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Synthesis and validation of dual Pi3k/mTOR inhibitors and probes for the treatment of cancer
No full textInternational audienc
3D models related to the publication: Taxonomy and evolutionary history of peradectids (Metatheria): new data from the early Eocene of France
No full textInternational audienceThis contribution contains the three-dimensional models of the most complete and/or informative fossil materialsattributed to Peradectes crocheti Gernelle, 2024, the earliest peradectid metatherian species of Europe, from itstype locality (Palette, Provence, ∼55 Ma). These specimens were analyzed and discussed in: Gernelle et al.(2024), Taxonomy and evolutionary history of peradectids (Metatheria): new data from the early Eocene of France.https://doi.org/10.1007/s10914-024-09724-
Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam
No full textInternational audienceThe feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean zebu in the founder ancestry. Comparative analysis of whole genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants.Interestingly, the population's success in the harsh environment can be attributed to pre-adaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts
GeCKO: user-friendly workflows for genotyping complex genomes using target enrichment capture. A use case on the large tetraploid durum wheat genome
No full textThe GeCKO workflows are freely available on a dedicated GitHub repository (https://github.com/GE2POP/GeCKO). The dataset supporting the conclusions of this article is available in the French dataverse repository: https://entrepot.recherche.data.gouv.fr (https://doi.org/10.57745/78MBZY). All scripts needed to reproduce these analyses are provided on a GitHub repository (https://github.com/GE2POP/GeCKO_UseCase).International audienceBackground: Genotyping of individuals plays a pivotal role in various biological analyses, with technology choice influenced by multiple factors including genomic constraints, number of targeted loci and individuals, cost considerations, and the ease of sample preparation and data processing. Target enrichment capture of specific polymorphic regions has emerged as a flexible and cost-effective genomic reduction method for genotyping, especially adapted to the case of very large genomes. However, this approach necessitates complex bioinformatics treatment to extract genotyping data from raw reads. Existing workflows predominantly cater to phylogenetic inference, leaving a gap in user-friendly tools for genotyping analysis based on capture methods. In response to these challenges, we have developed GeCKO (Genotyping Complexity Knocked-Out). To assess the effectiveness of combining target enrichment capture with GeCKO, we conducted a case study on durum wheat domestication history, involving sequencing, processing, and analyzing variants in four relevant durum wheat groups.Results: GeCKO encompasses four distinct workflows, each designed for specific steps of genomic data processing: (i) read demultiplexing and trimming for data cleaning, (ii) read mapping to align sequences to a reference genome, (iii) variant calling to identify genetic variants, and (iv) variant filtering. Each workflow in GeCKO can be easily configured and is executable across diverse computational environments. The workflows generate comprehensive HTML reports including key summary statistics and illustrative graphs, ensuring traceable, reproducible results and facilitating straightforward quality assessment. A specific innovation within GeCKO is its 'targeted remapping' feature, specifically designed for efficient treatment of targeted enrichment capture data. This process consists of extracting reads mapped to the targeted regions, constructing a smaller sub-reference genome, and remapping the reads to this sub-reference, thereby enhancing the efficiency of subsequent steps.Conclusions: The case study results showed the expected intra-group diversity and inter-group differentiation levels, confirming the method's effectiveness for genotyping and analyzing genetic diversity in species with complex genomes. GeCKO streamlined the data processing, significantly improving computational performance and efficiency. The targeted remapping enabled straightforward SNP calling in durum wheat, a task otherwise complicated by the species' large genome size. This illustrates its potential applications in various biological research contexts
Alternative cliques of coexisting species in complex ecosystems
No full textInternational audienceThe possibility that some ecosystems can exist in alternative stable states has profound implications for ecosystem conservation and restoration. Current ecological theory on multistability mostly relies on few-species dynamical models, in which alternative states are intrinsically related to specific non-linear dynamics. Recent theoretical advances, however, have shown that multiple stable ‘cliques’—small subsets of coexisting species—can be present in species-rich models even under linear interactions. Yet, the mechanisms governing the appearence and characteristics of these cliques remain largely unexplored. In the present work, we investigate cliques in the generalized Lotka–Volterra model with mathematical and computational techniques. Our findings reveal that simple probabilistic and dynamical constraints can explain the appearence, properties and stability of cliques. Our work contributes to the understanding of alternative stable states in complex ecological communities
Using non-addive effects in genome-wide association studies and genomic predictions to improve biotic stress tolerance in peach
