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Invasive species are permanently modifying the distribution and diversity of native species worldwide. For nearly two decades, a hornet, Vespa velutina nigrithorax (Hymenoptera: Vespidae), has been spreading in Europe. Due to its marked invasiveness, this yellow-legged hornet is of great economic and ecological concern, mainly because of the damage it causes to insects in general and bees in particular. Current management methods are sparse and ineffective. Naturally produced by insects, semio-chemicals have been proposed as integrated management tools in this context, either for disruption or mass trapping, as an alternative tool to conventional nonselective traps. Here, we focused on the venom gland, which produces the alarm pheromone. In previous studies, individuals showed marked diversity in their chemical profiles. However, to successfully conduct targeted pheromone-based trapping, the hornet's chemical ecology must be thoroughly characterized. Therefore, it was necessary to better understand the chemical composition of the alarm pheromone of not only workers but also other V. v. nigrithorax females. First, we evaluated the differences in venom gland profiles between the four types of females: queens, foundresses, pre-winter gynes, and workers. Next, we experimentally explored the venom gland profiles of V. velutina nigrithorax workers and pre-wintering gynes by in vivo and in vitro approaches. We found 13 new compounds in the venom gland, of which 9 were identified (chain lengths: C8 to C12). Two compounds were found exclusively in reproductive females. Profiles differed among pre-wintering gynes, foundresses, and queens but not between pre-wintering gynes and workers. This result indicates that the chemical signature of the female venom gland changes over the course of life history: from pre-wintering gynes to foundresses to queens., Les espèces invasives modifient en permanence la répartition et la diversité des espècesindigènes dans le monde entier. Depuis près de vingt ans, un frelon originaire d’Asie du Sud-Est,Vespa velutina nigrithorax (Hymenoptera : Vespidae), se répand en Europe. En raison de son caractèreinvasif marqué, ce frelon à pattes jaunes suscite de vives inquiétudes sur le plan économique etécologique, principalement en raison des dégâts qu’il cause aux insectes en général et aux abeillesen particulier. Les méthodes de gestion actuelles sont rares et inefficaces. Naturellement produits parles insectes, les produits sémio-chimiques ont été proposés comme outils de gestion intégrée. Dansce contexte, soit pour la perturbation, soit pour le piégeage de masse, en tant qu’outil alternatif auxpièges non sélectifs conventionnels. Ici, nous nous sommes concentrés sur la glande à venin, quiproduit la phéromone d’alarme. Des études antérieures ont montré que les femelles présentaientune variabilité dans les profils chimiques. Cependant, pour mener à bien un piégeage ciblé à basede phéromones, l’écologie chimique du frelon doit être caractérisée de manière approfondie. Il étaitdonc nécessaire de mieux comprendre la composition chimique de la phéromone d’alarme nonseulement des ouvrières, mais également des autres femelles de V. v. nigrithorax. Tout d’abord, nousavons examiné les différences dans les profils des glandes à venin entre les quatre types de femelles :les reines, les fondatrices, les gynes pré-hivernantes et les ouvrières. Ensuite, nous avons exploréexpérimentalement les profils des glandes à venin des ouvrières de V. velutina nigrithorax et des gynespré-hivernantes par des approches in vivo et in vitro. Nous avons constaté la présence de 13 nouveauxcomposés dans la glande à venin, dont 9 ont été identifiés (longueur des chaînes : C8 à C12). Deuxcomposés ont été trouvés exclusivement chez les femelles reproductrices. Les profils diffèrent entreles gynes pré-hivernantes, les fondatrices et les reines, mais pas entre les gynes pré-hivernantes et lesouvrières. Ce résultat indique que la signature chimique de la glande à venin femelle évolue au coursde l’histoire de vie : des gynes pré-hivernantes aux fondatrices, en passant par les reines.

Aging is the price to pay for acquiring and processing energy through cellular activity and life history productivity. Climate warming can exacerbate the inherent pace of aging, as illustrated by a faster erosion of protective telomere DNA sequences. This biomarker integrates individual pace of life and parental effects through the germline, but whether intra- and intergenerational telomere dynamics underlies population trends remains an open question. Here, we investigated the covariation between life history, telomere length (TL), and extinction risk among three age classes in a cold-adapted ectotherm ( Zootoca vivipara ) facing warming-induced extirpations in its distribution limits. TL followed the same threshold relationships with population extinction risk at birth, maturity, and adulthood, suggesting intergenerational accumulation of accelerated aging rate in declining populations. In dwindling populations, most neonates inherited already short telomeres, suggesting they were born physiologically old and unlikely to reach recruitment. At adulthood, TL further explained females’ reproductive performance, switching from an index of individual quality in stable populations to a biomarker of reproductive costs in those close to extirpation. We compiled these results to propose the aging loop hypothesis and conceptualize how climate-driven telomere shortening in ectotherms may accumulate across generations and generate tipping points before local extirpation.

International audience; The COVID-19 pandemic has led to a resurgence of the debate on whether host-parasite interactions should evolve towards avirulence. In this review, we first show that SARS-CoV-2 virulence is evolving, before explaining why some expect the mortality caused by the epidemic to converge towards that of human seasonal alphacoronaviruses. Leaning on existing theory, we then include viral evolution into the picture and discuss hypotheses explaining why the virulence has increased since the beginning of the pandemic. Finally, we mention some potential scenarios for the future.

The collection of animal position data via GPS tracking devices has increased in quality and usage in recent years. Animal position and movement, although measured discretely, follows the same principles of kinematic motion, and as such, the process is inherently continuous and differentiable. I demonstrate the functionality and visual elegance of smoothing spline models. I discuss the challenges and benefits of implementing such an approach, and I provide an analysis of movement and social interaction of seven jaguars inhabiting the Taiamã Ecological Station, Pantanal, Brazil, a region with the highest known density of jaguars. In the analysis, I derive measures for pairwise distance, cooccurrence, and spatiotemporal association between jaguars, borrowing ideas from density estimation and information theory. These measures are feasible as a result of spline model estimation, and they provide a critical tool for a deeper investigation of cooccurrence duration, frequency, and localized spatio‐temporal relationships between animals. In this work, I characterize a variety of interactive relationships between pairs of jaguars, and I particularly emphasize the relationships in movement of two male–female and two male–male jaguar pairs exhibiting highly associative relationships., I propose the use of smoothing spline models to explore animal movement and social interaction. I propose temporal‐state density estimation and localized mutual information measures to characterize behavior and strength of association between jaguars on a refined and unified time grid. I provide further characterization of time‐dependent male–male and female–male relationships in this region, an important step in determining conservation policy for an endangered neotropical predator.

L'écopastoralisme est une pratique de gestion écologique en plein essor, dont les bienfaits pour le maintien ou la restauration des milieux naturels ont été largement démontrés. Mais cette solution alternative de gestion obtient-elle les mêmes résultats sur des milieux fortement anthropisés et artificialisés ? Une étude menée sur les digues artificielles du Rhône de la réserve de chasse de Donzère-Mondragon s'est intéressée aux impacts des différents troupeaux sur les communautés végétales d’écosystèmes récents. Grâce à un suivi botanique sur plusieurs années, les scientifiques ont pu démontrer que la gestion par les herbivores s'avérait efficace pour maintenir l'ouverture des milieux et augmenter significativement le nombre et la diversité des espèces par rapport à l’absence de gestion ou aux interventions mécaniques.

International audience; The lipid fraction of birch pollen grains (BPGs) is not yet fully described, although pollen lipid molecules may play a role in the allergic immune response. The mechanisms by which atmospheric pollutants modify allergenic pollen grains (PGs) are also far from being elucidated despite high potential effects on allergic sensitization. This work is a contribution to a better description of the lipid profile (both external and cytoplasmic) of BPGs and of alterations induced by gaseous air pollutants. Several lipid extractions were performed using organic and aqueous solvents on BPGs following exposure to ozone and/or nitrogen dioxide and under conditions favoring the release of internal lipids. Ozone reacted with alkenes to produce aldehydes and saturated fatty acids, while nitrogen dioxide was shown to be unreactive with lipids. NO 2 exhibited a protective effect against the reactivity of alkenes with ozone, probably by competition for adsorption sites. The decreased reactivity of ozone during simultaneous exposure to NO 2 /O 3 raised the possibility of a Langmuir-Hinshelwood mechanism. Oxidation reactions induced by exposure of BPGs to ozone did not substantially modify the extraction of lipids by aqueous solvent, suggesting that the bioaccessibility of lipids was not modified by oxidation. On the contrary, the rupture of PGs appeared to be a key factor in enhancing the bioaccessibility of bioactive lipid mediators (linoleic and α-linolenic acids) in an aqueous solution. The internal lipid fraction of BPGs has specific characteristics compared with external lipids, with more abundant hexadecanoic acid, tricosanol, and particularly unsaturated fatty acids (linoleic and α-linolenic acids). Several mechanisms of action of gaseous pollutants on allergenic pollen were identified in this study: gaseous air pollutants can (i) modify the external lipid fraction by reactivity of alkenes, (ii) adsorb on the surface of PGs and be a source of oxidative stress after inhalation of PGs, and (iii) promote the release of cytoplasmic bioactive lipids by facilitating pollen rupture.

