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Fevola C, Rossi C, Rosso F, Girardi M, Rosà R, Manica M, Delucchi L, Rocchini D, Garzon-Lopez CX, Arnoldi D, Bianchi A, Buzan E, Charbonnel N, Collini M, Ďureje L, Ecke F, Ferrari N, Fischer S, Gillingham EL, Hörnfeldt B, Kazimírová M, Konečný A, Maas M, Magnusson M, Miller A, Niemimaa J, Nordström Å, Obiegala A, Olsson G, Pedrini P, Piálek J, Reusken CB, Rizzolli F, Romeo C, Silaghi C, Sironen T, Stanko M, Tagliapietra V, Ulrich RG, Vapalahti O, Voutilainen L, Wauters L, Rizzoli A, Vaheri A, Jääskeläinen AJ, Henttonen H, Hauffe HC. Geographical Distribution of Ljungan Virus in Small Mammals in Europe. Vector Borne Zoonotic Dis 2020; 20:692-702. [PMID: 32487013 DOI: 10.1089/vbz.2019.2542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
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.
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Affiliation(s)
- Cristina Fevola
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Chiara Rossi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Fausta Rosso
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Matteo Girardi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Roberto Rosà
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center for Agriculture Food Environment-C3A, University of Trento and Fondazione E. Mach, San Michele all'Adige, Italy
| | - Mattia Manica
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Luca Delucchi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Duccio Rocchini
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center for Agriculture Food Environment-C3A, University of Trento and Fondazione E. Mach, San Michele all'Adige, Italy.,Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Povo, Italy
| | - Carol X Garzon-Lopez
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Ecology and Vegetation Physiology Group (EcoFiv), Universidad de los Andes, Bogotá, Colombia
| | - Daniele Arnoldi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Alessandro Bianchi
- Istituto Zooprofilattico Sperimentale della Lombardia e Dell'Emilia Romagna "Bruno Ubertini," Brescia, Italy
| | - Elena Buzan
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Nathalie Charbonnel
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Margherita Collini
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - L'udovít Ďureje
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Studenec, Czech Republic
| | - Frauke Ecke
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Nicola Ferrari
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Stefan Fischer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Emma L Gillingham
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,School of Biosciences, Cardiff University, Cardiff, United Kingdom.,Department of Medical Entomology and Zoonoses Ecology, Emergency Response Department, Public Health England, Salisbury, United Kingdom.,Department of Climate Change and Health, Public Health England, London, United Kingdom
| | - Birger Hörnfeldt
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Mária Kazimírová
- Slovak Academy of Sciences (SAS), Institute of Zoology, Bratislava, Slovakia
| | - Adam Konečný
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Miriam Maas
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Magnus Magnusson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Andrea Miller
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department for Terrestrial Ecology, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Jukka Niemimaa
- Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Åke Nordström
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Anna Obiegala
- Comparative Tropical Medicine and Parasitology, Ludwig-Maximilians-Universität, Munich, Germany.,Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany
| | - Gert Olsson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Paolo Pedrini
- Sezione Zoologia dei Vertebrati, MUSE-Museo delle Scienze, Trento, Italy
| | - Jaroslav Piálek
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Studenec, Czech Republic
| | - Chantal B Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.,Department of Viroscience, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Franco Rizzolli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudia Romeo
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Cornelia Silaghi
- Comparative Tropical Medicine and Parasitology, Ludwig-Maximilians-Universität, Munich, Germany.,Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Stanko
- Slovak Academy of Sciences (SAS), Institute of Zoology, Bratislava, Slovakia.,Slovak Academy of Sciences (SAS), Institute of Parasitology, Košice, Slovakia
| | - Valentina Tagliapietra
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Olli Vapalahti
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Lucas Wauters
