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Inferring population size history from both modern and ancient genomes using Approximate Bayesian Computation
No full textInternational audienceOne of population genetics oldest challenges is the inferrence of effective population size (Ne), a central parameter that impacts the genetic diversity and resilience of a population. Population and conservation genetics are keenly interested in its estimation. The constant improvement of sequencing methods and the quickly growing amount of available genetic data have motivated the development of methods capable of screening vast quantities of whole-genome data to estimate past Ne trajectories for thousands of generations. Such algorithms include Sequentially Markovian Coalescent (SMC) approaches such as the PSMC (Li and Durbin, 2011) and MSMC (Schiffels and Durbin, 2014), but also methods based on Approximate Bayesian Computation (ABC, Tavaré et al. 1997). ABC methods use summary statistics to infer Ne, which allow them to take into account whole-genome data such as Single Nucleotide Polymorphism (SNP). The SNPs' abundance (how often a SNP is present in a population), their allele frequency distribution and linkage disequilibrium (how allele frequencies at two SNPs are correlated) are good indicators of past population size. However, all those methods use modern DNA samples for their calculations. Ancient DNA, or DNA extracted from archeological samples, is a potential way to improve past Ne estimates by giving us a glimpse in the population' past genetic diversity. To test this hypothesis, we updated PopSizeABC (Boitard et al. 2016), an ABC method using whole-genome SNP data to infer past Ne trajectories, so that it can take into consideration DNA data from several time points. Using simulated modern and ancient DNA under various population' histories, we show that the addition of new summary statistics accounting for allele frequency variations across generations reduces prediction error. In the future, we plan to apply PopSizeABC to empirical data, using the European Eel (Anguilla anguilla) as a test species. The European Eel, being a species supposed to be panmictic, is an especially interesting model as both ancient and modern samples can be assumed to come from the same population
Federated FAIR Semantic Artefacts Discovery and Search with OntoPortal Federation
No full textInternational audienceThe explosion in the number of ontologies and semantic artefacts has come with the importance of developing Semantic Artefact Catalogues to support diverse research communities to harvest, share and serve these artefacts as FAIR objects. However, the lack of interoperability of these catalogues hampers cross disciplinary studies and make semantic stakeholders work quite cumbersome juggling back and forth from one tool to another. In this paper, we define Semantic Artefact Catalogues interoperability and report on three approaches studied. We present the implementation of the OntoPortal Federation, i.e., the technical and collaboration processes engaged to federate multiple OntoPortal-based catalogues. We showcase how AgroPortal, EcoPortal, EarthPortal, and BiodivPortal, have been federated and now enable federated browsing and search, facilitating seamless access to distributed semantic artefacts and ontologies across their respective disciplines: agri-food, ecology, earth sciences and biodiversity. We discuss technical challenges and governance decisions and conclude by outlining future directions toward a sustainable and community-driven OntoPortal-based semantic layer for open science data infrastructures
Transition écologique territoriale : Faire dialoguer expertise scientifique et concertation citoyenne
No full textNational audienc
Wintering strategies of two king penguin populations of the Southern Indian Ocean
No full textInternational audienceThe king penguin Aptenodytes patagonicus is an important model species of the Southern Ocean. While there is extensive knowledge on the foraging movement of this species during the summer in the early chick-provisioning period, little information is available for the winter period. To fill this gap, we tracked 13 individuals during the winter from 2 neighboring populations of the Southern Indian Ocean, namely the Kerguelen and the Crozet Archipelagos, and examined penguin locations with respect to remote sensing data. Tracked penguins from Kerguelen mostly headed east of the archipelago, while those from Crozet islands headed southwest. This resulted in contrasting latitudes used between the 2 wintering locations. The different directions taken possibly result from the distinct oceanic features around the 2 islands: at Kerguelen, extensive spring blooms transported east of the island might sustain prey well until the winter, offering favorable conditions for penguins. At Crozet, blooms are reduced in intensity and penguins might instead head south to benefit from the better foraging conditions near the sea ice. Such distinct foraging distributions relative to the 2 archipelagos are consistent with the at-sea distribution of other penguin species (e.g. Eudyptes spp.) breeding in the same localities. We highlight 2 distinct winter foraging strategies in neighboring king penguin populations, shaped by the contrasting oceanographic conditions surrounding their breeding sites
Assessing the Future ODYSEA Satellite Mission for the Estimation of Ocean Surface Currents, Wind Stress, Energy Fluxes, and the Mechanical Coupling Between the Ocean and the Atmosphere
