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Evolutionary ecology of dispersal in biodiverse spatially structured systems: what is old and what is new?
No full textInternational audienceDispersal is a well-recognized driver of ecological and evolutionary dynamics, and simultaneously an evolving trait. Dispersal evolution has traditionally been studied in single-species metapopulations so that it remains unclear how dispersal evolves in metacommunities and metafoodwebs, which are characterized by a multitude of species interactions. Since most natural systems are both species-rich and spatially structured, this knowledge gap should be bridged. Here, we discuss whether knowledge from dispersal evolutionary ecology established in single-species systems holds in metacommunities and metafoodwebs and we highlight generally valid and fundamental principles. Most biotic interactions form the backdrop to the ecological theatre for the evolutionary dispersal play because interactions mediate patterns of fitness expectations across space and time. While this allows for a simple transposition of certain known principles to a multispecies context, other drivers may require more complex transpositions, or might not be transferred. We discuss an important quantitative modulator of dispersal evolution—increased trait dimensionality of biodiverse meta-systems—and an additional driver: co-dispersal. We speculate that scale and selection pressure mismatches owing to co-dispersal, together with increased trait dimensionality, may lead to a slower and more ‘diffuse’ evolution in biodiverse meta-systems. Open questions and potential consequences in both ecological and evolutionary terms call for more investigation. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'
La construction de l’engagement des collectivités sur la logistique des CCAP :perceptions des problématiques selon les territoires et les échelles
No full textNational audienc
Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity
No full textInternational audienceThough facing significant challenges, coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. In light of this, there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of northern and southern Haiti. We performed KASP-genotyping of SNP markers and HiPlex multiplex amplicon sequencing for haplotype calling on our samples, as well as several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realized. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another group that was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both mixed-variety farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures, and report the limited cultivation of C. canephora (Robusta coffee) in the study area. Our results show that some coffee farms are repositories of historical, widely-abandoned varieties while others are generators of new diversity through genetic mixing
Quantifying the impact of Great Green Wall and Corporate plantations on tree density and biomass in Sahelian Senegal
No full textInternational audienceThe Great Green Wall (GGW) is an international initiative to combat land degradation and restore native plant life in the Sahel, but due to a lack of monitoring tools, it remains unknown to be considered as success or failure. Here, we quantify the impact of GGW plantations and Corporate plantations (privately owned) in Sahelian Senegal based on remote sensing data and deep learning by mapping individual trees and their biomass across the Sahel region. Tree features (cover, density and above-ground biomass) have been computed in every hectare of 42 plantations (of both, corporate and GGW) and their surrounding non-planted areas, subsequently used for a comparative analysis of tree features. Results showed that gains in tree features varied substantially between plantations. At plot scale, among Corporate plantations, the average gain in tree density was 61.16 +/- 42.12 trees/ha while it was 5.7 +/- 5.8 trees/ha for GGW plantations. In regards to tree cover, the average gain was 618.5 +/- 588.5 m2/ha for Corporate plantations and 71.72 +/- 108.89 m2/ha for GGW plantations. For the above-ground biomass, the average gain was 3.36 +/- 3.29 tons/ha in the Corporate plantations and 0.46 +/- 0.67 tons/ha in the GGW plantations. The average gain in foliar biomass in the Corporate plantations was 0.15 +/- 0.13 tons/ha and in the GGW plantations, it was 0.02 +/- 0.03 tons/ha. The average gain in wood biomass was 3.21 +/- 3.12 tons/ha among the Corporate plantations and was 0.43 +/- 0.64 tons/ha among the GGW plantations. Notably, regarding the relative benefit in terms of ecosystem services per unit of density, each tree in GGW plantations contribute more to ecosystem services per unit of density compared to Corporate plantations. In GGW, each gained tree contributes 18 m2 of cover, 116.1 kg of above-ground biomass, 5.6 kg of foliar biomass, and 114.2 kg of woody biomass, while in corporate plantations, on the other hand, each gained tree adds 9 m2 of cover, 48.4 kg of above-ground biomass, 2.3 kg of foliar biomass, and 46.3 kg of woody biomass. These findings are opposed to conventional paradigms, suggesting that the Great Green Wall, while perhaps missing its tree density targets, has succeeded in its mission to produce ecosystem services per tree. This raises important questions about the redefinition of objectives in reforestation projects, focusing on quality rather than quantity, a perspective that could transform our understanding of the successes and failures of these essential ecological restoration initiatives. However, the assessment primarily relies on indicators such as cover and biomass, potentially overlooking other crucial ecosystem services. Therefore, while our conclusions underscore the effectiveness of reforestation initiatives, future research should aim to establish a more comprehensive understanding of ecosystem services by incorporating additional indicators beyond cover and biomass, such as species diversity, soil health, water retention, and habitat quality
