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88 results on '"Wildlife Conservation Society (WCS)"'

1. Conservation Medicine for Gorilla Conservation

Author: Mountain Gorilla Veterinary Project (MGVP, Inc.), Wildlife Conservation Society (WCS), Tuttle, Russell H., editor, Stoinski, T. S., editor, Steklis, H. D., editor, and Mehlman, P. T., editor
Published: 2008
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2. Eradication of Peste des Petits Ruminants Virus and the Wildlife-Livestock Interface

Author: Amanda E. Fine, Mathieu Pruvot, Camilla T. O. Benfield, Alexandre Caron, Giovanni Cattoli, Philippe Chardonnet, Maurizio Dioli, Thomas Dulu, Martin Gilbert, Richard Kock, Juan Lubroth, Jeffrey C. Mariner, Stephane Ostrowski, Satya Parida, Sasan Fereidouni, Enkhtuvshin Shiilegdamba, Jonathan M. Sleeman, Claudia Schulz, Jean-Jacques Soula, Yves Van der Stede, Berhe G. Tekola, Chris Walzer, Steffen Zuther, Felix Njeumi, Meeting Participants, Wildlife Conservation Society (WCS), Royal Veterinary College [London], University of London [London], Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Eduardo Mondlane University, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Joint FAO/IAEA Programme - Nuclear Techniques in Food and Agriculture, Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO)-International Atomic Energy Agency [Vienna] (IAEA), Auteur indépendant, Ministry of Agriculture, Livestock and Fisheries, Cornell University College of Veterinary Medicine, State University of New York (SUNY), Animal Production and Health Division [Rome], Food and Agriculture Organization of the United Nations, Cummings School of Veterinary Medicine, Tufts University [Medford], Pirbright Institute, Research Institute of Wildlife Ecology, University of Veterinary Medicine, University of Veterinary Medicine, National Wildlife Health Center, University of Veterinary Medicine Hannover, Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), European Food Safety Authority (EFSA), University of Veterinary Medicine [Vienna] (Vetmeduni), Association for the Conservation of Biodiversity of Kazakhstan, Frankfurt Zoological Society, FAO/OIE PPR GEP Secretariat and the Science for Nature and People Partnership (SNAPP), a partnership of The Nature Conservancy, the Wildlife Conservation Society (WCS), and the National Center for Ecological Analysis and Synthesis (NCEAS) at University of California, Santa Barbara. Additional organizational and financial support was provided by WCS, Royal Veterinary College, and the many institutions represented at the meeting that funded the participation of their respective experts including Agronomes et Veterinaires Sans Frontieres, Animal Production and Health Laboratory of the Joint FAO/IAEA Division for Nuclear Applications in Food and Agriculture, Association for the Conservation of Biodiversity of Kazakhstan, CIRAD, Cornell Wildlife Health Center, Denver Zoological Foundation, Frankfort Zoological Society, Friedrich-Loffler-Institut, Fondation Segre, Pirbright Institute, University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic, US Fish and Wildlife Service, USGS NationalWildlifeHealth Center, and theWild Sheep Foundation, and International Atomic Energy Agency [Vienna] (IAEA)-Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO)
Subjects: global eradication, [SDV]Life Sciences [q-bio], integrated management, L73 - Maladies des animaux, 0403 veterinary science, Interactions biologiques, Socioeconomics, Wildlife conservation, media_common, 0303 health sciences, lcsh:Veterinary medicine, 04 agricultural and veterinary sciences, Disease control, Épidémiologie, Geography, One Health, Perspective, wildlife conservation, Livestock, Psychological resilience, Bétail, 040301 veterinary sciences, media_common.quotation_subject, Wildlife, Virus peste petits ruminants, 03 medical and health sciences, one health, wildlife-livestock interface, 030304 developmental biology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, business.industry, Éradication des maladies, small ruminant morbillivirus, Global strategy, 15. Life on land, Animal sauvage, peste des petits ruminants, Peste-des-petits-ruminants virus, lcsh:SF600-1100, Veterinary Science, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract: Growing evidence suggests that multiple wildlife species can be infected with peste des petits ruminants virus (PPRV), with important consequences for the potential maintenance of PPRV in communities of susceptible hosts, and the threat that PPRV may pose to the conservation of wildlife populations and resilience of ecosystems. Significant knowledge gaps in the epidemiology of PPRV across the ruminant community (wildlife and domestic), and the understanding of infection in wildlife and other atypical host species groups (e.g., camelidae, suidae, and bovinae) hinder our ability to apply necessary integrated disease control and management interventions at the wildlife-livestock interface. Similarly, knowledge gaps limit the inclusion of wildlife in the FAO/OIE Global Strategy for the Control and Eradication of PPR, and the framework of activities in the PPR Global Eradication Programme that lays the foundation for eradicating PPR through national and regional efforts. This article reports on the first international meeting on, “Controlling PPR at the livestock-wildlife interface,” held in Rome, Italy, March 27–29, 2019. A large group representing national and international institutions discussed recent advances in our understanding of PPRV in wildlife, identified knowledge gaps and research priorities, and formulated recommendations. The need for a better understanding of PPRV epidemiology at the wildlife-livestock interface to support the integration of wildlife into PPR eradication efforts was highlighted by meeting participants along with the reminder that PPR eradication and wildlife conservation need not be viewed as competing priorities, but instead constitute two requisites of healthy socio-ecological systems.
Published: 2020

3. Safeguarding nutrients from coral reefs under climate change

Author: Camille Mellin, Christina C. Hicks, Damien A. Fordham, Christopher D. Golden, Marian Kjellevold, M. Aaron MacNeil, Eva Maire, Sangeeta Mangubhai, David Mouillot, Kirsty L. Nash, Johnstone O. Omukoto, James P. W. Robinson, Rick D. Stuart-Smith, Jessica Zamborain-Mason, Graham J. Edgar, Nicholas A. J. Graham, Australian Institute of Marine Science [Townsville] (AIMS Townsville), Australian Institute of Marine Science (AIMS), University of Adelaide, Lancaster Environment Centre, Lancaster University, Harvard T.H. Chan School of Public Health, Dalhousie University [Halifax], Wildlife Conservation Society (WCS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), University of Tasmania [Hobart, Australia] (UTAS), University of Alabama [Tuscaloosa] (UA), and Queen's University [Kingston, Canada]
Subjects: Ecology, [SDE.MCG]Environmental Sciences/Global Changes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; The sustainability of coral reef fisheries is jeopardized by complex and interacting socio-ecological stressors that undermine their contribution to food and nutrition security. Climate change has emerged as one of the key stressors threatening coral reefs and their fish-associated services. How fish nutrient concentrations respond to warming oceans remains unclear but these responses are probably affected by both direct (metabolism and trophodynamics) and indirect (habitat and species range shifts) effects. Climate-driven coral habitat loss can cause changes in fish abundance and biomass, revealing potential winners and losers among major fisheries targets that can be predicted using ecological indicators and biological traits. A critical next step is to extend research focused on the quantity of available food (fish biomass) to also consider its nutritional quality, which is relevant to progress in the fields of food security and malnutrition. Biological traits are robust predictors of fish nutrient content and thus potentially indicate how climate-driven changes are expected to impact nutrient availability within future food webs on coral reefs. Here, we outline future research priorities and an anticipatory framework towards sustainable reef fisheries contributing to nutrition-sensitive food systems in a warming ocean.
Published: 2022

4. Mosquito diversity (Diptera: Culicidae) and medical importance in four Cambodian forests

Author: Antsa Rakotonirina, Pierre-Olivier Maquart, Claude Flamand, Chea Sokha, Sébastien Boyer, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Wildlife Conservation Society [Phnom Penh, Cambodia], Wildlife Conservation Society (WCS), Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, and This study was by the Defense Advanced Research Projects Agency (DARPA).
Subjects: Infectious Diseases, Vector mosquitoes, [SDV]Life Sciences [q-bio], Parasitology, Forest, Cambodia, Entomology
Abstract: Background A total of 290 mosquito species are recorded in Cambodia among which 43 are known vectors of pathogens. As Cambodia is heavily affected by deforestation, a potential change in the dynamic of vector-borne diseases (VDBs) could occur through alteration of the diversity and density of sylvatic vector mosquitoes and induce an increase in their interactions with humans. Understanding mosquito diversity is therefore critical, providing valuable data for risk assessments concerning the (re)emergence of local VBDs. Consequently, this study mainly aimed to understand the spatial and temporal distribution of sylvatic mosquito populations of Cambodia by determining which factors impact on their relative abundance and presence. Methods A study was conducted in 12 sites from four forests in Cambodia. All mosquitoes, collected during the dry and rainy seasons, were morphologically identified. The diversity and relative density of mosquito species in each site were calculated along with the influence of meteorological and geographical factors using a quasi-Poisson generalized linear model. Results A total of 9392 mosquitoes were collected belonging to 13 genera and 85 species. The most represented genera were Culex, accounting for 46% of collected mosquitoes, and Aedes (42%). Besides being the most abundant species, Culex pseudovishnui and Aedes albopictus, which are known vectors of numerous arboviruses, were present in all sites during both dry and rainy seasons. The presence of mosquito species reported to be zoo-anthropophilic feeders was also observed in both forested and urban areas. Finally, this study demonstrated that altitude, temperature and precipitation impacted the abundance of mosquitoes but also influenced species community composition. Conclusion The results indicate an important diversity of mosquitoes in the four forests and an influence of meteorological and geographical factors on their community. Additionally, this work highlights in parallel the abundance of species considered to be of medical importance and therefore underlines the high risk of pathogen emergence/re-emergence in the region. Graphical Abstract
Published: 2023

5. The long lives of primates and the ‘invariant rate of ageing’ hypothesis

Author: Shirley C. Strum, Emma J. Stokes, Robert M. Seyfarth, Craig Packer, Klaus Zuberbühler, Jenny Tung, Zarin P. Machanda, Marie L. Manguette, Roman M. Wittig, Richard J. Parnell, Milou Groenenberg, Rebecca J. Lewis, Marina Cords, Francisco Villavicencio, Catherine Hobaiter, Anne E. Pusey, Martin N. Muller, Melissa Emery Thompson, Susan C. Alberts, James W. Vaupel, Joan B. Silk, Thomas Breuer, Karen B. Strier, Elizabeth A. Archie, Tara S. Stoinski, Richard R. Lawler, Anthony Collins, Christophe Boesch, Richard W. Wrangham, Claudia Fichtel, Catherine Crockford, Fernando A. Campos, Johanna Staerk, Dalia Amor Conde, Fernando Colchero, Linda M. Fedigan, Susan Perry, Martha M. Robbins, Peter M. Kappeler, José Manuel Aburto, Centre National de la Recherche Scientifique (CNRS), Interdisciplinary Center on Population Dynamics, University of Southern Denmark (SDU), Department of Biological Sciences [Notre Dame], University of Notre Dame [Indiana] (UND), Station d'écologie de Lamto, Université Abobo-Adjamé-Centre de Recherche en Ecologie, Wildlife Conservation Society (WCS), Instituto de Investigación Biosanitaria, University of St Andrews. School of Psychology and Neuroscience, University of St Andrews. Centre for Social Learning & Cognitive Evolution, and University of St Andrews. Institute of Behavioural and Neural Sciences
Subjects: 0301 basic medicine, Male, Aging, 1.2 Psychological and socioeconomic processes, [SDV]Life Sciences [q-bio], General Physics and Astronomy, 0302 clinical medicine, Models, Invariant (mathematics), media_common, Multidisciplinary, Evolutionary theory, Longevity, Age Factors, 3rd-DAS, Statistical, Female, Primates, Population dynamics, BF Psychology, media_common.quotation_subject, Science, BF, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Life Expectancy, Biological constraints, SDG 3 - Good Health and Well-being, Underpinning research, Animals, Humans, Mortality, Models, Statistical, Extramural, General Chemistry, Primates/physiology, Nonhuman primate, Ageing, 030104 developmental biology, Good Health and Well Being, Evolutionary biology, Life expectancy, Generic health relevance, 030217 neurology & neurosurgery
Abstract: Is it possible to slow the rate of ageing, or do biological constraints limit its plasticity? We test the ‘invariant rate of ageing’ hypothesis, which posits that the rate of ageing is relatively fixed within species, with a collection of 39 human and nonhuman primate datasets across seven genera. We first recapitulate, in nonhuman primates, the highly regular relationship between life expectancy and lifespan equality seen in humans. We next demonstrate that variation in the rate of ageing within genera is orders of magnitude smaller than variation in pre-adult and age-independent mortality. Finally, we demonstrate that changes in the rate of ageing, but not other mortality parameters, produce striking, species-atypical changes in mortality patterns. Our results support the invariant rate of ageing hypothesis, implying biological constraints on how much the human rate of ageing can be slowed., The ‘invariant rate of ageing’ hypothesis suggests that the rate of ageing tends to be constant within species. Here, Colchero et al. find support for the hypothesis across primates, including humans, suggesting biological constraints on the rate of ageing.
Published: 2021