- Department of Theoretical and Applied Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Annapaola Rizzoli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Antti Vaheri
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anne J Jääskeläinen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Heidi C Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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Zambrano J, Garzon-Lopez CX, Yeager L, Fortunel C, Cordeiro NJ, Beckman NG. The effects of habitat loss and fragmentation on plant functional traits and functional diversity: what do we know so far? Oecologia 2019; 191:505-518. [PMID: 31515618 DOI: 10.1007/s00442-019-04505-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/06/2019] [Indexed: 11/30/2022]
Abstract
Habitat loss and fragmentation result in significant landscape changes that ultimately affect plant diversity and add uncertainty to how natural areas will respond to future global change. This uncertainty is important given that the loss of biodiversity often includes losing key ecosystem functions. Few studies have explored the effects of landscape changes on plant functional diversity and evidence so far has shown far more pervasive effects than previously reported by species richness and composition studies. Here we present a review on the impact of habitat loss and fragmentation on (1) individual functional traits-related to persistence, dispersal and establishment-and (2) functional diversity. We also discuss current knowledge gaps and propose ways forward. From the literature review we found that studies have largely focused on dispersal traits, strongly impacted by habitat loss and fragmentation, while traits related to persistence were the least studied. Furthermore, most studies did not distinguish habitat loss from spatial fragmentation and were conducted at the plot or fragment-level, which taken together limits the ability to generalize the scale-dependency of landscape changes on plant functional diversity. For future work, we recommend (1) clearly distinguishing the effects of habitat loss from those of fragmentation, and (2) recognizing the scale-dependency of predicted responses when functional diversity varies in time and space. We conclude that a clear understanding of the effects of habitat loss and fragmentation on functional diversity will improve predictions of the resiliency and resistance of plant communities to varying scales of disturbance.
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Affiliation(s)
- Jenny Zambrano
- The School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - Carol X Garzon-Lopez
- Grupo de Ecología y Fisiología Vegetal, Departamento de Ciencias biológicas, Universidad de los Andes, Carrera 1 #18A-12, Bogotá, Colombia
| | - Lauren Yeager
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Claire Fortunel
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.,AMAP (botAnique et Modélisation de l'Architecture des Plantes et des végétations), IRD, CIRAD, CNRS, INRA, Université de Montpellier, Montpellier, France
| | - Norbert J Cordeiro
- Department of Biology (mc WB 816), Roosevelt University, 425 S. Wabash Avenue, Chicago, IL, 60605, USA.,Science and Education, The Field Museum, 1400 S. Lakeshore Drive, Chicago, IL, 60605, USA
| | - Noelle G Beckman
- Department of Biology and Ecology Center, Utah State University, Logan, UT, 84322, USA
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6
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Rocchini D, Garzon-Lopez CX, Marcantonio M, Amici V, Bacaro G, Bastin L, Brummitt N, Chiarucci A, Foody GM, Hauffe HC, He KS, Ricotta C, Rizzoli A, Rosà R. Anticipating species distributions: Handling sampling effort bias under a Bayesian framework. Sci Total Environ 2017; 584-585:282-290. [PMID: 28187937 DOI: 10.1016/j.scitotenv.2016.12.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/02/2016] [Accepted: 12/04/2016] [Indexed: 06/06/2023]
Abstract
Anticipating species distributions in space and time is necessary for effective biodiversity conservation and for prioritising management interventions. This is especially true when considering invasive species. In such a case, anticipating their spread is important to effectively plan management actions. However, considering uncertainty in the output of species distribution models is critical for correctly interpreting results and avoiding inappropriate decision-making. In particular, when dealing with species inventories, the bias resulting from sampling effort may lead to an over- or under-estimation of the local density of occurrences of a species. In this paper we propose an innovative method to i) map sampling effort bias using cartogram models and ii) explicitly consider such uncertainty in the modeling procedure under a Bayesian framework, which allows the integration of multilevel input data with prior information to improve the anticipation species distributions.