Bivalve predation by seabream has been observed worldwide and is a major concern for bivalve farmers. Farmed bivalve-seabream interactions must be better understood to ensure the sustainability of bivalve aquaculture. The objectives of this study were to characterize gilthead seabream Sparus aurata presence in a bivalve farm in Prevost Lagoon (Mediterranean Sea) using acoustic telemetry and to evaluate monthly losses of mussels Mytilus galloprovincialis and oysters Crassostrea gigas due to seabream predation over an 18 mo period inside the farm and at an unprotected experimental platform. Large (281 to 499 mm TL) seabream were more commonly detected in the bivalve farm than were small (200 to 280 mm TL) seabream. In contrast to small seabream, 90% of large seabream returned to and spent extended periods in the study area the following year, suggesting inter-annual site fidelity for large fish that used the bivalve farm as a feeding site. Signs of predation were observed on mussels and oysters throughout the year at the unprotected experimental platform. Farmers noted losses in the farm from April to September. Maximal losses (90 to 100%) were observed post-oyster ‘sticking’ and mussel socking. Despite the deployment of nets as mechanical protection to reduce predation, oyster losses represented 28% of the annual value of oysters sold while mussel losses were estimated at ca. 1%. These results suggest that bivalves must be protected by nets throughout the year to avoid predation, particularly post-handling. A collaboration between shellfish farmers and fishermen could be a sustainable solution for bivalve farming, by regularly fishing for seabream in farms, between tables and inside protective nets.

The current known distribution of Omura’s whale includes the tropical and warm temperate waters of the western Pacific, Indian, and Atlantic Oceans. Evidence of their presence in the Atlantic Ocean is based on beach cast specimens found on the coasts of Mauritania (North Atlantic) and Northeastern Brazil (South Atlantic). The present study characterizes the occurrence of this species in the São Pedro and São Paulo Archipelago (SPSPA), on the mid-Atlantic ridge between South America and Africa, based on autonomous recording systems. Acoustic signals were similar, but not identical, to B. omurai vocalizations recorded off the coast of Madagascar. Although these signals were recorded for only 11 months, there are peaks in vocal activity between May and June in the vicinities of SPSPA, suggesting either a shift in distribution within the Atlantic equatorial waters or seasonality in the species’ vocal behavior in this region. The first acoustic records of Omura’s whales in the Equatorial Atlantic suggest that these animals may also use deep-water habitats, in addition to the shallow-water habitat use observed in other regions., A atual distribuição conhecida da baleia-de-Omura (Balaenoptera omurai) inclui as águas tropicais e temperadas quentes dos oceanos Pacífico ocidental, Índico e Atlântico. A evidência de sua presença no oceano Atlântico baseia-se em espécimes encalhados encontrados em praias da Mauritânia (Atlântico Norte) e do Nordeste do Brasil (Atlântico Sul). O presente estudo caracteriza a ocorrência dessa espécie no Arquipélago de São Pedro e São Paulo (ASPSP), localizado sobre a Dorsal Mesoatlântica entre a América do Sul e a África, com base em sistemas de monitoramento acústico passivo. Os sinais acústicos detectados foram similares, mas não idênticos, às vocalizações de B. omurai gravadas na costa de Madagascar. Embora esses sinais tenham sido registrados por apenas 11 meses, há picos na atividade vocal entre maio e junho nas proximidades do ASPSP, sugerindo uma mudança na distribuição da espécie nas águas equatoriais do Atlântico ou uma sazonalidade no comportamento vocal nessa região. Os primeiros registros acústicos das baleias-de-Omura no Atlântico Equatorial sugerem que esses animais também podem utilizar habitats de águas profundas, além de habitats de águas rasas como observado em outras regiões.

International audience; Infectious disease transmission patterns in some outbreaks can be more heterogeneous than in others, with striking effects on the way epidemics unfold. Some studies show that the biological sources of heterogeneity may matter, but they tend to do so without controlling for the overall heterogeneity in the number of secondary cases caused by an infection. Here, we control for this important bias to explore the role of individual variation in infection duration and transmission rate on parasite emergence and spread. We simulate outbreaks using a stochastic SIR model, with and without parasite evolution. Consistently with existing studies, we show that the variance in the number of secondary infections has the strongest effect on outbreak emergence probability but has little effect on the epidemic dynamic once emergence is certain. The origin of heterogeneity also affects the probability of emergence, but its more striking effects are about properties of epidemics that do emerge. In particular, assuming more realistic variances in infection duration distributions lead to faster outbreaks and a higher peak of incidence. When the parasite requires evolutionary changes to be able to spread, the impact of heterogeneity depends on the underlying evolutionary model. If the parasite evolves within the host, decreasing the infection duration variance decreases the probability of emergence. These results show that using realistic distributions for infection duration is necessary to accurately capture the effect of individual heterogeneity on epidemiological dynamics, which has implications for the monitoring and control of infectious diseases, as well as data collection.

Mechanistic models of terrestrial ectotherms predict that climate warming will induce activity restriction due to heat stress and loss of shade, leading to the extinction of numerous populations. Such models rely on the assumption that activity patterns are dictated by simple temperature thresholds independent of changes in water availability. However, changes in water availability may further influence thermoregulation behaviour of ectotherms through dehydration risk perception, changes in water balance or changes in microclimatic conditions. Here, we experimentally assess the interactive effects of thermal conditions and water availability on activity patterns, shade selection and thermoregulation efficiency in a model ectothermic species. Thermoregulation behaviour of adult common lizards Zootoca vivipara was monitored in outdoor mesocosms as we manipulated water availability, providing water as mist in the morning and free-standing water during the daytime. We recorded operative temperatures and micro-meteorological conditions to infer thermal constraints and dehydration risk. Activity and shade selection were better predicted by continuous changes in thermal conditions and dehydration risk, respectively, than by threshold functions. In addition, water supplementation increased activity in males and reduced shade selection in both sexes, most probably as a behavioural response to the perception of a stronger dehydration risk. Water supplementation also influenced the thermal quality of the environment, which in turn altered daily activity patterns and thermoregulation statistics. This demonstrates that dual effects of heat and water stress on activity patterns may lead to stronger activity restriction as a result of climate change than currently predicted.

For large mammals, area expansion is a key conservation measure to prevent species’ decline and extinction. Yet, its success depends on whether animals discover and later use these areas. Here, using GPS data, we investigated how herds of elephants detected and used an area made available to them after the removal of a fence. We studied the elephants’ behaviour before and after the fence removal, accounting for seasonal changes in movement patterns. In contrast to previous studies, herds visited the newly available area within a month of the fence removal, and the maximum distance they moved into the new area was reached between 5 and 9 months after the fence removal. Yet, elephants did not preferentially visit the new area at night. By the second year, all herds had shifted their seasonal home ranges and incorporated the new area, in contrast to a previous range expansion event. Our analyses show that the regular proximity of elephants to the original fence, and the fact that the new area was generally composed of preferred habitats of the elephants, probably explained the rapid discovery and use of the area. Our study improves our understanding of animal exploration and the role of habitat quality, and thus may improve range expansion and corridor programmes.

Rapid shifts in biotic communities due to environmental variability challenge the detection of anthropogenic impacts by current biomonitoring programs. Metacommunity ecology has the potential to inform such programs, because it combines dispersal processes with niche-based approaches and recognizes variability in community composition. Using intermittent rivers—prevalent and highly dynamic ecosystems that sometimes dry—we develop a conceptual model to illustrate how dispersal limitation and flow intermittence influence the performance of biological indices. We produce a methodological framework integrating physical- and organismal-based dispersal measurements into predictive modeling, to inform development of dynamic ecological quality assessments. Such metacommunity-based approaches could be extended to other ecosystems and are required to underpin our capacity to monitor and protect ecosystems threatened under future environmental changes.