6. FunAndes : a functional trait database of Andean plants

Author: Selene Báez, Luis Cayuela, Manuel J. Macía, Esteban Álvarez-Dávila, Amira Apaza-Quevedo, Itziar Arnelas, Natalia Baca-Cortes, Guillermo Bañares de Dios, Marijn Bauters, Celina Ben Saadi, Cecilia Blundo, Marian Cabrera, Felipe Castaño, Leslie Cayola, Julia G. de Aledo, Carlos Iván Espinosa, Belén Fadrique, William Farfán-Rios, Alfredo Fuentes, Claudia Garnica-Díaz, Mailyn González, Diego González, Isabell Hensen, Ana Belén Hurtado, Oswaldo Jadán, Denis Lippok, M. Isabel Loza, Carla Maldonado, Lucio Malizia, Laura Matas-Granados, Jonathan A. Myers, Natalia Norden, Imma Oliveras Menor, Kerstin Pierick, Hirma Ramírez-Angulo, Beatriz Salgado-Negret, Matthias Schleuning, Miles Silman, María Elena Solarte-Cruz, J. Sebastián Tello, Hans Verbeeck, Emilio Vilanova, Greta Weithmann, Jürgen Homeier, Escuela Politécnica Nacional del Ecuador, Universidad Rey Juan Carlos [Madrid] (URJC), Universidad Autónoma de Madrid (UAM), Universidad Nacional Abierta a Distancia de Colombia, Universidad Mayor Real y Pontificia San Francisco Xavier de Chuquisaca, Universidad Técnica Particular de Loja (UTPL), Universidad de Nariño, Computational & Applied Vegetation Ecology (CAVElab), Universiteit Gent = Ghent University (UGENT), Universidad Nacional de Tucumán (UNT), Universidad Industrial de Santander [Bucaramanga] (UIS), Universidad Mayor de San Andrés (UMSA), University of Leeds, Missouri Botanical Garden, University of Florida [Gainesville] (UF), Instituto Vasco de Investigación de Recursos Biológicos Alexander von Humboldt, Conservación Internacional, Martin-Luther-University Halle-Wittenberg, Universidad de Cuenca (UCUENCA), The Morton Arboretum, Universidad Nacional de Jujuy, Department of Biology, Washington University, University of Washington [Seattle], Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), 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 [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), University of Oxford, Plant Ecology and Ecosystems Research, Georg-August-University = Georg-August-Universität Göttingen, Universidad de Los Andes [Mérida, Venezuela] (ULA), Universidad Nacional de Colombia [Bogotà] (UNAL), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Wake Forest University, Wildlife Conservation Society (WCS), and Living Earth Collaborative (LEC) at Washington University in St. LouisHerbario Nacional de BoliviaDeutscher Akademischer Austausch Dienst (DAAD)German Research Foundation (DFG)HE3041/20-1HO3296/2HO3296/4
Subjects: Statistics and Probability, Biodiversity, Library and Information Sciences, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Tropical ecology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, FRAMEWORK, Wood, Computer Science Applications, Education, Plant Leaves, COMMUNITY, Phenotype, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, HANDBOOK, Earth and Environmental Sciences, cavelab, Statistics, Probability and Uncertainty, Forest ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Information Systems
Abstract: We introduce the FunAndes database, a compilation of functional trait data for the Andean flora spanning six countries. FunAndes contains data on 24 traits across 2,694 taxa, for a total of 105,466 entries. The database features plant-morphological attributes including growth form, and leaf, stem, and wood traits measured at the species or individual level, together with geographic metadata (i.e., coordinates and elevation). FunAndes follows the field names, trait descriptions and units of measurement of the TRY database. It is currently available in open access in the FIGSHARE data repository, and will be part of TRY’s next release. Open access trait data from Andean plants will contribute to ecological research in the region, the most species rich terrestrial biodiversity hotspot.
Published: 2022

7. A novel SARS-CoV-2 related coronavirus in bats from Cambodia

Author: Deborah, Delaune, Vibol, Hul, Erik A, Karlsson, Alexandre, Hassanin, Tey Putita, Ou, Artem, Baidaliuk, Fabiana, Gámbaro, Matthieu, Prot, Vuong Tan, Tu, Sokha, Chea, Lucy, Keatts, Jonna, Mazet, Christine K, Johnson, Philippe, Buchy, Philippe, Dussart, Tracey, Goldstein, Etienne, Simon-Lorière, Veasna, Duong, Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Université Paris-Saclay, Unité de Virologie / Virology Unit [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université Paris Cité (UPCité), Wildlife Conservation Society [Phnom Penh, Cambodia], Wildlife Conservation Society (WCS), University of California [Davis] (UC Davis), University of California (UC), This study was made possible by the generous support of the American people through the United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00 and AID-OAA-A-14-00102), with a specific extension for the testing reported here. V.H. is supported by a scholarship from the French Government (BGF) for his Ph.D. E.S.L. acknowledges funding from the French Government’s Investissement d’Avenir program, ‘INCEPTION’ (ANR-16-CONV-0005), and Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID). In 2010, the fieldwork was supported by the National Authority for Preah Vihear, UNESCO, 'Société des amis du Muséum et du Jardin des Plantes', and the Muséum national d’Histoire naturelle., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut de Recherche Biomédicale des Armées (IRBA), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Dussart, Philippe, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, and Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID
Subjects: Epidemiology, viruses, MESH: Spike Glycoprotein, Coronavirus, MESH: Amino Acid Sequence, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Chiroptera, MESH: COVID-19, MESH: Animals, Viral, skin and connective tissue diseases, MESH: Phylogeny, Lung, Phylogeny, MESH: Evolution, Molecular, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genome, virus diseases, MESH: Chiroptera, Spike Glycoprotein, Infectious Diseases, Spike Glycoprotein, Coronavirus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Pneumonia & Influenza, MESH: Genome, Viral, Cambodia, Evolution, Science, MESH: Sequence Alignment, Genome, Viral, Article, Evolution, Molecular, Vaccine Related, Biodefense, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Animals, MESH: SARS-CoV-2, Amino Acid Sequence, SARS-CoV-2, Prevention, MESH: Cambodia, fungi, Molecular, COVID-19, Pneumonia, Coronavirus, body regions, Emerging Infectious Diseases, Good Health and Well Being, Molecular evolution, Metagenomics, Sequence Alignment
Abstract: Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identifies nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a region of the spike, which is not compatible with human ACE2-mediated entry. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously reported, and suggests that Southeast Asia represents a key area to consider for future surveillance for coronaviruses., In this study, Delaune et al., isolate and characterise a SARS-CoV-2-related coronavirus from two bats sampled in Cambodia. Their findings suggest that the geographic distribution of SARS-CoV-2-related viruses is wider than previously reported.
Published: 2021

8. Runs of homozygosity in killer whale genomes provide a global record of demographic histories

Author: Kelly M. Robertson, Rebecca Hooper, Rochelle Constantine, Renaud de Stephanis, Sara Tavares, Alana Alexander, Guangyi Fan, John A. Totterdell, Ruth Esteban, Nicholas J. Davison, Tim Gerrodette, Lisa T. Ballance, John W. Durban, Songhai Li, Paul Tixier, Phillip A. Morin, Michael D. Martin, C. S. Baker, Sarah L. Fordyce Martin, Robin W. Baird, Jay Barlow, Luciano Dalla Rosa, Filipa I. P. Samarra, Andrew Brownlow, Tim Collins, Laurent Excoffier, Andrew D. Foote, M. Bradley Hanson, Jochen B. W. Wolf, M. Thomas P. Gilbert, Karin A. Forney, Christophe Guinet, Paul R. Wade, Yaolei Zhang, NTNU University Museum [Trondheim], Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), School of Biological Sciences [Bangor], Bangor University, Institute of Ecology and Evolution [Bern, Switzerland], University of Bern, University of Exeter, University of Otago [Dunedin, Nouvelle-Zélande], Cascadia Research [Washington, USA], Marine Mammal Institute, Oregon State University (OSU), School of Biological Sciences [Auckland], University of Auckland [Auckland], Marine Mammal and Turtle Division (MMTD), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Scottish Marine Animal Stranding Scheme, SRUC Veterinary Service, Scotland's Rural College (SRUC), Wildlife Conservation Society (WCS), Laboratório de Ecologia e Conservação da Megafauna Marinha [Rio Grande, Brazil], Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), CIRCE (Conservation, Information and Research on Cetaceans), Moss Landing Marine Laboratories [CA, USA] (San José State University), San Jose State University [San Jose] (SJSU), Section for Evolutionary Genomics, IT University of Copenhagen (ITU)-GLOBE Institute, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Northwest Fisheries Science Center (NWFSC), Sanya Key Laboratory of Marine Mammal and Marine Bioacoustics, Institute of Deep-sea Science and Engineering, Vestmannaeyjar Research and Study Center, Scottish Oceans Institute [University of St Andrews] (SOI), School of Biology [University of St Andrews], University of St Andrews [Scotland]-University of St Andrews [Scotland], Fisheries and Oceans Canada (DFO), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), James Cook University (JCU), Alaska Fisheries Science Center (AFSC), Ludwig Maximilian University [Munich] (LMU), BGI Qingdao, Partenaires INRAE, Beijing Genomics Institute [Shenzhen] (BGI), China National GeneBank, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, Male, Demographic history, Population, inbreeding, Biology, Runs of Homozygosity, 010603 evolutionary biology, 01 natural sciences, Identity by descent, Polymorphism, Single Nucleotide, Coalescent theory, 03 medical and health sciences, Effective population size, Genetics, Inbreeding depression, Animals, Inbreeding, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Demography, Population Density, 0303 health sciences, education.field_of_study, whole genome sequencing, Genome, Orcinus orca, Homozygote, Killer whales, killer whale, Evolutionary biology, Whole genome sequencing, [SDE]Environmental Sciences, 570 Life sciences, biology, Whale, Killer
Abstract: International audience; Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
Published: 2021

9. No evidence for female kin association, indications for extragroup paternity, and sex‐biased dispersal patterns in wild western gorillas

Author: Masi, Shelly, Austerlitz, Frédéric, Chabaud, Chloé, Lafosse, Sophie, Marchi, Nina, Georges, Myriam, Dessarps‐Freichey, Françoise, Miglietta, Silvia, Sotto‐Mayor, Andrea, Galli, Aurore San, Meulman, Ellen, Pouydebat, Emmanuelle, Krief, Sabrina, Todd, Angelique, Fuh, Terence, Breuer, Thomas, Ségurel, Laure, Muséum national d'Histoire naturelle (MNHN), Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Mécanismes Adaptatifs et Evolution (MECADEV), World Wide Fund (WWF), Wildlife Conservation Society (WCS), 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), and Éco-Anthropologie (EA)
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, [SDV]Life Sciences [q-bio], western gorillas, polygynous species, paternity, dispersal, QH540-549.5, ComputingMilieux_MISCELLANEOUS, great apes, Original Research, kin association
Abstract: Characterizing animal dispersal patterns and the rational behind individuals’ transfer choices is a long‐standing question of interest in evolutionary biology. In wild western gorillas (Gorilla gorilla), a one‐male polygynous species, previous genetic findings suggested that, when dispersing, females might favor groups with female kin to promote cooperation, resulting in higher‐than‐expected within‐group female relatedness. The extent of male dispersal remains unclear with studies showing conflicting results. To investigate male and female dispersal patterns and extragroup paternity, we analyzed long‐term field observations, including female spatial proximity data, together with genetic data (10 autosomal microsatellites) on individuals from a unique set of four habituated western gorilla groups, and four additional extragroup males (49 individuals in total). The majority of offspring (25 of 27) were sired by the group male. For two offspring, evidence for extragroup paternity was found. Contrarily to previous findings, adult females were not significantly more related within groups than across groups. Consistently, adult female relatedness within groups did not correlate with their spatial proximity inferred from behavioral data. Adult females were similarly related to adult males from their group than from other groups. Using R ST statistics, we found significant genetic structure and a pattern of isolation by distance, indicating limited dispersal in this species. Comparing relatedness among females and among males revealed that males disperse farer than females, as expected in a polygamous species. Our study on habituated western gorillas shed light on the dispersal dynamics and reproductive behavior of this polygynous species and challenge some of the previous results based on unhabituated groups., We found evidence for extra‐group paternity for two offspring. Adult females were not significantly more related within groups than between groups and were similarly related to adult males from their group than from other groups. Comparing relatedness among females and among males revealed that males disperse farer than females.
Published: 2021

10. Epidemiology and pathological progression of erythematous lip lesions in captive sun bears (Helarctos malayanus)

Author: Kirsty Officer, Daniela Denk, Nev Broadis, Bethany Jackson, Paul F. Horwood, Vibol Hul, Mathieu Pruvot, Kris Warren, Philippe Dussart, Nhim Thy, Free the Bears [Phnom Penh, Cambodia], Free the Bears [Australia], Murdoch University, Wildlife Conservation Society (WCS), James Cook University (JCU), International Zoo Veterinary Group [Keighley, UK] (IZVG), Unité de Virologie / Virology Unit [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ministry of Agriculture, Forestry and Fisheries [Cambodia], and Laboratory testing at the Institut Pasteur du Cambodge was supported by funding from the European Union under the INNOVATE programme, through the LACANET project (DCIASIE/2013/315-151).
Subjects: Male, Artificial Gene Amplification and Extension, Pathology and Laboratory Medicine, Polymerase Chain Reaction, 0403 veterinary science, 0302 clinical medicine, MESH: Animals, MESH: Phylogeny, Phylogeny, Mammals, education.field_of_study, Eukaryota, MESH: Carcinoma, Squamous Cell, MESH: Lip, 3. Good health, MESH: Erythema, Oncology, Medical Microbiology, 030220 oncology & carcinogenesis, Viral Pathogens, Lip Neoplasms, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Carcinoma, Squamous Cell, Disease Progression, Medicine, MESH: Lip Neoplasms, MESH: Disease Progression, medicine.medical_specialty, Science, Bears, Surgical and Invasive Medical Procedures, Microbiology, 03 medical and health sciences, Tongue, education, Molecular Biology Techniques, Pathological, Microbial Pathogens, Molecular Biology, MESH: Prevalence, Lips, Mouth, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Organisms, Biology and Life Sciences, Lip Diseases, medicine.disease, Erythema, Face, Digestive System, MESH: Female, Biopsy, Risk Factors, MESH: Risk Factors, Epidemiology, Medicine and Health Sciences, Prevalence, MESH: Gammaherpesvirinae, Lip Squamous Cell Carcinoma, Multidisciplinary, medicine.diagnostic_test, 04 agricultural and veterinary sciences, medicine.anatomical_structure, Vertebrates, Viruses, MESH: Lip Diseases, Female, Anatomy, Pathogens, Cambodia, Ursidae, Research Article, Herpesviruses, Histology, 040301 veterinary sciences, MESH: Ursidae, Population, Research and Analysis Methods, Gammaherpesvirinae, medicine, Animals, Squamous Cell Carcinoma, business.industry, MESH: Cambodia, Carcinoma, Cancers and Neoplasms, Dermatology, Lip, MESH: Male, stomatognathic diseases, Dysplasia, Amniotes, business, DNA viruses, Head, Zoology
Abstract: International audience; This study investigates the occurrence of erythematous lip lesions in a captive sun bear population in Cambodia, including the progression of cheilitis to squamous cell carcinoma, and the presence of Ursid gammaherpesvirus 1. Visual assessment conducted in 2015 and 2016 recorded the prevalence and severity of lesions. Opportunistic sampling for disease testing was conducted on a subset of 39 sun bears, with histopathological examination of lip and tongue biopsies and PCR testing of oral swabs and tissue biopsies collected during health examinations. Lip lesions were similarly prevalent in 2015 (66.0%) and 2016 (68.3%). Degradation of lip lesion severity was seen between 2015 and 2016, and the odds of having lip lesions, having more severe lip lesions, and having lip lesion degradation over time, all increased with age. Cheilitis was found in all lip lesion biopsies, with histological confirmation of squamous cell carcinoma in 64.5% of cases. Single biopsies frequently showed progression from dysplasia to neoplasia. Eighteen of 31 sun bears (58.1%) had at least one sample positive for Ursid gammaherpesvirus 1. The virus was detected in sun bears with and without lip lesions, however due to case selection being strongly biased towards those showing lip lesions it was not possible to test for association between Ursid gammaherpesvirus 1 and lip squamous cell carcinoma. Given gammaherpesviruses can play a role in cancer development under certain conditions in other species, we believe further investigation into Ursid gammaherpesvirus 1 as one of a number of possible co-factors in the progression of lip lesions to squamous cell carcinoma is warranted. This study highlights the progressively neoplastic nature of this lip lesion syndrome in sun bears which has consequences for captive and re-release management. Similarly, the detection of Ursid gammaherpesvirus 1 should be considered in pre-release risk analyses, at least until data is available on the prevalence of the virus in wild sun bears.
Published: 2020

