Search

Your search keyword '"Jean-Baptiste Pons"' showing total 20 results
Start Over Author "Jean-Baptiste Pons"
20 results on '"Jean-Baptiste Pons"'

1. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

Author

Orianne Tournayre, Jean‐Baptiste Pons, Maxime Leuchtmann, Raphael Leblois, Sylvain Piry, Ondine Filippi‐Codaccioni, Anne Loiseau, Jeanne Duhayer, Inazio Garin, Fiona Mathews, Sébastien Puechmaille, Nathalie Charbonnel, and Dominique Pontier

Subjects
Chiroptera, connectivity, conservation, demographic inference, microsatellites, population genetics, Ecology, QH540-549.5
Abstract

Abstract The greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals, and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure, and the demographic history of R. ferrumequinum colonies in the western part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede R. ferrumequinum gene flow. These results provide important information to improve the delineation of R. ferrumequinum management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque Country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining high levels of genetic mixing between colonies. Smaller management units corresponding to English and northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in the near future.

Published
2019
Full Text
View/download PDF

2. Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

Author

Ondine Filippi-Codaccioni, Marie-Pauline Beugin, Damien M. de Vienne, Elodie Portanier, David Fouchet, Cecile Kaerle, Lina Muselet, Guillaume Queney, Eric J. Petit, Corinne Regis, Jean-Baptiste Pons, and Dominique Pontier

Subjects
Pteronotus cf. parnellii, Microsatellite, Mitochondrial DNA, Phylogeny, Echolocation, Population genetics, Evolution, QH359-425
Abstract

Abstract Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. Results A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1–4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). Conclusions The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species.

Published
2018
Full Text
View/download PDF

3. Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France

Author

Guillaume Castel, Mathilde Couteaudier, Frank Sauvage, Jean-Baptiste Pons, Séverine Murri, Angelina Plyusnina, Dominique Pontier, Jean-François Cosson, Alexander Plyusnin, Philippe Marianneau, and Noël Tordo

Subjects
Hantavirus, Puumala virus, complete genome, phylogeny, diversity, France, Microbiology, QR1-502
Abstract

Puumala virus (PUUV) is the agent of nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS) in Europe. NE incidence presents a high spatial variation throughout France, while the geographical distribution of the wild reservoir of PUUV, the bank vole, is rather continuous. A missing piece of the puzzle is the current distribution and the genetic variation of PUUV in France, which has been overlooked until now and remains poorly understood. During a population survey, from 2008 to 2011, bank voles were trapped in eight different forests of France located in areas known to be endemic for NE or in area from where no NE case has been reported until now. Bank voles were tested for immunoglobulin (Ig)G ELISA serology and two seropositive animals for each of three different areas (Ardennes, Jura and Orleans) were then subjected to laboratory analyses in order to sequence the whole S, M and L segments of PUUV. Phylogenetic analyses revealed that French PUUV isolates globally belong to the central European (CE) lineage although isolates from Ardennes are clearly distinct from those in Jura and Orleans, suggesting a different evolutionary history and origin of PUUV introduction in France. Sequence analyses revealed specific amino acid signatures along the N protein, including in PUUV from the Orleans region from where NE in humans has never been reported. The relevance of these mutations in term of pathophysiology is discussed.

Published
2015
Full Text
View/download PDF

4. Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions

Author

Stéphanie Jacquet, Michelle Culbertson, Chi Zhang, Adil El Filali, Clément De La Myre Mory, Jean-Baptiste Pons, Ondine Filippi-Codaccioni, M. Elise Lauterbur, Barthélémy Ngoubangoye, Jeanne Duhayer, Clément Verez, Chorong Park, Clara Dahoui, Clayton M. Carey, Greg Brennan, David Enard, Andrea Cimarelli, Stefan Rothenburg, Nels C. Elde, Dominique Pontier, Lucie Etienne, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Vaccine Related, Rare Diseases, Infectious Diseases, Emerging Infectious Diseases, Multidisciplinary, Prevention, Biodefense, [SDV]Life Sciences [q-bio], Genetics, Small Pox, Infection, Biotechnology
Abstract

Several bat species act as asymptomatic reservoirs for many viruses that are highly pathogenic in other mammals. Here, we have characterized the functional diversification of the protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats in contrast to all studied mammals that have a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. We determined that duplicated PKRs of the Myotis species have undergone genetic diversification, allowing them to collectively escape from and enhance the control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat-specific immunity.

Published
2022

5. Adaptive duplication and functional diversification of Protein kinase R contribute to the uniqueness of bat-virus interactions

Author

Stéphanie Jacquet, Michelle Culbertson, Chi Zang, Adil El Filali, Clément De La Myre Mory, Jean-Baptiste Pons, Ondine Filippi-Codaccioni, M. Elise Lauterbur, Barthélémy Ngoubangoye, Jeanne Duhayer, Clément Verez, Chorong Park, Clara Dahoui, Clayton M. Carey, Greg Brennan, David Enard, Andrea Cimarelli, Stefan Rothenburg, Nels C. Elde, Dominique Pontier, Lucie Etienne, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity
Abstract

Several bat species act as asymptomatic reservoirs for many viruses that are instead highly pathogenic in other mammals. Here, we have characterized the functional diversification of the Protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats, in contrast to all studied mammals that possess a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. More importantly, we determined that duplicated PKRs of the Myotis species have undergone functional diversification allowing them to collectively escape from and enhance control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat specific immunity.

Published
2022

6. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

Author

Raphaël Leblois, Jean-Baptiste Pons, Ondine Filippi-Codaccioni, Anne Loiseau, Dominique Pontier, Jeanne Duhayer, Fiona Mathews, Maxime Leuchtmann, Sylvain Piry, Sébastien J. Puechmaille, Nathalie Charbonnel, Inazio Garin, Orianne Tournayre, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Lyon, Nature environment, Partenaires INRAE, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of Sussex, GCMP, CREN, Toulouse, France, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), LABEX CEMEB : ANR-11-IDEX-0007, LABEX ECOFECT : ANR-11-LABX-0048 European Union (EU), DREAL Nouvelle-Aquitaine, Region Auvergne-Rhone-Alpes, Region Bourgogne-Franche-Comte, Region Hauts-de-France, Region Nouvelle-Aquitaine, ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226

Subjects
0106 biological sciences, Demographic history, Population, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, Chiroptera, lcsh:QH540-549.5, Biologie animale, IUCN Red List, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, connectivity, conservation, demographic inference, population genetics, 030304 developmental biology, Nature and Landscape Conservation, Isolation by distance, Animal biology, 0303 health sciences, education.field_of_study, Near-threatened species, Habitat fragmentation, Ecology, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Rhinolophus ferrumequinum, 15. Life on land, biology.organism_classification, Geography, Threatened species, Biological dispersal, lcsh:Ecology
Abstract

The greater horseshoe bat(Rhinolophus ferrumequinum)is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the EuropeanIUCN Red List of Threatened Animalsand it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure and the demographic history ofR. ferrumequinumcolonies in the Western European part of its distribution. We found high levels of genetic diversity and large population size on the European mainland and lower estimates in England and Northern France. Analyses of clustering and isolation by distance showed a barrier effect of the Channel and potentially of the Mediterranean Sea onR. ferrumequinumbat dispersal. Conversely, we could not reveal any gene flow disruption from both sides of the Western Pyrenees. These results provide important information to improve the delineation ofR. ferrumequinummanagement units in its western range. We suggest that a large management unit corresponding to the European mainland population must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining the high levels of genetic mixing between colonies. Smaller management units corresponding to English and Northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in a near future.

Published
2019

7. Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

Author

Orianne Tournayre, Dominique Pontier, Eric Pierre, Nathalie Charbonnel, Jean-Baptiste Pons, Maxime Galan, Maxime Leuchtmann, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), LabEx Ecofect, Eco-Evolutionary Dynamics of Infectious Diseases, Nature environment, Partenaires INRAE, This work was funded by the LabEx ECOFECT and the internal funding from the CBGP laboratory. Orianne Tournayre PhD is funded by the LabEx CeMEB. Part of this work (JBP, DP) was performed within the framework of the LabEx ECOFECT of Université de Lyon and the Poitou-Charentes Nature Feder project 'Grand Rhinolophe et trame verte bocagère : étude des facteurs environnementaux influant sur la dynamique des populations ' (ML, JBP, DP)., ANR-11-LABX-0048,ECOFECT,Dynamiques eco-évolutives des maladies infectieuses(2011), and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)

Subjects
0106 biological sciences, 0301 basic medicine, Conservation of Natural Resources, Arthropoda, predator-prey interactions, [SDV]Life Sciences [q-bio], Zoology, environmental DNA (eDNA), Biology, 010603 evolutionary biology, 01 natural sciences, Predation, Feces, 03 medical and health sciences, Chiroptera, Diet analysis, false positives, Genetics, False positive paradox, Animals, DNA Barcoding, Taxonomic, Species identification, 14. Life underwater, Arthropods, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, high-throughput sequencing, Feeding Behavior, Sequence Analysis, DNA, DNA extraction, Diet, 030104 developmental biology, Evolutionary biology, [SDE]Environmental Sciences, Taxonomic resolution, Identification (biology), Species richness, Biotechnology, Faecal pellet
Abstract

Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the ‘all at once’ taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity, and amplification biases. Our parallel identification strategy of predators and preys reduces the risk of mis-assigning preys to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing ‘chirosurveillance’ and conservation strategies.

Published
2018

9. Evolution of Hepatitis B Virus Receptor NTCP Reveals Differential Pathogenicities and Species Specificities of Hepadnaviruses in Primates, Rodents, and Bats

Author

Jean-Baptiste Pons, Dominique Pontier, François-Loïc Cosset, Lucie Etienne, Barthélémy Ngoubangoye, Stéphanie Jacquet, Corinne Régis, Ariel de Bernardo, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherches Médicales de Franceville (CIRMF), Virologie humaine, École normale supérieure - Lyon (ENS Lyon)-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), mulet-marquis, odile, Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), École normale supérieure de Lyon (ENS de Lyon)-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), and Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI)

Subjects
Primates, Hepatitis B virus, Rodent, Immunology, Organic Anion Transporters, Sodium-Dependent, Rodentia, medicine.disease_cause, Microbiology, Host Specificity, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Orthohepadnavirus, Viral envelope, Species Specificity, Viral Envelope Proteins, biology.animal, Chiroptera, Virology, medicine, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Animals, Humans, Primate, Receptor, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, biology, Symporters, Host (biology), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Virus Internalization, biology.organism_classification, Hepatitis B, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genetic Diversity and Evolution, Insect Science, Hepadnavirus, 030217 neurology & neurosurgery, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Human hepatitis B virus (HBV) is a global health problem, affecting more than 250 million people worldwide. HBV-like viruses, named orthohepadnaviruses, also naturally infect nonhuman primates, rodents, and bats, but their pathogenicity and evolutionary history are unclear. Here, we determined the evolutionary history of the HBV receptors NTCP and GPC5 over millions of years of primate, rodent, and bat evolution. We use this as a proxy to understand the pathogenicity of orthohepadnaviruses in mammalian hosts and to determine the implications for species specificity. We found that NTCP, but not GPC5, has evolved under positive selection in primates (27 species), rodents (18 species), and bats (21 species) although at distinct residues. Notably, the positively selected codons map to the HBV-binding sites in primate NTCP, suggesting past genetic “arms races” with pathogenic orthohepadnaviruses. In rodents, the positively selected codons fall outside and within the presumed HBV-binding sites, which may contribute to the restricted circulation of rodent orthohepadnaviruses. In contrast, the presumed HBV-binding motifs in bat NTCP are conserved, and none of the positively selected codons map to this region. This suggests that orthohepadnaviruses may bind to different surfaces in bat NTCP. Alternatively, the patterns may reflect adaptive changes associated with metabolism rather than pathogens. Overall, our findings further point to NTCP as a naturally occurring genetic barrier for cross-species transmissions in primates, which may contribute to the narrow host range of HBV. In contrast, this constraint seems less important in bats, which may correspond to greater orthohepadnavirus circulation and diversity. IMPORTANCE Chronic infection with hepatitis B virus (HBV) is a major cause of liver disease and cancer in humans. Mammalian HBV-like viruses are also found in nonhuman primates, rodents, and bats. As for most viruses, HBV requires a successful interaction with a host receptor for replication. Cellular receptors are thus key determinants of host susceptibility as well as specificity. One hallmark of pathogenic virus-host relationships is the reciprocal evolution of host receptor and viral envelope proteins, as a result of their antagonistic interaction over time. The dynamics of these so-called “evolutionary arms races” can leave signatures of adaptive selection, which in turn reveal the evolutionary history of the virus-host interaction as well as viral pathogenicity and the genetic determinants of species specificity. Here, we show how HBV-like viruses have shaped the evolutionary history of their mammalian host receptor, as a result of their ancient pathogenicity, and decipher the genetic determinants of cross-species transmissions.

Published
2018
Full Text
View/download PDF

10. Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

Author

Corinne Régis, Guillaume Queney, Dominique Pontier, Jean-Baptiste Pons, Lina Muselet, Cécile Kaerle, Elodie Portanier, Eric J. Petit, Damien M. de Vienne, Ondine Filippi-Codaccioni, David Fouchet, Marie-Pauline Beugin, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Ecologie et évolution des populations, Antagene - Animal Genomics Laboratory, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Lyon, ANR-11-LABX-0048, and ANR-11-IDEX-0007

Subjects
0106 biological sciences, 0301 basic medicine, Population genetics, 01 natural sciences, Haplogroup, Chiroptera, Phylogeny, education.field_of_study, biology, Reproduction, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Reproductive isolation, Mitochondrial DNA, French Guiana, Pteronotus cf, Sympatry, Genetic structure, Pteronotus cf. parnellii, Research Article, Species complex, Neotropics, Genotype, Evolution, Population, Introgression, 010603 evolutionary biology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Species Specificity, Pteronotus, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, QH359-425, otorhinolaryngologic diseases, Animals, parnellii, Microsatellite, Echolocation, Asymmetric introgression, education, Ecosystem, Ecology, Evolution, Behavior and Systematics, Cell Nucleus, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Acoustics, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Evolutionary biology, Microsatellite Repeats, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. Results A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1–4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). Conclusions The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1289-8) contains supplementary material, which is available to authorized users.

Published
2018

11. Additional file 1: of Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

Author

Filippi-Codaccioni, Ondine, Marie-Pauline Beugin, Vienne, Damien De, Portanier, Elodie, Fouchet, David, Kaerle, Cecile, Muselet, Lina, Queney, Guillaume, Petit, Eric, Regis, Corinne, Jean-Baptiste Pons, and Pontier, Dominique

Abstract

Table S1. Table. List of external COI sequences used in this study. The sequence in bold corresponds to type-locality of P. rubiginosus, caught in MatoGrosso, Brazil compared to P. sp4 in De Thoisy et al. (2014). Table S2. Characteristics of microsatellite markers. Figure S3. Graphical representation of assignation probabilities for Pteronotus A and Pteronotus B sampled. Each individual (x axis) is represented by a vertical bar divided in two parts according to its assignation probability (y axis) in each of the two clusters. Figure S4. Graphical representation of the difference between the Conservative and the Relaxed approach for the detection of hybrids. Table S5. Pairwise Fst values between caves for each species and both sexes. Table S6. Life cycle of Pteronotus A and B. PRE = Pregnant, LAC = Lactating females, PLAC = Post-lactating females, NS = No status (non pregnant, non-lactating, non post-lactating females, and non breeding males). n(A): number of Pteronotus A (number of adult females in parentheses); n(B): number of Pteronotus B (number of adult females in parentheses); n: total number of Pteronotus. (DOCX 319 kb)

Published
2018
Full Text
View/download PDF

12. Contrasting population trends at seabirds colonies: is food limitation a factor in Norway?

Author

Jean-Baptiste Pons, Francesco Bonadonna, Svein-Håkon Lorentsen, Lorien Pichegru, Robert T. Barrett, David Grémillet, and Emeline Pettex

Subjects
education.field_of_study, biology, food.dish, Haliaeetus albicilla, Ecology, Foraging, Population, Zoology, Clupea, biology.organism_classification, Predation, Geography, food, Nest, Pollachius virens, biology.animal, education, Northern gannet
Abstract

Norwegian Northern Gannet Morus bassanus populations exhibit contrasting trends on a regional scale, with several colony extinctions having occurred in recent decades. In an attempt to understand the ecological drivers of such variability, we tested whether resource availability is a factor limiting the current development of gannetries in the Lofoten/Vesteralen area. Between 2007 and 2010, we recorded arrival and departure times of breeding Northern Gannets from two colonies from regions showing contrasting population growth rates during the past two decades. We also recorded the duration of joint attendances by Northern Gannet parents at the nest, performed opportunistic diet sampling and counted numbers of occupied nests. Finally, we compiled ring recoveries over a 30-year period to assess inter-colony movements. Norwegian Gannet parents spent more time together, attending their chick, and performed shorter foraging trips than those in British and French colonies of similar size. This suggests that, despite some annual variations, their foraging effort was relatively low. Diet samples from both colonies mainly constituted fish of high energetic value, such as large herring Clupea harengus, mackerel Scomber scombrus, and saithe Pollachius virens, prey that are relatively abundant within the study area. Data from ringed birds revealed a northward movement of adults ringed as breeding birds and chicks from extinct Lofoten colonies that established a growing colony close to the North Cape. Recorded foraging features (trip duration, joint attendance and prey quality) during our study does not indicate food availability as a limiting factor explaining successive extinctions and re-colonisations of breeding sites in Lofoten/Vesteralen. White-tailed Eagles Haliaeetus albicilla are known to predate opportunistically on Northern Gannet adults or chicks and their populations are growing in the Lofoten area. Their potential impact on the Norwegian Northern Gannet population dynamics should be further investigated.

Published
2014

13. Bank vole immunoheterogeneity may limit Nephropatia Epidemica emergence in a French non-endemic region

Author

Anne Loiseau, Laure Benoit, Séverine Murri, Jean-Baptiste Pons, Coralie Pulido, Adelaide Dubois, Latifa Lakhdar, Guillaume Castel, Nathalie Charbonnel, Philippe Marianneau, Maxime Galan, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Lyon (COMUE), INRA-EFPA/ANSES fellowship, European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0301 basic medicine, experimental infections, Rodent, ecoimmunology, Gene Expression, Myodes glareolus, Population genetics, Antibodies, Viral, L73 - Maladies des animaux, Puumala virus, Serology, Zoonoses, Nephropathia epidemica, Non endemic, Puumala hantavirus, 2. Zero hunger, 0303 health sciences, Vegetal Biology, biology, Arvicolinae, rodent, 000 - Autres thèmes, 3. Good health, Bank vole, Infectious Diseases, Hemorrhagic Fever with Renal Syndrome, Zoology, 03 medical and health sciences, biology.animal, medicine, Animals, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Natural reservoir, population genetics, Disease Reservoirs, 030304 developmental biology, 030306 microbiology, biology.organism_classification, medicine.disease, Virology, Antiviral gene, 030104 developmental biology, Immunoglobulin G, Biological dispersal, Animal Science and Zoology, Parasitology, Biologie végétale
Abstract

Ecoevolutionary processes affecting hosts, vectors and pathogens are important drivers of zoonotic disease emergence. In this study, we focused on nephropathia epidemica (NE), which is caused by Puumala hantavirus (PUUV) whose natural reservoir is the bank vole,Myodes glareolus. Despite the continuous distribution of the reservoir in Europe, PUUV occurence is highly fragmented. We questioned the possibility of NE emergence in a French region that is considered to be NE-free but that is adjacent to a NE-endemic region. We first confirmed the epidemiology of these two regions using serological and virological surveys. We used bank vole population genetics to demonstrate the absence of spatial barriers that could have limited dispersal, and consequently, the spread of PUUV into the NE-free region. We next tested whether regional immunoheterogeneity could impact PUUV chances to establish, circulate and persist in the NE-free region. Immune responsiveness was phenotyped both in the wild and during experimental infections, using serological, virological and immune related gene expression assays. We showed that bank voles from the NE-free region were sensitive to experimental PUUV infection. We observed high levels of immunoheterogeneity between individuals and also between regions. In natural populations, antiviral gene expression (TnfandMx2genes) reached higher levels in bank voles from the NE-free region. During experimental infections, anti-PUUV antibody production was higher in bank voles from the NE endemic region. Altogether, our results indicated a lower susceptibility to PUUV for bank voles from this NE-free region, what might limit PUUV circulation and persistence, and in turn, the risk of NE.Graphical abstract

Published
2017

14. Experimental infections of wild bank voles (Myodes glareolus) from nephropatia epidemica endemic and non-endemic regions revealed slight differences in Puumala virological course and immunological responses

Author

Philippe Marianneau, Jean-Baptiste Pons, Adelaide Dubois, Anne Loiseau, Coralie Pulido, Séverine Murri, Laure Benoit, Maxime Galan, Latifa Lakhdar, Guillaume Castel, Nathalie Charbonnel, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de Virologie, Institut de Recherches Biomédicales des Armées, Plateforme d’expérimentation animale (PFEA), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Plateforme Expérimentation Animale, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
0301 basic medicine, Cancer Research, Nephropathia epidemica, [SDV]Life Sciences [q-bio], Immunology, Myodes glareolus, Biology, Antibodies, Viral, Puumala virus, Wild bank vole, 03 medical and health sciences, Human disease, Virology, medicine, Animals, Humans, Viral rna, Non endemic, Disease Reservoirs, Virulence, Arvicolinae, biology.organism_classification, medicine.disease, Bank vole, 030104 developmental biology, Infectious Diseases, Hemorrhagic Fever with Renal Syndrome, Immunoglobulin G, Experimental infections, RNA, Viral, Disease Susceptibility, France, Regional differences
Abstract

A. Dubois et N. Charbonnel : contributions égales au travail; In Europe, the occurrence of nephropathia epidemica (NE), a human disease caused by Puumala virus (PUUV), exhibits considerable geographical heterogeneity despite the continuous distribution of its reservoir, the bank vole Myodes glareolus. To better understand the causes of this heterogeneity, wild voles sampled in two adjacent NE endemic and non-endemic regions of France were infected experimentally with PUUV. The responses of bank voles to PUUV infection, based on the levels of anti-PUUV IgG and viral RNA, were compared. Slight regional differences were highlighted despite the high inter-individual variability. Voles from the NE non-endemic region showed greater immune responsiveness to PUUV infection, but lower levels of RNA in their organs than voles from the endemic region. These results suggest the existence of regional variations in the sensitivity of bank voles that could contribute to the apparent absence of PUUV circulation among voles and the absence of NE in the non endemic region.

Published
2017

15. Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France

Author

Mathilde Couteaudier, Noël Tordo, Guillaume Castel, Dominique Pontier, Angelina Plyusnina, Frank Sauvage, Alexander Plyusnin, Jean-Baptiste Pons, Jean-François Cosson, Séverine Murri, Philippe Marianneau, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecoevolutionary Dynamics of Infectious Diseases, LabEx ECOFECT, Laboratoire de Lyon, Unité Virologie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Department of Virology [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre collaborateur de l'OMS Arbovirus et Fièvres Hémorragiques virales - Stratégies antivirales (CC-OMS), Institut Pasteur [Paris], project ECOFECT (ANR-11-LABX-0048, ANR-11-IDEX-0007) - Anses (Afsset grant EST-2007-75) - EU grants FP7-261504 EDENext - FP7- 278976 ANTIGONE, European Project: 261504, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Unité Virologie, Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Institut Pasteur [Paris] (IP), Medicum, Department of Virology, Castel, Guillaume, Centre de Biologie pour la Gestion des Populations (CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) - Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro) - Institut national de la recherche agronomique [Montpellier] (INRA Montpellier) - Université de Montpellier (UM) - Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) - Institut National de la Recherche Agronomique (INRA) - Institut National de Recherche en Informatique et en Automatique (Inria) - Université de Montpellier (UM) - Centre National de la Recherche Scientifique (CNRS), UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), Laboratoire de Biométrie et Biologie Evolutive (LBBE), Université Claude Bernard Lyon 1 (UCBL) - Institut National de Recherche en Informatique et en Automatique (Inria) - Centre National de la Recherche Scientifique (CNRS), Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES Maisons-Alfort), Haartman Institute, Institut National de la Recherche Agronomique (INRA) - Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12) - Ecole Nationale Vétérinaire d'Alfort - AFSSA, ANR-11-IDEX-0007-02/11-LABX-0048, ECOFECT, Dynamiques eco-évolutives des maladies infectieuses(2011), European Project : 261504, EC:FP7:HEALTH, FP7-HEALTH-2010-single-stage, EDENEXT(2011), and European Project : 278976, EC:FP7:HEALTH, FP7-HEALTH-2011-two-stage, ANTIGONE(2011)

Subjects
Male, Disease reservoir, [SDV]Life Sciences [q-bio], TULA, lcsh:QR1-502, Sequence Homology, phylogeny, Puumala virus, lcsh:Microbiology, INFECTION, Nephropathia epidemica, Cluster Analysis, biology, Arvicolinae, MAJOR ANTIGENIC DOMAIN, 3. Good health, [SDV] Life Sciences [q-bio], Bank vole, Phylogeography, Infectious Diseases, diversité génétique, ANALYSIS RESOURCE, RNA, Viral, Female, France, Hantavirus, GENETICS, BIOINFORMATICS DATABASE, Molecular Sequence Data, complete genome, Zoology, Genome, Viral, analyse phylogénétique, Article, diversity, Phylogenetics, Virology, Genetic variation, medicine, Animals, Disease Reservoirs, technique elisa, VIRUS NUCLEOCAPSID PROTEIN, STRAINS, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, MOLECULAR EVOLUTION, PATTERNS, campagnol roussatre, 3111 Biomedicine
Abstract

Puumala virus (PUUV) is the agent of nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS) in Europe. NE incidence presents a high spatial variation throughout France, while the geographical distribution of the wild reservoir of PUUV, the bank vole, is rather continuous. A missing piece of the puzzle is the current distribution and the genetic variation of PUUV in France, which has been overlooked until now and remains poorly understood. During a population survey, from 2008 to 2011, bank voles were trapped in eight different forests of France located in areas known to be endemic for NE or in area from where no NE case has been reported until now. Bank voles were tested for immunoglobulin (Ig)G ELISA serology and two seropositive animals for each of three different areas (Ardennes, Jura and Orleans) were then subjected to laboratory analyses in order to sequence the whole S, M and L segments of PUUV. Phylogenetic analyses revealed that French PUUV isolates globally belong to the central European (CE) lineage although isolates from Ardennes are clearly distinct from those in Jura and Orleans, suggesting a different evolutionary history and origin of PUUV introduction in France. Sequence analyses revealed specific amino acid signatures along the N protein, including in PUUV from the Orleans region from where NE in humans has never been reported. The relevance of these mutations in term of pathophysiology is discussed.

Published
2015

16. Irreplaceable area extends marine conservation hotspot off Tunisia: insights from GPS‑tracking Scopoli’s shearwaters from the largest seabird colony in the Mediterranean

Author

Clara Péron, Jean-Baptiste Pons, Jérôme Fort, Ridha Ouni, Matthieu Authier, Mathieu Thévenet, David Grémillet, DST-NRF Centre of Excellence at the Percy FitzPatrick Institute, University of Cape Town, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Société d’Echantillonnage et d’Ingénierie Scientifique en Environnement, Faculté des Sciences de Monastir (FSM), Université de Monastir - University of Monastir (UM), Observatoire PELAGIS UMS 3462 (PELAGIS), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Conservatoire du Littoral, Ministère de l'Ecologie, Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Observatoire pour la Conservation de la Mégafaune Marine (PELAGIS), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Mediterranean climate, Marine conservation, Calonectris diomedea, Ecology, biology, 010604 marine biology & hydrobiology, Foraging, Pelagic zone, Aquatic Science, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Shearwater, biology.animal, Marine protected area, 14. Life underwater, Seabird, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract

International audience; Recent meta-analyses identified conservation hotpots at the scale of the Mediterranean, yet those may be crude by lack of detailed information about the spatial ecology of the species involved. Here, we identify an irreplaceable marine area for >95 % of the world population of the Scopoli’s shearwater (Calonectris diomedea), which is endemic to the Mediterranean and breeds on the island of Zembra off Tunis. To this end, we studied the three dimensional at-sea movements of 50 breeding adults (over a total of 94 foraging trips) in 2012 and 2013, using GPS and temperature–depth recorders. Feathers were also collected on all birds to investigate their trophic status. Despite Zembra being the largest seabird colony in the Mediterranean (141,000 pairs), the per capita home-range of Scopoli’s shearwaters foraging from this colony was not larger than that of birds from much smaller colonies, indicating highly beneficial feeding grounds in the Gulf of Tunis and off Cap Bon. Considering depleted Mediterranean small pelagic fish stocks, supposed to be Scopoli’s shearwater prey base, we therefore speculate that birds may now also largely feed on zooplankton, something which is supported by our stable isotopic analyses. Crucially, shearwater at-sea feeding and resting areas showed very little overlap with a conservation hotspot recently defined on the western side of the Gulf of Tunis using meta-analyses of species distributions relative to anthropogenic threats. We therefore propose a major extension to this conservation hotspot. Our study stresses the importance of detailed biotelemetry studies of marine megafauna movement ecology for refining large-scale conservation schemes such as marine protected area networks.

Published
2014

17. Movements and space use of feral cats in Kerguelen archipelago: a pilot study with GPS data

Author

Jean-Baptiste Pons, Dominique Pontier, Jodie Martin, Eugenia Natoli, Benjamin Rey, Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, education.field_of_study, geography, geography.geographical_feature_category, biology, business.industry, Ecology, 010604 marine biology & hydrobiology, Home range, [SDV]Life Sciences [q-bio], Population, 010603 evolutionary biology, 01 natural sciences, Predation, Fishery, biology.animal, Assisted GPS, Archipelago, Global Positioning System, Spatial ecology, 14. Life underwater, Seabird, General Agricultural and Biological Sciences, education, business
Abstract

The domestic cat has been introduced on several sub-Antarctic islands such as the Kerguelen archipelago (48°28′–50°S, 68°28′–70°35E), causing a worrying impact on the viability of some seabird populations. A better understanding of the biology of this introduced predator is needed to help design appropriate management actions. To investigate the effectiveness of a GPS study on feral cats living on the Kerguelen main island and to gain preliminary results on cat space use and fine-scale movement patterns, we fitted GPS collars on three young adult males and recorded cat location at a high frequency (every 5 min) for 2–3 weeks, during the austral summer. Home-range sizes varied from 0.30 to 0.73 km², with large overlaps in space but not in time. Cats were active during the warmest hours of the day, with a peak of activity around 2:00 p.m. This preliminary result suggests that trapping for management of the population should therefore yield the highest number of captures in the afternoon and before sunrise, when cats are more active. Our pilot study demonstrated the potential of using GPS to track feral cats in sub-Antarctic islands, opening up opportunities to get deep insights in the spatial ecology of these introduced predators.

Published
2013

18. Multi-scale foraging variability in Northern gannet (Morus bassanus) fuels potential foraging plasticity

Author

Francesco Bonadonna, Olivier Gimenez, Céline Le Bohec, Jean-Baptiste Pons, Robert T. Barrett, Emeline Pettex, Svein-Håkon Lorentsen, and David Grémillet

Subjects
food, Ecology, food.dish, Foraging, Flight speed, Aquatic Science, Biology, Ecology, Evolution, Behavior and Systematics, Northern gannet, Predation
Abstract

The survival of marine predators depends on behavioural plasticity to cope with changes in prey distribution. Variability in behaviour might predict plasticity and is easier to assess than plasticity. Using miniaturized GPS loggers over several breeding seasons in two Norwegian Northern gannet (Morus bassanus) colonies, we investigated if and how the variability within and between individuals, but also between colonies and years, affected foraging strategies. Results revealed strong individual variability (foraging trip durations, foraging effort and different foraging areas). Individuals from both colonies showed preferred commuting routes, flight bearings and feeding hotspots. Individuals from the largest colony used larger and more foraging areas than individuals from the small colony. Feeding hotspots and foraging ranges varied amongst years in the largest colony only. Our study demonstrated that gannets show flexibility by changing prey fields that are driven by shifting oceanographic conditions.

