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1. From local spectral species to global spectral communities: A benchmark for ecosystem diversity estimate by remote sensing

Author

Kate S. He, Harini Nagendra, Michael Förster, Martin Wegmann, Thomas W. Gillespie, Vítĕzslav Moudrý, Birgit Kleinschmit, Duccio Rocchini, Carl Beierkuhnlein, Jean-Baptiste Féret, Marco Malavasi, Nicole Salvatori, Florian de Boissieu, Davnah Payne, Heidi C. Hauffe, Carol X. Garzon-Lopez, Alessandro Chiarucci, Petra Šímová, Jonathan Lenoir, Michele Torresani, University of Bologna/Università di Bologna, Università degli Studi di Udine - University of Udine [Italie], University of Bayreuth, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Technical University of Berlin / Technische Universität Berlin (TU), Universidad de los Andes [Bogota] (UNIANDES), University of California (UC), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Czech University of Life Sciences Prague (CZU), PES University [Bengaluru], University of Bern, Free University of Bozen-Bolzano, Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Horizon 2020 Framework ProgrammeCentre National d’Etudes Spatiales, ANR-17-CE32-0001,BioCop,Suivi de la biodiversité tropicale avec les satellites Sentinel-2 du programme Copernicus(2017), Rocchini D., Salvatori N., Beierkuhnlein C., Chiarucci A., de Boissieu F., Forster M., Garzon-Lopez C.X., Gillespie T.W., Hauffe H.C., He K.S., Kleinschmit B., Lenoir J., Malavasi M., Moudry V., Nagendra H., Payne D., Simova P., Torresani M., Wegmann M., Feret J.-B., Rocchini, D., Salvatori, N., Beierkuhnlein, C., Chiarucci, A., de Boissieu, F., Forster, M., Garzon-Lopez, C. X., Gillespie, T. W., Hauffe, H. C., He, K. S., Kleinschmit, B., Lenoir, J., Malavasi, M., Moudry, V., Nagendra, H., Payne, D., Simova, P., Torresani, M., Wegmann, M., Feret, J. -B., University of Bologna, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Technical University Berlin, and University of California

Subjects
0106 biological sciences, Earth observation, Ecological informatic, Biodiversity, Earth Observations, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010603 evolutionary biology, 01 natural sciences, Modelling, Settore BIO/07 - ECOLOGIA, Satellite imagery, Ecosystem diversity, Imaging Spectroscopy, Ecology, Evolution, Behavior and Systematics, Remote sensing, Ecological informatics, Spectral signature, Ecology, 010604 marine biology & hydrobiology, Applied Mathematics, Ecological Modeling, 15. Life on land, Field (geography), Computer Science Applications, Computational Theory and Mathematics, 13. Climate action, Modeling and Simulation, [SDE]Environmental Sciences, Environmental science, Species richness, Rapideye, Global biodiversity
Abstract

In the light of unprecedented change in global biodiversity, real-time and accurate ecosystem and biodiversity assessments are becoming increasingly essential. Nevertheless, estimation of biodiversity using ecological field data can be difficult for several reasons. For instance, for very large areas, it is challenging to collect data that provide reliable information. Some of these restrictions in Earth observation can be avoided through the use ofremote sensingapproaches. Various studies have estimated biodiversity on the basis of the Spectral Variation Hypothesis (SVH). According to this hypothesis, spectral heterogeneity over the different pixel units of a spatial grid reflects a higher niche heterogeneity, allowing more organisms to coexist. Recently, the spectral species concept has been derived, following the consideration that spectral heterogeneity at a landscape scale corresponds to a combination of subspaces sharing a similarspectral signature. With the use of high resolution remote sensing data, on a local scale, these subspaces can be identified as separate spectral entities, the so called “spectral species”. Our approach extends this concept over wide spatial extents and to a higher level of biological organization. We applied this method toMODISimagery data across Europe. Obviously, in this case, a spectral species identified by MODIS is not associated to a singleplant speciesin the field but rather to a species assemblage, habitat, or ecosystem. Based on such spectral information, we propose a straightforward method to deriveα- (local relative abundance and richness of spectral species) andβ-diversity (turnover of spectral species) maps over wide geographical areas.

Published
2021
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2. Geographical Distribution of Ljungan Virus in Small Mammals in Europe