11. Floristic evidence for alternative biome states in tropical Africa

Author: Aleman, J. C., Fayolle, A., Favier, C., Staver, A. C., Dexter, K. G., Ryan, C. M., Azihou, A. F., Bauman, D., Te Beest, M., Chidumayo, E. N., Comiskey, J. A., Cromsigt, J. P. G. M., Dessard, H., Doucet, J.-l., Finckh, M., Gillet, J.-f., Gourlet-fleury, S., Hempson, G. P., Holdo, R. M., Kirunda, B., Kouame, F. N., Mahy, G., Gonçalves, F. Maiato P., Mcnicol, I., Quintano, P. Nieto, Plumptre, A. J., Pritchard, R. C., Revermann, R., Schmitt, C. B., Swemmer, A. M., Talila, H., Woollen, E., Swaine, M. D., Spatial Ecology and Global Change, Environmental Sciences, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Département de géographie, Université de Montréal, Montréal, Canada, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), 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, Department of Ecology and Evolutionary Biology, Yale University, School of Geosciences [Edinburgh], University of Edinburgh, Royal Botanical Garden Edinburgh, Royal Botanical Garden, Laboratory of Applied Ecology, Université d’Abomey-Calavi (UAC), School of Geography and the Environment [Oxford] (SoGE), University of Oxford [Oxford], Plant Ecology and Biogeochemistry, Faculté des Sciences [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Copernicus Institute for Sustainable Development, Utrecht University [Utrecht], Centre for African Conservation Ecology, Nelson Mandela Metropolitan University [Port Elizabeth, South Africa], Grasslands-Wetlands-Forests Node, SAEON, Makeni Savanna Research Project, Inventory & Monitoring Program, National Park Service, Smithonian Institution, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences (SLU), Forêts et Sociétés (UPR Forêts et Sociétés), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Environnements et Sociétés (Cirad-ES), Institute of Plant Science and Microbiology, University of Hamburg, Odum School of Ecology, University of Georgia [USA], Wildlife Conservation Society (WCS), Université Nangui Abrogoua, Herbário do Lubango, Instituto Superior de Ciências da Educação da Huíla, Department of Zoology [Cambridge], University of Cambridge [UK] (CAM), Global Development Institute, University of Manchester [Manchester], Faculty of Natural Resources and Spatial Sciences, Namibia University of Science and Technology (NUST), University of Bonn, Chair for Nature Conservation and Landscape Ecology, South African Environmental Observation Network [Pretoria] (SAEON), College of Agriculture and Natural Resource, Madda Walabu University, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, 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), Royal Botanic Garden [Edinburgh], Université d’Abomey-Calavi = University of Abomey Calavi (UAC), University of Oxford, Nelson Mandela University [Port Elizabeth], Université Nangui Abrogoua (UNA), Universität Bonn = University of Bonn, and Biotechnology and Biological Sciences Research Council (BBSRC)-Aberystwyth University
Subjects: F40 - Écologie végétale, Climate, Rain, forêt tropicale, Forests, compostion, Fires, Trees, données spatiales, tree species, Alternative stable states, Savane, Ecosystem, Tropical Climate, tropical biomes, precipitation and seasonality, F70 - Taxonomie végétale et phytogéographie, Biological Sciences, Grassland, cartographie des fonctions de la forêt, Succession végétale, Africa, Écosystème forestier, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, fire, Communauté végétale, Index de végétation
Abstract: International audience; The idea that tropical forest and savanna are alternative states is crucial to how we manage these biomes and predict their future under global change. Large-scale empirical evidence for alternative stable states is limited however and comes mostly from the multimodal distribution of structural aspects of vegetation. These approaches have been criticized, as structure alone cannot separate out wetter savannas from drier forests for example, and there are also technical challenges to mapping vegetation structure in unbiased ways. Here, we develop an alternative approach to delimit the climatic envelope of the two biomes in Africa, using tree species lists gathered for a large number of forest and savanna sites distributed across the continent. Our analyses confirm extensive climatic overlap of forest and savanna, supporting the alternative stable states hypothesis for Africa, and this result is corroborated by paleo-ecological evidence. Further, we find the two biomes to have highly divergent tree species compositions and to represent alternative compositional states. This allowed us to classify tree species as forest vs savanna specialists, with some generalist species that span both biomes. In conjunction with geo-referenced herbarium records, we mapped the forest and savanna distributions across Africa and quantified their environmental limits, which are primarily related to precipitation and seasonality, with a secondary contribution of fire. These results are important for the ongoing efforts to restore African ecosystems, which depend on accurate biome maps to set appropriate targets for the restored states, but also provide novel empirical evidence for broad scale bistability. Significance statement: We develop a biogeographic approach to analyzing the presence of alternative stable states in tropical biomes. Whilst forest-savanna bistability has been widely hypothesized and modeled, empirical evidence has remained scarce and controversial, and here, applying our method to Africa, we provide large scale evidence that there are alternative states in tree species composition of tropical vegetation. Furthermore, our results have produced novel and more accurate maps of the forest and savanna distributions in Africa, which takes into account differences in tree species composition, and a complex suite of determinants. This result is not only important for understanding the biogeography of the continent, but also to guide large-scaled tree planting and restoration efforts planned for the region.
Published: 2020

12. Variability in coral reef fish baseline and benchmark biomass in the central and western Indian Ocean provinces

Author: Pascale Chabanet, J. Henrich Bruggemann, Tim R. McClanahan, Nicholas A. J. Graham, Alan M. Friedlander, Wildlife Conservation Society (WCS), National Geographic Society, University of Hawaii at Manoa, Partenaires INRAE, Lancaster University, Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA)
Subjects: 0106 biological sciences, Unfished biomass, Coral reef fish, Biodiversity, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Human gravity, human gravity, Marine reserves, 14. Life underwater, Sustainable fishing, Reef, Nature and Landscape Conservation, Seascape, Biomass (ecology), geography, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, wilderness, Marine reserve, unfished biomass, marine reserves, Coral reef, 15. Life on land, sustainable fishing, Fishery, Fishing impacts, Habitat, Wilderness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Reef fish biomass is increasingly recognized as a key indicator of fishery and biodiversity status linked to ecosystem integrity on coral reefs, and yet the evaluation of appropriate baselines for biomass, and what drives variation in potential baselines, is sparse. Variability in reef fishable biomass was assessed to test for the existence of baselines or benchmarks (B&Bs), based on field studies of 223 reef sites in remote uninhabited reefs, in high‐compliance closures of >5 km2, and among the increasing number of small and recent closures. The purpose of the study was to examine the effects of human habitation, travel time and distance to cities, habitat, depth, benthic cover, and environmental variables on fish B&Bs. There were large differences in the three categories of ‘no fishing’, with human habitation being the single best predictor of biomass. In remote areas without people (>9 hours of travel time), fish biomass had a mean of 2,450 kg ha–1 (95% confidence interval, 95% CI, 2,130–2,770 kg ha–1; median = 1,885 kg ha–1). In these remote areas, biomass was weakly associated with human travel time to the site and, to a lesser extent, wave energy. In high‐compliance closures, fish biomass peaked at 20 years and 5–10 km2, and levelled at 910 kg ha–1 (95% CI 823–989 kg ha–1) for both closure age and size. There was little evidence that human travel time and environmental factors influenced biomass greatly in these established closures. In small and recent closures (
Published: 2020

13. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats

Author: Feng Zhu, Veasna Duong, Xiao Fang Lim, Vibol Hul, Tanu Chawla, Lucy Keatts, Tracey Goldstein, Alexandre Hassanin, Vuong Tan Tu, Philippe Buchy, October M. Sessions, Lin-Fa Wang, Philippe Dussart, Danielle E. Anderson, Duke-NUS Medical School [Singapore], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Wildlife Conservation Society (WCS), University of California [Davis] (UC Davis), University of California (UC), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Vietnam Academy of Science and Technology (VAST), University of Melbourne, and DEA and L-FW were supported by Grants NRF2012NRFCRP001-056 and NRF2016NRF-NSFC002-013 from the Singapore National Research Foundation. This study was made possible by the generous support of the American people through the United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00 and AID-OAA-A-14-00102). The contents of this paper are the responsibility of the authors and do not necessarily reflect the views of the US Agency for International Development or the US Government. The fieldwork was supported in part by the National Authority for Preah Vihear, UNESCO, 'Société des amis du Muséum et du Jardin des Plantes', and the Muséum national d’Histoire naturelle.
Subjects: Recombination, Genetic, China, Coronaviridae, Coronaviridae Infections, [SDV]Life Sciences [q-bio], viruses, bats, coronavirus, virus diseases, cross-species transmission, Genome, Viral, zoonosis, recombination, respiratory tract diseases, Evolution, Molecular, Phylogeography, co-infection, Infectious Diseases, Chiroptera, Virology, Animals, GCCDC1, Cambodia, Phylogeny, Disease Reservoirs
Abstract: International audience; Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.
Published: 2022

14. Perception of health risks in Lao market vendors

Author: Bounlom Douangngeun, Watthana Theppangna, Kongsy Khammavong, Paul N. Newton, Daniel Reinharz, Mayfong Mayxay, Chanfong Philavong, Amanda E. Fine, Paul F. Horwood, Matthew T. Robinson, Philippe Dussart, Mathieu Pruvot, Sayapeth Rattanavong, Phonesavanh Milavong, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, Ministry of Health [Laos], Institut de la Francophonie pour la Médecine Tropicale (IFMT), Wildlife Conservation Society (WCS), Université Laval [Québec] (ULaval), University of Oxford [Oxford], University of Health Sciences [Vientiane, Laos] (UHS), Wildlife Conservation Society [Vientiane, Laos] (WCS), James Cook University (JCU), Unité de Virologie / Virology Unit [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ministry of Agriculture and Forestry of Laos, and This work was funded by the European Union under the INNOVATE program, through the LACANET project (DCIASIE/2013/315-151) and the Wellcome Trust. PNN and MTR are funded by the Wellcome Trust.
Subjects: 0301 basic medicine, Male, Health Knowledge, Attitudes, Practice, Epidemiology, MESH: Health Knowledge, Attitudes, Practice, Ethnic group, Pilot Projects, 0302 clinical medicine, Risk Factors, MESH: Risk Factors, Pandemic, MESH: Animals, Longitudinal Studies, Socioeconomics, MESH: Longitudinal Studies, Risk management, health care economics and organizations, 2. Zero hunger, MESH: Meat, MESH: Aged, MESH: Middle Aged, Commerce, Middle Aged, Infectious Diseases, Laos, MESH: Young Adult, MESH: Livestock, Original Article, Female, MESH: Zoonoses, Adult, MESH: Pandemics, Livestock, Meat, Adolescent, Vendor, wildlife, 030106 microbiology, 030231 tropical medicine, Wildlife, Legislation, Animals, Wild, 03 medical and health sciences, Young Adult, one health, MESH: Cross-Sectional Studies, risk perception, markets, Animals, Humans, MESH: Animals, Wild, Bushmeat, Pandemics, Aged, MESH: Adolescent, health risk, MESH: Humans, General Veterinary, General Immunology and Microbiology, business.industry, food, Public Health, Environmental and Occupational Health, MESH: Adult, Original Articles, MESH: Pilot Projects, MESH: Male, zoonoses, Risk perception, MESH: Commerce, Cross-Sectional Studies, MESH: Laos, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, bushmeat, business, MESH: Female
Abstract: International audience; Wet markets are a critical part of South-East Asian culture and economy. However, their role in circulation and transmission of both endemic and emerging disease is a source of concern in a region considered a hotspot of disease emergence. In the Lao People's Democratic Republic (Lao PDR, Laos), live and dead wild animals are fre- quently found in wet markets, despite legislation against the bushmeat trade. This is generally considered to increase the risk of disease transmission and emergence, al- though whether or not wildlife vendors themselves have indeed increased incidence of zoonotic disease has rarely been assessed. In preparation for a future longitudi- nal study of market vendors investigating vendors’ exposure to zoonotic pathogens, we conducted a pilot survey of Lao market vendors of wildlife meat, livestock meat and vegetables, to identify demographic characteristics and potential control groups within markets. We also investigated baseline risk perception for infectious diseases among market vendors and assessed the association between risk perception and risk mitigation behaviours. The surveys conducted with 177 vendors revealed simi- lar age, sex, ethnic background and geographical origin between vendor types, but differences in professional background and work history for livestock meat vendors. The perception of disease risk was very low across all vendors, as was the reported use of personal protective equipment, and the two appeared unrelated. Personal risk discounting and assumptions about transmission routes may explain this lack of association. This information will help inform the development of future research, risk communication and risk mitigation policy, especially in the light of the COVID-19 pandemic.
Published: 2020
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15. Creating a space for place and multidimensional well-being: lessons learned from localizing the SDGs