International audience; Background No circulating biomarker is available for endometrial carcinoma (EC). We aimed to identify DNA positions universally hypermethylated in EC, and to develop a digital droplet PCR (ddPCR) assay for detection of hypermethylated circulating tumor DNA (meth-ctDNA) in plasma from patients with EC. Methods DNA positions hypermethylated in EC, and without unspecific hypermethylation in tissue/cell types releasing circulating cell-free DNA in plasma, were identified in silico from TCGA/Gene Expression Omnibus (GEO) data. A methylation-specific ddPCR (meth-ddPCR) assay following bisulfite conversion of DNA extracted from plasma was optimized for detection of meth-ctDNA according to dMIQE guidelines. Performances were validated on a retrospective cohort (n = 78 tumors, n = 30 tumor-adjacent tissues), a prospective pilot cohort (n = 33 stage I–IV patients), and 55 patients/donors without cancer.Results Hypermethylation of zinc finger and SCAN domain containing 12 (ZSCAN12) and/or oxytocin (OXT) classified EC samples from multiple noncancer samples with high diagnostic specificity/sensitivity [>97%; area under the curve (AUC) = 0.99; TCGA/GEO tissues/blood samples]. These results were confirmed in the independent retrospective cohort (AUC = 0.99). Meth-ddPCR showed a high analytical specificity (limit of blank = 2) and sensitivity (absolute lower threshold of detection = 50 pgmethDNA/mLplasma). In the pilot cohort, meth-ctDNA was detected in pretreatment plasma samples from 9/11 and 5/20 patients with advanced and non-advanced EC, respectively. 2 of 9 patients had ctDNA detected after macroscopic complete surgery and experienced progression within 6 months. No healthy donors had any copy of hypermethylated DNA detected in plasma.Conclusions Meth-ddPCR of ZSCAN12/OXT allows a highly specific and sensitive detection of ctDNA in plasma from patients with EC and appears promising for personalized approaches for these patients.

Animals regulate their diet in order to maximise the expression of fitness traits that often have different nutritional needs. These nutritional trade-offs have been experimentally uncovered using the Geometric framework for nutrition (GF). However, current analytical methods to measure such responses rely on either visual inspection or complex models applied to multidimensional performance landscapes, making these approaches subjective, or conceptually difficult, computationally expensive, and in some cases inaccurate. This limits our ability to understand how animal nutrition evolved to support life-histories within and between species. Here, we introduce a simple trigonometric model to measure nutritional trade-offs in multidimensional landscapes (‘Nutrigonometry’). Nutrigonometry is both conceptually and computationally easier than current approaches, as it harnesses the trigonometric relationships of right-angle triangles instead of vector calculations. Using landmark GF datasets, we first show how polynomial (Bayesian) regressions can be used for precise and accurate predictions of peaks and valleys in performance landscapes, irrespective of the underlying structure of the data (i.e., individual food intakes vs fixed diet ratios). Using trigonometric relationships, we then identified the known nutritional trade-off between lifespan and reproductive rate both in terms of nutrient balance and concentration. Nutrigonometry enables a fast, reliable and reproducible quantification of nutritional trade-offs in multidimensional performance landscapes, thereby broadening the potential for future developments in comparative research on the evolution of animal nutrition.

Genetic structure, i.e. intra-population genetic diversity and inter-population genetic differentiation, is influenced by the amount and spatial configuration of habitat. Measuring the amount of reachable habitat (ARH) makes it possible to describe habitat patterns by considering intra-patch and inter-patch connectivity, dispersal capacities and matrix resistance. Complementary ARH metrics computed under various resistance scenarios are expected to reflect both drift and gene flow influence on genetic structure. Using an empirical genetic dataset concerning the large marsh grasshopper (Stethophyma grossum), we tested whether ARH metrics are good predictors of genetic structure. We further investigated (i) how the components of the ARH influence genetic structure and (ii) which resistance scenario best explains these relationships. We computed local genetic diversity and genetic differentiation indices in genetic graphs, and ARH metrics in the unified and flexible framework offered by landscape graphs, and we tested the relationships between these variables. ARH metrics were relevant predictors of the two components of genetic structure, providing an advantage over commonly used habitat metrics. Although allelic richness was significantly explained by three complementary ARH metrics in the best PLS regression model, private allelic richness and MIW indices were essentially related with the ARH measured outside the focal patch. Considering several matrix resistance scenarios was also key for explaining the different genetic responses. We thus call for further use of ARH metrics in landscape genetics to explain the influence of habitat patterns on the different components of genetic structure.

International audience; Aim: Seasonal bird migration is one of the most fascinating global ecological phenomena. Yet, the biogeographic scenarios and climatic drivers that led single species or entire lineages to evolve seasonal migration between disjunct breeding and wintering ranges remain unclear. Based on distribution and phylogenetic data for all birds worldwide, we explored the biogeographic and climatic context of the evolutionary emergence of seasonal geographic migration in birds. Location: Global. Taxon: The Aves class (9,819 species). Methods: We used the worldwide phylogeny of all birds, with a new backbone tree, to test the link between birds' migration distance (short, variable, long) and strategy (resident, mixed, strict migrant) with four different metrics depicting species' thermal niches in their breeding and wintering ranges. We also performed ancestral state reconstructions for the main migratory orders to reconstruct past events of appearance and loss of migration behaviour, and past biogeographic scenarios that led to the emergence of seasonal geographic migration. Results: Migratory species generally experience warmer climates in their wintering range compared to their breeding one, although notable exceptions exist. This thermal niche change due to migration was found to be much larger for species travelling large distances. We also found that geographic migration emerged at different time periods through varied biogeographic paths (i.e. both from temperate and tropical ancestors) and that migration behaviour was likely ancestral to Passeriformes, with several subsequent episodes of loss of migration behaviour. Main conclusions: We report an evolutionary correlation between long-distance migration and the tendency of birds to seek warmer climates during their non-breeding period , compared to short-distance migrants. Migration behaviour was likely ancestral to Passeriformes, and migratory lineages in general seem to have often adapted to novel ecological opportunities by returning to a resident state. Our results provide the first large-scale study of biogeographic and climatic origins of bird migration worldwide. K E Y W O R D S ancestral state reconstructions, biogeographic scenarios, bird migration, climatic niche conservatism, migration distance, phylogenetic comparative methods

Analysis of genetic diversity represents a fundamental component of ecological risk assessments in contaminated environments. Many studies have assessed the genetic implications of chronic radiation exposure at Chernobyl, generally recording an elevated genetic diversity and mutation rate in rodents, plants, and birds inhabiting contaminated areas. Only limited studies have considered genetic diversity in aquatic biota at Chernobyl, despite the large number of freshwater systems where elevated dose rates will persist for many years. Consequently, the present study aimed to assess the effects of chronic radiation exposure on genetic diversity in the freshwater crustacean, Asellus aquaticus, using a genome‐wide SNP approach (Genotyping‐by‐sequencing). It was hypothesized that genetic diversity in A. aquaticus would be positively correlated with dose rate. A. aquaticus was collected from six lakes in Belarus and the Ukraine ranging in dose rate from 0.064 to 27.1 µGy/hr. Genotyping‐by‐sequencing analysis was performed on 74 individuals. A significant relationship between geographical distance and genetic differentiation confirmed the Isolation‐by‐Distance model. Conversely, no significant relationship between dose rate and genetic differentiation suggested no effect of the contamination gradient on genetic differentiation between populations. No significant relationship between five measures of genetic diversity and dose rate was recorded, suggesting that radiation exposure has not significantly influenced genetic diversity in A. aquaticus at Chernobyl. This is the first study to adopt a genome‐wide SNP approach to assess the impacts of environmental radiation exposure on biota. These findings are fundamental to understanding the long‐term success of aquatic populations in contaminated environments at Chernobyl and Fukushima., This study utilized a genotyping by sequencing method to provide a novel assessment of the impacts of chronic radiation exposure at Chernobyl on a freshwater crustacean. No significant impact of over 30 years of radiation exposure on genetic variation was recorded. These findings are fundamental to understanding the long‐term success of aquatic populations in contaminated environments at Chernobyl and Fukushima.

