When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that “Everything is everywhere, but the environment selects”, we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.France. Agence nationale de la recherche (grant PHYTBACK (ANR-10-BLAN-7109))European Union (EU Micro B3 project)European Research Council (ERC Diatomite project)Gordon and Betty Moore Foundation (Grant #3778

Compétition par interférence, température et dynamique des populations structurées (étude expérimentale et théorique chez le collembole folsomia candida)

La compétition par interférence et ses effets sur la dynamique des populations suscitent un intérêt croissant. La température a aussi un fort effet sur la physiologie et les comportements individuels ainsi que sur les dynamiques des populations. Face au changement climatique, comprendre les interactions compétition-température-dynamique des populations est un enjeu majeur en biologie des populations. Les interactions entre individus sont liées à leur taille corporelle. La structure en taille de populations de deux clones du collembole Folsomia candida a été suivie pendant 2 à 4 ans à 4 températures. L'analyse des séries temporelles de leur structure à 21C a révélé une dépendance de la dynamique aux conditions individuelles d¿accès à la ressource, liées aux plus grands individus. Nous avons modifié la structure de populations à 21C et observé leur retour à l'équilibre, puis observé le comportement d'accès à la ressource. Cela a démontré le rôle des grands adultes dans la régulation des populations, en interférant avec les plus petits pour l'accès aux ressources. Grâce à un modèle de populations structurées intégrant l'interférence, nous avons montré que son intensité croissante cause : l'amortissement des cycles de générations, la survie de grands individus, des cycles induits par l'interférence. Nous avons enfin comparé les normes de réactions à la température sur des individus isolés et dans des populations afin de comprendre les interactions compétition-température dans la régulation des populations. Plusieurs niveaux de complexité permettent de comprendre l'effet des changements environnementaux sur les populations.Interference competition and its effects on population dynamics are of growing interest. Temperature also plays an important role on the physiology and individual behavior as well as on population dynamics populations. In the context of climate change, understanding the effect of interactions between individuals on population dynamics and their interactions with temperature is an important issue for population biology. Interactions between individuals are related to their body size. The size structure of several populations of two clones of Collembola Folsomia candida was monitored for 2-4 years at four temperatures from 11 C to 26 C. The time series analysis of their structure at 21 C revealed a dependence of the dynamics on individual access to the resource related to the presence of large individuals. We then changed some population structures at 21 C and observed their return to equilibrium. We observed real-time access to the resource behavior. These studies have shown the role of large adults in population control by interfering with smaller individuals for access to resources. Through a structured model incorporating interference competition, we have shown that its intensity may have different effects on the dynamics of structured populations: damping single generation cycles, allowing the survival of large individuals, and causing interference induced cycles. Finally, we compared the reaction norms to temperature on isolated individuals and populations in order to understand the competition-temperature interactions in regulating populations. Several levels of complexity allow us to understand the effect of environmental change on populationsPARIS-JUSSIEU-Bib.électronique (751059901) / SudocSudocFranceF

Effects of finite-range interactions on the one-electron spectral properties of TTF-TCNQ

The electronic dispersions of the quasi-one-dimensional organic conductor TTF-TCNQ are studied by angle-resolved photoelectron spectroscopy (ARPES) with higher angular resolution and accordingly smaller step width than in previous studies. Our experimental results suggest that a refinement of the single-band 1D Hubbard model that includes finite-range interactions is needed to explain these photoemission data. To account for the effects of these finite-range interactions we employ a mobile quantum impurity scheme that describes the scattering of fractionalized particles at energies above the standard Tomonaga-Luttinger liquid limit. Our theoretical predictions agree quantitatively with the location in the (k,ω) plane of the experimentally observed ARPES structures at these higher energies. The nonperturbative microscopic mechanisms that control the spectral properties are found to simplify in terms of the exotic scattering of the charge fractionalized particles. We find that the scattering occurs in the unitary limit of (minus) infinite scattering length, which limit occurs within neutron-neutron interactions in shells of neutron stars and in the scattering of ultracold atoms but not in perturbative electronic condensed-matter systems. Our results provide important physical information on the exotic processes involved in the finite-range electron interactions that control the high-energy spectral properties of TTF-TCNQ. Our results also apply to a wider class of 1D and quasi-1D materials and systems that are of theoretical and potential technological interest.We thank Claus S. Jacobsen for providing the single crystals used in our ARPES studies. J.M.P.C. acknowledges the late Adilet Imambekov for discussions that were helpful in writing this paper. He also would like to thank Boston University's Condensed Matter Theory Visitors Program for support and the hospitality of MIT. J.M.P.C. and T.C. acknowledge the support from Fundacao para a Ciencia e Tecnologia (FCT) through the Grants No. UID/FIS/04650/2013 and No. PTDC/FIS-MAC/29291/2017, J.M.P.C. acknowledges that from the FCT Grants No. SFRH/BSAB/142925/2018 and No. POCI-01-0145-FEDER-028887, and T.C. acknowledges the support from the National Natural Science Foundation of China Grant No. 11650110443