Diagnostic partagé des opportunités et contraintes liées à l'agriculture en zone inondable et péri-urbaine.: Synthèse de l'atelier participatif avec des agriculteurs.ices, représentant.e.s d'institutions et chercheurs.euses du système d'observation des impacts des inondations (so-ii) - 18 janvier 2024
No full textCe rapport est une synthèse d'un atelier participatif, qui s'est tenu le 18 janvier 2024, ayant réuni des agriculteurs.ices et représentant.e.s d'institutions du système d'observation des impacts des inondations (so-ii) localisé autour de la métropole de Montpellier et des chercheurs. euses du projet CAFRUA (Challenges pour l'adaptation de l'agriculture en zone inondable et péri-urbaine) afin de faire un diagnostic partagé des opportunités et contraintes liées à l’agriculture en zone inondable et péri-urbaine. Le projet CAFRUA, dans lequel cet atelier s'inscrit, porte sur la prise en compte de l'agriculture en zone inondable et péri-urbaine dans les stratégies de gestion et d'aménagement du territoire.Dans ce projet, une série d'atelier a été programmé en 2023 et 2024 dont les premier et deuxième ateliers se sont tenus respectivement les 13 février 2023 avec des agriculteurs.ices et 03 juillet 2023 avec les représentants.es d'institutions. Ces deux ateliers ont eu le même objectif : aboutir à un état des lieux des opportunités et contraintes de l'agriculture en zone inondable et péri-urbaine. Le troisième atelier, dont il est question dans ce rapport, a permis de réaliser un diagnostic partagé sur les base de ceux faits précédemment et d'explorer des propositions de solutions dans le cadre d’un exercice de prospective.Les opportunités identifiées font globalement consensus entre les différents groupes d’acteurs. Pour autant, de nombreux points de vigilances (désaccords au sein du même groupe, nuances, condition(s) pour que ce soit une opportunité, association à une contrainte) ont été émis. Il a notamment été dit que « quasiment chaque opportunité est conditionnée par des contraintes ». Il a également été identifié que les opportunités au maintien de l’agriculture en zone péri-urbaine et inondable bénéficient majoritairement à la collectivité en particulier la gestion des inondations et la sécurité alimentaire.Concernant les contraintes, les participant.e.s se sont mis d'accord sur le fait que la plupart des contraintes portent sur les agriculteurs.ices. Pour autant, certaines contraintes concernant initialement l'agriculture ont également été rapprochées du côté de la collectivité, comme par exemple l'élévation du prix du foncier en zone péri-urbaine qui empêche la facilitation d'achat de foncier par la collectivité pour la mise en place de projets agricoles. Ont été partagé par exemple les contraintes agro-économiques pour les exploitations, la non-constructibilité de bâti agricole en zone inondable, le flou autour de la gestion des fossés, les conflits d'usage de l'eau, les transferts de pollution, la spéculation foncière autour des friches et des zones péri-urbaines, etc
Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice
No full textInternational audienceFaecal microbiota plays a critical role in human health, but its relationship with nutritional status among schoolchildren remains under-explored. Here, in a double-blinded cluster-randomized controlled trial on 380 Cambodian schoolchildren, we characterize the impact of six months consumption of two types of rice fortified with different levels of vitamins and minerals on pre-specified outcomes. We investigate the association between the faecal microbiota (16SrRNA sequencing) and age, sex, nutritional status (underweight, stunting), micronutrient status (iron, zinc and vitamin A deficiencies, anaemia, iron deficient anaemia, hemoglobinopathy), inflammation (systemic, gut), and parasitic infection. We show that the faecal microbiota is characterised by a surprisingly high proportion of Lactobacillaceae . We discover that deficiencies in specific micronutrients, such as iron and vitamin A, correlate with particular microbiota profiles, whereas zinc deficiency shows no such association. The nutritional intervention with the two rice treatments impacts both the composition and functions predicted from compositional analysis in different ways. (ClinicalTrials.gov (Identifier: NCT01706419)
Orchestrating data flows throughout their whole life cycle: Key stages and partners for success
No full textInternational audienceMost life science domains rely on the massive production of data via different technologies (sequencing, imaging, proteomics, metabolomics, phenomics, …). In this context, data management becomes critical to enhance the value of the data to its full extent. This situation translates into regulatory obligations for research projects, with incentives for researchers to adopt best practice in data management. The FAIR principles, which aim at making the data Findable, Accessible, Interoperable, and Reusable, are a cornerstone of best practice. They are widely promoted at the political level, but they require appropriate software tools to be put into practice. We present here a general schema describing the successive steps for seamless data management from the conception of a research project until result publication and data deposition in relevant repositories. Data management plans (DMPs), often perceived as a tedious administrative requirement, could turn into much-appreciated support for researchers if they were adapted to fit their concrete needs (e.g. identifying datasets for reuse, reprocessing, etc.). This would require user-friendly tools to handle DMPs, which should not only