The Warburg effect is one of the hallmarks of cancer cells in humans. It is a true metabolic reprogramming to aerobic glycolysis, allowing cancer cells to meet their particular energy needs for growth, proliferation, and resistance to apoptosis, depending on the microenvironment they encounter within the tumor. We have recently discovered that the Crassostrea gigas oyster can naturally reprogram its metabolism to the Warburg effect. Thus, the oyster becomes a new invertebrate model useful for cancer research. Due to its lifestyle, the oyster C. gigas has special abilities to adapt its metabolism to the extreme changes in the environment in which it is located. The oyster C. gigas is therefore a model of interest to study how the environment can control the Warburg effect under conditions that could not be explored in vertebrate model species., L’effet Warburg est l’une des caractéristiques des cellules cancéreuses chez l’homme. C’est une véritable reprogrammation métabolique vers la glycolyse aérobie, permettant aux cellules cancéreuses de satisfaire leurs besoins énergétiques en fonction du microenvironnement qu’elles rencontrent au sein de la tumeur. De par son mode de vie, l’huître Crassostrea gigas possède des capacités particulières afin d’adapter son métabolisme aux changements extrêmes du milieu dans lequel elle se trouve. Elle est naturellement capable de reprogrammer son métabolisme vers l’effet Warburg. C. gigas représente ainsi un modèle d’intérêt pour étudier comment l’environnement peut contrôler l’effet Warburg dans des conditions qui ne pourraient être explorées chez des espèces modèles vertébrés.

[EN] In many Mediterranean areas, citrus orchards exhibit high soil loss rates because of the expansion of drip irrigation that allows cultivation on sloping terrain and the widespread use of glyphosate. To mitigate these non-sustainable soil losses, straw mulch could be applied as an efficient solution but this has been poorly studied. Therefore, the main goal of this paper was to assess the use of straw mulch as a tool to reduce soil losses in clementine plantations, which can be considered representative of a typical Mediterranean citrus orchard. A total of 40 rainfall simulation experiments were carried out on 20 pairs of neighbouring bare and mulched plots. Each experiment involved applying 38.8 mm of rain at a constant rate over 1 h to a circular plot of 0.28 m(2) circular plots. The results showed that a cover of 50% of straw (60 g m(-2)) was able to delay the time to ponding from 32 to 52 s and the time to runoff initiation from 57 to 129 s. Also, the mulching reduced the runoff coefficient from 65.6 to 50.5%. The effect on sediment transport was even more pronounced, as the straw mulch reduced the sediment concentration from 16.7 g l(-1) to 3.6 g l(-1) and the soil erosion rates from 439 g to 73 g. Our results indicated that mulching can be used as a useful management practice to control soil erosion rates due to the immediate effect on high soil detachment rate and runoff initiation reduction in conventional clementine orchards on sloping land, by slowing down runoff initiation and by reducing runoff generation and, especially, sediment losses. We indirectly concluded that straw mulch is also a sustainable solution in glyphosate-treated citrus plantations., This paper is part of the results of research projects GL2008-02879/BTE, LEDDRA 243857 and RECARE-FP7 (ENV.2013.6.2-4).

International audience; Mountain social-ecological systems (SES) supply important ecosystem services that are threatened by climate change. In mountain SES there is a paradox between high community capacity to cope with extremes, and governance structures and processes that constrain that capacity from being realised. Climate adaptation that maintains livelihoods and supply of ecosystem services can catalyse this innate adaptive capacity if new adaptive governance arrangements can be created. Using the French Alps as a case study, we outline a participative framework for transformative adaptation that links adaptive capacity and governance to provide social innovation and ecosystem-based adaptation solutions for mountain SES. Grassland management was the main entry point for adaptation: bundles of adaptation services supplied by the landscape mosaic of biodiverse grassland types can maintain agricultural production and tourism and facilitate income diversification. Deliberate management for core adaptation services like resilient fodder production, erosion control, shade or aesthetic value generates co-benefits for future transformation ability. People activate bundles of adaptation services along adaptation pathways and realise benefits via co-production with other forms of capital including traditional knowledge or social networks. Common and distinctive adaptation services in each pathway create options for transformation if barriers from interactions between values and rules across scales can be overcome. For example conserving mown terraces which is a critical adaptation nexus reflects a complex interplay of values, markets and governance instruments from local to European scales. We conclude that increasing stakeholders capacity to mobilise adaptation services is critical for empowering them to implement adaptation to global change.

A new species of the genusStygepactophanesMoeschler & Rouch, 1984 (Copepoda, Harpacticoida, Canthocamptidae) is established to accommodate a small canthocamptid population collected from a spring system in the “Parc du Mercantour”, Var catchment, southern France. The population analysed in the present study is defined by a set of morphological characters of the female, namely a very large maxilliped, a rudimentary mandibular palp, P1 with 3-segmented exopod and 2-segmented endopod, a falcate terminal claw of the P1 endopod, dorsal seta of caudal rami inserted on the inner margin, and anal operculum not overreaching the insertion of the caudal rami, thus supporting its assignment into the genusStygepactophanes. The new speciesStygepactophanesoccitanusshows marked differences with the nominotypical species of the genus that was originally described by monotypy with the speciesStygepactophanesjurassicusMoeschler & Rouch, 1984. The main diagnostic traits ofS.jurassicusare the absence of the P5 and a falcate outer terminal claw of P1 endopod.Stygepactophanesjurassicusalso shows a reduced armature of the antennal exopod, bearing one seta, 1-segmented P2–P4 endopods, a reduced armature of P2–P4 exopodal segments 3 (3,4,4 armature elements, respectively), P6 bearing only one long seta, a rounded short and smooth anal operculum. Conversely the female ofS.occitanusGalassi & Fiers,sp. n.has a well-developed P5, with rudimentary intercoxal sclerite, together with a falcate outer terminal claw of P1 endopod, antennal exopod bearing two elements, P4 endopod 1-segmented versus 2-segmented in P2–P3, P2–P4 exopodal segment 3 with five armature elements, P6 with three setae of different lengths, rounded anal operculum, bearing 3–4 strong spinules.According to our present knowledge,S.occitanusGalassi & Fiers,sp. n.is assigned to the genusStygepactophanesas the most conservative solution, waiting for the male to be discovered. The genusStygepactophanesrepresents a distinct lineage within the harpacticoid family Canthocamptidae that colonised southern European groundwater, the genus being known only from the saturated karst in Switzerland and a fissured saturated aquifer in southern France. Both species of the genus are stygobites and narrow endemics, the nominotypical species being known from the type locality Source de la Doux in Délemont (Switzerland), andS.occitanusGalassi & Fiers,sp. n.described herein from a spring system of the Var catchment (France).

International audience; With forest fragmentation continuing in many parts of the tropics, it is likely that fragmented forests will become the rule for most remaining global tropical forests in the next decades. In this context, there is a need for practical tools to assess and monitor fragmented forests if we are to conserve tree species diversity as much as possible. Several methods, either using (1) field-based or (2) remote-sensing approaches could be used to achieve this goal. This paper aims at providing a state-of-the-art review of both approaches in order to make recommendations for rapid and cost-effective assessments of tree species diversity and forest structure, with specific applications in studies of fragmented tropical forests. Overall both methods have pros and cons, depending on the type of data needed to address the research objectives and the quantity of resources available. We suggest combining the use of both field-based and remotely-sensed methods as they can be complementary. Remote-sensing data should be used to predict and map the tree species diversity and stand structure at regional scales, while field-inventories provide accurate information at local scales and allow validation of remotely-sensed data. For field-inventories, we recommend the use of small (e.g. 20 × 50 m) plots with a 10 cm DBH minimum measurement. In terms of remotely-sensed techniques, if funding is sufficient, airborne imagery seems the best regarding the quality of information (i.e. hyperspectral and hyperspatial imagery, LiDAR). If funding is limited, a cost-effective alternative providing reasonably accurate estimates would be the use of high-resolution satellite imagery such as Worldview. Ultimately, for studies where data accessible for free is the only possible option, we recommend the use of Sentinel-2, although it is relatively coarser in terms of quality. However, further research needs to be done to validate these approaches in fragmented tropical forests.