Author: Jamie Tanguay, Jennifer E. Caselle, Winifereti Nainoca, Kanoeʻulalani Morishige, John Aini, John Parks, Manuel Mejia, Emily S. Darling, Puaʻala Pascua, Alexander Mawyer, Ron Vave, Joachim Claudet, Joe McCarter, Lisa Mandle, Stacy D. Jupiter, Simon Albert, Chris Filardi, Nadav Gazit, Samantha H. Cheng, Erin Betley, Eleanor J. Sterling, Veronica Wase, Rachel Dacks, Supin Wongbusarakum, Tamara Ticktin, Sophie Caillon, Amanda Sigouin, American Museum of Natural History (AMNH), School of Civil Engineering, The University of Queensland, School of Civil Engineering, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 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), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-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), Wildlife Conservation Society (WCS), Université Paul-Valéry - Montpellier 3 (UPVM)-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), 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), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), and Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE)
Subjects: Health (social science), Process management, 010504 meteorology & atmospheric sciences, Sociology and Political Science, [SDE.MCG]Environmental Sciences/Global Changes, Geography, Planning and Development, Context (language use), 010501 environmental sciences, Management, Monitoring, Policy and Law, Space (commercial competition), Pacific Islands, 01 natural sciences, Indigenous, 12. Responsible consumption, [SHS]Humanities and Social Sciences, Political science, Sustainable development, 11. Sustainability, Resilience (network), 0105 earth and related environmental sciences, Nature and Landscape Conservation, Global and Planetary Change, International call, Ecology, 1. No poverty, [SDE.ES]Environmental Sciences/Environmental and Society, Indigenous Peoples and local communities, International development, Transformational leadership, 13. Climate action, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, Sustainability, [SDE]Environmental Sciences, Place-based
Abstract: Achieving sustainable development globally requires multilevel and interdisciplinary efforts and perspectives. Global goals shape priorities and actions at multiple scales, creating cascading impacts realized at the local level through the direction of financial resources and implementation of programs intended to achieve progress towards these metrics. We explore ways to localize global goals to best support human well-being and environmental health by systematically comparing the UN Sustainable Development Goals (SDGs) with regionally-derived well-being dimensions that encompass components of social–ecological resilience across the Pacific Islands. Our research shows that, in the context of the Pacific, there are overlaps but also significant gaps between regional conceptions of well-being and the globally-derived SDGs. Some dimensions, related to human health and access to infrastructure and finances, are well represented in the SDGs. Other dimensions of high importance when localizing perspectives of well-being, such as those regarding connections between and across people and place and Indigenous and local knowledge, are not. Furthermore, internationally generated indicators may result in trade-offs and measurement challenges in local contexts. Creating space for place-based values in global sustainability planning aligns with international calls for transformational changes needed to achieve global goals. We identify challenges in applying SDG indicators at the local level and provide lessons learned to foster equitable and holistic approaches and outcomes for sustainability.
Published: 2020

16. Assessing ecological function in the context of species recovery

Author: E. J. Milner-Gulland, Erik Meijaard, Simon Hedges, Ana S. L. Rodrigues, P. J. Stephenson, David A. Keith, Molly K. Grace, H. Resit Akçakaya, David P. Mallon, Eric W. Sanderson, Barney Long, Department of Ecology and Evolution, Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), IUCN Species Survival Commission (IUCN SSC), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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]), Centre for Ecosystem Sciences, University of New South Wales [Sydney] (UNSW), NSW Office of Environment and Heritage, Department of Zoology [Oxford], University of Oxford [Oxford], Merton College, University of Oxford, U.K., Wildlife Conservation Society (WCS), Asian Arks, Division of Biology and Conservation Ecology, Manchester Metropolitan University (MMU), Global Wildlife Conservation (GWC), Center of Excellence for Environmental Decision, University of Queensland [Brisbane], Ecosystem Management Group, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), WWF-US funded several of the meetings. Stony Brook University OVPR Seed Grant Program supported H.R.A. NERC Knowledge Exchange Fellowship supported M.K.G., Université Paul-Valéry - Montpellier 3 (UPVM)-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 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), University of Oxford, 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), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)
Subjects: 0106 biological sciences, Conservation of Natural Resources, Computer science, Context (language use), [SDV.BID]Life Sciences [q-bio]/Biodiversity, Ecological systems theory, 010603 evolutionary biology, 01 natural sciences, Species level, Animals, Ecosystem, Conservation planning, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Functional ecology, Ecology, business.industry, 010604 marine biology & hydrobiology, Environmental resource management, Endangered Species, Biodiversity, 15. Life on land, Species recovery, Conservation optimism, Ecological process, business, Conservation impact, Green List of Species, Demographic structure
Abstract: Species interactions matter to conservation. Setting an ambitious recovery target for a species requires considering the size, density, and demographic structure of its populations such that they fulfill the interactions, roles, and functions of the species in the ecosystems in which they are embedded. A recently proposed framework for an International Union for Conservation of Nature Green List of Species formalizes this requirement by defining a fully recovered species in terms of representation, viability, and functionality. Defining and quantifying ecological function from the viewpoint of species recovery is challenging in concept and application, but also an opportunity to insert ecological theory into conservation practice. We propose 2 complementary approaches to assessing a species' ecological functions: confirmation (listing interactions of the species, identifying ecological processes and other species involved in these interactions, and quantifying the extent to which the species contributes to the identified ecological process) and elimination (inferring functionality by ruling out symptoms of reduced functionality, analogous to the red-list approach that focuses on symptoms of reduced viability). Despite the challenges, incorporation of functionality into species recovery planning is possible in most cases and it is essential to a conservation vision that goes beyond preventing extinctions and aims to restore a species to levels beyond what is required for its viability. This vision focuses on conservation and recovery at the species level and sees species as embedded in ecosystems, influencing and being influenced by the processes in those ecosystems. Thus, it connects and integrates conservation at the species and ecosystem levels.Evaluación de la Función Ecológica en el Contexto de Recuperación de Especies Resumen Las interacciones entre especies son de importancia para la conservación. La definición de una meta ambiciosa de recuperación para una especie requiere considerar el tamaño, la densidad y la estructura demográfica de sus poblaciones de tal manera que lleven a cabo las interacciones, papeles y funciones de las especies en los ecosistemas donde viven. Un marco de referencia propuesto recientemente para una Lista Verde de Especies de la Unión Internacional para la Conservación de la Naturaleza (UICN)formaliza este requerimiento mediante la definición de una especie completamente recuperada en términos de su representación, viabilidad y funcionalidad. La definición y cuantificación de la función ecológica desde la perspectiva de la recuperación de especies es un reto conceptual y de aplicación, pero también es un oportunidad para insertar la teoría ecológica en la práctica de la conservación. Proponemos 2 métodos complementarios para evaluar las funciones ecológicas de una especie: confirmación (listado de interacciones de la especie, identificación de procesos ecológicos y otras especies involucradas en estas interacciones) y eliminación (inferencia de la funcionalidad descartando los síntomas de reducción en la funcionalidad, análogo al método de la lista roja que enfoca los síntomas de reducción en la viabilidad). A pesar de los retos, la incorporación de la funcionalidad en la planificación de la recuperación de especies es posible en la mayoría de los casos y es esencial para una visión de la conservación que vaya más allá de la prevención de extinciones y que tenga como objetivo restaurar a una especie a niveles más allá de lo que se requiere para su viabilidad. Su visión se centra en la conservación y recuperación a nivel de especies y ve a las especies como componentes de los ecosistemas, influyendo y siendo influenciadas por los procesos en esos ecosistemas. Así, conecta e integra la conservación a nivel de especies y ecosistemas.物种间的相互作用对保护至关重要。设定远大的物种恢复目标需要考虑其种群大小、密度和种群统计结构, 以确保物种能在其所处的生态系统中实现种间互作和物种自身的作用与功能。最近提出的《国际自然保护联盟 (IUCN) 绿色物种名录》框架正式纳入了这项需求, 提出从代表性、生存力和功能性三个方面来定义完全恢复的物种。从物种恢复的角度来定义和量化其生态功能, 在概念和应用上都具有挑战性, 但这也是在保护实践中引入生态学理论的重要机遇。我们提出了两种互补的方法来评估物种的生态功能: 一是直接确认, 即列出物种的互作、确定互作中涉及的生态学过程和其它物种, 并量化物种对该生态过程的贡献;二是消除法, 即通过排除功能性受损后的症状来推断功能, 这与红色名录中关注生存力降低后的症状的方法类似。虽然还存在上述挑战, 但在大多数情况下将功能性纳入物种恢复计划是可行的, 而且这对于不仅旨在防止灭绝、更要将物种恢复到生存所需水平的保护愿景来说至关重要。这一愿景强调物种水平的保护和恢复, 将物种视为生态系统的一部分, 影响着生态系统过程的同时也受其影响。因此, 它也连接和整合了物种及生态系统水平的保护。【翻译: 胡怡思; 审校: 聂永刚】.
Published: 2020

17. Peste des Petits Ruminants at the Wildlife–Livestock Interface in the Northern Albertine Rift and Nile Basin, East Africa

Author: Margaret Driciru, Xavier Fernández Aguilar, Arnaud Bataille, Gladys Kalema-Zikusoka, Johan Espunyes, Alexandre Caron, David Solomon Adwok, Jean-Paul Kabemba Lukusa, Chrisostom Ayebazibwe, Jesús Muro, Natascha V Meunier, Satya Parida, Richard Kock, Michael D. Kock, Andreu Colom-Cadena, Mattia Begovoeva, Geneviève Libeau, Oscar Cabezón, Krupali Parekh, Ignasi Marco, Mana Mahapatra, Producció Animal, Sanitat Animal, Royal Veterinary College [London], University of London [London], University of Calgary, Pirbright Institute, Università degli studi di Torino (UNITO), Conservation Through Public Health (CTPH), UWA - Uganda Wildlife Authority, National Animal Disease Diagnostics and Epidemiology Centre (NADDEC), Ministry of Animal Resources and Fisheries, Wildlife Conservation Society (WCS), Mountain Gorilla Veterinary Program (MGVP), Andorrana de Cooperació Veterinària a l'Àfrica de l'Est (Daktari), Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Edifici V, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Centre de Recerca en Sanitat Animal [UAB, Spain] (CReSA), Universitat Autònoma de Barcelona (UAB)-Institute of Agrifood Research and Technology (IRTA), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Eduardo Mondlane University, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and This study was primarily funded by the Biotechnology and Biological Sciences Research Council (UK) and the Animal Health and Welfare Network from the European Commission through the project, Improved Understanding of the Epidemiology of Peste-des-Petits Ruminants, led by The Pirbright Institute (BB/L013657/1) and the Royal Veterinary College (BB/L013592/1). The Government of Andorra funded the veterinary activities in which livestock samples from western Uganda were collected.
Subjects: 0301 basic medicine, Male, Veterinary medicine, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Antibodies, Viral, L73 - Maladies des animaux, lcsh:Microbiology, Disease Outbreaks, 0403 veterinary science, Interactions biologiques, Seroepidemiologic Studies, Geography, Medical, 2. Zero hunger, Rift, National park, Goats, 04 agricultural and veterinary sciences, Maladie transfrontière, Africa, Eastern, democratic republic of the congo, Épidémiologie, Infectious Diseases, Geography, Livestock, Female, transboundary emerging diseases, epidemiology, south sudan, Bétail, 040301 veterinary sciences, wildlife, Wildlife, host range, Animals, Wild, Enzyme-Linked Immunosorbent Assay, Article, Peste-des-petits-ruminants virus, Virus peste petits ruminants, 03 medical and health sciences, uganda, Virology, Peste-des-Petits-Ruminants, parasitic diseases, medicine, Animals, Epizootic, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Sheep, business.industry, Outbreak, L70 - Sciences et hygiène vétérinaires - Considérations générales, 15. Life on land, Animal sauvage, medicine.disease, ppr, peste des petits ruminants, 030104 developmental biology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract: In the recent past, peste des petits ruminants (PPR) emerged in East Africa causing outbreaks in small livestock across different countries, with evidences of spillover to wildlife. In order to understand better PPR at the wildlife&ndash, livestock interface, we investigated patterns of peste des petits ruminants virus (PPRV) exposure, disease outbreaks, and viral sequences in the northern Albertine Rift. PPRV antibodies indicated a widespread exposure in apparently healthy wildlife from South Sudan (2013) and Uganda (2015, 2017). African buffaloes and Uganda kobs &lt, 1-year-old from Queen Elizabeth National Park (2015) had antibodies against PPRV N-antigen and local serosurvey captured a subsequent spread of PPRV in livestock. Outbreaks with PPR-like syndrome in sheep and goats were recorded around the Greater Virunga Landscape in Kasese (2016), Kisoro and Kabale (2017) from western Uganda, and in North Kivu (2017) from eastern Democratic Republic of the Congo (DRC). This landscape would not be considered typical for PPR persistence as it is a mixed forest&ndash, savannah ecosystem with mostly sedentary livestock. PPRV sequences from DRC (2017) were identical to strains from Burundi (2018) and confirmed a transboundary spread of PPRV. Our results indicate an epidemiological linkage between epizootic cycles in livestock and exposure in wildlife, denoting the importance of PPR surveillance on wild artiodactyls for both conservation and eradication programs.
Published: 2020

18. Fishing restrictions and remoteness deliver conservation outcomes for Indonesia's coral reef fisheries

Author: Eva Maire, Estradivari, Gabby N. Ahmadia, Emily S. Darling, Amkieltiela, Shinta Pardede, Stuart Campbell, Sangeeta Mangubhai, Wildlife Conservation Society (WCS), Rare Indonesia, Department of Ecology and Evolutionary Biology [University of Toronto] (EEB), University of Toronto, World Wildlife Fund, Washington, World Wide Fund (WWF), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Lancaster Environment Centre, Lancaster University, and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, lcsh:QH1-199.5, Coral reef fish, gear restrictions, Fishing, lcsh:General. Including nature conservation, geographical distribution, Data-poor fisheries, South East Asia, 010603 evolutionary biology, 01 natural sciences, Marine protected areas, Dominance (ecology), 14. Life underwater, Reef, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Trophic level, geography, Gear restrictions, Small-scale fisheries, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, small-scale fisheries, Food webs, Pelagic zone, Coral reef, small‐scale fisheries, 15. Life on land, data‐poor fisheries, Fishery, food webs, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, Marine protected area, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, data-poor fisheries, marine protected areas
Abstract: International audience; Coral reef fisheries depend on reef fish biomass to support ecosystem functioning and sustainable fisheries. Here, we evaluated coral reefs across 4,000 km of the Indonesian archipelago to reveal a large gradient of biomass, from 17,000 kg/ha.Trophic pyramids characterized by planktivore dominance emerged at high biomass, suggesting the importance of pelagic pathways for reef productivity. Total biomass and the biomass of most trophic groups were higher within gear restricted and no-take management, but the greatest biomass was found on unmanaged remote reefs. Within marine protected areas (MPAs), 41.6% and 43.6% of gear restricted and no-take zones,respectively, met a global biomass target of 500 kg/ha, compared with 71.8% of remote sites. To improve conservation outcomes for Indonesia’s biodiverse and economically important coral reef fisheries, our results suggest to: (1) strengthen management within Indonesia’s existing MPAs and (2) precautionarily manage remote reefs with high biomass.
Published: 2020