serve as landmarks at the onset, mid-term, and termination of a project but offer interactive interfaces enabling their continuous follow-up throughout the project, and designed modularly to cope with the diversity of data combined in a project. DMPs should also promote the adoption of international standards and specifications established by communities of experts for each data type, which become an absolute requirement to deposit data in international repositories. Validating the compliance and quality of the metadata along the project’s life will save the painful efforts necessary to recollect mandatory information at the moment of data submission, months or years after their generation. Metadata standardization should rely on domain-specific ontologies such as EDAM, to describe the data types, formats, and operations, as well as general purpose lightweight ontologies (e.g. Schema.org/Bioschemas, DC-Terms, DCAT) to increase findability and reuse. Data management software environments should also handle provenance metadata such as the location of primary and secondary data generated at each step of a project, to optimize storage usage, avoid data loss, and ensure data securing without excessive duplication. It should also include user-friendly interfaces to simplify data and metadata submission to international repositories, and to automate their indexing in national and international catalogs. Beyond the description of these conceptual requirements, we will present the software tools and standards required to accompany each event associated with the data and metadata (production, curation, storage, archiving, …). Some of these tools have been developed by the Institut Français de Bioinformatique or by the European bioinformatics infrastructure ELIXIR. Other tools are under development or have to be developed to achieve a comprehensive software environment supporting the orchestration of data flows throughout their life cycle
Genome-wide association analysis and transgenic characterization for amylose content regulating gene in tuber of Dioscorea zingiberensis
No full textThe raw sequencing data are available at NCBI SRA under the project number: 716093 (https://www.ncbi.nlm.nih.gov/bioproject/716093). Codes and scripts used for data analysis are available in Supplementary file 1. Any intermediary file and all phenotypic data can be provided upon request to the corresponding authors.International audienceBackground: Amylose, a prebiotic found in yams is known to be beneficial for the gut microflora and is particularly advantageous for diabetic patients’ diet. However, the genetic machinery underlying amylose production remains elusive. A comprehensive characterization of the genetic basis of amylose content in yam tubers is a prerequisite for accelerating the genetic engineering of yams with respect to amylose content variation.Results: To uncover the genetic variants underlying variation in amylose content, we evaluated amylose content in freshly harvested tubers from 150 accessions of Dioscorea zingibensis. With 30,000 high-quality single nucleotide polymorphisms (SNP), we performed a genome-wide association analysis (GWAS). The population structure analysis classified the D. zingiberensis accessions into three groups. A total of 115 significant loci were detected on four chromosomes. Of these, 112 significant SNPs (log10(p) = 5, q-value < 0.004) were clustered in a narrow window on the chromosome 6 (chr6). The peak SNP at the position 75,609,202 on chr6 could explain 63.15% of amylose variation in the population and fell into the first exon of the ADP-glucose pyrophosphorylase (AGPase) small subunit gene, causing a non-synonymous modification of the resulting protein sequence. Allele segregation analysis showed that accessions with the rare G allele had a higher amylose content than those harboring the common A allele. However, AGPase, a key enzyme precursor of amylose biosynthesis, was not expressed differentially between accessions with A and G alleles. Overexpression of the two variants of AGPase in Arabidopsis thaliana resulted in a significantly higher amylose content in lines transformed with the AGPase-G allele.Conclusions: Overall, this study showed that a major genetic variant in AGPase probably enhances the enzyme activity leading to high amylose content in D. zingiberensis tuber. The results provide valuable insights for the development of amylose-enriched genotypes
Les interactions entre diverses exploitations agricoles : un levier pour les collectivités territoriales dans le Morbihan
No full textInternational audienceEn Bretagne, malgré la spécialisation agricole régionale héritée des politiques de modernisation, les exploitations et profils d’agriculteurs et agricultrices demeurent diversifiés dans un certain nombre de territoires de cette région. En réponse aux interrogations des élus d'un territoire rural du sud-est morbihannais, une étude a permis d'analyser la différenciation des systèmes de production et d'examiner comment s'opèrent localement les interactions entre les différentes catégories d’exploitations et d’agriculteurs. Cette communication rend donc compte d'un diagnostic agraire réalisé en 2023 sur les 13 communes rurales de ce territoire breton, totalisant environ 300 exploitations, dont 80 % conduisent une activité d'élevage, principalement laitière. Après une présentation du cadre et de la méthodologie de travail, cette communication détaille à grands traits les dynamiques agricoles actuellement en cours sur le territoire. Après avoir identifié les principales interactions existantes entre les différentes catégories d'exploitations du territoire, nous discutons comment le tissu d'interdépendances et de coordinations entre la diversité des fermes locales constitue selon nous des ressources territoriales à saisir par les collectivités locales