] Fellous | Adaptation due to symbionts and conflicts between heritable agents of biological information[END_REF]. Adaptation due to symbionts and conflicts between heritable agents of biological information. Nature Reviews Genetics.[START_REF] Fellous | Potential for evolutionary coupling and decoupling of larval and adult immune gene expression[END_REF] 663.

(Correspondence) Duncan*, Fellous*, Accot, Alart, Chantung-Sobandi, Cosiaux & Kaltz, 2010. Parasitemediated protection against osmotic stress for Paramecium caudatum infected by Holospora undulata is host genotype specific. FEMS Microbiology Ecology, (74) 353-360. *Equal authorship Fellous & Salvaudon, 2009. How can your parasites become your allies? Trends in Parasitology, (25) 62-66.

Table 1 : list of the students I whose projects I supervised or co-supervised, starting

 1 Master 1 level.22 Sterile Insecte Technique, SIT, consists in the large scale release of sterilised males of a given pest that mates with local females. Mated females produce unviable eggs, hence impacting population dynamics.

	YEAR	NAME OF STUDENT	DEGREE	TOPIC AND CO-SUPERVISION			FUTURE
		Joel	M2	Parasite	manipulation	of	PhD,	Now	CNRS
		Meunier		behaviour			researcher
				Main supervisor J. Koella
		Lideric	M2	G*G	interactions.	unknown
		Aubert		Main supervisor J. Koella
		Romain	M1	I forgot, but he was impressive.	PhD, Now researcher
		Levayer		Main supervisor J. Koella

23

People from the AFIDOL, Association Française Interprofessionnelle de l'Olive.

24

Actually 3, as the paper of Antoine Rombaut correspond to work carried out during his PhD.

Challenges

These metrics reflect little of the challenges of guiding and supervising younger colleagues. Every time I have had difficulties knowing when to stop helping them, be it with reasoning,

  Julie Collet is the first postdoc under my supervision. It is too early to have perspective and draw conclusions. Relationship with Allan Debelle, when he was paid by Ted Morrow but worked at CBGP, was too horizontal to qualify as supervision.This section would not be complete without evoking Anne Xuéreb. She is the first Technician 27 I really worked with. It feels we each taught each other how to work together. Trust is essential. We both rely on each other daily. CBGP, the project of deciphering the invasion routes of D. suzukii with population genetics data was recently concluded with a publication(Fraimout et al. 2017). This project, quite remote from my usual aspiration began with my first INRA grant in October 2013. The 15k euros were not sufficient to carry out the submitted project. However, with this money it was possible to initiate the population genetics project, pay for molecular biology reagents and the trips of PhD Antoine Fraimout (MNHN) from Paris to Montpellier. At the time, Vincent Debat, his main supervisor and I thought essential to know how independent were American and European populations of D. suzukii because we wanted to study their phenotypic divergence. Arnaud Estoup (CBGP) was interested by D. suzukii -he now has several projects on the fly -and happily offered his expertise. With time, the population genetics project has become more and more ambitious, naturally reducing my relative contribution.Two other projects involve CBGP colleagues. First, common interest for Drosophila bacterial symbionts has led to an on-going collaboration with Marie-Pierre Chapuis and Laure Benoit (CIRAD researcher and technician, respectively). Marie-Pierre, an expert in population genetics and meta-barcoding, is involved in the PhD project of Robin Guilhot and co-authored the first article of Antoine Rombaut. Second, the transcriptomics project of postdoc Julie Collet necessitates expertise and advice from NGS experts. This is the role taken by Sabine Nidelet, INRA technician, whose input and guidance has become vital.

	Within

Collaborations

Regarding collaborations, several have been described above (plus see list in the first chapters in French). And numerous others are on going (e.g. with the group Darren Obbard, Edinburgh, UK, on the viruses of D. suzukii; that of Francis Jiggins, Cambridge, UK, on metamorphosis and resistance to parasitoids in D. melanogaster; with Kate Howell, University of Melbourne, Australia, on yeast symbionts of Drosophila flies) or close to publication (e.g. with Jaka Razinger, Ljubljana, Slovenia, on plant protection).

  32 Our lab's advisory panel33 INRA's advisory board, in charge of advising both INRA and the french Agriculture Council.

34

aren't these good final words?

