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Detecting flowers on imagery with computer vision to improve continental scale grassland biodiversity surveying
No full textInternational audienceLarge-scale biodiversity monitoring is essential for assessing biodiversity trends, yet traditional surveying methods are limited in the spatial/temporal scale they can cover. Recent technological developments have led to computer vision-based species identification tools, such as the Pl@ntNet application. Increasing accuracy of such algorithms presents an opportunity of integrating computer vision into larger monitoring schemes and could lead to automating ground-based evidence provision related to agri-environmental measures (e.g. flower strips, field margins). However, images from surveys or farmer declarations do not live up to the standards of current applications. In order to integrate these automated methods into biodiversity monitoring, more generalized models are needed. We create a dataset using 500 manually delineated images of vegetation patches in European grasslands taken during the Land Use/cover Area Survey (LUCAS) grassland module. We train the Faster R-CNN model to detect and extract individual flower objects. Using this model, we extract the abundance of flowers in an image, analyse their colour distribution, and use the Pl@ntNet application to identify the species of the individual flowers detected. The best model reaches precision and recall of 0.89/0.61 and predicts 1377 flowers on the 100 test images distributed between 10 colours. Using Pl@ntNet, only 52 flowers were identified with a certainty score above 0.5 due to the limitations in image size and quality. Of these flowers, 30% were correctly automatically identified at the species level and 42% at the genus level. The results show that we can automatically extract valuable information on floral abundances, colours, and sizes from images of vegetation patches, though in most cases better images are needed for species identification. Despite limitations with image quality, integrating this workflow into large-scale monitoring could speed up the sampling process and allow for better spatial and temporal data on floral diversity and abundance
Développement et validation d'une méthode d'évaluation de la durabilité des exploitations agricoles. IDEA4, ses outils et ses usages
No full textCe numéro traite de résultats de projets lauréats en 2017 et 2018 de l'appel à projet CASDAR (Compte d'Affectation Spéciale Développement Agricole et Rural), "Innovation et Partenariat" et "Recherche Technologique. Ces projets sont financés par le ministère de l'Agriculture et de la Souveraineté Alimentaire.National audienceThe ACTION project validated the use of the IDEA4 method (Farm Sustainability Indicators 4th version)with three major outcomes: 1) its ability to be used for various purposes (education, research Farmadvisory, support, advisory, public action) and for the majority of farming systems (crops, livestock,orchards, viticulture, and market gardening), 2) its functionality with its three freely accessible tools (Excelcalculator, IDEATools, and the WEB-IDEA platform), 3) the establishment of a broad collaborativecommunity of around 300 IDEA4 users (advisors, teachers, researchers and farmers) who carried out justover 800 IDEA’s farm diagnosis. In education, its dual sustainability approach (3 dimensions and 5properties of sustainability) enhances its pedagogical performance. In research, IDEA4 expandsknowledge on the sustainability of transitions. The future WEB-IDEA 2.0 platform paves the way fornational open data on sustainability of the French agriculture.Le projet ACTION a validé l’usage de la méthode IDEA4 (Indicateurs de Durabilité d’une ExploitationAgricole version 4) avec trois résultats majeurs : 1) sa capacité à être utilisée pour différents usages(enseignement, recherche conseil, accompagnement, action publique) et pour la majorité des systèmes(grandes cultures, élevages, arboriculture, viticulture et maraîchage), 2) son opérationnalité avec ses troisoutils libres d’accès (calculateur Excel, IDEATools et plateforme WEB-IDEA), 3) la création d’une largecommunauté collaborative d’environ 300 utilisateurs d’IDEA4 (conseillers, enseignants, chercheurs etagriculteurs) ayant réalisé un peu plus de 800 diagnostics d’exploitation. Dans l’enseignement, sa doublelecture de la durabilité (3 dimensions et 5 propriétés de la durabilité) renouvelle sa capacité pédagogique.En recherche, IDEA4 élargit les connaissances sur la durabilité des transitions. La future plateforme WEB-IDEA 2.0 ouvre la voie de l’open data national des données de la durabilité de la Ferme France