19. Contrasting patterns in the abundance of fish communities targeted by fishers on two coral reefs in southern Mozambique

Author: Anna L. Flam, Sébastien Jaquemet, Mark G. Meekan, Alexandra M. Watts, Conrad W. Speed, T Sancelme, Jordan Goetze, Australian Institute of Marine Science (AIMS), The University of Western Australia (UWA), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Bentley University, Wildlife Conservation Society (WCS), Marine Megafauna Foundation, Partenaires INRAE, Manchester Metropolitan University (MMU), and Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, marine reserve, rarefaction curves, Biodiversity, fish community structure, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Abundance (ecology), parasitic diseases, 14. Life underwater, western Indian Ocean, fishing pressure, Ecology, Evolution, Behavior and Systematics, biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, geography.geographical_feature_category, 010604 marine biology & hydrobiology, Baseline (sea), Marine reserve, Coral reef, 15. Life on land, Fishery, Geography, Habitat, Marine protected area, Species richness, baited remote underwater video, Bazaruto Archipelago
Abstract: International audience; Coastal populations of maritime countries in eastern Africa rely on fish as a primary source of protein, but baseline information on the abundance of fish communities on these coastlines is often lacking. We used baited remote underwater video stations to compare the abundance and diversity of reef fishes targeted by fishing at two sites in southern Mozambique, one at Lighthouse Reef within the Bazaruto Archipelago National Park and the other to the south at San Sebastian Reef on the San Sebastian Peninsula. Fish that are known targets of fisheries (mostly small-scale and artisanal) had an abundance that was almost three-times greater at San Sebastian Reef (80.22 ind. h–1 [SE 18.00]) than at Lighthouse Reef (29.70 ind. h–1 [SE 8.91]). Similarly, there was greater mean species richness at San Sebastian Reef (38.74 species h–1 [SE 2.79]) than at Lighthouse Reef (25.37 species h–1 [SE 3.66]). The main drivers of targeted fish abundance were habitat and depth, with shallow (
Published: 2020

20. Threatened fish spawning area revealed by specific metabarcoding identification of eggs and larvae in the Beni River, upper Amazon

Author: Miranda-Chumacero, Guido, Mariac, Cédric, Duponchelle, Fabrice, Painter, Lilian, Wallace, Robert, Cochonneau, Gérard, Molina-Rodriguez, Jorge, Garcia-Davila, Carmen, Renno, Jean-François, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), University of Iowa [Iowa City], Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Wildlife Conservation Society (WCS), Universidad Mayor de San Andrés (UMSA), Laboratoire Mixte International – Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)
Subjects: Prochilodus, lcsh:QH540-549.5, [SDE.MCG]Environmental Sciences/Global Changes, Ichthyoplankton, Zungaro, lcsh:Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Arid extraction, Brachyplatystoma, Dams
Abstract: WOS:000608479300001; International audience; Identifying fish spawning areas is of great ecological and conservation importance as fishes are suffering increasing threat levels from anthropogenic activities. However, to date very few studies have done so in the Amazon basin. In the Beni River located in the upper Madeira basin, fishers reported that a particular ecotone near the town of Rurrenabaque was a fish reproduction area. To test the importance of this zone as a spawning site, we conducted an ichthyoplankton survey during the month when reproduction is most likely to occur. The specific identification of larvae and eggs was made with a metabarcoding analysis. With this approach 13 different fish species of high importance for regional and local fisheries were identified, including the long-distance migratory gilded catfish (Brachyplatystoma rousseauxii), considered as endangered in the upper Madeira. Combining the development time of morula-gastrula egg stages with the integrated current velocity of the river, we identified a spawning area that ranges between the last gravel beaches close to Altamarani community and the San Miguel del Bala community on top of Suse strait, the last foothill of the Andes. This spawning area further extends upstream in the Madidi and Pilon Lajas protected areas and Tacana and T’simane indigenous communities, when considering eggs in final embryo stage. This portion of the Beni River, at the Andean foothills, is heavily impacted by anthropogenic activities, ranging from unmanaged fisheries to contamination coming from the extraction of fluvial aggregates, upstream gold mining, deforestation associated with a sugar cane mill, an existing downstream dam, and projected upstream dam projects. Some urgent solutions for the conservation of this already impacted area are proposed. Confirming fish spawning zones, although difficult, is crucial to inform the definition of priority areas for conservation and management measures, in particular when these sites host endangered species.
Published: 2020

21. Research Priorities for Achieving Healthy Marine Ecosystems and Human Communities in a Changing Climate

Author: Whitney R. Friedman, Benjamin S. Halpern, Elizabeth McLeod, Michael W. Beck, Carlos M. Duarte, Carrie V. Kappel, Arielle Levine, Robert D. Sluka, Steven Adler, Casey C. O’Hara, Eleanor J. Sterling, Sebastian Tapia-Lewin, Iñigo J. Losada, Tim R. McClanahan, Linwood Pendleton, Margaret Spring, James P. Toomey, Kenneth R. Weiss, Hugh P. Possingham, Jensen R. Montambault, Universidad de Cantabria, University of California, The Nature Conservancy, King Abdullah University of Science and Technology (KAUST), San Diego State University (SDSU), University of California [Santa Barbara] (UCSB), American Museum of Natural History (AMNH), University of Cantabria, Wildlife Conservation Society (WCS), Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer (AMURE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Public Health Genomics Unit, University of Queensland [Brisbane], Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), University of California (UC), and University of California [Santa Barbara] (UC Santa Barbara)
Subjects: 0106 biological sciences, social equity, 010504 meteorology & atmospheric sciences, Ecological health, lcsh:QH1-199.5, [SDE.MCG]Environmental Sciences/Global Changes, media_common.quotation_subject, Ocean Engineering, Context (language use), Aquatic Science, lcsh:General. Including nature conservation, geographical distribution, Oceanography, human health, 01 natural sciences, [SHS]Humanities and Social Sciences, marine sustainability, Need to know, Multidisciplinary approach, Political science, 11. Sustainability, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, lcsh:Science, Environmental planning, 0105 earth and related environmental sciences, Water Science and Technology, media_common, Global and Planetary Change, priority research, Equity (economics), 010604 marine biology & hydrobiology, sustainable development goals, [SDE.ES]Environmental Sciences/Environmental and Society, climate change, 13. Climate action, [SDE]Environmental Sciences, Sustainability, lcsh:Q, Psychological resilience, Social equality
Abstract: International audience; The health of coastal human communities and marine ecosystems are at risk from a host of anthropogenic stressors, in particular, climate change. Because ecological health and human well-being are inextricably connected, effective and positive responses to current risks require multidisciplinary solutions. Yet, the complexity of coupled social–ecological systems has left many potential solutions unidentified or insufficiently explored. The urgent need to achieve positive social and ecological outcomes across local and global scales necessitates rapid and targeted multidisciplinary research to identify solutions that have the greatest chance of promoting benefits for both people and nature. To address these challenges, we conducted a forecasting exercise with a diverse, multidisciplinary team to identify priority research questions needed to promote sustainable and just marine social–ecological systems now and into the future, within the context of climate change and population growth. In contrast to the traditional reactive cycle of science and management, we aimed to generate questions that focus on what we need to know, before we need to know it. Participants were presented with the question, “If we were managing oceans in 2050 and looking back, what research, primary or synthetic, would wish we had invested in today?” We first identified major social and ecological events over the past 60 years that shaped current human relationships with coasts and oceans. We then used a modified Delphi approach to identify nine priority research areas and 46 questions focused on increasing sustainability and well-being in marine social–ecological systems. The research areas we identified include relationships between ecological and human health, access to resources, equity, governance, economics, resilience, and technology. Most questions require increased collaboration across traditionally distinct disciplines and sectors for successful study and implementation. By identifying these questions, we hope to facilitate the discourse, research, and policies needed to rapidly promote healthy marine ecosystems and the human communities that depend upon them. © Copyright © 2020 Friedman, Halpern, McLeod, Beck, Duarte, Kappel, Levine, Sluka, Adler, O’Hara, Sterling, Tapia-Lewin, Losada, McClanahan, Pendleton, Spring, Toomey, Weiss, Possingham and Montambault.
Published: 2020

22. 'Too Big To Ignore': A feasibility analysis of detecting fishing events in Gabonese small-scale fisheries

Author: Raul Vilela, Matthew J. Witt, Catherine M. McClellan, Floriane Cardiec, Richard J. Parnell, Brendan J. Godley, Sophie Bertrand, François Le Loc'h, Kristian Metcalfe, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Wildlife Conservation Society (WCS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Hatherly Laboratories [Exeter], University of Exeter, College of Life and Environmental Sciences [Exeter], Institut de Recherche pour le Développement (IRD), This work was supported by US Fish and Wildlife Service, AFR-1427/F14AP00555, https://www.fws.gov/.The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. BJG, KM, and MJW were supported by the Darwin Initiative (Projects 17-005/20-009/23-011/26-014) through funding from the Department for Environment, Food and Rural Affairs in the UK. SB was supported by the LMI TAPIOCA, program CAPES/COFECUB (88881.142689/2017-01) and EU H2020 TRIATLAS project under Grant Agreement 817578. FL was supported by Arc Emeraude Project (ANPN/AFD). We thank all the members of the fishing communities who participated in the study. We thank Direction Generale des Peches et de l'Aquaculture (DGPA) and Agence Nationale des Parcs Nationaux (ANPN) to have allowed and supported data collection., European Project: 817578,TRIATLAS(2019), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Computer science, Markov models, Social Sciences, Transportation, 01 natural sciences, context, Food Supply, Geographical Locations, vms, Psychology, Hidden Markov models, Multidisciplinary, Food security, Data Processing, Animal Behavior, Sampling (statistics), Eukaryota, Agriculture, Animal Tagging, Markov Chains, Physical sciences, Vertebrates, Global Positioning System, Medicine, Engineering and Technology, movement, Information Technology, management, Research Article, Computer and Information Sciences, Science, Fishing, Fisheries, Context (language use), Research and Analysis Methods, 010603 evolutionary biology, Humans, Animals, Resource management, 14. Life underwater, Gabon, Behavior, business.industry, 010604 marine biology & hydrobiology, Scale (chemistry), ACL, Organisms, Biology and Life Sciences, Probability theory, space, tracks, Boats, Fishery, Fish, example, People and Places, Africa, Geographic Information Systems, Animal Studies, Feasibility Studies, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Zoology, Mathematics
Abstract: WOS:000542969500001; International audience; In many developing countries, small-scale fisheries provide employment and important food security for local populations. To support resource management, the description of the spatiotemporal extent of fisheries is necessary, but often poorly understood due to the diffuse nature of effort, operated from numerous small wooden vessels. Here, in Gabon, Central Africa, we applied Hidden Markov Models to detect fishing patterns in seven different fisheries (with different gears) from GPS data. Models were compared to information collected by on-board observers (7 trips) and, at a larger scale, to a visual interpretation method (99 trips). Models utilizing different sampling resolutions of GPS acquisition were also tested. Model prediction accuracy was high with GPS data sampling rates up to three minutes apart. The minor loss of accuracy linked to model classification is largely compensated by the savings in time required for analysis, especially in a context of nations or organizations with limited resources. This method could be applied to larger datasets at a national or international scale to identify and more adequately manage fishing effort.
Published: 2019

23. Revisiting the Pneumocystis host specificity paradigm and transmission ecology in wild Southeast Asian rodents

Author: Magali Chabé, Johan Michaux, Alex Stuart, Fedelino F. Malbas, Alice Latinne, Hsuan-Wien Chen, Christine Demanche, Serge Morand, Chi Chien Kuo, Grant R. Singleton, Renee P. Lorica, Wildlife Conservation Society [Hanoi, Vietnam] (WCS), Wildlife Conservation Society (WCS), Université de Liège - Faculté des sciences appliquées (ULIEGE FSA), Université de Liège, National Chiayi University (NCYU), National Chiayi University, National Taiwan Normal University (NTNU), International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Greenwich, Research Institute for Tropical Medicine [Muntinlupa City, Philippines], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), 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, Kasetsart University (KU), Field work was supported by ANR 07 BDIV 012 CERoPath project (Community ecology of rodents and their pathogens in a changing environment in Southeast Asia), ANR 11 CPEL 002 BiodivHealthSEA project (Local impacts and perceptions of global changes: biodiversity, health, and zoonoses in Southeast Asia), ANR-17-CE35-0003-02 FutureHealthSEA (Predictive scenarios of health in Southeast Asia) and CORIGAP (Project 7F-08412.02) funded by the Swiss Agency for Development and Cooperation (SDC). Laboratory work was supported by a Marie Curie COFUND postdoctoral fellowship from the University of Liege to A.L., ANR-07-BDIV-0012,CEROPATH,Ecologie des communautés rongeurs - pathogènes en Asie du Sud-Est : effets des changements de biodiversité et implications pour l'écologie de la santé(2007), ANR-11-CEPL-0002,BiodivHealthSEA,Impacts et perceptions locales des changements globaux : santé, biodiversité et zoonoses en Asie du Sud-Est(2011), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), 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), LESUR, Hélène, Biodiversité - Ecologie des communautés rongeurs - pathogènes en Asie du Sud-Est : effets des changements de biodiversité et implications pour l'écologie de la santé - - CEROPATH2007 - ANR-07-BDIV-0012 - BDIV - VALID, Changements Environnementaux Planétaires et Sociétés - Impacts et perceptions locales des changements globaux : santé, biodiversité et zoonoses en Asie du Sud-Est - - BiodivHealthSEA2011 - ANR-11-CEPL-0002 - CEP&S - VALID, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: 0301 basic medicine, Microbiology (medical), Nuclear gene, Rodent, Philippines, [SDV]Life Sciences [q-bio], 030106 microbiology, Taiwan, Animals, Wild, Southeast asian, Rodents, Microbiology, Rodent Diseases, 03 medical and health sciences, biology.animal, Genetics, Animals, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Habitat fragmentation, biology, Pneumocystis, Ecology, Host (biology), Bandicota, 15. Life on land, Thailand, biology.organism_classification, Southeast Asia, Pneumocystis Infections, [SDV] Life Sciences [q-bio], Muridae, 030104 developmental biology, Infectious Diseases, Laos, Host specificity, Genetic structure, Sundamys, Murinae, Cambodia
Abstract: International audience; Pneumocystis fungi are opportunistic parasites of mammalian lungs whose evolution, ecology and host specificity in natural host populations remain poorly understood and controversial. Using an extensive collection of 731 lung samples from 27 rodent species sampled in five Southeast Asian countries, and nested PCR amplification of mitochondrial and nuclear genes, we investigated the host specificity and genetic structure of Pneumocystis lineages infecting wild rodents. We also identified the rodent species playing a central role in the transmission of these parasites using network analysis and centrality measurement and we characterized the environmental conditions allowing Pneumocystis infection in Southeast Asia using generalized linear mixed models. Building upon an unprecedented Pneumocystis sampling from numerous rodent species belonging to closely related genera, our findings provide compelling evidence that the host specificity of Pneumocystis lineages infecting rodents is not restricted to a single host species or genus as often presented in the literature but it encompasses much higher taxonomic levels and more distantly related rodent host species. The phylogenetic species status at both mitochondrial and nuclear genetic markers of at least three new Pneumocystis lineages, highly divergent from Pneumocystis species currently described, is also suggested by our data. Our models show that the probability of Pneumocystis infection in rodent hosts is positively correlated to environmental variables reflecting habitat fragmentation and landscape patchiness. Synanthropic and habitat-generalist rodents belonging to the Rattus, Sundamys and Bandicota genera played a role of bridge host species for Pneumocystis spreading in these heterogeneous habitats, where they can reach high population densities. These are critical findings improving our understanding of the ecology of these enigmatic parasites and the role played by cospeciation and host switches in their evolution. Our results also confirmed the role of land-use change and habitat fragmentation in parasite amplification and spillover in rodents.
Published: 2021