No full textInternational audienceAccounting for genetic architecture is crucial to breed for sustainable disease resistances and tolerances in plants. Indeed, (i) harnessing together minor and major effects genes allows to design a more durable plant immunity with large spectrum (ii) access to non-additive variance allows for a better exploitation of the total genetic variance when it comes to breeding, which is particularly relevant for clonally propagated crops. Our study system, Prunus persica (peach tree), is a major temperate fruit crop characterized by an overall high susceptibility to several pests and diseases, illustrated by a frequency treatment index around five times higher than in cereals. In this work, we phenotyped symptoms of two pests (leafhopper and twig moth) and four diseases (rust, leaf curl, mildew and shot hole) under low pesticide cover over three years in a peach core-collection replicated at three sites. This population consists in 192 unique accessions representing peach worldwide diversity and has been genotyped with the IRSC 16K SNP array. We used linear mixed models and the natural orthogonal interactions approach (Vitezica et al. 2017) to explicitly decompose genetic variance into additive, dominant and epistatic effects, and genotype x environment interactions. Genome-wide associations studies (GWAS) were performed with single-locus mixed models including kinships accounting for different dominance inheritance patterns. Genomic predictions consisted in a comparison of five GBLUP models incorporating different combinations of non-additive and inbreeding effects. After describing significant non-additive genetic variance and inbreeding effects across traits, we show that in addition to additive quantitative trait loci (QTLs), three to eight additional QTLs have been detected when accounting for dominant architecture. We were also able to improve genomic predictions by up to +0.05 in predictive ability with models incorporating non-additive and inbreeding terms in comparison to the additive baseline GBLUP model. Our results indicate the presence of very contrasted genetic architectures within the six biotic stress responses studied, traits being more strongly influenced either by dominance, epistasis or inbreeding effects. We also present the exploitation of GxE variance to find robust QTLs and improve environment-specific predictions. Finally, we introduce a multitrait approach to exploit jointly the complementary between resistance and tolerance to several biotic stresses. Our results could translate into high genetic gain in peach given its long juvenile phase, and could contribute to a long-term reduction of pesticide reliance in fruit production
Characterization of the starting conditions of the rainy season in Senegal: highlighting the constraints of crop establishment
No full textInternational audienceThe start of the rainy season in Senegal is characterized by critical variability, resulting in many crop failures after seed planting when a long dry spell occurs. The objective of this study is to characterize the starting conditions of the rainy season in different areas of Senegal in relation to crop success at the early stage. An analysis of four seasonal components determined from a daily rainfall database of 95 stations from 1950 to 2015. These seasonal components are the sowing date (Sowing), the Onset of the rainy season date (Onset), the length of the longest dry spell (DryMax), and the total rainfall (TotRain) during the 30 days after sowing. Statistical methods of time series homogeneity determination such as the Pettitt test, the Buishand test, the Von Newmann test, and the segmentation method have been applied to determine actual breakpoints and to obtain the most recent and homogeneous period to define the component in each site. The results indicate that these components have not exhibited statistically significant changes since 1950. Indeed, 3% of the stations show breakpoints for the Sowing, 4% for the TotRain, and 2% for the Onset. The start of the season follows a South East-North West gradient. It begins in the extreme South-East part of the country in the second decade of June while the first waves of sowing take place in the South-East center part from the second half of June. The north zone remains exposed to false start events with important seasonality. In the Northern and Central zones, the early or late character of the sowing passes more on the DryMax than the TotRain. It would be interesting to elucidate the effects of the rainfall regime at the early stage on the rainy season profile to gain better control of the pluvial crop yields
Social-ecological modelling as a boundary object to implement inter- and transdisciplinary approaches of forests in transitions
No full textInternational audienceFrench forests are at the crossroads of multiple dynamics and expectations: while they are supposed to be managed to ensure multifunctionality, national policies mostly focus on their role of carbon sink as a remedy for climate change mitigation. Simultaneously, French forests are increasingly impacted by on-going climate change (droughts, heat waves, bio-aggressors, fires), which alters their functioning and survival – and raises adaptation issues. As a result, forest management is currently facing a key challenge: how can we promote forests’ ability to maintain wood production and carbon sequestration, without impacting their other contributions (such as providing biodiversity habitats, air and water filtering, soil protection, leisures…), while also considering their sensitivity to climate change? This is the question addressed by the FISSA project (ForecastIng forest Socio-ecosystems’ Sensitivity and Adaptation to climate change) – whose ultimate aim is to test complex forest management scenarios at national and local levels within three regional natural parks (Pyrénées Ariégeoises, Luberon and Morvan) – in a context of climate change. FISSA has been designed to enlighten ongoing controversy, in this context of tensions between mitigation and adaptation