Premier signalement de la fourmi d'Argentine, Linepithema humile (Mayr, 1868) (Hymenoptera : Formicidae), pour la région Malgache
No full textInternational audienceThe Argentine ant, Linepithema humile (Mayr, 1868), is a highly invasive species with serious detrimental consequences to native fauna and flora in invaded territories. Native to South-Central South America, it was first reported from continental Africa in 1893 but, to date, had never been recorded from the Malagasy region (encompassing Madagascar, Comoros, Seychelles, and Mascarene archipelago). Here, we report the first record of this invasive species on the island of La Reunion, a French overseas territory part of the Mascarene archipelago. The species was identified using both morphological and molecular analysis. We discuss potential ecological consequences of the presence of this ant on the insular ecosystems of La Réunion.La fourmi d’Argentine, Linepithema humile (Mayr, 1868), est une espèce hautement invasive générant des conséquences considérables sur la faune et la flore des territoires envahis. Originaire du Centre-Sud de l’Amérique du Sud, cette espèce a été découverte en Afrique continentale dès 1893 mais n’avait, jusqu’à présent, pas été signalée de la région Malgache (comprenant Madagascar, les Comores, Seychelles et l’archipel des Mascareignes). Nous rapportons ici la première découverte de cette espèce invasive sur l’ile de La Réunion, territoire français d’outre-mer faisant partie des Mascareignes. L’identité de l’espèce a été confirmée grâce à des analyses moléculaires et morphologiques. Nous discutons ensuite des conséquences écologiques potentielles de la présence de cette espèce sur les écosystèmes insulaires de La Réunion
Agrarian Change in the Central Plain of Thailand (1950-2020): A Longitudinal Study of Farm Characteristics
No full textA measure of the DNA barcode gap for applied and basic research
No full textInternational audienceDNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a “DNA barcode gap” ⎯ the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives. Furthermore, both theory and empirical work indicate a gap may not occur for related pairs of biological species. Here, we present a novel evaluation approach in the form of an easily calculated set of nonparametric metrics to quantify the extent of proportional overlap in inter- and intraspecific distributions of pairwise differences among target species and their conspecifics. The metrics are based on a simple count of the number of overlapping records for a species falling within the bounds of maximum intraspecific distance and minimum interspecific distance. Our approach takes advantage of the asymmetric directionality inherent in pairwise genetic distance distributions, which has not been previously done in the DNA barcoding literature. We apply the metrics to the predatory diving beetle genus Agabus as a case study because this group poses significant identification challenges due to its morphological uniformity despite both relative sampling ease and well-established taxonomy. Results herein show that target species and their nearest neighbour species were found to be tightly clustered, and therefore difficult to distinguish. Such findings demonstrate that DNA barcoding can fail to fully resolve species in certain cases. Moving forward, we suggest the implementation of the proposed metrics be integrated into a common framework to be reported in any study that uses DNA barcoding for identification. In so doing, the importance of the DNA barcode gap and its components on the success of DNA-based identification using DNA barcodes can be better appreciated
Trend analysis of reference evapotranspiration and climate variables in the main hydrosystems of Senegal: Senegal, Gambia and Casamance River Basins
No full textInternational audienceAbstract. Analysis of reference evapotranspiration (ET0) trends is essential for understanding the impacts of climate change on water resources. Thus, despite the continuous rise in temperatures, a decrease in evapotranspiration is noted in some parts of the world. This contrast is called the “evaporation paradox” and is thought to be related to the variation in wind speed, relative humidity and solar radiation. The objective of this work is to analyze the annual and seasonal trends of ET0 and climate variables at the scale of the Senegal, Gambia and Casamance river basins. The reanalyze data of NASA/POWER are used over the period 1984–2019. Mann Kendall's test and Sen slope were used to analyze trends in ET0 and climate variables. Results show that on annual scale, ET0 increases significantly in 32 % of the Senegal basin and decreases in less than 1 % of it. In contrast, in the Casamance and Gambia basins, the annual ET0 drops by 65 % and 18 %, respectively. On an annual scale, temperature and relative humidity show an increasing trend over all basins while wind speed and radiation decrease significantly. This confirms the existence of the “evaporation paradox” in the three basins. This phenomenon is explained by the increase in relative humidity and the decrease in wind speed and solar radiation