Characterization of the worldwide genetic diversity of 447 P. vivax strains shows evidence for a Southeast Asian origin., Plasmodium vivax is the most common and widespread human malaria parasite. It was recently proposed that P. vivax originates from sub-Saharan Africa based on the circulation of its closest genetic relatives (P. vivax-like) among African great apes. However, the limited number of genetic markers and samples investigated questions the robustness of this hypothesis. Here, we extensively characterized the genomic variations of 447 human P. vivax strains and 19 ape P. vivax-like strains collected worldwide. Phylogenetic relationships between human and ape Plasmodium strains revealed that P. vivax is a sister clade of P. vivax-like, not included within the radiation of P. vivax-like. By investigating various aspects of P. vivax genetic variation, we identified several notable geographical patterns in summary statistics in function of the increasing geographic distance from Southeast Asia, suggesting that P. vivax may have derived from a single area in Asia through serial founder effects.

This map presents the distribution of all bird species which were counted during the 2021 Vigur Island research campaign by Milesi-Gaches, D. and Lhériau, A., Cette carte présente la répartition de toutes les espèces d'oiseaux qui ont été dénombrées lors de la campagne de recherche 2021 de l'île Vigur par Milesi-Gaches, D. et Lhériau, A., Þetta kort sýnir dreifingu allra fuglategunda sem voru taldar í Vigur-eyju rannsóknarátakinu 2021 af Milesi-Gaches, D. og Lhériau, A.

International audience; Pour des raisons techniques et économiques, toutes les masses d’eau européennes ne bénéficient pas d’un suivi direct de leur qualité établi à partir d’une collecte régulière de données biologiques. En France, cela représente environ dix mille sites. Pour combler ces lacunes, des chercheurs d’INRAE ont mis au point un ensemble de modèles capables de prédire avec un bon taux de réussite l’état écologique de ces masses d’eau à partir d’un jeu de données de pressions. Si ce type d’outil prédictif est d’un intérêt majeur pour les gestionnaires, il ne doit cependant pas être considéré comme une approche antagoniste à l'amélioration du réseau de surveillance mais plutôt comme un moyen de fournir un cadre général pour aider les politiques de l'eau.

Multi-type infection processes are ubiquitous in ecology, epidemiology and social systems, but remain hard to analyze and to understand on a fundamental level. Here, we study a multi-strain susceptible-infected-susceptible model with coinfection. A host already colonized by one strain can become more or less vulnerable to co-colonization by a second strain, as a result of facilitating or competitive interactions between the two. Fitness differences between N strains are mediated through \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N^2$$\end{document}N2 altered susceptibilities to secondary infection that depend on colonizer-cocolonizer identities (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$K_{ij}$$\end{document}Kij). By assuming strain similarity in such pairwise traits, we derive a model reduction for the endemic system using separation of timescales. This ‘quasi-neutrality’ in trait space sets a fast timescale where all strains interact neutrally, and a slow timescale where selective dynamics unfold. We find that these slow dynamics are governed by the replicator equation for N strains. Our framework allows to build the community dynamics bottom-up from only pairwise invasion fitnesses between members. We highlight that mean fitness of the multi-strain network, changes with their individual dynamics, acts equally upon each type, and is a key indicator of system resistance to invasion. By uncovering the link between N-strain epidemiological coexistence and the replicator equation, we show that the ecology of co-colonization relates to Fisher’s fundamental theorem and to Lotka-Volterra systems. Besides efficient computation and complexity reduction for any system size, these results open new perspectives into high-dimensional community ecology, detection of species interactions, and evolution of biodiversity. Electronic supplementary material The online version of this article (10.1007/s11538-020-00816-w) contains supplementary material, which is available to authorized users.

Background To describe the effect of mechanical ventilation on diaphragm mitochondrial oxygen consumption, ATP production, reactive oxygen species (ROS) generation, and cytochrome c oxidase activity and content, and their relationship to diaphragm strength in an experimental model of sepsis. Methods A cecal ligation and puncture (CLP) protocol was performed in 12 rats while 12 controls underwent sham operation. Half of the rats in each group were paralyzed and mechanically ventilated. We performed blood gas analysis and lactic acid assays 6 h after surgery. Afterwards, we measured diaphragm strength and mitochondrial oxygen consumption, ATP and ROS generation, and cytochrome c oxidase activity. We also measured malondialdehyde (MDA) content as an index of lipid peroxidation, and mRNA expression of the proinflammatory interleukin-1β (IL-1β) in diaphragms. Results CLP rats showed severe hypotension, metabolic acidosis, and upregulation of diaphragm IL-1β mRNA expression. Compared to sham controls, spontaneously breathing CLP rats showed lower diaphragm force and increased susceptibility to fatigue, along with depressed mitochondrial oxygen consumption and ATP production and cytochrome c oxidase activity. These rats also showed increased mitochondrial ROS generation and MDA content. Mechanical ventilation markedly restored mitochondrial oxygen consumption and ATP production in CLP rats; lowered mitochondrial ROS production by the complex 3; and preserved cytochrome c oxidase activity. Conclusion In an experimental model of sepsis, early initiation of mechanical ventilation restores diaphragm mitochondrial function.

International audience; This book presents some of the most recent tools, methods and concepts in historical ecology. It introduces students and researchers to state-of-the-art techniques and showcases a wide array of methods dedicated to understanding the history of tropical landscapes. The chapters cover the detection and characterisation of archaeological features, living organisms as witnesses of past human activities, ethnoecological knowledge of ancient anthropogenic landscapes and societal impacts of historical ecology. Whilst mainly based on Amazonian experiences, the contributions aim to strengthen synergies between disciplines and to propose solutions that can be applied elsewhere in the field.

Interstitial cystitis/Bladder Pain Syndrome (IC/BPS) is a chronic inflammatory disease characterized by visceral pain and voiding symptoms. IC/BPS is still an unsolved enigma with ineffective diagnosis criteria and treatment. A main limitation in IC/BPS understanding is the lack of appropriate preclinical model. Cyclophosphamide (CYP) is commonly used as an experimental model for IC/BPS in rodent. However, the proposed models are very aggressive, contrasting with what occurs in clinic, and often associated with severe toxicity and high mortality rate. In addition, visceral pain, the hallmark symptom of IC/BPS, has been validated in only few of them. In this study, we developed a chronic model of CYP-induced IC/BPS in female rat. In our protocol, no severe weight loss occurred and the survival rate was 100%. In accordance to human pathology, chronic CYP-injected rats developed severe painful behavior whereas only sparse inflammation was observed. Inflammatory response was characterized by bladder edema and focal urothelial damage but absence of massive infiltrate. This chronic model showed persistent symptoms indicative for a central sensitization mechanism. We further demonstrate that CYP-induced chronic visceral pain was significantly reduced by curative treatment with clinically relevant compounds (gabapentin, ibuprofen, and Ialuril ®). We therefore developed and validated a rat model of chronic cystitis that shares strong similarity with human non-ulcerative IC/BPS features without overtly affecting the animal health. This model will thus provide mechanistic insights of the disease and help to evaluate therapeutic agents for IC/BPS.

Ecological systems are undeniably complex, including many species interacting in different ways with each other (e.g., predation, competition, facilitation, parasitism). One way of visualizing, describing, and studying this complexity is to represent them as networks, where nodes are typically species and links are interactions between these species. The study of these networks allows understanding of the rules governing the topology of their links, and assessing how network structure drives ecological dynamics. Studies on different types of ecological networks have suggested that they exhibit structural regularities, which in turn affect network dynamics and resilience to perturbations. Although the use of networks to represent ecological communities dates back to the early stages of the discipline, the last two decades have seen rapid progresses in our understanding of ecological networks, as data are collected at a faster rate and better resolution, as metrics are continuously developed to better characterize network structure and as numerical simulations of mathematical models have allowed investigating how network structure and dynamics are related in more comprehensive and realistic ecological networks. This chapter describes some of the recent developments and challenges related to the study of ecological networks. After defining networks in general, and ecological networks more specifically, recent results regarding the structure of different types of ecological networks, and what is known about their dynamics and resilience, are presented.

International audience; Marine noise pollution (MNP) can cause a multitude of impacts on many organisms, but information is often scattered and general outcomes difficult to assess. We have reviewed the literature on MNP impacts on Mediterranean fish and invertebrates. Both chronic and acute MNP produced by various human activities - e.g. maritime traffic, pile driving, air guns - were found to cause detectable effects on intra-specific communication, vital processes, physiology, behavioral patterns, health status and survival. These effects on individuals can extend to inducing population- and ecosystem-wide alterations, especially when MNP impacts functionally important species, such as keystone predators and habitat forming species. Curbing the threats of MNP in the Mediterranean Sea is a challenging task, but a variety of measures could be adopted to mitigate MNP impacts. Successful measures will require more accurate information on impacts and that effective management of MNP really becomes a priority in the policy makers' agenda.