24. Carbon stocks in central African forests enhanced by elephant disturbance

Author: Marcos Longo, François Bretagnolle, Giuseppe Scarascia-Mugnozza, Stephen Blake, Christopher E. Doughty, Fabio Berzaghi, Philippe Ciais, Simone Aparecida Vieira, M. A. Scaranello, Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali, University of Tuscia, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Embrapa Agricultural Informatics, Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), ICOS-ATC (ICOS-ATC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Department of Biology, Saint Louis University (SLU), Wildlife Conservation Society (WCS), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Núcleo de Estudos e Pesquisas Ambientais, Universidade Estadual de Campinas (UNICAMP), School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University [Flagstaff], the Max-Planck-Society, the German Ministry of Education and Research and le Conseil Regional de Bourgogne., Università degli studi della Tuscia [Viterbo], Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), and Universidade Estadual de Campinas = University of Campinas (UNICAMP)
Subjects: Herbivore, Forest inventory, 010504 meteorology & atmospheric sciences, Ecology, media_common.quotation_subject, Primary production, Rainforest, 15. Life on land, 010502 geochemistry & geophysics, 01 natural sciences, Competition (biology), Geography, Productivity (ecology), Disturbance (ecology), General Earth and Planetary Sciences, Ecosystem, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 0105 earth and related environmental sciences, media_common
Abstract: Large herbivores, such as elephants, can have important effects on ecosystems and biogeochemical cycles. Yet, the influence of elephants on the structure, productivity and carbon stocks in Africa’s rainforests remain largely unknown. Here, we quantify those effects by incorporating elephant disturbance in the Ecosystem Demography model, and verify the modelled effects by comparing them with forest inventory data from two lowland primary forests in Africa. We find that the reduction of forest stem density due to the presence of elephants leads to changes in the competition for light, water and space among trees. These changes favour the emergence of fewer and larger trees with higher wood density. Such a shift in African’s rainforest structure and species composition increases the long-term equilibrium of aboveground biomass. The shift also reduces the forest net primary productivity, given the trade-off between productivity and wood density. At a typical density of 0.5 to 1 animals per km2, elephant disturbances increase aboveground biomass by 26–60 t ha−1. Conversely, the extinction of forest elephants would result in a 7% decrease in the aboveground biomass in central African rainforests. These modelled results are confirmed by field inventory data. We speculate that the presence of forest elephants may have shaped the structure of Africa’s rainforests, which probably plays an important role in differentiating them from Amazonian rainforests. Elephant disturbance favours the emergence of larger trees with higher wood density, and thereby increases the aboveground biomass in central African forests by up to 60 t ha–1, according to simulations with the Ecosystem Demography model.
Published: 2019

25. Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Author: Paul R. Wade, Cory J. D. Matthews, Steven H. Ferguson, Ana Amaral, Nicholas J. Davison, Michael D. Martin, Wayne Hoggard, Marie Louis, Sara Tavares, Andrew Brownlow, Andrew D. Foote, Jay Barlow, Phillip A. Morin, Ruth Esteban, Luciano Dalla Rosa, Paul Tixier, Willy Dabin, Tim Gerrodette, M. Thomas P. Gilbert, Robin W. Baird, Jochen B. W. Wolf, Laurent Excoffier, Tim Collins, John A. Totterdell, Lisa T. Ballance, C. S. Baker, Kelly M. Robertson, Renaud de Stephanis, M. Bradley Hanson, Rochelle Constantine, John W. Durban, Mikkel-Holger S. Sinding, George Pacheco, Christophe Guinet, Filipa I. P. Samarra, Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, NTNU University Museum [Trondheim], Norwegian University of Science and Technology [Trondheim] (NTNU), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Scottish Oceans Institute, University of St Andrews [Scotland], Marine Mammal and Turtle Division (MMTD), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), American Museum of Natural History (AMNH), Cascadia Research [Washington, USA], Department of Fisheries and Wildlife, Marine Mammal Institute [Oregon, USA], Oregon State University (OSU), Wildlife Conservation Society (WCS), School of Biological Sciences [Auckland, New Zealand], University of Auckland [Auckland], 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), Laboratório de Ecologia e Conservação da Megafauna Marinha [Rio Grande, Brazil], Universidade Federal do Rio Grande do Sul (UFRGS), Animal Health and Veterinary Laboratories Agency, CIRCE (Conservation, Information and Research on Cetaceans), Fisheries & Oceans Canada [Canada], Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service [Mississippi, USA], Southeast Fisheries Science Center [USA], Repositório da Universidade de Lisboa, Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), 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), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Gene Flow, Population, Antarctic Regions, Genomics, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, 03 medical and health sciences, Genetic drift, Phylogenetics, biology.animal, Genetics, Vicariance, genomics, Animals, 14. Life underwater, secondary contact, education, Ecology, Evolution, Behavior and Systematics, Alleles, Phylogeny, Cell Nucleus, education.field_of_study, Principal Component Analysis, Genome, biology, Base Sequence, Geography, Models, Genetic, Whale, drift, Genetic Drift, Genetic Variation, population structure, Markov Chains, 030104 developmental biology, Sympatric speciation, Evolutionary biology, [SDE]Environmental Sciences, Biological dispersal, admixture, Whale, Killer
Abstract: Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
Published: 2019

26. Rethinking spatial costs and benefits of fisheries in marine conservation

Author: Thomas F. Allnutt, Marissa L. Baskett, Merrill Baker-Médard, Claire Kremen, Erwinn Lagabrielle, Reg Watson, Middlebury College, Wildlife Conservation Society (WCS), University of California [Davis] (UC Davis), University of California, Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), and University of British Columbia (UBC)
Subjects: 0106 biological sciences, Marine conservation, Resource (biology), 010504 meteorology & atmospheric sciences, Fishing, Fisheries, Developing country, Management, Monitoring, Policy and Law, Aquatic Science, Oceanography, 01 natural sciences, Marine reserves, Marxan, Madagascar, 14. Life underwater, Life Below Water, Spatial planning, 0105 earth and related environmental sciences, Cost–benefit analysis, 010604 marine biology & hydrobiology, Marine reserve, [SDE.ES]Environmental Sciences/Environmental and Society, Fishery, Studies in Human Society, Earth Sciences, Business, Environmental Sciences
Abstract: International audience; Fishing catch is often used as a cost in marine conservation planning to avoid areas of high fishing activity when identifying potential marine reserve locations. However, the theory of marine reserves indicates that reserves are more likely to benefit fisheries in areas of heavy fishing activity that would otherwise be overfished. Whether or not fishing catch is calculated as a cost depends on the balance of conservation and fisheries goals for a reserve, and thus is critical for policymakers to consider when designing marine reserve networks. This research shows the utility of running an inverted cost model of fishery catches during marine reserve spatial prioritization as a first step in a marine planning process oriented towards stabilizing local fisheries. This technique serves as a heuristic tool that may help conservation planners explore regions that would otherwise be overlooked if fisheries data were absent or integrated purely as a cost in the planning process. Drawing on data from Madagascar to illustrate our approach, this research demonstrates that the regions most frequently selected using the inverted cost model not only meet conservation targets, but are also those most accessible to community-based resource managers, the dominant management paradigm in Madagascar as well as in many developing countries.
Published: 2019

27. Extreme temperature event and mass mortality of insectivorous bats

Author: Veasna Duong, Neil M. Furey, Vibol Hul, Paul F. Horwood, Mathieu Pruvot, Julien Cappelle, Philippe Dussart, Huy Sreang Heng, Wildlife Conservation Society [Fort Collins, CO] (WCS), Wildlife Conservation Society (WCS), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Fauna and Flora International [Cambodia], Fauna and Flora International [Cambridge, UK], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Australian Institute of Tropical Health and Medicine (AITHM), James Cook University (JCU), and This study was funded by the European Union under the INNOVATE program, through the two projects LACANET (DCI-ASIE/2013/315-151) and ComAcross (DCI-ASIE/2013/315-047).
Subjects: 0106 biological sciences, P40 - Météorologie et climatologie, Short Communication, Event (relativity), Outbreak investigation, Wildlife, Management, Monitoring, Policy and Law, Mortalité, Bat paramyxovirus, L73 - Maladies des animaux, 010603 evolutionary biology, 01 natural sciences, Santé publique, Heat stress, 010605 ornithology, Ecosystem services, Extreme weather, Die-off, Chiroptera, chaleur, L50 - Physiologie et biochimie animales, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, biology, Ecology, Taphozous, Outbreak, Insectivore, 15. Life on land, biology.organism_classification, Mass mortality, événements météorologiques extrêmes, 13. Climate action, Enquête pathologique, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, L20 - Écologie animale, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Extreme weather event
Abstract: International audience; A mass mortality event involving Chaerephon plicatus and Taphozous theobaldi bats occurred during a heat wave in April 2016 in Cambodia. This was investigated to clarify the causes of the die-off and assess the risk to public health. Field evidences, clinical signs, and gross pathology findings were consistent with a heat stress hypothesis. However, the detection of a novel bat paramyxovirus raises questions about its role as a contributing factor or a coincidental finding. Systematic documentation of bat die-offs related to extreme weather events is necessary to improve understanding of the effect of changing weather patterns on bat populations and the ecosystem services they provide.
Published: 2019

28. Toward a quantification of risks at the nexus of conservation and health: The case of bushmeat markets in Lao PDR

Author: Pruvot, M, Khammavong, K, Milavong, P, Philavong, C, Reinharz, D, Mayxay, M, Rattanavong, S, Horwood, P, Dussart, P, Douangngeun, B, Theppangna, W, Fine, A, Olson, S, Robinson, M, Newton, P, Wildlife Conservation Society (WCS), Wildlife Conservation Society [Vientiane, Laos] (WCS), Ministry of Health [Laos], Institut de la Francophonie pour la Médecine Tropicale (IFMT), Université Laval [Québec] (ULaval), Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, University of Oxford [Oxford], Australian Institute of Tropical Health and Medicine (AITHM), James Cook University (JCU), Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Ministry of Agriculture and Forestry of Laos, and This study was funded by the European Union under the INNOVATE program and the LACANET project (DCI-ASIE/2013/315-151).
Subjects: MESH: Meat, MESH: Socioeconomic Factors, Conservation of Natural Resources, Meat, Risk analysis, Commerce, Food security, Bushmeat consumption, Article, MESH: Commerce, MESH: Laos, Socioeconomic Factors, Laos, Wildlife conservation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Conservation of Natural Resources, Animals, MESH: Animals, Public Health, One Health, MESH: Public Health, Zoonotic diseases
Abstract: Trade of bushmeat and other wildlife for human consumption presents a unique set of challenges to policy-makers who are confronted with multiple trade-offs between conservation, food security, food safety, culture and tradition. In the face of these complex issues, risk assessments supported by quantitative information would facilitate evidence-based decision making. We propose a conceptual model for disease transmission risk analysis, inclusive of these multiple other facets. To quantify several processes included in this conceptual model we conducted questionnaire surveys with wildlife consumers and vendors in semi-urban centers in Lao People's Democratic Republic (Lao PDR, Laos) and direct observations of consumer behaviors. Direct observation of market stalls indicated an estimated average of 10 kg bushmeat biomass per stall per hour. The socio-demographic data suggested that consumption of bushmeat in urban areas was not for subsistence but rather driven by dietary preference and tradition. Consumer behavioral observations indicated that each animal receives an average of 7 contacts per hour. We provide other key parameters to estimate the risk of disease transmission from bushmeat consumption and illustrate their use in assessing the total public health and socio-economic impact of bushmeat consumption. Pursuing integrative approaches to the study of bushmeat consumption is essential to develop effective and balanced policies that support conservation, public health, and rural development goals., Graphical abstract Unlabelled Image, Highlights • Bushmeat trade in Lao PDR is considerable and likely exceeds sustainable levels. • Bushmeat consumption in urban centers is not a necessity but a preference. • High contact rates between consumers and bushmeat add to the transmission risk. • Integrated assessment of conservation, food security and food safety risks needed
Published: 2018

