HAL-Université de Bretagne Occidentale
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Allocating individual fishing possibilities through producer organisations: The case of the Bay of Biscay common sole fishery in France
No full textInternational audienceManagement of the economically important Bay of Biscay common sole fishery has long relied on the setting of annual Total Allowable Catches (TACs). Allocation of these fishing possibilities at the French level is largely administered by six Producer Organisations (POs) for the fraction of the national quota they are responsible for, depending on the catch history of vessels belonging to their members. We surveyed representatives of these POs with the aim to understand the principles and processes that have evolved for determining allocation of sole quota among their members. Survey results show that the move away from derby fishing and towards the setting of individual catch allocations, initiated in the years 2000, has continued, along with the development of strategies at different levels to reconcile members’ demand for catch allocations with quota constraints. While one might have expected these individual allocations to reflect the track records of fishing vessels, we find that POs have developed alternative allocation rules to satisfy the needs of their members. POs thus play a key role in the definition of fishing possibilities in this and most of the TAC-managed fisheries in which French fleets operate. In so doing, POs bear the brunt of the transaction costs associated with quota allocation
Escherichia coli in the Niger River: Links to environmental variables and anthropogenic activities in Niamey city, Niger
No full textInternational audienceStudy region: Middle Niger River, upstream to downstream of Niamey city, Sahel, West Africa.Study focus: Understanding surface water pollution dynamics and identifying its main drivers isparticularly important in regions where surface waters are largely used without proper treatment.This study is focused on the Niger River water and assesses E. coli numbers, and physicochemicalparameters upstream and downstream of Niamey. Data collected over three years, supplementedby occasional campaigns, aimed to determine the spatial and temporal variability of waterquality.New hydrological insights for the region: SPM and E. coli showed high values during the rainyseason, peaking before the Red flood. E. coli increased from the first rainfall events in Niameywith a peak occurring before SPM peak. Distinct sources play an important role on their seasonaldynamics; E. coli mainly originates from urban areas along the Niger River, while SPM comesfrom right-hand tributaries upstream of Niamey. Downstream of Niamey, E. coli were significantlyhigher than upstream, highlighting the city’s substantial contribution to fecal contaminationthrough wastewater discharges, particularly on the left bank. No significant differences betweenupstream and downstream were observed in the other physicochemical parameters analyzed.Considering spatial distribution in E. coli sources and environmental parameters such as rainfalland SPM is of major and global importance for understanding and addressing fecal contaminationin urban environments
Comparison of star-allele caller performances on genotyping and sequencing data at different geographic scales
No full textInternational audiencePharmacogenetics is the study of genetic variants responsible for variable response tomedication. These variants can explain alternate drug responses, and understanding their effects thusrepresents a key public health issue. To standardize pharmacogenetics studies, a specific nomenclatureis used: the star-alleles, which associates haplotypes with the activity of a given pharmacogene. Suchhaplotype calling can be influenced by population origin, the complexity of the genomic region inquestion and choice of reference data; many star-allele callers have been developed with little insighton their performance in different scenarios.The objective of this study is to determine the performances of the different tools available.To do this, we used sequencing data from the 1000 Genomes and FranceGenRef projects.To this end, we have benchmarked different pipelines of star-allele annotation. We haveobserved some discrepancies between the output of star-allele annotation pipelines, coming fromdifferences in the reference database used, the method employed and the range of each pipeline interms of gene coverage and variant detection. We have also evaluated the impact of imputation onstar-allele calling, examining its influence on calling accuracy and downstream phenotype predictionto assess the reliability of imputed data. We provide recommendations on which tools to use regardingthe data available, the population observed and the gene studied.This study provides insights into the strengths and limitations of different star-allele callersused for inferring unobserved data. These findings contribute to the assessment of the potentialbenefits of personalized care informed by pharmacogenetic variant information
