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Graph-structured variable selection with Gaussian Markov random field horseshoe prior
No full textA graph structure is commonly used to characterize the dependence between variables, which may be induced by time, space, biological networks or other factors. Incorporating this dependence structure into the variable selection procedure can improve the identification of relevant variables, especially those with subtle effects. The Bayesian approach provides a natural framework to integrate this information through the prior distributions. In this work, we propose combining two priors that have been well studied separately-the Gaussian Markov random field prior and the horseshoe prior-to perform selection on graph-structured variables. Local shrinkage parameters that capture the dependence between connected covariates are specified to encourage similar amount of shrinkage for their regression coefficients, while a standard horseshoe prior is used for non-connected variables. After evaluating the performance of the method on different simulated scenarios, we present three applications: one in quantitative trait loci mapping with block sequential structure, one in near-infrared spectroscopy with sequential non-disjoint dependence and another in gene expression study with a general dependence structure
An organizational capacity self-assessment for innovation support service providers (OCATI) - approach and results from application in Madagascar
Get PDFPurpose: This paper introduces the Organisational Capacity Assessment Approach for Innovation Support (OCATI) and presents findings from its application with a farmer-based organisation in Madagascar. Design/method/approach: OCATI has been co-designed within the EU–Africa collaborative research project SERVInnov, reflecting conditions in the global South, particularly Madagascar, Cameroon, and Burkina Faso. It assesses organisational, technical, and functional capacities, skill needs, and structural conditions for delivering innovation support services (ISS). Findings: Results from its application in Madagascar, show disparities in performance across five capacity components with the highest performance in delivering ISS and the weakest in networking and policy engagement. Recommendations include initiating policy lobbying, institutionalisation, updating knowledge of the innovation ecosystem, new collaborations, ISS mapping tools, and clear communication channels. More so, enhancements in risk management, service diversification, human resource expansion, and ISS-type awareness are equally seen as crucial. Theoretical implications: Realising an OCATI assessment fosters organisational evolution, complements widely used monitoring and evaluation (M&E) tools, and supports experiential learning approaches for extension and advisory service (EAS) organisations. Practical implications: Practically, the results provide an opportunity for reflexive thinking about organisations' own position in supporting innovation, raising awareness for ISS, and revealing how support for innovation processes in agriculture matters and can be enhanced. The approach help organisations extract and develop core competencies in innovation support, thereby becoming more professionalised and recognised. Original Value: This study addresses a significant research gap in organisational capacity assessment for innovation support and introduces a novel self-assessment tool for use by innovation support service providers
Coconut palms of Samoa
Get PDFThis website returns the information collected during four scientific visits conducted in 2001, 2010, 2012 and 2017 on behalf the Ministry of Agriculture of Samoa, the International Coconut Genetic Resources Network, the Secretariat of the South Pacific Community, the Global Crop Diversity Trust, Bioversity International, CIRAD (French Centre for Agricultural Research and Development), the Coconut Industry Development for the Pacific (CIDP project) and the Darwin Initiative "Saving Pacific Coconuts"
Mission report to Colombia, Montes de Maria : Visioning workshop SASI-SPI. Module 2 - Action-Learning Program 2025 (Juin 2025)
No full textObjective of the mission: combine participatory learning and strategic visioning to foster a collaborative, multi-level approach to transforming territorial food systems. The mission involved two main components: (i) the Visioning workshop led by CIRAD and AGROSAVIA, with the FAO-CFI, has built on the analytical work undertaken to understand the specificities of the food system in the four territories and to identify one transition challenge per territory (WS3), and (ii) the implementation of the Learning in Action program led by iCRA to strengthen the capacities of the territorial actors (WS4)
Projecting trends of arabica coffee yield under climate change: A process-based modelling study at continental scale
Get PDFCONTEXT: Climate change may lead to negative impacts on coffee production, such as reduced yields. Addressing this issue requires identifying climate risks and assessing the adaptation potential of agronomic practices across spatial and environmental gradients. OBJECTIVE: This study aimed to evaluate climate change impacts on arabica coffee yields at continental scale and evaluate a specific adaptation measure, i.e. increasing shade tree density in agroforestry settings, by simulating the physiological links between coffee growth, climatic factors and agronomic management. METHODS: After evaluating the performance of the process-based model DynACof in simulating arabica yields (using data from previous studies), we developed a new tool called G-DynACof, a modelling framework for spatializing DynACof on a regional scale using extensive climate projections and soil geodata. We used G-DynACof to simulate trends of potential coffee yields in Latin America and Africa using an ensemble of downscaled and bias-corrected climate projections for the period 2036–2065 compared to a historical period 1985–2014. RESULTS AND CONCLUSIONS: Despite considerable uncertainties due to the scarcity of information on agronomic management at the regional scale, our results indicate that potential yields could decrease between 23 % and 35 % in Latin America and between 16 % and 21 % in Africa, depending on the Shared Socioeconomic Pathway (SSP) considered (SSP1–2.6 and SSP5–8.5, respectively). Yield variations were very heterogeneous in space, with yields increasing at high altitudes and low latitudes, indicating a possible future shift of production areas. In our simulations, the effect of increased shade tree density on productivity was also spatially variable, and its potential for adaptation to climate change remains uncertain, requiring further investigation. SIGNIFICANCE: Impact analyses and adaptation modelling of coffee agrosystems, together with socio-economic indicators, can delineate realistic, comprehensive, integrated risk assessments and support effective adaptation recommendations
Using near-infrared spectroscopy as a cost-effective method to characterise soil and leaf properties in native forest