Viral diseases cause significant losses in aquaculture. Prophylactic measures, such as immune priming, are promising control strategies. Treatment of the Pacific oyster (Crassostrea gigas) with the double-stranded RNA analog poly(I·C) confers long-term protection against infection with ostreid herpesvirus 1, the causative agent of Pacific oyster mortality syndrome. In a recent article in mBio, Lafont and coauthors (M. Lafont, A. Vergnes, J. Vidal-Dupiol, J., Viral diseases cause significant losses in aquaculture. Prophylactic measures, such as immune priming, are promising control strategies. Treatment of the Pacific oyster (Crassostrea gigas) with the double-stranded RNA analog poly(I·C) confers long-term protection against infection with ostreid herpesvirus 1, the causative agent of Pacific oyster mortality syndrome. In a recent article in mBio, Lafont and coauthors (M. Lafont, A. Vergnes, J. Vidal-Dupiol, J. de Lorgeril, et al., mBio 11:e02777-19, 2020, https://doi.org/10.1128/mBio.02777-19) characterized the transcriptome of oysters treated with poly(I·C). This immune stimulator induced genes related to the interferon and apoptosis pathways. This response overlaps the response to viral infection, and high expression levels of potential effector genes are maintained for up to 4 months. This work opens the door to characterization of the phenomena of immune priming in a poorly studied invertebrate model. It also highlights the importance of interferon-like responses for invertebrate antiviral immunity.

International audience

20 pages; International audience; Molluscs are one of the most diversified phyla among metazoans. Most of them produce an external calcified shell, resulting from the secretory activity of a specialized epithelium of the calcifying mantle. This biomineralization process is controlled by a set of extracellular macromolecules, the organic matrix. In spite of several studies, these components are mainly known for bivalves and gastropods. In the present study, we investigated the physical and biochemical properties of the internal planispiral shell of the Ram's Horn squid Spirula spirula. Scanning Electron Microscope investigations of the shell reveal a complex microstructural organization. The saccharides constitute a quantitatively important moiety of the matrix, as shown by Fourier-transform infrared and solid-state nuclear magnetic resonance spectroscopies. NMR identified β-chitin and additional polysaccharides for a total amount of 80% of the insoluble fraction. Proteomics was applied to both soluble and insoluble matrices and in silico searches were performed, first on heterologous metazoans models, and secondly on an unpublished transcriptome of Spirula spirula. In the first case, several peptides were identified, some of them matching with tyrosinase, chitinase 2, protease inhibitor, or immunoglobulin. In the second case, 39 hits were obtained, including transferrin, a serine protease inhibitor, matrilin, or different histones. The very few similarities with known molluscan shell matrix proteins suggest that Spirula spirula uses a unique set of shell matrix proteins for constructing its internal shell. The absence of similarity with closely related cephalopods demonstrates that there is no obvious phylogenetic signal in the cephalopod skeletal matrix.

17 pages; International audience; AimSpecies distribution modelling (SDM) represents a valuable alternative to predict species distribution over vast and remote areas of the ocean. We tested whether reliable SDMs can be generated for benthic marine organisms at the scale of the Southern Ocean. We aimed at identifying the main large‐scale factors that determine the distribution of the selected species. The robustness of SDMs was tested with regards to sampling effort, species niche width and biogeography.LocationSouthern Ocean.MethodsThe impact of sampling effort was tested using two sets of data: one set with all presence‐only data available until 2005, and a second set using all data available until 2015 including recent records from campaigns carried out during the Census of Antarctic Marine Life (CAML) and the International Polar Year (IPY) period (2005–2010). The accuracy of SDMs was tested using a ground‐truthing approach by comparing recent presence/absence data collected during the CAML and IPY period to pre‐CAML model predictions.ResultsOur results show the significance of the SDM approach and the role of abiotic factors as important drivers of species distribution at broad spatial scale. The addition of recent data to the models significantly improved the prediction of SDM and changed the respective contributions of environmental predictors. However, the intensity of change varied between models depending on sampling tools, species ecological niche width and biogeographic barriers to dispersal.Main conclusionsWe highlight the need for new data and the significance of the ground‐truthing approach to test the accuracy of SDMs. We show the importance of data collected through international initiatives, su ch as the CAML and IPY to the improvement of species distribution modelling at broad spatial scales. Finally, we discussed the relevance of SDM as a relevant marine conservation tool particularly in the context of climate change and the definition of Marine Protected Areas.

International audience; 1. High mountain lakes are a network of sentinels, sensitive to any events occurring within their waterbodies, their surrounding catchments and their airsheds. By modifying nutrient balance and availability in water, both local and global changes are expected to alter primary productivity and to trigger strong ecological impacts in these ecosystems. 2. Predicting ecological trajectories under future change is a key challenge for both scientists and conservation managers. French alpine lakes, in the most southern and western part of the European Alps, have received surprisingly little attention to date. In this article, we address how variations in nitrogen (N) and phosphorus (P) supply are likely to impact the area's phytoplankton growth. We performed N and/or P enrichment microcosm experiments under controlled conditions on 12 phytoplankton assemblages sampled during the summer 2016 in four French alpine lakes with contrasting catchments and N-deposition regimes. 3. The nutrients limiting phytoplankton growth varied according to the nutrient sto-ichiometry of the lake water. In the lakes exposed to high N-deposition rates (≈700 kg N km-2 year-1), the water contained more N than P and phytoplankton growth in microcosms was either limited by P or not limited by either N or P. In the lakes exposed to low N-deposition rates (≈500 kg N km-2 year-1), N availability relative to P was lower in the lake with vegetated catchment than in the lake with rocky catchment, resulting in a switch from P to NP colimitation of the phytoplankton in microcosms. 4. Our data clearly indicate that French alpine lakes do not host the same diversity and structure of phytoplankton communities and that phytoplankton composition influenced phytoplankton growth in microcosms. First, we show that nonmotile colonial chlorophytes appeared in late summer assemblages, with lower growth rates but P-storage abilities. Second, our findings indicate that the growth of phytoplankton assemblages dominated by diatoms was increasingly limited by sil-ica (SiO 2) throughout the summer, along with a 70% decrease in SiO 2 concentration in lake water. 5. The forecast global changes in the French Alps should increase phytoplankton growth in most high mountain lakes where P is the main limiting nutrient, beforeNP colimitation. These changes are likely to be of lesser extent in lakes with large vegetated catchments in the northern area with lower N-deposition rates and of greater extent in the southern area with higher N-deposition rates and future P-deposition rates. 6. By investigating the relationship between nutrient availability, phytoplankton composition and phytoplankton growth rate, this experimental laboratory microcosm study will help interpret current multifactorial data from in situ monitoring networks in the Alps. It will also be helpful to develop models to better predict the sentinel lake responses to local and global changes.

Paleogenetics, the genetic study of organisms and populations of the past, became possible when the methods of molecular biology allowed the analysis of degraded DNA preserved in trace amounts in certain ancient biological remains, such as bones, teeth, hair or soft tissue of mummies. This has contributed significantly to archeology, paleontology, paleopathology or paleoecology. Recently, the progress of DNA sequencing has brought about a new quantum leap of the field since next-generation sequencing allows the analysis of whole genomes of past organisms. This led to the revision of our view of the last stages of the evolution of humans and of the peopling of Eurasia and the Americas, but also of the domestication of animals and some plants, the evolution of wild populations in response to climate changes, the evolution of pathogens responsible for past epidemics, etc. Paleogenomics revolutionized already the idea we had about the recent evolution of our species, but it is legitimate to expect the field to make further important contributions to archeology., La paléogénétique, l’étude génétique des organismes et populations du passé, est devenue possible quand les méthodes de la biologie moléculaire ont permis l’analyse de l’ADN préservé en état très dégradé et en très faible quantité dans certains restes biologiques anciens comme des ossements, des dents, des poils, ou encore des tissus mous de momies. Ces études ont contribué de manière très significative à l’archéologie, la paléontologie, la paléopathologie ou encore la paléoécologie. Plus récemment, le progrès des méthodes de séquençage de l’ADN a conduit à un nouveau saut quantique de ce domaine puisque le séquençage de nouvelle génération rend possible non seulement l’analyse de quelques gènes mais aussi de génomes entiers des organismes du passé augmentant de plusieurs ordres de grandeur la quantité d’informations que l’on peut obtenir. Ceci a permis une révision de notre vision des dernières étapes de l’évolution humaine et du peuplement de l’Eurasie et de l’Amérique, mais aussi des processus de domestication des animaux et de certaines plantes, de l’évolution des populations sauvages animales et végétales en réponse aux changements climatiques, de l’évolution des pathogènes responsables d’épidémies, etc. La paléogénomique a ainsi déjà réussi à révolutionner l’idée que nous nous sommes faites de l’évolution récente de notre espèce, et on peut légitimement attendre d’elle d’autres très belles contributions à l’archéologie.