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Affiliation(s)
- Duccio Rocchini
- Fondazione Edmund Mach, Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Via E. Mach 1, S. Michele all'Adige 38010, TN, Italy.
| | - Carol X Garzon-Lopez
- UR "Ecologie et Dynamique des Systèmes Anthropisés" (EDYSAN, FRE 3498 CNRS), 9 Université de Picardie Jules Verne, 1 rue des Louvels, Amiens Cedex 1 FR-80037, France
| | - Matteo Marcantonio
- Fondazione Edmund Mach, Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Via E. Mach 1, S. Michele all'Adige 38010, TN, Italy; Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, USA
| | - Valerio Amici
- Department of Life Sciences, University of Siena, Via P.A. Mattioli 4, Siena 53100, Italy
| | - Giovanni Bacaro
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 10, Trieste 34127, Italy
| | - Lucy Bastin
- School of Computer Science, Aston University, UK; European Commission, Joint Research Centre (JRC), Directorate D - Sustainable Resources
| | - Neil Brummitt
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alessandro Chiarucci
- BIGEA, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum, University of Bologna, Via Irnerio 42, Bologna 40126, Italy
| | - Giles M Foody
- University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Heidi C Hauffe
- Fondazione Edmund Mach, Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Via E. Mach 1, S. Michele all'Adige 38010, TN, Italy
| | - Kate S He
- Department of Biological Sciences, Murray State University, Murray, KY 42071, USA
| | - Carlo Ricotta
- Department of Environmental Biology, University of Rome "La Sapienza", Rome 00185, Italy
| | - Annapaola Rizzoli
- Fondazione Edmund Mach, Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Via E. Mach 1, S. Michele all'Adige 38010, TN, Italy
| | - Roberto Rosà
- Fondazione Edmund Mach, Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Via E. Mach 1, S. Michele all'Adige 38010, TN, Italy
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Garzon-Lopez CX, Ballesteros-Mejia L, Ordoñez A, Bohlman SA, Olff H, Jansen PA. Indirect interactions among tropical tree species through shared rodent seed predators: a novel mechanism of tree species coexistence. Ecol Lett 2015; 18:752-760. [PMID: 25939379 DOI: 10.1111/ele.12452] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/01/2015] [Accepted: 04/14/2015] [Indexed: 11/27/2022]
Abstract
The coexistence of numerous tree species in tropical forests is commonly explained by negative dependence of recruitment on the conspecific seed and tree density due to specialist natural enemies that attack seeds and seedlings ('Janzen-Connell' effects). Less known is whether guilds of shared seed predators can induce a negative dependence of recruitment on the density of different species of the same plant functional group. We studied 54 plots in tropical forest on Barro Colorado Island, Panama, with contrasting mature tree densities of three coexisting large seeded tree species with shared seed predators. Levels of seed predation were far better explained by incorporating seed densities of all three focal species than by conspecific seed density alone. Both positive and negative density dependencies were observed for different species combinations. Thus, indirect interactions via shared seed predators can either promote or reduce the coexistence of different plant functional groups in tropical forest.
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Affiliation(s)
- Carol X Garzon-Lopez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, Groningen, 9700 CC, The Netherlands.,GIS and Remote Sensing Unit, Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy
| | - Liliana Ballesteros-Mejia
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, Groningen, 9700 CC, The Netherlands.,Laboratorio de Genetica e Biodiversidade, ICB, Universidade Federal de Goias (UFG), Campus Samambaia 74001-970 Goiania, Goias, Brazil
| | - Alejandro Ordoñez
- Department of Bioscience, Section for Ecoinformatics and Biodiversity, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Stephanie A Bohlman
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Republic of Panama.,School of Forest Resources and Conservation, University of Florida, Box 110410, Gainesville, FL, 32611-0410, USA
| | - Han Olff
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, Groningen, 9700 CC, The Netherlands
| | - Patrick A Jansen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, Groningen, 9700 CC, The Netherlands.,Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Republic of Panama.,Department of Environmental Sciences, Wageningen University, Box 47, 6700, AA Wageningen, The Netherlands
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