29. Taxonomy of the order Mononegavirales: update 2018

Author: Kang Seuk Choi, Nikos Vasilakis, Claudio Verdugo, Janusz T. Paweska, Thomas Briese, Víctor Manuel Neira Ramírez, Andrew J. Bennett, Masayuki Horie, Charles H. Calisher, Robert Kityo, Anthony R. Fooks, Martin Schwemmle, Sunil K. Mor, Nidia G. Aréchiga Ceballos, Timothy H. Hyndman, Ayato Takada, Yíngyún Caì, Robert A. Lamb, Alexander Bukreyev, Paul A. Rota, Tony L. Goldberg, Lin-Fa Wang, Benhur Lee, Kartik Chandran, Hideki Ebihara, Michael R. Wiley, Ralf G. Dietzgen, Anna E. Whitfield, Mark D. Stenglein, Piet Maes, Andrew J. Easton, Jean L. Patterson, Valerian V. Dolja, Olga Dolnik, Eugene V. Koonin, James F. X. Wellehan, Ralf Dürrwald, Peter L. Collins, Qisheng Song, Susan Payne, Jonathan S. Towner, Sina Bavari, Sonia Vázquez-Morón, Pierre Formenty, Sophie J. Smither, Keizō Tomonaga, Leslie L. Domier, Dàohóng Jiāng, Gael Kurath, Robert B. Tesh, Sergey V. Netesov, Elodie Ghedin, Andrea Maisner, Denise A. Marston, Cristine Campos Lawson, Elke Mühlberger, Christopher F. Basler, Conrad M. Freuling, Yǒng Zhèn Zhāng, Dennis Rubbenstroth, Peter J. Walker, Gōngyín Yè, David Wang, Ron A. M. Fouchier, Gustavo Palacios, Gary P. Kobinger, Yuri I. Wolf, Timothy Song, Hideki Kondō, Mart Krupovic, Karla Prieto, David M. Stone, Luciano M. Thomazelli, Colin A. Chapman, Ashley C. Banyard, Jens H. Kuhn, Stuart G. Siddell, Noël Tordo, John M. Dye, Terry Fei Fan Ng, Charles Y. Chiu, Kim R. Blasdell, Bertus K. Rima, Victoria Wahl, Eric M. Leroy, Gaya K. Amarasinghe, Juan Emilio Echevarría, Norbert Nowotny, Roger Hewson, Thomas Müller, Viktor E. Volchkov, Washington University School of Medicine (WUSM), University of Washington [Seattle], Laboratorio de Rabia, Instituto de Diagnóstico y Referencias Epidemiológicos, Animal and Plant Health Agency [Weybridge] (APHA), Georgia State University, University System of Georgia (USG), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), School of Veterinary Medicine, Department of Pathobiological Sciences, University of Wisconsin-Madison-Influenza Research Institute, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, Columbia University [New York], The University of Texas Medical Branch (UTMB), Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Department of Anthropology [Montréal], McGill University = Université McGill [Montréal, Canada], Wildlife Conservation Society (WCS), Primate Research Institute, Kyoto University, University of California [San Francisco] (UC San Francisco), University of California (UC), Avian Disease Research Division, Animal and Plant Quarantine Agency, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Department of Botany and Plant Pathology, Oregon State University (OSU), Center for Genome Research and Biocomputing, Philipps Universität Marburg = Philipps University of Marburg, University of Chicago, IDT Biologika, School of Life Sciences, University of Warwick [Coventry], Department of Biochemistry and Molecular Biology, University of Rochester [USA], Institute of Health Carlos III, Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Institute of Molecular Virology and Cell Biology, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Public Health England [Salisbury] (PHE), Kagoshima University, Murdoch University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University [Wuhan] (HZAU), Makerere University [Kampala, Ouganda] (MAK), Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Centre International de Recherches Médicales de Franceville (CIRMF), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Neuromuscular Diagnostic Laboratory, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Universidad de Chile = University of Chile [Santiago] (UCHILE), Novosibirsk State University (NSU), Department of Medicine [San Francisco], University of California (UC)-University of California (UC), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], University of Bristol [Bristol], Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), University of Missouri [Columbia] (Mizzou), University of Missouri System, Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Universidade de São Paulo - USP (BRAZIL), Institute for Virus Research, Stratégies antivirales, Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Facultad de Ciencias Veterinarias [Buenos Aires], Universidad de Buenos Aires [Buenos Aires] (UBA), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), 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)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), 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), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], University of Florida [Gainesville] (UF), University of Nebraska Medical Center, University of Nebraska System, Kansas State University, State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), State Key Laboratory for Infectious Disease prevention and Control, Beijing Institute of Technology (BIT), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Albert Einstein College of Medicine, McGill University, Kyoto University [Kyoto], University of California [San Francisco] (UCSF), University of California, Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Philipps University of Marburg, Warwick University, Public Health England [Porton Down, Salisbury], Huazhong Agricultural University, Makerere University (MAK), Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Institut Pasteur [Paris], Centre International de Recherches Médicales de Franceville, University of Minnesota [Twin Cities], Universidad de Chile, University of California-University of California, Texas Biomedical Research Institute [San Antonio, Texas], National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], University of Bristol (School of Cellular and Molecular Medicine), University of Missouri [Columbia], Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Duke NUS Medical School, University of Florida [Gainesville], and Virology
Subjects: 0301 basic medicine, Order Mononegavirales, 040301 veterinary sciences, Mononegavirales Infections, 04 agricultural and veterinary sciences, General Medicine, Biology, Data science, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Article, 0403 veterinary science, 03 medical and health sciences, 030104 developmental biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, Animals, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology), Mononegavirales, Phylogeny
Abstract: International audience; In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
Published: 2018

30. Quantifying species recovery and conservation success to develop an IUCN Green List of Species

Author: Erik Meijaard, Jon Paul Rodríguez, David P. Mallon, Michael R. Hoffmann, Thomas M. Brooks, E. J. Milner-Gulland, H. Resit Akçakaya, Richard P. Young, Craig Hilton-Taylor, Simon Hedges, David A. Keith, Barney Long, Molly K. Grace, P. J. Stephenson, Simon N. Stuart, Ana S. L. Rodrigues, Elizabeth L. Bennett, Anna Heath, Department of Ecology and Evolution, Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), IUCN Species Survival Commission (IUCN SSC), Wildlife Conservation Society (WCS), International Union for Conservation of Nature (IUCN), World Agroforestry Centre, University of the Philippines, Institute for Marine & Antarctic Studies, University of Tasmania (UTAS), Department of Zoology [Oxford], University of Oxford [Oxford], Synchronicity Earth, Red List Unit, Conservation and Policy, Zoological Society of London - ZSL (UNITED KINGDOM), Centre for Ecosystem Sciences, University of New South Wales [Sydney] (UNSW), NSW Office of Environment and Heritage, Global Wildlife Conservation (GWC), Division of Biology and Conservation Ecology, Manchester Metropolitan University (MMU), Durrell Institute of Conservation and Ecology, University of Kent [Canterbury], 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), Instituto Venezolano de Investigaciones Cientificas (IVIC), Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Durrell Wildlife Conservation Trust, Institute of Trinity Jersey, University of the Philippines (UP System), University of Tasmania [Hobart, Australia] (UTAS), University of Oxford, 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), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), 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, Counterfactual thinking, Conservation of Natural Resources, threatened species, Range (biology), Computer science, conservation impact, conservation optimism, recovered species, red lists, Saiga tatarica, especies recuperadas, Endangered species, Biodiversity, especies amenazadas, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, 01 natural sciences, Animals, IUCN Red List, impacto de la conservación, 14. Life underwater, Taxonomic rank, listas rojas, optimismo de conservación, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Wildlife conservation, Ecology, business.industry, Data Collection, 010604 marine biology & hydrobiology, Endangered Species, Environmental resource management, 15. Life on land, Vertebrates, Threatened species, business
Abstract: Stopping declines in biodiversity is critically important, but it is only a first step toward achieving more ambitious conservation goals. The absence of an objective and practical definition of species recovery that is applicable across taxonomic groups leads to inconsistent targets in recovery plans and frustrates reporting and maximization of conservation impact. We devised a framework for comprehensively assessing species recovery and conservation success. We propose a definition of a fully recovered species that emphasizes viability, ecological functionality, and representation; and use counterfactual approaches to quantify degree of recovery. This allowed us to calculate a set of 4 conservation metrics that demonstrate impacts of conservation efforts to date (conservation legacy); identify dependence of a species on conservation actions (conservation dependence); quantify expected gains resulting from conservation action in the medium term (conservation gain); and specify requirements to achieve maximum plausible recovery over the long term (recovery potential). These metrics can incentivize the establishment and achievement of ambitious conservation targets. We illustrate their use by applying the framework to a vertebrate, an invertebrate, and a woody and an herbaceous plant. Our approach is a preliminary framework for an International Union for Conservation of Nature (IUCN) Green List of Species, which was mandated by a resolution of IUCN members in 2012. Although there are several challenges in applying our proposed framework to a wide range of species, we believe its further development, implementation, and integration with the IUCN Red List of Threatened Species will help catalyze a positive and ambitious vision for conservation that will drive sustained conservation action. ISSN:0888-8892 ISSN:1523-1739
Published: 2018

31. The status of marine biodiversity in the Eastern Central Atlantic (West and Central Africa)

Author: Polidoro, B. A., Ralph, G. M., Strongin, K., Harvey, M., Carpenter, K. E., Arnold, R., Buchanan, J. R., Camara, K. M. A., Collette, B. B., Comeros-Raynal, M. T., De Bruyne, G., Gon, O., Harold, A. S., Harwell, H., Hulley, P. A., Iwamoto, T., Knudsen, S. W., Lewembe, J. D., Linardich, C., Lindeman, K. C., Monteiro, V., Munroe, T., Nunoo, F. K. E., Pollock, C. M., Poss, S., Russell, B., Sayer, C., Sidibe, A., Smith-Vaniz, W., Stump, E., Sylla, M., Tito de Morais, Luis, Vie, J. C., Williams, A., International Union for Conservation of Nature (IUCN), Old Dominion University [Norfolk] (ODU), Arizona State University [Tempe] (ASU), Institut Mauritanien de Recherches Océanographiques et des Pêches (IMROP), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Wildlife Conservation Society (WCS), South African Cultural History Museum of Cape Town, Grice Marine Laboratory [Charleston], College of Charleston, Christopher Newport University, California Academy of Sciences, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Direction Générale des Pêches et de l'Aquaculture (DGPA), Florida Institute of Technology [Melbourne], Instituto Nacional de Desenvolvimento das Pescas (INDP), University of Ghana, Florida Museum of Natural History [Gainesville], University of Florida [Gainesville] (UF), University of British Columbia (UBC), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Nigerian Institute for Oceanography & Marine Research, Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: Mammals, fish, Red List, ACL, coastal, invertebrates, urban development, Invertebrates, ocean, red list, pollution, mammals, Fishing, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, fishing, conservation evaluation
Abstract: International audience; The status of marine biodiversity in the Eastern Central Atlantic (ECA), especially of coastal and pelagic fishes, is of concern owing to a number of threats including overharvesting, habitat loss, pollution, and climate change combined with inadequate policy responses, legislation, and enforcement. This study provides the first comprehensive documentation of the presence, status, and level of extinction risk, based on IUCN Red List assessment methodology, for more than 1800 marine species, including all taxonomically described marine vertebrates (marine mammals, sea turtles, seabirds, fishes); complete clades of selected marine invertebrates (sea cucumbers, cone snails, cephalopods, lobsters, reef-building corals); and marine plants (mangroves, seagrasses). Approximately 8% of all marine species assessed in the ECA are in threatened categories, while 4% are listed as Near Threatened, 73% are Least Concern, and 15% are Data Deficient. Fisheries and overharvesting are the biggest threats to living marine resources in the ECA, with 87% of threatened species across all taxonomic groups affected by both large- and small-scale targeted fisheries, excessive capture as by-catch, or unsustainable harvest. The results of this study will transform the current state of knowledge and increase capacity for regional stakeholders to identify and enact marine conservation and research priorities, as a number of species are identified as having high conservation and/or research priorities in the region. Through the process of marine species data collection and risk assessments conducted over the past 5 years, several key conservation actions and research needs are identified to enable more effective conservation of marine biodiversity in the ECA, including increased governance, multilateral collaboration, taxonomic training, and improved reporting of fisheries catch and effort.
Published: 2017

32. Satellite telemetry of humpback whales off Madagascar reveals insights on breeding behavior and long-range movements within the southwest Indian Ocean

Author: Jean-Benoît Charrassin, Howard C. Rosenbaum, Salvatore Cerchio, Jean-Luc Jung, Francois Xavier Mayer, Norbert Andrianarivelo, Olivier Adam, Ygor Geyer, Laurène Trudelle, Alexandre N. Zerbini, Woods Hole Oceanographic Institution (WHOI), Processus de couplage à Petite Echelle, Ecosystèmes et Prédateurs Supérieurs (PEPS), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), National Marine Mammal Laboratory (MML), Alaska Fisheries Science Center (AFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Instituto Aqualie, Cetamada [Madagascar], Institut Halieutique et des Sciences Marines, Université de Toliara, Laboratoire de Biologie et génétique des mammifères marins dans leur environnement (BioGEMME), Université de Brest (UBO), Institut Jean le Rond d'Alembert (DALEMBERT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Wildlife Conservation Society (WCS), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636))
Subjects: 0106 biological sciences, Ecology, Satellite telemetry, Range (biology), [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], 010604 marine biology & hydrobiology, Population structure, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Fishery, Indian ocean, Geography, Oceanography, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2016

33. Influence of environmental parameters on movements and habitat utilization of humpback whales ( Megaptera novaeangliae ) in the Madagascar breeding ground

Author: Stéphane Pous, Howard C. Rosenbaum, Jean-Baptiste Sallée, Ygor Geyer, Maxime R. Hervé, Olivier Adam, Jean-Luc Jung, Laurène Trudelle, Jean-Benoît Charrassin, Alexandre N. Zerbini, François-Xavier Mayer, Salvatore Cerchio, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Woods Hole Oceanographic Institution (WHOI), New England Aquarium, NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Cascadia Research Collective, Instituto Aqualie, Cetamada [Madagascar], Laboratoire de Biologie et génétique des mammifères marins dans leur environnement (BioGEMME), Université de Brest (UBO), Institute of Plant Sciences [Berne], Universität Bern [Bern] (UNIBE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Department of Oceanography [Cape Town], University of Cape Town, Processus de couplage à Petite Echelle, Ecosystèmes et Prédateurs Supérieurs (PEPS), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Wildlife Conservation Society (WCS), Institut Jean le Rond d'Alembert (DALEMBERT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Ocean Giants Program, Wildlife Conservation Society, Total Foundation to NeuroPSI, BIOTOPE, Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Université de Berne, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut Jean Le Rond d'Alembert (DALEMBERT), 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)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, habitat, environmental parameters, 580 Plants (Botany), humpback whales, 010603 evolutionary biology, 01 natural sciences, Humpback whale, satellite telemetry, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Madagascar, 14. Life underwater, lcsh:Science, Behavioural state, Shore, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, geography, Multidisciplinary, geography.geographical_feature_category, biology, 010604 marine biology & hydrobiology, Ocean current, Megaptera Novaeangliae, habitat use, effet de l'environnement, biology.organism_classification, movement patterns, Current (stream), Fishery, Habitat, Human pressure, Philopatry, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Assessing the movement patterns and key habitat features of breeding humpback whales is a prerequisite for the conservation management of this philopatric species. To investigate the interactions between humpback whale movements and environmental conditions off Madagascar, we deployed 25 satellite tags in the northeast and southwest coast of Madagascar. For each recorded position, we collated estimates of environmental variables and computed two behavioural metrics: behavioural state of ‘transiting’ (consistent/directional) versus ‘localized’ (variable/non-directional), and active swimming speed (i.e. speed relative to the current). On coastal habitats (i.e. bathymetry aconcentrations. Active swimming speed accounts for a large proportion of observed movement speed; however, breeding humpback whales probably exploit prevailing ocean currents to maximize displacement. This study provides evidence that coastal areas, generally subject to strong human pressure, remain the core habitat of humpback whales off Madagascar. Our results expand the knowledge of humpback whale habitat use in oceanic habitat and response to variability of environmental factors such as oceanic current and chlorophyll level.
Published: 2016

34. Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia

Author: Vibol Hul, Hull Davun, Watthana Theppangna, Kongsy Khammavong, Amanda E. Fine, Roger Frutos, Philippe Buchy, Aneta Afelt, Keo Omaliss, Alexandre Hassanin, Veasna Duong, Audrey Lacroix, Sinpakone Singhalath, Damien O. Joly, Zoe Greatorex, Lucy Keatts, Sorn San, Philippe Dussart, Soubanh Silithammavong, Sokha Chea, Tracey Goldstein, Sarah H. Olson, Unité de Virologie / Virology Unit [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ministry of Agriculture, Forestry and Fisheries [Cambodia], Wildlife Conservation Society [Phnom Penh, Cambodia], Wildlife Conservation Society (WCS), 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), Ministry of Agriculture and Forestry of Laos, Wildlife Conservation Society [Vientiane, Laos] (WCS), Metabiota Inc. [Vientiane, Laos], Metabiota Inc. [San Francisco], Wildlife Conservation Society [Hanoi, Vietnam] (WCS), University of California [Davis] (UC Davis), University of California (UC), Metabiota Inc. [Nanaimo, British Columbia, Canada], University of Warsaw (UW), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), GlaxoSmithKline Vaccines [Singapore], GlaxoSmithKline [Headquarters, London, UK] (GSK), This study was made possible by the generous support of the American people through the United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00)., Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and University of California
Subjects: 0301 basic medicine, Pipistrellus coromandra, Phylogénie, Identification, MESH: Sequence Analysis, DNA, Genes, Viral, Coronaviruses, viruses, MESH: Base Sequence, medicine.disease_cause, L73 - Maladies des animaux, Coronavirinae, Genetic diversity, Génétique des populations, Chiroptera, Bats, MESH: Coronavirus, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, Coronavirus, MESH: Genes, Viral, biology, Megaerops niphanae, virus diseases, MESH: Chiroptera, 3. Good health, Phylogeography, Infectious Diseases, Vecteur de maladie, Laos, MESH: Phylogeography, MESH: RNA-Dependent RNA Polymerase, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Biodiversité, Cambodia, Microbiology (medical), zoonose, Myotis horsfieldii, 030106 microbiology, Microbiology, Article, Evolution, Molecular, 03 medical and health sciences, Macroglossus, Viral Proteins, Variation génétique, Maladie de l'homme, Lao PDR, Genetics, medicine, Animals, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Disease Reservoirs, MESH: Disease Reservoirs, Base Sequence, MESH: Cambodia, Outbreak, Genetic Variation, Sequence Analysis, DNA, biology.organism_classification, RNA-Dependent RNA Polymerase, Virology, MESH: Viral Proteins, 030104 developmental biology, MESH: Laos, Enquête pathologique
Abstract: South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n = 55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii, Graphical abstract Image 1, Highlights • Coronaviruses detected in bats from Lao PDR and Cambodia. • High diversity of αCoVs and βCoVs circulating in bats in Cambodia and Lao PDR. • One strain of βCoV, a new member of the MERS-CoV sister-clade, detected from Pipistrellus coromandra. • A αCoV strain genetically related to PEDV-CoV, detected from Myotis horsfieldii. • CoVs detected for the first time in Megaerops niphanae, Myotis horsfieldii and Macroglossus sp.
Published: 2016

35. Diversity of bat astroviruses in Lao PDR and Cambodia

Author: Philippe Dussart, Vibol Hul, Soubanh Silithammavong, Watthana Theppangna, Veasna Duong, Philippe Buchy, Kongsy Khammavong, Aneta Afelt, Roger Frutos, Zoe Greatorex, Sinpakone Singhalath, Sorn San, Keo Omaliss, Alexandre Hassanin, Audrey Lacroix, Lucy Keatts, Sokha Chea, Tracey Goldstein, Holl Davun, Damien O. Joly, Amanda E. Fine, Sarah H. Olson, Unité de Virologie / Virology Unit [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ministry of Agriculture, Forestry and Fisheries [Cambodia], Wildlife Conservation Society [Phnom Penh, Cambodia], Wildlife Conservation Society (WCS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Ministry of Agriculture and Forestry of Laos, Wildlife Conservation Society [Vientiane, Laos] (WCS), Metabiota Inc. [Vientiane, Laos], Metabiota Inc. [San Francisco], University of Warsaw (UW), University of California [Davis] (UC Davis), University of California, Metabiota Inc. [Nanaimo, British Columbia, Canada], Réseau International des Instituts Pasteur (RIIP), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), GlaxoSmithKline Vaccines [Singapore], GlaxoSmithKline [Headquarters, London, UK] (GSK), This study was made possible by the generous support of the American people through the United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00)., 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), and University of California (UC)
Subjects: 0301 basic medicine, Phylogénie, Range (biology), viruses, L73 - Maladies des animaux, Genetic diversity, MESH: Mouth, Hôte, Feces, fluids and secretions, Génétique des populations, MESH: Rectum, MESH: Astroviridae Infections, Astroviridae Infections, Chiroptera, Bats, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, Lung, Phylogeny, Yinpterochiroptera, biology, Phylogenetic tree, Astroviruses, 000 - Autres thèmes, virus diseases, MESH: Chiroptera, MESH: Feces, Infectious Diseases, Yangochiroptera, Laos, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Biodiversité, Cambodia, MESH: Astroviridae, Microbiology (medical), 030106 microbiology, Zoology, Microbiology, Article, Astrovirus, Virus des animaux, 03 medical and health sciences, Variation génétique, Lao PDR, Phylogenetics, Genetics, Animals, MESH: Lung, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Mouth, MESH: Cambodia, Rectum, Genetic Variation, biology.organism_classification, Virology, 030104 developmental biology, MESH: Laos, Enquête pathologique, Astroviridae, Mammifère, Rousettus
Abstract: Astroviruses are known to infect humans and a wide range of animal species, and can cause gastroenteritis in their hosts. Recent studies have reported astroviruses in bats in Europe and in several locations in China. We sampled 1876 bats from 17 genera at 45 sites from 14 and 13 provinces in Cambodia and Lao PDR respectively, and tested them for astroviruses. Our study revealed a high diversity of astroviruses among various Yangochiroptera and Yinpterochiroptera bats. Evidence for varying degrees of host restriction for astroviruses in bats was found. Furthermore, additional Pteropodid hosts were detected. The astroviruses formed distinct phylogenetic clusters within the genus Mamastrovirus, most closely related to other known bat astroviruses. The astrovirus sequences were found to be highly saturated indicating that phylogenetic relationships should be interpreted carefully. An astrovirus clustering in a group with other viruses from diverse hosts, including from ungulates and porcupines, was found in a Rousettus bat. These findings suggest that diverse astroviruses can be found in many species of mammals, including bats., Highlights • Diverse astroviruses detected in bats in Lao PDR and Cambodia • High polymorphism of astroviruses found in insectivorous and frugivorous bats • High level of genome saturation and hypermutation potential evidenced in astrovirus • Detection of additional astrovirus bat hosts, i.e. nectar bats from the genus Eonycteris • Discovery of a new species of astrovirus in fruit bats (Rousettus sp.), Graphical abstract. Image 1
Published: 2016

36. Contrasting effects of defaunation on aboveground carbon storage across the global tropics

Author: Francesco Rovero, David Kenfack, Jayashree Ratnam, Varun Varma, Mireille Ndoundou-Hockemba, Mahesh Sankaran, Andrew R. Marshall, B. R. Ramesh, Johanna Hurtado Astaiza, Patrick A. Jansen, Christine Fletcher, Anand M. Osuri, Patricia Alvarez-Loayza, Matt Bradford, Tata Institute for Fundamental Research (TIFR), Nature Conservation Foundation, Duke University [Durham], Organization for Tropical Studies, CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Forest Research Institute Malaysia (FRIM), Wildlife Conservation Society (WCS), Smithsonian Tropical Research Institute, Wageningen University, Department of Environmental Sciences, Smithsonian Conservation Biology Institute, Center for Conservation Education and Sustainability, MRC 705, Box 37012, Washington, DC, VA 20013-7012, USA, University of York [York, UK], Flamingo Land Ltd., Institut Français de Pondichéry (IFP), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), MUSE – Science Museum of Trento, and University of Leeds
Subjects: 0106 biological sciences, Conservation of Natural Resources, 010504 meteorology & atmospheric sciences, Defaunation, Seed dispersal, Science, Biome, General Physics and Astronomy, Forests, Biology, Carbon sequestration, Southeast asian, 010603 evolutionary biology, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Trees, tropics, mammiferi, tropici, Seed Dispersal, Tropical climate, Animals, Life Science, Ecosystem, 0105 earth and related environmental sciences, tropical forests, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Tropical Climate, Multidisciplinary, Ecology, General Chemistry, 15. Life on land, carbon storage, PE&RC, Carbon, Wildlife Ecology and Conservation, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Distribution
Abstract: Defaunation is causing declines of large-seeded animal-dispersed trees in tropical forests worldwide, but whether and how these declines will affect carbon storage across this biome is unclear. Here we show, using a pan-tropical data set, that simulated declines of large-seeded animal-dispersed trees have contrasting effects on aboveground carbon stocks across Earth's tropical forests. In our simulations, African, American and South Asian forests, which have high proportions of animal-dispersed species, consistently show carbon losses (2–12%), but Southeast Asian and Australian forests, where there are more abiotically dispersed species, show little to no carbon losses or marginal gains (±1%). These patterns result primarily from changes in wood volume, and are underlain by consistent relationships in our empirical data (∼2,100 species), wherein, large-seeded animal-dispersed species are larger as adults than small-seeded animal-dispersed species, but are smaller than abiotically dispersed species. Thus, floristic differences and distinct dispersal mode–seed size–adult size combinations can drive contrasting regional responses to defaunation., Defaunation is linked to the decline of tree species that depend on large animals for seed dispersal, but it is unclear if this affects carbon storage. Here the authors show that defaunation effects on carbon storage vary across continents, driven by relationships between seed dispersal strategies and adult tree size.
Published: 2016

37. Anthropogenic Stressors, Inter-Specific Competition and ENSO Effects on a Mauritian Coral Reef

Author: Tim R. McClanahan, Yves Letourneur, René Galzin, Nicholas A. J. Graham, Queen's University [Kingston, Canada], Wildlife Conservation Society (WCS), Diversité, évolution et écologie fonctionnelle marine (DIMAR), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Coral bleaching, [SDV]Life Sciences [q-bio], Coastal fish, Mascarene Islands, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Tourism, Stegastes, Climate change, Acropora, 14. Life underwater, Aquaculture of coral, Reef, Ecology, Evolution, Behavior and Systematics, geography, geography.geographical_feature_category, biology, Ecology, 010604 marine biology & hydrobiology, Coral reef, biology.organism_classification, Community structure, Fishery, Reef fishes, Western Indian Ocean, Species richness
Abstract: Much of the western Indian Ocean suffered widespread loss of live coral in 1998 and interest is now focussed on the indirect effects of this coral loss on other components of the ecosystem, in particular fishes. However, it is just as important to identify changes in fish assemblages at locations that did not suffer coral mortality to understand local versus regional drivers. We surveyed benthic and fish communities on a reef flat in Mauritius five times between 1994 and 2005. The design allowed for comparison through time, along the coast and between inshore and offshore reef locations. The benthic community demonstrates a clear trend along the coast, likely in response to a dredged water ski lane, but little change through time. Branching Acropora colonies dominate much of the live coral and best explain patterns in the fish assemblage (P < 0.01). Few changes in overall fish species richness through time were identified, and observed changes were within fishery target families rather than species reliant on live coral. Departure from expected levels of taxonomic distinctness suggests degradation in the community associated with the dredged ski lane. Non-metric multi-dimensional scaling of the fish assemblage demonstrates a similar pattern to that seen in the benthos; greater differences along the coast (Global R = 0.34) than through time (Global R = 0.17) and no trend between reef positions. SIMPER analysis identified two species of Stegastes as the main drivers of trends in the MDS plot and the most dominant of these, S. lividus, appears to be reducing species richness of the remaining fish community. The study highlights Mauritius as a regional refugia of thermally-sensitive corals and specialised fish, suggesting a need for careful management.
Published: 2006

38. Serologic Evidence of Lyssavirus Infection in Bats, Cambodia

Author: Laurent Audry, Jean-Marc Reynes, Sopheak Ngin, Joe Walston, Hervé Bourhy, Sophie Molia, Sotheara Hout, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur [Paris] (IP), Wildlife Conservation Society [Phnom Penh, Cambodia], Wildlife Conservation Society (WCS), and Institut Pasteur [Paris]
Subjects: Epidemiology, MESH: Lyssavirus, lcsh:Medicine, L73 - Maladies des animaux, Antibodies, Viral, Serology, 0302 clinical medicine, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chiroptera, Immunologie, MESH: Animals, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, medicine.diagnostic_test, MESH: Chiroptera, dispatch, 3. Good health, Épidémiologie, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Antibody, Infection, Cambodia, Microbiology (medical), 030231 tropical medicine, bats, Biology, Immunofluorescence, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Rhabdoviridae Infections, medicine, Animals, Surveillance épidémiologique, lcsh:RC109-216, