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1. Spatiotemporal large-scale networks shaped by air mass movements

Author

Choufany, Maria, Martinetti, Davide, Senoussi, Rachid, Morris, Cindy E., and Soubeyrand, Samuel

Subjects
Statistics - Applications
Abstract

The movement of atmospheric air masses can be seen as a continuous and complex flow of particles hovering over our planet. It can however be locally simplified by considering three-dimensional trajectories of air masses connecting distant areas of the globe during a given period of time. In this paper, we present a mathematical framework to construct spatial and spatiotemporal networks where the nodes are the subsets of a partition of a geographical area and the links between these nodes are inferred from sampled trajectories of air masses passing over and across the nodes. We propose different estimators of link intensities relying on different bio-physical hypotheses and covering adjustable time periods. This approach leads to a new class of spatiotemporal networks characterized by adjacency matrices. We applied the approach in two real geographical contexts: the watersheds of the French region Provence-Alpes-C\^ote d'Azur and the coastline of the Mediterranean Sea. The analysis of the constructed networks allowed identifying a marked seasonal pattern in air mass movements in the study areas. These constructed networks can be used to investigate issues, e.g., in aerobiology and epidemiology of airborne plant pathogens. Similar networks could be estimated from other types of trajectories, such as animal trajectories.

Published
2019

9. Spatiotemporal Large-Scale Networks Shaped by Air Mass Movements

Author

Choufany, Maria, Martinetti, Davide, Senoussi, Rachid, Morris, Cindy E., Soubeyrand, Samuel, Biostatistique et Processus Spatiaux (BioSP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Pathologie Végétale (PV), PHYTOSENTINEL project (Grant No. IB–2019–SPE)., ANR-17-CE32-0004,SPREE,Stratégie préemptive de surveillance de l'air et de l'eau pour anticiper l'émergence de maladies des plantes liés aux changements paysagers(2017), Institut National de la Recherche Agronomique (INRA), SPREE project from the French National Research Agency (grant n0 ANR-17-CE32-0004-01), and PHYTOSENTINEL project (grant n0 IB-2019-SPE)

Subjects
[PHYS.PHYS.PHYS-AO-PH]Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph], FOS: Computer and information sciences, [STAT.AP]Statistics [stat]/Applications [stat.AP], aerobiology, air masses dynamics, lcsh:T57-57.97, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Statistics - Applications, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, trajectory, connectivity, spatiotemporal network, [SDE]Environmental Sciences, lcsh:Applied mathematics. Quantitative methods, Applications (stat.AP), lcsh:Probabilities. Mathematical statistics, lcsh:QA273-280, spatial network
Abstract

The movement of atmospheric air masses can be seen as a continuous and generally complex flow of gases and particles hovering over our planet. It can however be locally simplified by considering three-dimensional trajectories of air masses connecting distant areas of the globe during a given period of time. In this paper, we present a mathematical framework to construct spatial and spatiotemporal networks where the nodes are the subsets of a partition of a geographical area and the links between these nodes are inferred from sampled trajectories of air masses passing over and across the nodes. We propose different estimators of link intensities relying on different bio-physical hypotheses and covering adjustable time periods. This approach leads to a new class of spatiotemporal networks characterized by adjacency matrices giving, e.g., the probability of connection between distant areas during a chosen period of time. To illustrate the effectiveness of this approach, we applied it to characterize tropospheric connectivity in two real geographical contexts: the watersheds of the French region Provence-Alpes-Côte d'Azur and the coastline of the Mediterranean Sea. The analysis of the constructed networks allowed identifying a marked seasonal pattern in air mass movements in the two study areas. The networks constructed from air mass trajectories can be used to investigate issues, e.g., in aerobiology and epidemiology of airborne plant pathogens. Similar networks could be estimated from other types of trajectories, such as animal trajectories, to characterize connectivity between different components of the landscape where the animals live.

Published
2021
Full Text
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12. Estimating virus effective population size and selection without neutral markers

Author

Rousseau, Elsa, Moury, Benoît, Mailleret, Ludovic, Senoussi, Rachid, Palloix, Alain, Simon, Vincent, Valière, Sophie, Grognard, Frédéric, Fabre, Frédéric, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Biological control of artificial ecosystems (BIOCORE), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Biostatistique et Processus Spatiaux (BioSP), Génétique et Amélioration des Fruits et Légumes (GAFL), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Animalerie Rongeurs (UAR), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), SMaCH (Sustainable Management of Crop Health) metaprogramme of INRA, grant over-seen by the French National Research Agency (ANR) as part of the 'Blanc2013' program (ANR-13-BSV7- 0011, FunFit project), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Biostatistique et Processus Spatiaux (BIOSP), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), GeT PlaGe, Genotoul, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
lcsh:Immunologic diseases. Allergy, Evolutionary Genetics, Genetic Markers, Leaves, Evolutionary Processes, Heredity, Genotype, Population Size, [SDV]Life Sciences [q-bio], Potyvirus, Variant Genotypes, Plant Science, Microbiology, Viral Evolution, Evolution, Molecular, [SPI]Engineering Sciences [physics], Population Metrics, Effective Population Size, Virology, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Genetics, Selection, Genetic, [MATH]Mathematics [math], lcsh:QH301-705.5, Plant Diseases, Evolutionary Biology, Population Biology, Models, Genetic, Plant Anatomy, Genetic Drift, Biology and Life Sciences, High-Throughput Nucleotide Sequencing, food and beverages, Organismal Evolution, Genetic Mapping, lcsh:Biology (General), Microbial Evolution, lcsh:RC581-607, Capsicum, Population Genetics, Research Article
Abstract

By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and variant frequencies were determined by HTS in eight plants of each pepper line at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes Ne at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (Ne ∈ [10, 2000]) and selection (|s| ∈ [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of Ne were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation., Author summary A growing number of experimental evolution studies are using an “evolve-and-resequence” approach to observe the within-host dynamics of pathogen variants of biomedical or ecological interest. The resulting data are particularly appropriate for studying the effects of evolutionary forces, such as selection and genetic drift, on the emergence of new pathogen variants. However, it remains challenging to unravel the effects of selection and genetic drift in the absence of neutral markers, a situation frequently encountered for microbes, such as viruses, due to their small constrained genomes. Using such an approach on a plant virus, we observed that the same set of virus variants displayed highly diverse dynamics in closely related plant genotypes. We developed and validated a method that does not require neutral markers, for estimating selection coefficients and effective population sizes from these experimental evolution data. We found that the viruses experienced considerable diversity in genetic drift regimes, depending on host genotype. Importantly, genetic drift experienced by virus populations was shown to be a heritable plant trait. These findings pave the way for the breeding of plant varieties exposing viruses to strong genetic drift, thereby slowing virus adaptation.

Published
2017
Full Text
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13. Estimating virus effective population size and selection without neutral markers

Author

Moury, Benoit, Mailleret, Ludovic, Senoussi, Rachid, Palloix, Alain, Simon, Vincent, Valiere, Sophie, Grognard, Frédéric, Rousseau, Elsa, and Fabre, Frédéric

Subjects
sélection génétique, Phytopathology and phytopharmacy, Virologie, dérive génétique, food and beverages, taille de la population, Phytopathologie et phytopharmacie, virus y de la pomme de terre, Agricultural sciences, modèle mathématique, Virology, marqueur neutre, évolution génétique des populations, virologie végétale, pathologie végétale, Sciences agricoles
Abstract

By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and variant frequencies were determined by HTS in eight plants of each pepper line at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes Ne at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (Ne ∈ [10, 2000]) and selection (|s| ∈ [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of Ne were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation.

Published
2017

14. Joint estimation of effective population size and selection coefficient without neutrel markers: method validation and application to experimental evolution of viruses

Author

Rousseau, Elsa, Moury, Benoit, Mailleret, Ludovic, Senoussi, Rachid, Palloix, Alain, Simon, Vincent, Grognard, Frédéric, Valiere, Sophie, and Fabre, Frédéric

Subjects
virus phytopathogène, sélection génétique, modèle statistique, dérive génétique, séquençage, modèle mécanique, comparaison de génotypes, évolution génétique des populations, simulation numérique, pathologie végétale, Sciences agricoles, virus y de la pomme de terre, Agricultural sciences
Abstract

Experimental evolution studies deserve considerable attention to the estimation of basic evolutionary forces such as selection and genetic drift. With the advent of high-throughput sequencing techniques, these studies gained a renewed attention. However the joint estimation of selection and genetic drift still remain challenging when no neutral markers are available, a common situation with many microbes, such as viruses, due to their small tightly packed genomes.

Published
2016

15. Joint estimation of the strength of genetic drift and selection from next generation sequencing time-sampled data : a case study on the adaptation of virus populations to host plant resistance

Author

Rousseau, Elsa, Fabre, Frédéric, Coville, Jérôme, Mailleret, Ludovic, Palloix, Alain, Senoussi, Rachid, Moury, Benoît, Grognard, Frédéric, Biological control of artificial ecosystems (BIOCORE), Institut National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Biostatistique et Processus Spatiaux (BIOSP), Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Station de Pathologie Végétale (AVI-PATHO), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Unité de Pathologie Végétale (PV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Santé et agroécologie du vignoble (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Biostatistique et Processus Spatiaux (BioSP), Génétique et Amélioration des Fruits et Légumes (GAFL), Society for molecular biology and evolution (SMBE). Lawrence, USA., Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), and Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, résistance variétale, virus phytopathogène, dérive génétique, [SDV]Life Sciences [q-bio], poivron, culture legumiere, modèle d'évolution, maladie des plantes, virus y de la pomme de terre, Agricultural sciences, durabilité des résistances, [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, évolution génétique des populations, population virale, lutte génétique, pathologie végétale, ComputingMilieux_MISCELLANEOUS, Sciences agricoles
Abstract

National audience

Published
2015

16. Joint estimation of effective population sizes and selection coefficients from time-sampled data: a case study on virus populations submitted to plant resistance

Author

Rousseau, Elsa, Coville, Jérôme, Mailleret, Ludovic, Palloix, Alain, Senoussi, Rachid, Grognard, Frédéric, Moury, Benoit, and Fabre, Frédéric

Subjects
résistance variétale, virus phytopathogène, épidémiologie moléculaire, poivron, analyse de qtl, culture legumiere, modèle d'évolution, virus y de la pomme de terre, maladie des plantes, Agricultural sciences, durabilité des résistances, gestion du paysage, évolution génétique des populations, lutte génétique, pathologie végétale, Sciences agricoles
Published
2015

17. Joint estimation of effective population sizes and selection coefficients from time-sampled data: a case study on virus populations exposed to plant resistance

Author

Rousseau, Elsa, Coville, Jérôme, Mailleret, Ludovic, Palloix, Alain, Senoussi, Rachid, Grognard, Frédéric, Moury, Benoit, and Fabre, Frédéric

Subjects
résistance variétale, virus phytopathogène, épidémiologie moléculaire, poivron, analyse de qtl, culture legumiere, modèle d'évolution, maladie des plantes, virus y de la pomme de terre, Agricultural sciences, durabilité des résistances, évolution génétique des populations, lutte génétique, pathologie végétale, Sciences agricoles
Published
2015

19. Méthodes statistiques de détection d'anomalies spatio-temporelles en épidémiologie

Author

Senoussi, Rachid, Gay, Emilie, Jacob, Christine, Biostatistique et Processus Spatiaux (BioSP), Institut National de la Recherche Agronomique (INRA), Unité de biométrie et intelligence artificielle de jouy, Jacques Barnouin (Directeur), and Ivan Sache (Directeur)

Subjects
public health, risk prevention, gestion de risques, anomaly, modélisation spatiale, statistique spatiale, spatial statistic, modèle mathématique, anomalie, santé publique, épidémiologie, epidemiology, [INFO]Computer Science [cs], [MATH]Mathematics [math], prévention des risques
Abstract

Chapitre numéro 11; National audience

Published
2010

21. Effet d'une haie composite sur la distribution de la faune auxiliaire en verger de poirier

Author

Debras, Jean Francois, Rieux, René, Senoussi, Rachid, Dutoit, Thierry, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Biostatistique et Processus Spatiaux (BioSP), Unité mixte de recherche Ecologie des invertébrés (UAPV), and Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU)

Subjects
haies, protection raisonnée, cacopsylla pyri L, auxiliaires, poirier, diversité, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [INFO]Computer Science [cs], [MATH]Mathematics [math]
Abstract

International audience; L’intensification de l’agriculture, s’est faite au détriment du linéaire des haies, de nombreuses études ont tentée d’évaluer l’impact de cette perte sur les agrosystèmes. Peu d’entre elles ont été réalisées en prenant en compte l’entomofaune globale de la parcelle et de la haie simultanément. C’est pourquoi nous avons échantillonné pendant 3 années consécutives, de 1999 à 2001, la communauté globale d’un verger de Poirier et d’une haie adjacente. Nous tentons dans cette étude d’évaluer l’impact écologique de la présence de la haie sur les distributions dans le verger du psylle Cacopsylla pyri L. et des différents prédateurs. Nos résultats soulignent que la proximité des distributions des peuplements des prédateurs dans le verger et la haie est significativement observée avec la mise en évidence d’un gradient spatial de la diversité décroissant localisé dans le temps et en relation avec les effectifs du psylle.

Published
2006

23. Should I stay or should I go? A habitat-dependent dispersal kernel improves prediction of movement

Author

Vinatier, Fabrice, Lescourret, Françoise, Duyck, Pierre François, Martin, Olivier, Senoussi, Rachid, Tixier, Philippe, Vinatier, Fabrice, Lescourret, Françoise, Duyck, Pierre François, Martin, Olivier, Senoussi, Rachid, and Tixier, Philippe

Abstract

The analysis of animal movement within different landscapes may increase our understanding of how landscape features affect the perceptual range of animals. Perceptual range is linked to movement probability of an animal via a dispersal kernel, the latter being generally considered as spatially invariant but could be spatially affected. We hypothesize that spatial plasticity of an animal's dispersal kernel could greatly modify its distribution in time and space. After radio tracking the movements of walking insects (Cosmopolites sordidus) in banana plantations, we considered the movements of individuals as states of a Markov chain whose transition probabilities depended on the habitat characteristics of current and target locations. Combining a likelihood procedure and pattern-oriented modelling, we tested the hypothesis that dispersal kernel depended on habitat features. Our results were consistent with the concept that animal dispersal kernel depends on habitat features. Recognizing the plasticity of animal movement probabilities will provide insight into landscape-level ecological processes.

Published
2011

29. Narrow Bottlenecks Affect Pea Seedborne Mosaic Virus Populations during Vertical Seed Transmission but not during Leaf Colonization.

Author

Fabre, Frédéric, Moury, Benoît, Johansen, Elisabeth Ida, Simon, Vincent, Jacquemond, Mireille, and Senoussi, Rachid

Subjects
MOSAIC viruses, PLANT viruses, GENETIC drift, BIOLOGICAL evolution, GENETICS
Abstract

The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Populations having high Ne adapt faster, as selection acts more intensely, than populations having low Ne, where random effects of genetic drift dominate. Estimating Ne for various steps of plant virus life cycle has been the focus of several studies in the last decade, but no estimates are available for the vertical transmission of plant viruses, although virus seed transmission is economically significant in at least 18% of plant viruses in at least one plant species. Here we study the co-dynamics of two variants of Pea seedborne mosaic virus (PSbMV) colonizing leaves of pea plants (Pisum sativum L.) during the whole flowering period, and their subsequent transmission to plant progeny through seeds. Whereas classical estimators of Ne could be used for leaf infection at the systemic level, as virus variants were equally competitive, dedicated stochastic models were needed to estimate Ne during vertical transmission. Very little genetic drift was observed during the infection of apical leaves, with Ne values ranging from 59 to 216. In contrast, a very drastic genetic drift was observed during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. A simple model of vertical transmission, assuming a cumulative action of virus infectious particles and a virus density threshold required for vertical transmission to occur fitted the experimental data very satisfactorily. This study reveals that vertically-transmitted viruses endure bottlenecks as narrow as those imposed by horizontal transmission. These bottlenecks are likely to slow down virus adaptation and could decrease virus fitness and virulence. [ABSTRACT FROM AUTHOR]

Published
2014
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30. Estimation of the number of virus particles transmitted by an insect vector.

Author

Mouty, Benoît, Fabre, Frédéric, and Senoussi, Rachid

Subjects
PLANT viruses, PLANT invasions, APHIDS, POTYVIRUSES, INSECTS, INVASIVE plants, PHYTOPATHOGENIC microorganisms, BIOLOGICAL invasions
Abstract

Plant viruses are submitted to narrow population bottlenecks both during infection of their hosts and during horizontal transmission between host individuals. The size of bottlenecks exerted on virus populations during plant invasion has been estimated in a few pathosystems but is not addressed yet for horizontal transmission. Using competition for aphid transmission between two Potato virus V variants, one of them being noninfectious but equally transmissible, we obtained estimates of the size of bottlenecks exerted on an insect-borne virus during its horizontal transmission. We found that an aphid transmitted on average 0.5–3.2 virus particles, which is extremely low compared with the census viral population into a plant. Such narrow bottlenecks emphasize the strength of stochastic events acting on virus populations, and we illustrate, in modeling virus emergence, why estimating this parameter is important. [ABSTRACT FROM AUTHOR]

Published
2007
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31. Estimating virus effective population size and selection without neutral markers.

Author

Rousseau E, Moury B, Mailleret L, Senoussi R, Palloix A, Simon V, Valière S, Grognard F, and Fabre F

Subjects
Evolution, Molecular, Genetic Drift, Genetic Markers, Genotype, High-Throughput Nucleotide Sequencing, Models, Genetic, Potyvirus physiology, Selection, Genetic, Capsicum virology, Plant Diseases virology, Potyvirus genetics
Abstract

By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and variant frequencies were determined by HTS in eight plants of each pepper line at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes Ne at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (Ne ∈ [10, 2000]) and selection (|s| ∈ [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of Ne were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation.

Published
2017
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