Published
2012

19. Meta-population evidence of oriented chain migration in northern gannets (Morus bassanus)

Author

François Siorat, Jean Baptiste Pons, Stefan Garthe, William A. Montevecchi, Yann Tremblay, Svein-Håkon Lorentsen, W. James Grecian, Robert W. Furness, Emeline Pettex, Jérôme Fort, Stuart Bearhop, David Grémillet, Stephen C. Votier, Department of Biological Sciences, Aarhus University, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UMR 212 EME 'écosystèmes marins exploités' (EME), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM), Norwegian Institute for Nature Research (NINA), Research and Technology Centre (FTZ), University of Kiel, Marine Biology and Ecology Research Centre, Plymouth University, Station ornithologique de l'Ile Grande, Ligue Pour la Protection des Oiseaux, Faculty of Biomedical and Life Sciences, Graham Kerr Building, University of Glasgow, Marine Spatial Ecology Lab, School of BioSciences, University of Exeter, University of Exeter, Memorial University of Newfoundland [St. John's], DST/NRF Centre of Excellence, University of Cape Town-Percy FitzPatrick Institute of African Ornithology, FitzPatrick Institute of African Ornithology, Faculty of Science, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Ligue pour la Protection des Oiseaux (LPO), Memorial University of Newfoundland = Université Memorial de Terre-Neuve [St. John's, Canada] (MUN), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
0106 biological sciences, National Health Programs, Range (biology), Disaster Planning, Meta population, 010603 evolutionary biology, 01 natural sciences, South Africa, Flyway, Chain migration, biology.animal, Seasonal breeder, Humans, Mass Casualty Incidents, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Societies, Medical, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, biology, 010604 marine biology & hydrobiology, Pelagic zone, 15. Life on land, Marine biodiversity, Geography, Practice Guidelines as Topic, Seabird, Burns
Abstract

International audience; Although oriented migrations have been identified in many terrestrial bird species, the post-breeding-season movements of seabirds are generally regarded as dispersive. We used geolocator tags to reveal post-breeding movements and winter distribution of northern gannets (Morus bassanus) at a meta-population scale. By focusing on five breeding colonies of European gannets, we show that their breeding and wintering grounds areconnected by a major flyway running along the coasts of Western Europe and Africa. Moreover, maximum winter distance to colony was similar across colonies despite their wide latitudinal range. In contrast with the general opinion that large pelagic birds such as gannets have unlimited ranges beyond the breeding season, our findings strongly suggest oriented chain migration in northern gannets (a pattern in which populations move uniformly southward) and highlight the benefit of meta-population approaches for studying seabird movements. We argue that the inclusion of such processes in ocean management plans is essential to improve efforts in marine biodiversity conservation.

Published
2012
Full Text
View/download PDF

20. Ecological changes in recent land-bridge islands in French Guiana, with emphasis on vertebrate communities

Author

Ambroise Dalecky, J.F. Villiers, Jean-Baptiste Pons, Stéphane Ringuet, Olivier Claessens, Jean-François Cosson, J.-C. De Massary, Laurent Granjon, Laboratoire de la Faune Sauvage, Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
0106 biological sciences, Ecology, 010604 marine biology & hydrobiology, [SDV]Life Sciences [q-bio], Fragmentation (computing), Species diversity, Rainforest, 15. Life on land, Generalist and specialist species, 010603 evolutionary biology, 01 natural sciences, [SDV] Life Sciences [q-bio], Geography, Habitat, Guild, Biological dispersal, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Nature and Landscape Conservation, Tropical rainforest
Abstract

In 1993 a multidisciplinary project investigating the effects of tropical rainforest fragmentation on land-bridge islands created by a hydroelectric reservoir was initiated in French Guiana (the Saint Eugene Fragmentation Project, SEFP). The main focus of the study is documenting changes in vertebrate groups, including lizards, birds, non-flying small mammals, bats and primates, that have marked differences in dispersal capacities. Here we summarize results of the first 4 years of research on SEFP (1 year pre-fragmentation, 3 years post-fragmentation), comparing islands with nearby control plots in continuous forest. Our results suggest that forest fragmentation has rapidly modified vertebrate diversity, regardless of the ability of species to disperse over water. Species present on islands do not represent a random sample of those present before isolation. Rather, a common suite of species has rapidly become dominant on each island, and these species share the following ecological traits: (1) they exhibit some of the largest body sizes in their guild, (2) they are generalists in habitat and food requirements, (3) they are naturally abundant in undisturbed forests, and (4) they have a wide geographic range yet are restricted to tropical rainforest. These results are interpreted in light of other studies of rainforest fragmentation.

Published
1999

Catalog

Books, media, physical & digital resources
See catalog results