Uncertainties in future ecosystem services under land and climate scenarios: The case of erosion in the Alps
No full textInternational audienceHow ecosystems will provide ecosystem services in the future given uncertain changes in climate and land use is an open question that challenges decision-making on adaptation to climate change. Prospective assessments of ecosystem services should carefully include and communicate the sources of uncertainties that affect the predictions. We used the ecosystem service of soil protection against erosion in the Maurienne Valley (French Alps) as a case study to illustrate how several sources of uncertainties can be integrated into an assessment of future ecosystem service supply. We modeled future erosion rates in the Maurienne Valley for years 2020 and 2085 using the Revised Universal Soil Loss Equation (RUSLE) and six climatic and socioeconomic scenarios. We quantified how the ecosystem service supply will be likely affected by climate and land-use change, separately and jointly. We assessed the effects of different sources of uncertainty on projected erosion rates: scenarios, climate models choice, and methods to parametrize the ecosystem service model. Land-use change increased erosion (+ 3.3 ton.ha-1.yr-1 on average, with significant increases in 81 % of the study site), while climate change contributed to a slight reduction (-0.21 ton.ha-1.yr-1 on average with significant decrease 20 % of the study site). The uncertainty of the ecosystem service model parameterization explained 93 % of the variance in erosion values. Furthermore, uncertainty linked to climate models and future scenarios contributed almost equally to the variability in the direction (positive or negative) of erosion change (41 % and 38 % respectively). The uncertainties surrounding the direction of future changes in ecosystem services come mainly from uncertainties in climate models and future scenarios rather than from uncertainties in the ecosystem service model parameters. Assessing the likelihood of future changes in ecosystem services helps prioritize locations where adaptation solutions are likely to be needed
A Paleozoic history of Armorica recounted through anorogenic to vaugneritic magmatism
No full textInternational audienceThe Plouaret-Commana-Huelgoat (PCH) vaugnerite-granite complex, emplaced at around 315 Ma on both sides of the North Armorican Shear Zone (NASZ) in the Armorican Massif (France), can be regarded as the "axial pivot" around which a large part of the history of the Armorican magmatism was revolving. Indeed, four main magmatic cycles can be distinguished in the Ordovician/Early Permian time-span over much of the considered areas, i.e. North and Central Armorican Domains (N/CAD): (1) several anorogenic mafic complexes (plutons, dykes and/or lavas) were successively emplaced from the Ordovician to Early Carboniferous; (2) near the Bashkirian/Moscovian time-boundary, when the N/CAD started to record the effects of the Variscan collision, magmatism became predominantly lamprophyric/vaugneritic (K-rich West-Armorican kersantites and PCH vaugnerites), prior to (3) the generalized granitic peak during the Moscovian-Kasimovian ages, in turn followed by (4) a K-rich intermediate magmatic activity, including again vaugnerites and the last granitic intrusions, during the late-/post-collision stages in the upper Pennsylvanian-Early Permian time-period. The sharp geochemical break evidenced in the present work between an early anorogenic magmatic group and a syn- to post-collisional system in the N/CAD emphasizes the original magmatic history recorded by part of Armorica, including probably the Central Iberian Zone (CIZ), during the nearly entire Paleozoic era compared to those commonly applied to the rest of the European Variscan orogen. This evolution is assumed to result from: (1) large-scale asthenospheric upheavals due to the downward straightening and retreat of variously plunging slabs during the Paleozoic times, (2) partial melting of metasomatized lithospheric/asthenospheric mantle due to fluid release from fragments of buried continental crust, and (3) crustal anatexis
Deep-learning-based detection of underwater fluids in multiple multibeam echosounder data
No full textInternational audienceetecting and locating emitted fluids in the water column is necessary for studying margins, identifying natural resources, and preventing geohazards. Fluids can be detected in the water column using multibeam echosounder data. However, manually analyzing the huge volume of this data for geoscientists is a very time-consuming task. Our study investigated the use of a YOLO-based deep learning supervised approach to automate the detection of fluids emitted from cold seeps (gaseous methane) and volcanic sites (liquid carbon dioxide). Several thousand annotated echograms collected from three different seas and oceans during distinct surveys were used to train and test the deep learning model. The results demonstrate first that this method surpasses current machine learning techniques, such as Haar-Local Binary Pattern Cascade. Additionally, we thoroughly analyzed the composition of the training dataset and evaluated the detection performance based on various training configurations. The tests were conducted on a dataset comprising hundreds of thousands of echograms i) acquired with three different multibeam echosounders (Kongsberg EM302 and EM122 and Reson Seabat 7150) and ii) characterized by variable water column noise conditions related to sounder artefacts and the presence of biomass (fishes, dolphins). Incorporating untargeted echoes (acoustic artefacts) in the training set (through hard negative mining) along with adding images without fluid-related echoes are the most efficient way to improve the performance of the model and reduce the false positives. Our fluid detector opens the door for near-real time acquisition and post-acquisition detection with efficiency, reliability and rapidity
Statistical learning methods applied to stratigraphic and pottery data: An aid to establishing archaeological periodisation
No full textInternational audienceChronology, and hence periodisation of archaeological sites according to the major transformations that affect them, is an essential prerequisite for any historical discourse. The main sources that can be used to establish this periodisation, the temporality of archaeological sites, are (i) stratigraphy, which corresponds to the succession of anthropic levels at the origin of the construction of a relative chronology, and (ii) archaeological material, and more specifically pottery that is omnipresent in excavations, with a typology that evolves rapidly over time; these two factors make pottery a highly valuable chronological source. This work presents an original interdisciplinary approach in which archaeology and statistics work together to produce a periodisation using pottery and stratigraphy. We apply this approach to data collected in the mythic city of Angkor Thom (Cambodia), capital of the Khmer Empire between the 9th and 15th centuries. The first step in the process is to construct stable, interpretable pottery facies using a compromise-based clustering approach. In the second step, the predictions provided by supervised classification models make it possible to integrate less reliable pottery assemblages that are essential to the overall construction of the chronological model of the Angkor Thom city. Our approach offers the advantage of automatically processing large volumes of data and integrating uncertainty into the forecasts obtained for the least chronologically reliable sets
Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households
No full textInternational audienceFood loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, Penicillium spp. were the most common representing more than 50 % of mold isolates followed by Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %) spp. Hanseniaspora uvarum and Aureobasidium pullulans were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with Pseudomonas spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in household
Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti
No full textInternational audienceElucidating the genomic architecture of quantitative traits is essential for our understanding of adaptation and for breeding in domesticated organisms. Penicillium roqueforti is the mold used worldwide for the blue cheese maturation, contributing to flavors through proteolytic and lipolytic activities. The two domesticated cheese populations display very little genetic diversity, but are differentiated and carry opposite mating types. We produced haploid F1 progenies from five crosses, using parents belonging to cheese and non-cheese populations. Analyses of high-quality genome assemblies of the parental strains revealed five large translocations, two having occurred via a circular intermediate, one with footprints of Starship giant mobile elements. Offspring genotyping with genotype-by-sequencing (GBS) revealed several genomic regions with segregation distortion, possibly linked to degeneration in cheese lineages. We found transgressions for several traits relevant for cheese making, with offspring having more extreme trait values than parental strains. We identified quantitative trait loci (QTLs) for colony color, lipolysis, proteolysis, extrolite production, including mycotoxins, but not for growth rates. Some genomic regions appeared rich in QTLs for both lipid and protein metabolism, and other regions for the production of multiple extrolites, indicating that QTLs have pleiotropic effects. Some QTLs corresponded to known biosynthetic gene clusters, e.g., for the production of melanin or extrolites. F1 hybrids constitute valuable strains for cheese producers, with new traits and new allelic combinations, and allowed identifying target genomic regions for traits important in cheese making, paving the way for strain improvement. The findings further contribute to our understanding of the genetic mechanisms underlying rapid adaptation, revealing convergent adaptation targeting major gene regulators