Distributed System Contract Monitoring

The use of behavioural contracts, to specify, regulate and verify systems, is particularly relevant to runtime monitoring of distributed systems. System distribution poses major challenges to contract monitoring, from monitoring-induced information leaks to computation load balancing, communication overheads and fault-tolerance. We present mDPi, a location-aware process calculus, for reasoning about monitoring of distributed systems. We define a family of Labelled Transition Systems for this calculus, which allow formal reasoning about different monitoring strategies at different levels of abstractions. We also illustrate the expressivity of the calculus by showing how contracts in a simple contract language can be synthesised into different mDPi monitors.Comment: In Proceedings FLACOS 2011, arXiv:1109.239

Using crop-pathogen modeling to identify plant traits to control Zymoseptoria tritici epidemics on wheat

Diversification in pathogen control methods to reduce the severity of economically important foliar diseases such as Zymoseptoria tritici on wheat is needed. One way is to identify plant physiological and architectural traits that influence disease development and that can be selected in the process of crop breeding. Such traits may be used for improving tolerance or disease escape. Traits favoring disease escape, the focus of our work, may significantly decrease crop epidemics (Robert et al., 2018). However, understanding the role of such traits in crop-pathogen interactions is a daunting task because the interactions are multiple and dynamic in time. To characterize and quantify crop-pathogen interactions, an innovative trait-based and resource-based modeling framework was developed (Precigout et al., 2017). In this framework, the pathosystem is assumed to respond dynamically to both architecture and physiological status of the host canopy. A canopy consists of plenty of small patches, i.e. small functional and infectable units of leaf tissue. Production of new patches, for canopy growth and renewal of photosynthetically active plant tissues, is a function of the available resources produced by the other patches. Pathogen spores can contaminate nearby healthy patches. The definition of patch proximity depends on dispersal abilities of the pathogen and canopy architecture. We used and adapted this modeling framework to quantify the effects of several plant traits on Zymoseptoria tritici epidemics for varied climate scenarios. The complex infection cycle of Z. tritici characterized by a long symptomless incubation period was implemented in the model. We studied plant architectural traits such as leaf size or stem height, and plant physiological traits such as leaf lifespan or leaf metabolite contents. In our simulations, these traits impacted the epidemics dynamics though their effects on pathogen dispersal and on the amount of resources available for the pathogen. Sensitivity analyses showed how disease severity depended on plant traits and pathogen virulence. The importance of several plant and pathogen traits could be linked to the pathogen’s ability to manage the race for the colonization of the canopy in the face of canopy growth. Playing on host traits also made it possible to simulate different wheat varieties - with contrasted heights, pathogen resistance or precocity - to characterize the behavior of the pathosystem of interest for different host ideotypes. We argue that this kind of trait-based modeling approach is a valuable tool to identify plant traits promoting more resilient agroecosystems in particular for crop breeding in a context of innovative and sustainable crop protection

<特集>「生徒は何を読んでいるか、読書は何を育てるか」 自立した読書人となるように

Recent size-structured cannibalistic models point to the importance of the energy gain by cannibals and also show that this gain may result in the emergence of giant individuals. We use a combination of a 10-year field study of a perch (Perca fluviatilis) population and quantitative within-season modeling of individual and population-level dynamics to investigate which mechanisms are most likely to drive the dynamics of the studied perch population. We focused on three main aspects to explain observed discrepancies between earlier model predictions and data: (1) introduction of more than one shared resource between cannibals and victims, (2) whether or not several victim age cohorts are necessary to allow giant growth, and (3) the intensity of inter-cohort competition between young-of-the-year (YOY) perch and 1-yr-old perch. At the start of the study period, the perch population was dominated by “stunted” perch individuals, and recruitment of perch to an age of 1-yr-old was negligible. Following a major death in adult perch, strong recruitments of perch to 1-yr-old were thereafter observed for a number of years. As 1-yr-olds these successful recruiters subsequently starved to death due to competition with the new YOY. The few surviving adult perch accelerated substantially in growth and became “giants.” At the end of the study period, the perch population moved back to the situation with stunted individuals. There was a high agreement between observed diets of cannibalistic perch and those predicted by the model for both the stunted and the giant phases. Analyses of growth rates showed that cannibalistic perch could become giants on a diet of YOY perch only, but that a supplement with the second shared resource (macroinvertebrates) was needed to reach the observed sizes. Modeling of growth and diet in the giant phase showed an exploitative competitive effect of YOY perch on 1-yr-old perch, but a restriction in habitat use of 1-yr-old perch had to be assumed to yield the observed growth rate and diet. The resource dynamics of zooplankton and macroinvertebrates were both accurately predicted by the model. Also, YOY perch mortality was accurately predicted and, furthermore, suggested that one of the trawling methods used may underestimate the number of YOY perch when they increase in size. We conclude that the presence of a second shared resource and the restricted habitat use and absence of cannibalistic consumption by 1-yr-old perch individuals are two important mechanisms to explain the discrepancy between model predictions and data. Our results also point to the fact that that the dynamics observed may be explained by complex dynamics not involving the presence of a giant and dwarf cycle