We used ringed-recoveries to assess: 1) the connectivity (movements of individuals) between the three putative flyways (north–west Europe, central Europe, south–west Asia) of common pochards in the Western Palearctic, 2) possible spatio-temporal variations in the distribution of the species, and, 3) temporal evolution in spring and autumn migration dates. Based on winter counts of common pochards in the north–west European flyway, we distinguished three periods in the analyses (1960–1990, 1991–2000 and 2001–2016), which correspond to successive periods of population increase, peak and decline, respectively. Whatever the season (wintering or breeding) and period of ringing, large probabilities of ring-recoveries outside the flyway of origin (ringing) were recorded, suggesting a high connectivity between the three putative flyways. There was a significant trend towards an earlier departure from the wintering area, and an eastward shift of spring recoveries over periods. In contrast, neither autumn/winter recovery locations, nor departure dates from the breeding area in Latvia and Russia changed over periods. The latter results do not support the hypothesis that short-stopping (i.e. a reduction of fall migration distances/delaying of departure dates from the breeding area) could explain the observed decline of wintering common pochards in the north–west European flyway. Indirect recoveries support that large proportions of individuals wintering in western Europe may originate from the south–west Asia flyway and more particularly from a region in Siberia located in the Ob river catchment area. Considering trends in numbers for the three flyways together confirmed the “vulnerable” IUCN status of common pochard in the Western Palearctic as a whole, with a 35% decline over the last decade. The important connectivity between the northwest, central European and southwest Asian flyways call for considering such conservation problems at a much broader scale than the regional flyway.

Bioindicators of running freshwaters in Central African Republic : benthic macroinvertebrates and anthropogenic stress in the Nguitto Stream. This study of benthic macroinvertebrates in Central African Republic (CAR) aimed at determining the structure of their assemblages in relation to the physico-chemical quality of the Nguitto River. The data were collected monthly from May 2015 to April 2016, in five selected sampling points on the Nguitto River. The physico-chemical parameters were measured using standard methods while the benthic macrofauna was collected using a handnet sampler of 150 μm mesh size on a total area of about 6 m² per station. The physico-chemical analysis revealed a satisfactory water quality in the forest belt and an eutrophication in the urban area. A number of 2052 individuals of benthic macroinvertebrates belonging to 71 taxa were identified and counted. Arthropods was the most diversified (53 taxa) and the most abundant (80.75 %) taxonomic group, followed by molluscs (17 taxa ; 23.94 %) and annelids (1 taxon ; 0.24 %). The sampling points in the forest belt, which exhibit the lowest anthropogenic activity, were composed mostly of arthropods and dominated by insects. In the urban zone, the strong abundance of molluscs and the presence of annelids indicated an anthropogenic pressure and the usefulness of invertebrates as bioindicators of waste waters in this area., Cette étude sur les macro-invertébrés benthiques en République Centrafricaine (RCA) visait à déterminer la structure de leurs peuplements en relation avec la qualité physico-chimique de l’eau dans le ruisseau Nguitto. Les données ont été collectées de mai 2015 à avril 2016 avec une fréquence mensuelle dans cinq stations d’échantillonnage de l’amont vers l’aval du cours d’eau. Les analyses physico-chimiques ont été effectuées par des méthodes standards tandis que la macrofaune benthique a été récoltée à l’aide d’un filet troubleau avec un vide de maille de 150 μm sur une superficie totale d’environ 6 m² par station. Les analyses physico-chimiques ont révélé une qualité de l’eau satisfaisante à bonne dans la zone forestière et une eutrophisation en zone urbaine. Au total, 2052 macro-invertébrés benthiques, répartis en 71 taxa, ont été identifiés et dénombrés. Les arthropodes sont les plus diversifiés avec 53 taxa et les plus abondants (80,75 % de l’effectif total), suivis des mollusques (17 taxa ; 23,94 %) et des annélides (1 taxon ; 0,24 %). Les stations en zone forestière sont composées en majorité d’arthropodes dominés par les insectes confirmant un faible niveau de perturbation par les activités anthropiques. En zone urbaine, la forte abondance des mollusques et la présence des annélides indiquent une pression anthropique plus forte, illustrant l’intérêt de ces organismes comme bioindicateurs des petits cours d’eau dans ce pays., Ngoay-Kossy Jean Clair,Zébazé Togouet Serge Hubert,Wango Solange Patricia,Bolevane Ouantinam Serge Florent,Tchakonté Siméon,Piscart Christophe. Bioindicateurs des milieux aquatiques lotiques en république centrafricaine : macro-invertébrés benthiques et pression anthropique du cours d’eau Nguitto. In: Revue d'Écologie (La Terre et La Vie), tome 73, n°4, 2018. pp. 603-616.

In this study we present a list of invasive/potential invasive alien species in the East and South European Network for Invasive Alien Species (ESENIAS) countries with marine borders. The species were classified according to the existing literature and experts’ judgment, as established, casual, invasive and expected. Finally, factsheets were compiled for ten species of high importance based on their expanding/invading character. Of the 160 species comprising the list, 149 were already present in the ESENIAS countries, while eleven were invasive species either present in the Mediterranean or in other European Seas, likely to be recorded in the ESENIAS countries. The majority of the species were of Red Sea/IndoPacific origin (97 species; 60.6%). Italy, Turkey and Greece were the countries with the highest representation of species (159, 152 and 139 species respectively), due to their extended coastline and the number of scholars working on marine invasive species. The highest number of established species was recorded in Turkey (116 species), whereas in Italy and Greece the most numerous species were the “expected” ones (85 and 48 species, respectively). The eastern Adriatic Sea countries (i.e. Albania, Croatia, Montenegro and Slovenia) had generally low numbers of species in this list, many of which are still “expected” to arrive from the neighbouring countries of Greece and Italy. Finally, the most frequently potential pathway was transfer stowaways (ship ballast water: 41 cases; ship hull fouling: 55), whereas unaided spread of Lessepsian immigrants followed (95 cases). This list is intended to serve as an early warning system that through horizon scanning process would assist ESENIAS countries to prioritise invasive alien species, their pathways and the areas of higher likelihood to appear, in order to take management measures., U ovom radu predstavljamo popis invazivnih i potencijalno invazivnih vrsta na istoku i jugu Europske mreže za invazivne vrste (ESENIAS) u zemljama s morskim granicama. Vrste su klasificirane prema postojećoj literaturi i procjeni stručnjaka, pa su tako utvrđene grupe povremenih, invazivnih i očekivanih vrsta. Podaci su dati za deset vrsta čija se važnost temelji na njihovom širenju i invazivnom karakteru. Od 160 vrsta koje sadrži popis, 148 je već bilo prisutno u ESENIAS zemljama, dok je 9 invazivnih vrsta bilo prisutno u Sredozemnom ili u drugim europskim morima, a vjerojatno je da će se zabilježiti i u zemljama udruženim u ESENIAS. Većina vrsta je bile iz Crvenog mora / indopacifičkog podrijetla (97 vrsta, 60,6%). Italija, Turska i Grčka su zemlje s najvišom zastupljenošću vrsta (159, 152 i 139), zbog njihove proširene obale i broja znanstvenika koji rade na morskim invazivnim vrstama. Najveći broj utvrđenih vrsta zabilježen je u Turskoj (116 vrsta), dok su u Italiji i Grčkoj najbrojnije vrste bile “očekivane” (85 i 48 vrsta, respektivno). Istočne zemlje Jadranskog mora (npr. Albanija, Hrvatska, Crna Gora i Slovenija) imale su općenito nizak broj vrsta na ovom popisu, od kojih mnoge još “očekujemo” da pristignu iz susjednih zemalja: Grčke i Italije. Konačno, najčešće su potencijalni putovi bili „transferni putnici“ (balastna voda broda: 41 slučaj, obraštaj brodskog trupa: 55), dok je slijedilo i širenje lesepsijskih migranata (95 slučajeva). Ovaj popis je namijenjen da služi kao sustav ranog upozorenja koji bi kroz proces skeniranja pomogao državama ESENIAS da daju prioritet invazivnim stranim vrstama, njihovim putovima i područjima veće vjerojatnosti pojavljivanja, kako bi se poduzele potrebne mjere upravljanja.

Les échantillons sanguins ou urinaires prélevés dans les laboratoires de biologie médicale sont aujourd’hui dirigés vers des plateformes d’analyse centralisées permettant l’optimisation des analyses, tant sur le plan technique qu’économique. Ces plateformes sont équipées d’automates spécialisés utilisant de nombreux réactifs chimiques. Ces réactifs contiennent parfois des substances très écotoxiques qui peuvent ainsi être rejetées au réseau d’assainissement urbain sans traitement préalable. Dans le but de caractériser les dangers environnementaux liés à ces rejets liquides méconnus, un programme de caractérisation chimique et écotoxicologique a été mis en place sur les rejets d’un laboratoire pilote situé dans la région lyonnaise. Ce programme a montré la forte écotoxicité des rejets de certains automates. Il a également mis en évidence l’écotoxicité des rejets liquides traités à l’Eau de Javel dans le laboratoire, dans le but d’éliminer les germes pathogènes. Après consolidation par la réalisation de mesures sur d’autres sites, ces résultats pourront être utilisés par les responsables des plateformes en vue de l’amélioration de la gestion de leurs rejets : remplacement de certains réactifs par des composés moins écotoxiques, prétraitement de certains rejets sur le site même du laboratoire, évacuation des rejets les plus écotoxiques, ou difficilement traitables in situ, vers des filières de traitement adaptées., The blood and urine samples taken in local medical laboratories are today treated in large analytical centres that enable the optimization of analyses, technically and economically. These centres are equipped with automatic machines that use various chemical reactants. These reactants sometimes contain very toxic substances, which can be released into urban sewage networks without treatment. In order to characterize the environmental hazard linked to these unknown liquid wastes, a chemical and ecotoxicological program was set up to investigate the liquid wastes of a pilot laboratory situated in the Lyon area. This program has demonstrated the strong ecotoxicity of liquid wastes from certain automatic analysis machines. It has also revealed the ecotoxicity of liquid wastes that are treated with bleach before release into the sewage network, in order to eliminate pathogenic germs. These results can be used by managers of analytical centres in order to improve the management of their liquid wastes: replacement of some reactants by less ecotoxic compounds, in situ pretreatment of certain liquid wastes, elimination of the most toxic liquid wastes in specialized treatment plants.

The success of oral infection by viruses depends on their capacity to overcome the gut epithelial barrier of their host to crossing over apical, mucous extracellular matrices. As orally transmitted viruses, densoviruses, are also challenged by the complexity of the insect gut barriers, more specifically by the chitinous peritrophic matrix, that lines and protects the midgut epithelium, how capsids stick to and cross these barriers to reach their final cell destination where replication goes has been poorly studied in insects. Here, we analyzed the early interaction of the Junonia coenia densovirus (JcDV) with the midgut barriers of caterpillars from the pest Spodoptera frugiperda. Using combination of imaging, biochemical, proteomic and transcriptomic analyses, we examined in vitro, ex vivo and in vivo the early interaction of the capsids with the peritrophic matrix and the consequence of early oral infection on the overall gut function. We show that the JcDV particle rapidly adheres to the peritrophic matrix through interaction with different glycans including chitin and glycoproteins, and that these interactions are necessary for oral infection. Proteomic analyses of JcDV binding proteins of the peritrophic matrix revealed mucins and non-mucins proteins including enzymes already known to act as receptors for several insect pathogens. In addition, we show that JcDV early infection results in an arrest of N-Acetylglucosamine secretion and a disruption in the integrity of the peritrophic matrix, which may help viral particles to pass through. Finally, JcDV early infection induces changes in midgut genes expression favoring an increased metabolism including an increased translational activity. These dysregulations probably participate to the overall dysfunction of the gut barrier in the early steps of viral pathogenesis. A better understanding of early steps of densovirus infection process is crucial to build biocontrol strategies against major insect pests.

We report four draft genome sequences of Nocardia spp. The strains are the Nocardia cyriacigeorgica DSM 44484 pathogenic type strain; two environmental isolates, Nocardia cyriacigeorgica EML446 and EML1456; and the Nocardia asteroides ATCC 19247 nonpathogenic type strain, with estimated genome sizes of 6.3 to 6.8 Mb. The study of these isolates will provide insight into physiology, evolution, and pathogenicity of Nocardia spp.

Trabajo presentado en la EGU General Assembly 2019, celebrada en Viena del 3 al 8 de mayo de 2019., There are many studies assessing the regulating ecosystem services of cover crops in woody crops (e.g. soilfertility or erosion control) but rarely the landscape and their associated cultural ecosystem services have beenevaluated, especially in relatively small agricultural areas. The region is in southern Spain and encompass 17municipalities with a surface of 5052 ha of vines assigned to the Appellation.Within the project VineDivers, several studies were carried out in the region at different spatial scales(from landscape to vineyard): i) elaboration of an inventory of the landscape elements of one representativemunicipality (Aguilar de la Frontera) [1], ii) digitization and analysis of landscape buffers corresponding to 750m circles radius around the centroid of 16 commercial vineyards [2], and iii) field measurements of vegetationinter-rows at the vineyards under a range of soil management intensities [3]. Furthermore, iv) stakeholders weresurveyed to study if landscape complexity and soil management practices provide cultural ecosystem services [4,5].This communication presents the results obtained from these studies. Numerous possible areas of actionhave been identified in which the implementation of diversification measures of the landscape elements wouldbe essential for controlling erosion and preserving environmental sustainability. Olive orchards are the dominantlandscape elements around the studied vineyards. Our results highlighted the effect of landscape complexity andsoil management intensity on cultural ecosystem services provision. In general terms, the interrow managementof the vineyards and vegetation typology determines the appreciation of the landscape by the respondents, beingaesthetically better valued the cover crop vineyards.

Pl@ntNet is a participatory platform and information system dedicated to the production of botanical data through deep learning-based plant identification. It includes 3 main front-ends, an Android app (the most advanced and the most used one), an iOs app (being currently re-developed) and a web version. The main feature of the application is to return the ranked list of the most likely species providing an image or an image set of an individual plant. In addition, Pl@ntNet’s search engine returns the images of the dataset that are the most similar to the queried observation allowing interactive validation by the users. The back-office running on the server side of the platform is based on Snoop visual search engine (a software developed by ZENITH) and on NewSQL technologies for the data management. The application is distributed in more than 180 countries (10M downloads) and allows identifying about 20K plant species at present time.

International audience; Over the past decades, research on insect cognition has made considerable advances in describing the ability of model species (in particular bees and fruit flies) to achieve cognitive tasks once thought to be unique to vertebrates, and investigating how these may be implemented in a miniature brain. While this lab-based research is critical to understand some fundamental mechanisms of insect brains and cognition, taking a more integrative and comparative view will help making sense of this rich behavioural repertoire and its evolution. Here we argue that there is a need to reconsider insect cognition into an ecological context in order to design experiments that address the cognitive challenges insects face in nature, identify competing hypotheses about the cognitive abilities driving the observed behavioural responses, and test them across different populations and species. Reconnecting with the tradition of naturalistic observations, by testing animals in the field or in ecologically-inspired setups and comparing their performances, is complementary to mechanistic research in the lab, and will greatly improve our understanding of the role of insect cognition, its diversity, and the influence of ecological factors in its evolution.

International audience

WOS:000579910600080; International audience; A simple ICP-MS procedure for the determination of trace element concentrations in GBCAs is described here. Abundances of most of the REEs, Y, Ba and Pb concentrations were determined. We confirm that GBCAs contain traces of non-Gd REEs, Y, Ba and Pb. REE patterns of the five GBCAs actually administered in France have been obtained. They display specific shapes that make it possible to identify the different Gd oxides oxides used by pharmaceutical laboratories to produce them. Our method enables us to quickly evaluate the quantities of impurities in these products and, if necessary, to follow the evolution of their quality in the future. The presence of small but not negligible quantities of Y and REEs other than Gd cannot be ignored in these products, and their behaviour in the human body must be considered. The concentrations measured for Pb and Ba, on the other hand, are much lower and do not pose any particular problems.