No full textInternational audienceOver the past decade, several studies based on coupled ocean–atmosphere simulations have shown that the oceanic surface current feedback to the atmosphere (CFB) leads to a slow-down of the mean oceanic circulation and, overall, to the so-called eddy killing effect, i.e., a sink of kinetic energy from oceanic eddies to the atmosphere that damps the oceanic mesoscale activity by about 30%, with upscaling effects on large-scale currents. Despite significant improvements in the representation of western boundary currents and mesoscale eddies in numerical models, some discrepancies remain when comparing numerical simulations with satellite observations. These discrepancies include a stronger wind and wind stress response to surface currents and a larger air–sea kinetic energy flux from the ocean to the atmosphere in numerical simulations. However, altimetric gridded products are known to largely underestimate mesoscale activity, and the satellite observations operate at different spatial and temporal resolutions and do not simultaneously measure surface currents and wind stress, leading to large uncertainties in air–sea mechanical energy flux estimates. ODYSEA is a new satellite mission project that aims to simultaneously monitor total surface currents and wind stress with a spatial sampling interval of 5 km and 90% daily global coverage. This study evaluates the potential of ODYSEA to measure surface winds, currents, energy fluxes, and ocean–atmosphere coupling coefficients. To this end, we generated synthetic ODYSEA data from a high-resolution coupled ocean–wave–atmosphere simulation of the Gulf Stream using ODYSIM, the Doppler scatterometer simulator for ODYSEA. Our results indicate that ODYSEA would significantly improve the monitoring of eddy kinetic energy, the kinetic energy cascade, and air–sea kinetic energy flux in the Gulf Stream region. Despite the improvement over the current measurements, the estimates of the coupling coefficients between surface currents and wind stress may still have large uncertainties due to the noise inherent in ODYSEA, and also due to measurement capabilities related to wind stress. This study evidences that halving the measurement noise in surface currents would lead to a more accurate estimation of the surface eddy kinetic energy and wind stress coupling coefficients. Since measurement noise in surface currents strongly depends on the square root of the transmit power of the Doppler scatterometer antenna, noise levels can be reduced by increasing the antenna length. However, exploring other alternatives, such as the use of neural networks, could also be a promising approach. Additionally, the combination of wind stress estimation from ODYSEA with other satellite products and numerical simulations could improve the representation of wind stress in gridded products. Future efforts should focus on the assessment of the potential of ODYSEA in quantifying the production of eddy kinetic energy through horizontal energy fluxes and air–sea energy fluxes related to divergent and rotational motions
Demandes de justice et traitement des injustices socio-spatiales et environnementales dans les pays du Sud.: Note conceptuelle
No full textMany rural people in the Global South are experiencing strong processes of land exclusion and exposure to health and environmental risks (pollution, etc.), often linked to particularly brutal extractivist logics. The concepts of socio-spatial and environmental justice are increasingly being used in research aimed at describing these situations and analyzing the various forms of resistance or contestation they generate. The result of a collective project, this text proposes a conceptual framework for identifying and analyzing local perceptions of injustice, the forms of their expression, the demands for justice and the responses they receive, in varied political and institutional contexts, but all marked by a colonial history and the forms of layered citizenship it induced.De nombreuses populations rurales dans les pays du Sud connaissent des processus forts d’exclusion foncière et d’exposition à des risques sanitaires et environnementaux (pollutions, etc.), souvent liés à des logiques extractivistes particulièrement brutales. Face à ces situations, on observe une mobilisation croissante des concepts de justice socio-spatiale et environnementale dans les travaux de recherche visant à les décrire et à analyser les différentes formes de résistance ou de contestation qu’elles suscitent. Issue d’un chantier collectif, ce texte propose un cadre conceptuel pour penser les perceptions locales de l’injustice, les formes de leur expression, les demandes de justice et les réponses qu’elles reçoivent, dans des contextes politiques et institutionnels variés, mais tous marqués par une histoire coloniale et les formes de citoyenneté feuilletée qu’elle a induit
Otolith shape variability of labrid fish from Rapa Nui (Easter Island), southeastern Pacific
No full textInternational audienceFish otolith shape provides valuable insights into fish species' taxonomic, phylogenetic, and ecological traits. This study aimed to assess and compare the phenotypic variation in otolith shape among four labrid species (Anampses femininus, Coris debueni, Pseudolabrus fuentesi, and Thalassoma lutescens) inhabiting Rapa Nui (Easter Island) in the southeastern Pacific Ocean, utilizing geometric morphometrics and aging methods. Age estimation based on otolith structure indicated that collected specimens were adults, ranging between 1 and 3 years old. Allometric analysis revealed low but significant variation (5.40%), primarily driven by changes in otolith width, resulting in distinct morphologies. Principal Component Analysis (PCA) of sagittal otoliths elucidated significant morphospace variation among species, with the first two PCs explaining 60.3% of the total variance. PC1 distinguished between elongated sagittal shapes (e.g., P. fuentesi) and robust sagittae (e.g., T. lutescens), while PC2 correlated with otolith roundness, delineating variations within species. Canonical variate analysis further highlighted differences in otolith shape, with significant variations detected among all species. The Discriminant function analysis showed high levels of discrimination accuracy for most of species' pairs. Except for C. debueni-P. fuentesi (89%) and C. debueni-T. lutescens (96%), all other species pairs achieved 100% discrimination, highlighting the reliability of otolith shape as a distinguishing characteristic for the studied species. Overall, our findings emphasize the value of otolith shape analysis for characterizing and distinguishing Rapa Nui labrid species. This offers potential applications such as identifying prey within the digestive systems of large fish or bird predators near this isolated island in the South Pacific Ocean or archaeofauna studies