No full textForests conservation and sustainable management of forests require an understanding of ecological traits that influence carbon and nutrient turnover in forest ecosystems. This study evaluates the potential of Near Infrared Spectroscopy (NIRS) as a rapid, non-destructive and cost-effective tool for characterising soil and trees in natural forests and forest-frontier ecosystems. Soil samples were collected at four depths from three land uses (native forest, grazed grassland, and horticultural land), while leaf samples were obtained from two provenances of Nothofagus alpina. Spectra were used to classify samples, predict biological and chemical properties, estimate relatedness matrices for both soils and leaves and compared them with those obtained from genetic data. Principal component analysis separated soil samples from different land uses and depths as well as leaf samples from the two provenances. NIRS-based models showed high predictive accuracy for soil microbial biomass, biological activity and total carbon (R2 = 0.80, 0.94, and 0.86, respectively), although leaf pigment estimation was less reliable (R2 = 0.60–0.40). Correlations between genetic and NIRS relatedness matrices were low, highlighting that both methodologies are relevant for sample characterisation. These findings demonstrate that NIRS is a useful method for assessing soil ecological traits associated with nutrient cycling offering a practical and cost-efficient alternative for ecological monitoring in forest ecosystems. However, further methodological improvements are needed to enhance its accuracy, particularly for leaf traits characterisation. This study highlights the broader potential of NIRS for large-scale forest management, conservation strategies, and ecological research
Canopy functional trait variation across Earth's tropical forests
Get PDFTropical forest canopies are the biosphere's most concentrated atmospheric interface for carbon, water and energy1,2. However, in most Earth System Models, the diverse and heterogeneous tropical forest biome is represented as a largely uniform ecosystem with either a singular or a small number of fixed canopy ecophysiological properties3. This situation arises, in part, from a lack of understanding about how and why the functional properties of tropical forest canopies vary geographically4. Here, by combining field-collected data from more than 1,800 vegetation plots and tree traits with satellite remote-sensing, terrain, climate and soil data, we predict variation across 13 morphological, structural and chemical functional traits of trees, and use this to compute and map the functional diversity of tropical forests. Our findings reveal that the tropical Americas, Africa and Asia tend to occupy different portions of the total functional trait space available across tropical forests. Tropical American forests are predicted to have 40% greater functional richness than tropical African and Asian forests. Meanwhile, African forests have the highest functional divergence—32% and 7% higher than that of tropical American and Asian forests, respectively. An uncertainty analysis highlights priority regions for further data collection, which would refine and improve these maps. Our predictions represent a ground-based and remotely enabled global analysis of how and why the functional traits of tropical forest canopies vary across space
Study of the development of cashew (Anacadium occidentale L.) yield components at tree level in northern Côte d'Ivoire
Get PDFThe study was conducted at the Lataha research station in the Poro region, which has a Sudanese climate with two distinct seasons. The aim was to assess cashew yield components through agromorphological and phenological analysis in three orchards of different ages (8, 12 and 39 years). An experimental block design was set up with three 50 m × 50 m plots. Twelve trees were selected and monitored. Span, height and trunk circumference were measured. Quadras were used to monitor twig development (vegetative, flowering, fruiting) every two days. Statistical analysis revealed that trunk span and circumference were strongly correlated with the number of vegetative shoots (r = 0.94 and r = 0.77). A strong linear regression was observed between span and the number of vegetative shoots (R² = 0.97). Branching and fruit production increased with tree age. East and west directions favoured higher shoot and fruit production, probably related to exposure to light. Male flowers are the most common, regardless of cardinal direction, followed by hermaphroditic flowers, which are more common in the east and south. The length of the flowering cycle increases with age: 34 days for young trees, 45 days for intermediate trees and 51 days for old cashew trees. Fruit production was significantly higher in the oldest trees. The study concludes that the age of the tree, its morphological characteristics and the cardinal orientation of the branches have a strong influence on flowering, fruiting and therefore yield
A spatial perspective on flowering in cauliflorous cacao: Architecture defines flower cushion location, not its early activity
Get PDFBackground and Aims: Theobroma cacao L., a tropical sciaphilous tree, exhibits cauliflory, with persistent flowering sites known as flower cushions. Cushions develop from floral buds located at the axils of leaves or cataphylls. They can sustain recurrent flowering and contribute to the fruit production of the tree throughout its lifespan. However, factors influencing their formation and flowering activity remain poorly understood. Methods: Architectural and geometrical measurements, combined with weekly monitoring of flowering activity at the node scale, were conducted on plagiotropic branches of two cacao genotypes under medium and heavy shade. We investigated how architecture and geometry influence cushion formation, frequency and duration of flowering episodes, and synchrony of flowering among cushions at different scales. Key Results: Flower cushions developed once a flush (growth unit) had reached a specific ontogenetic age, defined by its position along the shoot (axis). The probability of flower cushion formation was then determined primarily by the position of the node (phytomer) within the flush and its basal diameter. Heavy shade (90 % light reduction) greatly limited cushion formation, regardless of the architectural traits or growth characteristics of the node, flush or shoot. In contrast, the temporal activity of the flower cushions was not related to architectural or geometrical factors, and flowering occurred with moderate synchrony at the growth unit, axis and branch scales. Conclusions: These findings indicate the dual importance of shoot ontogeny and node-specific traits in flower cushion formation in this cauliflorous species. They also demonstrate the overall negative influence of heavy shade on flower cushion development, and the absence of architectural constraints on the flowering activity of cushions during the first reproductive phase of the tree. Further analyses are needed to gain a better understanding of the hormonal and carbohydrate regulation of flowering and fruiting in productive trees of this cauliflorous species