Author

Annapaola Rizzoli, Alessandro Bianchi, Roberto Rosà, Daniele Arnoldi, Claudia Romeo, Mattia Manica, Gert E. Olsson, Heidi C. Hauffe, Fausta Rosso, Anne J. Jääskeläinen, Magnus Magnusson, Anna Obiegala, Chiara Rossi, Carol X. Garzon-Lopez, Birger Hörnfeldt, Cornelia Silaghi, Olli Vapalahti, Frauke Ecke, Valentina Tagliapietra, Andrea L. Miller, Cristina Fevola, Nathalie Charbonnel, Nicola Ferrari, Antti Vaheri, Luca Delucchi, Åke Nordström, Jaroslav Piálek, Lucas A. Wauters, Miriam Maas, Franco Rizzolli, Jukka Niemimaa, Rainer G. Ulrich, Tarja Sironen, Adam Konečný, Michal Stanko, Paolo Pedrini, Liina Voutilainen, Emma L. Gillingham, Heikki Henttonen, Margherita Collini, Duccio Rocchini, Elena Buzan, Matteo Girardi, Ľudovít Ďureje, Stefan Fischer, Mária Kazimírová, Chantal Reusken, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Trento [Trento], Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini' (IZSLER), University of Primorska, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), Dipartimento di Scienza dei Materiali = Department of Materials Science [Milano-Bicocca], Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Czech Academy of Sciences [Prague] (CAS), Swedish University of Agricultural Sciences (SLU), Università degli Studi di Milano = University of Milan (UNIMI), Friedrich-Loeffler-Institut (FLI), Cardiff University, Public Health England [London], Slovak Academy of Sciences (SAS), Masaryk University [Brno] (MUNI), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Norwegian Institute for Nature Research (NINA), Natural Resources Institute Finland (LUKE), Ludwig-Maximilians-Universität München (LMU), Museo delle Scienze, Department of Virology [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], 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, Laboratory work was funded by the European Union grant FP7-261504 EDENext - Biology and control of vector-borne infections in Europe to A.R., H.H., R.G.U., and H.C.H. and by Sigrid Juselius Foundation. Sample collection in Sweden was financed by grants from the Swedish Environmental Protection Agency (by the National Environmental Monitoring Programme for small rodents and Alvins fond) to B.H., the Stiftelsen Oscar och Lili Lamms minne to B.H. and F.E., VINNOVA - Swedish Governmental Agency for Innovation Systems (Verket For Innovations system) (P32060-1) to F.E., the Swedish Research Council Formas (221-2012-1562) to F.E., B.H., and G.O., the National Environmental and Wildlife Monitoring and Assessment program (FoMA, www.slu.se/en/environment) to G.O., and the Helge Ax:son Johnsons Stiftelse to M.M., European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), Virology, University of Helsinki, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Università degli Studi di Milano [Milano] (UNIMI), University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Sigrid Juselius Foundation, Swedish Environmental Protection Agency (National Environmental Monitoring Programme for small rodents and Alvins fond), Stiftelsen Oscar och Lili Lamms minne, Vinnova : P32060-1, Swedish Research Council, Swedish Research Council Formas : 221-2012-1562, National Environmental and Wildlife Monitoring and Assessment program (FoMA), and Helge Ax:son Johnsons Stiftelse

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Tundra vole, Parechovirus, Zoology, rodent vector, Rodentia, Picornaviridae, Alexandromys, Microbiology, 03 medical and health sciences, Crocidura leucodon, 0302 clinical medicine, Virology, biology.animal, Animals, reservoir host, bank vole, Settore VET/06 - PARASSITOLOGIA E MALATTIE PARASSITARIE DEGLI ANIMALI, Microtus, Phylogeny, Picornaviridae Infections, biology, Reverse Transcriptase Polymerase Chain Reaction, Body Weight, Shrew, Eulipotyphla, 030108 mycology & parasitology, biology.organism_classification, Europe, Infectious Diseases, Ljungan virus, Vole, Seasons, GLM, cartogram
Abstract

International audience; Ljungan virus (LV), which belongs to the Parechovirus genus in the Picornaviridae family, was first isolated from bank voles (Myodes glareolus) in Sweden in 1998 and proposed as a zoonotic agent. To improve knowledge of the host association and geographical distribution of LV, tissues from 1685 animals belonging to multiple rodent and insectivore species from 12 European countries were screened for LV-RNA using reverse transcriptase (RT)-PCR. In addition, we investigated how the prevalence of LV-RNA in bank voles is associated with various intrinsic and extrinsic factors. We show that LV is widespread geographically, having been detected in at least one host species in nine European countries. Twelve out of 21 species screened were LV-RNA PCR positive, including, for the first time, the red vole (Myodes rutilus) and the root or tundra vole (Alexandromys formerly Microtus oeconomus), as well as in insectivores, including the bicolored white-toothed shrew (Crocidura leucodon) and the Valais shrew (Sorex antinorii). Results indicated that bank voles are the main rodent host for this virus (overall RT-PCR prevalence: 15.2%). Linear modeling of intrinsic and extrinsic factors that could impact LV prevalence showed a concave-down relationship between body mass and LV occurrence, so that subadults had the highest LV positivity, but LV in older animals was less prevalent. Also, LV prevalence was higher in autumn and lower in spring, and the amount of precipitation recorded during the 6 months preceding the trapping date was negatively correlated with the presence of the virus. Phylogenetic analysis on the 185 base pair species-specific sequence of the 5 ' untranslated region identified high genetic diversity (46.5%) between 80 haplotypes, although no geographical or host-specific patterns of diversity were detected.

Published
2020
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3. Lyme borreliosis in Europe

Author

Annapaola Rizzoli, Gwenaël Vourc’h, Heidi C. Hauffe, Roberto Rosà, Markus Neteler, Giovanna Carpi, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Unité de Recherche d'Épidémiologie Animale (UR EpiA), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
medicine.medical_specialty, Ixodes ricinus, EUROPE, Epidemiology, [SDV]Life Sciences [q-bio], Disease, LYME BORRELIOSIS, Tick, 03 medical and health sciences, Risk Factors, Virology, Environmental health, medicine, Animals, Humans, Serologic Tests, Borrelia burgdorferi, Settore VET/06 - PARASSITOLOGIA E MALATTIE PARASSITARIE DEGLI ANIMALI, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Lyme Disease, biology, Ixodes, 030306 microbiology, Ecology, Transmission (medicine), Risk of infection, Incidence, Public Health, Environmental and Occupational Health, Malattie trasmesse da zecche, Tick-borne disease, biology.organism_classification, 3. Good health, [SDV] Life Sciences [q-bio], 13. Climate action, Lyme disease microbiology, Arachnid Vectors
Abstract

International audience; Despite improvements in prevention, diagnosis and treatment, Lyme borreliosis (LB) is still the most common arthropod-borne disease in temperate regions of the northern hemisphere, with risk of infection associated with occupation (e.g. forestry work) and certain outdoor recreational activities (e.g. mushroom collecting). In Europe, LB is caused by infection with one or more pathogenic European genospecies of the spirochaete Borrelia burgdorferi sensu lato, mainly transmitted by the tick Ixodes ricinus. Recent surveys show that the overall prevalence of LB may be stabilising, but its geographical distribution is increasing. In addition, much remains to be discovered about the factors affecting genospecific prevalence, transmission and virulence, although avoidance of tick bite still appears to be the most efficient preventive measure. Uniform, European-wide surveillance programmes (particularly on a local scale) and standardisation of diagnostic tests and treatments are still urgently needed, especially in the light of climate change scenarios and land-use and socio-economic changes. Improved epidemiological knowledge will also aid development of more accurate risk prediction models for LB. Studies on the effects of biodiversity loss and ecosystem changes on LB emergence may identify new paradigms for the prevention and control of LB and other tick-borne diseases.

Published
2011

4. The Genetic Impact of Translocations and Habitat Fragmentation in Chamois (Rupicapra) spp

Author

Giorgio Bertorelle, B. Crestanello, Cristiano Vernesi, Heidi C. Hauffe, Marián Janiga, Elena Pecchioli, Natália Martínková, Stefano Mona, Research and Innovation Centre, Edmund Mach Foundation (FEM), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of York [York, UK], Czech Academy of Sciences [Prague] (CAS), Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), and Università degli Studi di Ferrara = University of Ferrara (UniFE)

Subjects
Gene Flow, Conservation of Natural Resources, Population, Molecular Sequence Data, MtDNA, Zoology, Conservation, Subspecies, DNA, Mitochondrial, Gene flow, Evolution, Molecular, Rupicapra pyrenaica, Species Specificity, Genetic variation, Genetics, Animals, education, Microsatellites, Molecular Biology, Hybridization, Genetics (clinical), Ecosystem, Phylogeny, Demography, Taxonomy, education.field_of_study, Likelihood Functions, Habitat fragmentation, biology, Base Sequence, Geography, Models, Genetic, Cytochrome b, Ecology, Computational Biology, Genetic Variation, Management, Rupicapra, Bayes Theorem, Sequence Analysis, DNA, biology.organism_classification, Europe, Genetics, Population, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biotechnology, Microsatellite Repeats
Abstract

The chamois is a useful species with which to investigate the combined genetic impact of habitat fragmentation, over hunting, and translocations. Genetic variation within and between chamois (genus Rupicapra) populations was analyzed in 259 individuals from 16 sampling sites located in Italy, Spain, Slovakia, and the Czech Republic. Two mitochondrial DNA markers (control region and cytochrome b) and 11 nuclear microsatellites were typed. The principal results of this study can be summarized as follows: 1) high and significant differentiation between almost all chamois populations is observed even on a microgeographical scale, probably caused by the patchy distribution of this species, sharp geographical barriers to gene flow, and drift effects related to recent bottlenecks; 2) historical translocation events have left a clear genetic signature, including interspecific hybridization in some Alpine localities; 3) the Apennine subspecies of chamois, Rupicapra pyrenaica ornata, shows a high and similar level of divergence (about 1.5 My) from the Pyrenean (Rupicapra pyrenaica pyrenaica) and the Alpine (Rupicapra rupicapra) chamois; therefore, the specific status of these taxa should be revised. These results confirm the potential of population genetic analyses to dissect and interpret complex patterns of diversity in order to define factors important to conservation and management.

Published
2009
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