Science fondamentale: questions génériques sur le fonctionnement de l'univers, et processus biologiques.

Science appliquée: questions issues d'enjeux societaux visant à éclairer des actions et décisions déjà identifées.

Parasite: any organism that developps by taking resources from another organism without necessarily killing it.

Couple is doable, trouple is trouble

Virulence: the detrimental effects parasites have on their hosts.

Infectious dose: the number of infectious forms of a given parasite the host is exposed to.

Neutral genetic variation referres to DNA sequence polymorphisms that are not related (yet) to phenotypic variations.

genotype-by-environment (i.e. G*E) interactions: the phenotypic responses of individual genotypes to environmental factors.

Dispersal: the movements of individuals between the site they were born and the site they reproduce.

range expension refers to the spatial spread of a species.

In fact, of the numerous species of holometabolous insects, fruit flies are among the ones which have the most similar larval and adult environments. Mosquitoes, for example, have aquatic larvae that feed on microorganisms and flying adults that suck blood of vertebrates.

Symbionts: any group of organisms that live together. Symbiotic relationships can be either beneficial, neutral or costly. Symbiosis is distinct from sociality as social interactions refer to relationships between members of a same species.

This one was too nice to be true. It is apparently a case of blatant fraud.

Anne, Antoine, sorry for having wasted so much of your time.

My appologises to Michael, Johan and Elodie who are the victims of my lack of reliability.

The consequence of life cycle complexity on pest ecology and, with D. suzukii in mind.

To be fair, Anne Xuéreb was the one performing the experiments.

It is not possible to describe the nature of our reppelent in this document as it may affect intellectual property rights.

Tephritid flies are the true fruit flies. They are mostly a problem in tropical regions, but the olive fly, Batrocera oleae, is an example of Tephritid causing damages in Europe.

That is about 8 people I reckon, and probably even less will read this note. Actually, if you do read it please tell me, it will give more sens to this whole HDR thing.

Although those who have worked in the lab with me know how little I like repetitive tasks. To be fair, I suspect most of them think I could have helped more. They don't realize I would have ruined their work

This probably has to do with my own experience as a PhD student ; according to my own supervisor I was excessively independent.

"Assistante Ingenieur" in fact, it is substanically different but the difference does not translate well to english.

Network for the study of symbiosis ecology.

To those who saw the movie "REID is (not) dead".

It should be noted that a large, international network of tephritid workers already exists (https://nucleus.iaea.org/sites/naipc/twd/Pages/TEAM.aspx). Our aim is not to compete with this well-established group. Instead, we want to focus on sustainability rather than target species.

Acknowledgements

This section obviously is the first one most readers will look at... and be disappointed with.

IV. FULL TEXT ARTICLES

List of articles in appendix

Focus article 1: Fellous and Koella, 2009. Infectious dose affects the outcome of the within-host competition between parasites. The American Naturalist, (173) E177-84.


Scott Love

Marine Siwiaszczyk

Marie Auge

Christophe Destrieux

Frédéric Andersson

Elodie Chaillou

Surface-based cortical parcellation and atlas creation of the sheep brain

à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Introduction

• The sheep model is a compelling yet underused model for understanding structure and function of the cortex.

• Brain atlases have largely focused on subcortical regions in sheep, very little information is available about the cortical parcellation.

• Neuroanatomical labeling facilitates the generalizability and comparability of experimental results across studies and laboratories.

• The current work aimed to produce a surface-based labeling of the entire sheep cortex.

Atlas of the Sheep Neocortex

Methods

• High-resolution (0.6 mm 3 ) T1-weighted MR images were collected from 20, two-year old Ile de France ewes using a 3T Siemens Magnetom Verio.

Conclusions

• A computerized labeling of the entire sheep neocortex containing 28 regions (12 gyri, 16 sulci) per hemisphere is provided.

• We also aim to produce a probabilistic parcellation that will optimize automatic labelling of the entire sheep brain. • As well as providing an atlas of the sheep cortex it is hoped that the atlas, along with the pipelines used to create it, will also facilitate neuroimaging research of this valuable large animal model.

Project NeuroGeo (00091714) Funded by Region Centre Val de Loire

  • Standard processing streams of the Freesurfer software suite (http://freesurfer.net, Dale 1999; Fischl 1999) that produce automatically labeled cortical surfaces of the human cortex (Destrieux 2010) were modified to enable semi-automatic labelling of the sheep cortex. • Anatomical nomenclature is based on previous literature (e.g., Landacre 1930) and the Nomina Anatomica Veterinaria (5 th Edition). correction 1 6) Normalize white-matter 7) Extract the cortex 8) Bias correction 2 9) Segment white-matter 10) Separate hemispheres 1) Image denoising 2) Talairach-like orientation 3) Neocortex mask 4) Conform the image • 1mm 3 voxel size • 256 3 matrix size 11) Surface reconstruction: • White-matter surface • Inflated white-matter • Pial surface • Local mean curvature 12) Manual parcellation


est destinée au dépôt

=

  Investigating the drivers of Atlantic salmon populations decline at the North Atlantic basin scale through a Bayesian life cycle modelling approach Maxime Olmos, Mark Payne, Gerald Chaput, Marie Nevoux, Etienne Prévost, Etienne Rivot To cite this version: Maxime Olmos, Mark Payne, Gerald Chaput, Marie Nevoux, Etienne Prévost, et al.. Investigating the drivers of Atlantic salmon populations decline at the North Atlantic basin scale through a Bayesian life cycle modelling approach. NASCO Symposium: Managing the Atlantic salmon in a rapidly changing environment. Management Challenges and Possibles Responses, Jun 2019, Tromso, Norway. 2019. hal-02289538 Want to know more ? Olmos et al., 2019. Evidence for spatial coherence in time trends of marine life history traits of Atlantic salmon in the North Atlantic. Fish and Fisheries, 20(2), 322-342. https://doi.org/10.1111/faf.12345 An unified framework to explore ecological mechanisms and forecast the response of populations to management strategies while accounting for the effect of environmental changes at the North Atlantic basin scale -Outperforms existing models -Highly expandable (incorporate new data and new ecological hypothesis) drivers and mechanisms of this decline ?  Develop a risk analysis framework to evaluate fisheries management strategies at the North Atlantic basin scale MATERIAL & METHODS RESULTS Is the decline in post-smolt survival a response of populations to changes in the marine ecosystem (bottom-up processes)? Zoo PP SST Prey  Age-and stage based life cycle model  Intra and inter-populations variability of life histories  A 𝛅 𝐭 +𝛂 𝐭,𝐜 + ε t , r + β r + Effect of environmental variables Environmental variables (PP or SST) The probability to reach CL for a particular scenario is contrasted between SU  But the probability to reach CL simultaneously for all SU for the same continental stock group is ~0 whatever the management scenarios  Decline of all populations is likely a synchronous response to large scale bottom up environmentally driven changes susceptible to synchronize post-smolt survival during the first year at sea  Stock status is depressed -the probability to reach management objectives remains low whatever the fishing quotas (although it may be high for local populations) Develop a life cycle model to draw ecological inferences on the temporal and spatial variability of the processes  Use hierarchical models to separating out the effects of local from global pressures  Analyze scenarios through probabilistic forecasting  A model working at the scale of all stock units in the North Atlantic Hindcasting What is the probability to reach Conservation Limits given management strategies of mixed stock fisheries (Greenland and Faroes)? Forecasting  Decline in the post-smolt survival is likely a response to environmental changes operating in the spacetime domains occupied by large groups of populations scale component common to the 24 SUs 𝛂 𝐭,𝐜 : Specific CSG component 𝛆 𝐭 , 𝐫 : Specific SU component


C Martinez

P Courtois

M Tidball

G Thébaud

Coordination problems and the control of epidemics affecting fruit trees

A complex management problem production by private owners distributed within a landscape economic losses due to the infection outbreak diffusion of pathogens intra and inter-patch finite horizon, multi-year production treatment by (partially inefficient) detection and removal of infected trees, (discrete binary choice) Our objective: understand better the decentralized behavior. Emerging literature: [Atallah et al., 2017], [Fenichel et al., 2014], [Costello et al., 2017] We analyze classical questions... coordination issues, inefficiency characterization... with specific modeling constraints Modeling: infection diffusion within a period Management options: ρ i ∈ {0, ρ max }; 0 < ρ max < 1 State variables:

I i Quantity of infected in patch i. S i Quantity of uninfected trees.
Growth and diffusion of the infection: r ij Evolutionary law (discrete time model), with I << S: Economic model: profit function

(I t+1 i , S t+1 i ) = f (S t , I t , ρ t ) I t+1 i = I t i (1 -ρ i ) + N j=1 I t j (1 -ρ j )r ji S t+1 i = S t i - N j=1 I t j (1 -ρ j )r ji
π t i (I t , S t , ρ t ) = S t+1 i v i + I t+1 i u i - ρ t i ρ max (c a + c h A i )
subject to:

(I t+1 , S t+1 ) = f (S t , I t , ρ t ).
v i production value by an uninfected tree in patch i u i production value by an infected tree i c a access cost c h per ha -1 inspection cost A i patch i surface

Results

Impact of the initial condition in the 2 patches 2 steps model: Maximal effort as a FNE

An
Proposition: Within the initial condition state space, there is a zone where initial infection is sufficiently high so that both players do maximal effort: (ρ max , ρ max , ρ max , ρ max ) is the unique Nash equilibrium if and only if (I 0 1 , I 0 2 ) ∈ ∆ max , where ∆ max is defined by the set of inequalities:

           I 0 2 > α 1 -I 0 1 (1-ρmax )(1+r 11 ) (1-ρmax )r 21 I 0 2 > α 2 -I 0 1 (1-ρmax )r 12 (1-ρmax )(1+r 22 ) I 0 2 > k 2 I 0 1 > k 1 where α i ≡ 1 F i (c a + c h 1 ρmax A i ) where F i ≡ (v i -u i )r ii -u i ,

Maximal effort and initial infection

Illustration for ρ max as a unique Nash equilibrium

β i ≡ 1 D i (c a + c h 1 ρmax A i ) where D i ≡ (v i -u i )r ii + (v j -u j )r ij -u i α i ≡ 1 F i (c a + c h 1 ρmax A i ) where F i ≡ (v i -u i )r ii -u i C. Martinez (INRA,CEE-M) 23/05/2018 11 / 19
Number of Nash equilibria Proposition: Multiplicity might arise... even in a symmetric case (proof using an example).

Example, Nash equilibria according to the initial condition Symmetric example, inefficiency

Conclusion

Main results

When infection is still small, (I << S), and detection imperfect, and given parameters (T , R, U, V ...)

Nash

Figure :

 : Figure: Sharka example

Modeling:

  Infection diffusion, two patches modelDiffusion in a two patches model

  and k 1 and k 2 are some constants. Private efficiency in the case of maximal effort C. Martinez (INRA,CEE-

Figure :

 : Figure: Map of Nash equilibria according to initial state variables values. The C. Martinez (INRA,CEE-M) 23/05/2018 13 / 19

Figure

  Figure: Pareto optimum, symmetric example

  Costello, C., Querou, N., and Tomini, A. (2017). Private eradication of mobile public bads. European Economic Review, 94:23-44.Fenichel, E. P., Richards, T. J., and Shanafelt, D. W. (2014). The control of invasive species on private property with neighbor-to-neighbor spillovers. Environmental and Resource Economics, 59(2):231-255.

	Conclusion Atallah, S. S., Gómez, M. I., and Conrad, J. M. (2017). Specification of spatial-dynamic externalities and implications for Temporal structure
	strategic behavior in disease control.
	Land Economics, 93(2):209-229.
	Perspectives
	Introduce asymmetry in the case study, look at the impact of other parameters Thanks for listening !
	feedback resolution of the game shows equilibria depending on Study de-synchronization of production cycles and longer time
	the initial infection level horizons
	Geometric characterization of efficiency and inefficiency zones as a Apply this framework to analyze real life problems (find some data);
	function of the initial infectious state question large scale management programs using known parameters
	Coordination issues: multiplicity of equilibria for some (I 0 1 , I 0 2 )
	C. Martinez (INRA,CEE-M)	23/05/2018	18 / 19

C. Martinez (INRA,CEE-M) 23/05/2018 19 / 19

C. Martinez (INRA,CEE-M) 23/05/2018

Conceptual framework

Framework

Resolution for the closed loop feedback-Nash equilibrium concept. Comparison with the Pareto optimum.