Towards solar metallurgy: iron ore reduction by ammonia under concentrated light flux
No full textInternational audienceIron and steel making are responsible for around 7% of global CO2 emissions. The use of fossil fuels to provide both the heat needed to reduce iron ore into iron and the reducing agent is the principal cause of these emissions. Here, we focus on an alternative pathway for direct iron ore reduction using concentrated light power as the heat source and ammonia as the reducing gas. Experiments were performed on industrial iron ore pellets and compared to the ones obtained using hydrogen as a reducer. We showed that below 600°C, reduction with ammonia proceeds via iron nitrides formation. Reduction dynamics is slower for ammonia for short exposure times but is rapidly caught up, so that reduction ratios as high as the ones obtained for hydrogen are observed. Notably, degrees of reduction exceeding 90% in 5 min were obtained on disks cut from industrial iron ore pellets. This work therefore opens a promising route towards ammonia-based solar metallurgy
Hemolymph microbiota and immune effectors’ expressions driven by geographical rearing acclimation of the aquacultured Penaeus stylirostris
No full textInternational audienceBackground : In holobiont, microbiota is known to play a central role on the health and immunity of its host. Then, understanding the microbiota, its dynamic according to the environmental conditions and its link to the immunity would help to react to potential dysbiosis of aquacultured species. While the gut microbiota is highly studied, in marine invertebrates the hemolymph microbiota is often set aside even if it remains an important actor of the hemolymph homeostasis. Indeed, the hemolymph harbors the factors involved in the animal homeostasis that interacts with the microbiota, the immunity. In the Southwest Pacific, the high economical valued shrimp Penaeus stylirostris is reared in two contrasted sites, in New Caledonia (NC) and in French Polynesia (FPResults: We characterized the active microbiota inhabiting the hemolymph of shrimps while considering its stability during two seasons and at a one-month interval and evidenced an important microbial variability between the shrimps according to the rearing conditions and the sites. We highlighted specific biomarkers along with a common core microbiota composed of 6 ASVs. Putative microbial functions were mostly associated with bacterial competition, infections and metabolism in NC, while they were highly associated with the cell metabolism in FP suggesting a rearing site discrimination. Differential relative expression of immune effectors measured in the hemolymph of two shrimp populations from NC and FP, exhibited higher level of expression in NC compared to FP. In addition, differential relative expression of immune effectors was correlated to bacterial biomarkers based on their geographical location. Conclusions: Our data suggest that, in Pacific shrimps, both the microbiota and the expression of the immune effectors could have undergone differential immunostimulation according to the rearing site as well as a geographical adaptative divergence of the shrimps as an holobiont, to their rearing sites. Further, the identification of proxies such as the core microbiota and site biomarkers, could be used to guide future actions to monitor the bacterial microbiota and thus preserve the productions
Guadeloupe and Haiti's coffee genetic resources reflect the crop's regional and global history
No full textThe data and related documentations that support the findings of this study are available on request in DataSuds repository (IRD, France) at: https://doi.org/10.23708/MRPVHL.International audienceSocietal Impact Statement: Despite strong historical declines, Guadeloupe and Haiti's coffee sectors remain important to rural communities' livelihood and resilience. Coffee also holds value as part of the islands' historical legacy and cultural identities. Furthermore, it is often grown in agroforestry systems providing important ecosystem services, which will become more important as these vulnerable islands work to adapt to a changing climate. Current efforts to revitalize coffee farms and target strategically important specialty markets would benefit from understanding existing genetic resources and the historical factors that shaped them. Our study reveals the rich history reflected in current coffee stands on the islands.Summary: . The West Indies, particularly former French colonies like Haiti and Guadeloupe, were central to the spread of coffee in the Americas. The histories of these Islands are shared until the 19th century, where they diverged significantly. Still, both Islands experienced a strong decline in their coffee sector. Characterizing the genetic and varietal diversity of their coffee resources and understanding historical factors shaping them can help support revitalization efforts.. To that end, we performed Kompetitve Allele-Specific PCR (KASP) genotyping of 80 informative single nucleotide polymorphism (SNP) markers on field samples from across main coffee-growing region of Guadeloupe, and two historically important ones in Haiti, as well as 146 reference accessions from international collections. We also compared bioclimatic variables from sampled geographic areas and searched for historical determinants of present coffee resources.. At least five Coffea arabica varietal groups were found in Haiti, versus two in Guadeloupe, with admixed individuals in both. The traditional Typica variety is still present in both islands, growing across a variety of climatic environments. We also found Coffea canephora on both islands, with multiple likely origins, and identified C. liberica var. liberica in Guadeloupe.. These differences are explained by the Islands' respective histories. Overall, Guadeloupe experienced fewer, but older introductions of non-Typica coffee. By contrast, several recent introductions have taken place in Haiti, driven by local and global factors and reflecting the history of Arabica varietal development and spread. Diversity on these islands is dynamic, and our results reveal opportunities and limits to the future of Guadeloupean and Haitian coffee