strategies, between our multiple expectations regarding forests’ roles, and regarding the practices to promote to respond to such a challenge. To do so, it relies on an interdisciplinary approach: while social sciences inform dynamics of discourses and practices through social surveys at both national and local levels, natural sciences assess the effects of different forest management and climate scenarios on forests’ contributions through process-based models of forest dynamics and functioning. At the interface, transdisciplinary approaches are implemented to collectively define the management scenarios to be implemented both at local and national levels. In this presentation, we highlight how inter- and transdisciplinarity are promoted in the project, and how they can shape the original assumptions of modelers. First, we discuss how this project ensures the inter- and transdisciplinary dialogue through diverse boundary objects, both conceptual (social-ecological system), methodological (participatory modelling) and practical (common field work and promotion of dialogue among the participants). Second, we illustrate the changes in the modelling process brought by inter- and transdisciplinary contributions. Qualitative surveys, focus groups and dialogue have shown that expectations towards modelling are multiple depending on the territories, the stakeholders involved and the considered scale: (i) nourish a scientific and societal debate and controversy around adaptation and mitigation, but also (ii) respond to an extreme and unknown event such as major forest diebacks; or (iii) anticipate a shift from traditional sylvicultural practices and inherited forests towards more desirable practices in the face of environmental and climate urges. We conclude on the interests and limits of participatory social-ecological modelling approaches to promote collective action in a context where uncertainties and tensions are unavoidable
Dominance and rarity in tree communities across the globe: Patterns, predictors and threats
No full textInternational audienceAim: Ecological and anthropogenic factors shift the abundances of dominant and rare tree species within local forest communities, thus affecting species composition and ecosystem functioning. To inform forest and conservation management it is important to understand the drivers of dominance and rarity in local tree communities. We answer the following research questions: (1) What are the patterns of dominance and rarity in tree communities? (2) Which ecological and anthropogenic factors predict these patterns? And (3) what is the extinction risk of locally dominant and rare tree species? Location Global. Time period 1990–2017. Major taxa studied Trees. Methods: We used 1.2 million forest plots and quantified local tree dominance as the relative plot basal area of the single most dominant species and local rarity as the percentage of species that contribute together to the least 10% of plot basal area. We mapped global community dominance and rarity using machine learning models and evaluated the ecological and anthropogenic predictors with linear models. Extinction risk, for example threatened status, of geographically widespread dominant and rare species was evaluated. Results: Community dominance and rarity show contrasting latitudinal trends, with boreal forests having high levels of dominance and tropical forests having high levels of rarity. Increasing annual precipitation reduces community dominance, probably because precipitation is related to an increase in tree density and richness. Additionally, stand age is positively related to community dominance, due to stem diameter increase of the most dominant species. Surprisingly, we find that locally dominant and rare species, which are geographically widespread in our data, have an equally high rate of elevated extinction due to declining populations through large-scale land degradation. Main conclusions: By linking patterns and predictors of community dominance and rarity to extinction risk, our results suggest that also widespread species should be considered in large-scale management and conservation practices
Belowground traits and crop performance under stress in field-grown durum wheat mixtures
No full textInternational audienceIncreasing intra-specific diversity in agroecosystems is a promising practice, but belowground mechanismsshaping plant-plant interactions in mixtures remain unclear. We explored how belowground traits andassociated microbial communities influence durum wheat performance under limited resources, testingwhether traits in monogenotypic wheat stands could explain mixture performance. In a field experiment, 14durum wheat genotypes were cultivated alone or in pairs under two stress levels (control versus combinedwatering and N-fertilizer reduction). We measured root morphological traits, mycorrhizal colonization rate andmicrobial communities (mycorrhizal fungi, fungi, and bacteria) via Illumina metabarcoding on wheat roots andrhizospheric soil. Wheat performances were assessed by shoot biomass, N and P uptake. Mixed models wereused to assess which traits best explained wheat performances. In the stressed condition, mixtures exhibited11% higher shoot biomass compared to monogenotypic stands. Also only under stress, wheat performances(shoot biomass and P uptake) were significantly correlated to root biomass and colonization byMucoromycotina fungi, which are mycorrhizal fungi recently distinguished from the well-knownGlomeromycota. However, belowground traits and microbiome composition of monogenotypic stands failed toexplain mixture performances, pointing the need to explore different traits and integrate more diverse wheatgenotypes as 11 were modern cultivars. Although a definitive framework is lacking, our study offers promisingresults, urging further research in designing mixtures meeting farmers' need