Les élites managériales prennent conscience du caractère insécable du lien entre résilience des entreprises et résilience écologique [Tribune au journal Le Monde]
No full textNational audienceLa mesure de l’impact des entreprises sur l’environnement sert surtout à calculer les « compensations » qui permettent de légitimer la poursuite de leur activité, observent les chercheurs Nicolas Balas et Clara Roussey
A taxonomy of multiple stable states in complex ecological communities
No full textInternational audienceNatural systems are built from multiple interconnected units, making their dynamics, functioning and fragility notoriously hard to predict. A fragility scenario of particular relevance concerns so-called regime shifts: abrupt transitions from healthy to degraded ecosystem states. An explanation for these shifts is that they arise as transitions between alternative stable states, a process that is well-understood in few-species models. However, how multistability upscales with system complexity remains a debated question. Here, we identify that four different multistability regimes generically emerge in models of species-rich communities and other archetypical complex biological systems assuming random interactions. Across the studied models, each regime consistently emerges under a specific interaction scheme and leaves a distinct set of fingerprints in terms of the number of observed states, their species richness and their response to perturbations. Our results help clarify the conditions and types of multistability that can be expected to occur in complex ecological communities.We often use simple models to talk about regime shifts and alternative stable states in nature. But how does multistability really look like in complex systems? We find that high-dimensional models with random interactions can unfold up to four different multistability regimes. More importantly, each regime shows the same fingerprints across biological systems, suggesting a general taxonomy.imag
Rice yellow mottle virus is a suitable amplicon vector for an efficient production of an anti-leishmianiasis vaccine in Nicotiana benthamiana leaves
No full textInternational audienceBackground Since the 2000's, plants have been used as bioreactors for the transient production of molecules of interest such as vaccines. To improve protein yield, "amplicon" vectors based on plant viruses are used. These viral constructs, engineered to carry the gene of interest replicate strongly once introduced into the plant cell, allowing significant accumulation of the protein. Here, we evaluated the suitability of the monocot-infecting RNA virus Rice yellow mottle virus (RYMV) as an amplicon vector. The promastigote surface antigen (PSA) of the protozoan Leishmania was considered as a protein of interest due to its vaccine properties against canine leishmaniasis. Results Since P1 (ORF1) and CP (ORF3) proteins are not strictly necessary for viral replication, ORF1 was deleted and the PSA gene was substituted to ORF3 in the RYMV-based vector. We evaluated its expression in the best described plant bioreactor system, Nicotiana benthamiana which, unlike rice, allows transient transformation by Agrobacterium. Despite not being its natural host, we demonstrated a low level of RYMV-based vector replication in N. benthamiana leaves. Under optimized ratio, we showed that the P19 silencing suppressor in combination with the missing viral CP ORF significantly enhanced RYMV amplicon replication in N. benthamiana. Under these optimized CP/P19 conditions, we showed that the RYMV amplicon replicated autonomously in the infiltrated N. benthamiana cells, but was unable to move out of the infiltrated zones. Finally, we showed that when the RYMV amplicon was expressed under the optimized conditions we set up, it allowed enhanced PSA protein accumulation in N. benthamiana compared to the PSA coding sequence driven by the 35S promoter without amplicon background. Conclusion This work demonstrates that a non-dicot-infecting virus can be used as an amplicon vector for the efficient production of proteins of interest such as PSA in N. benthamiana leaves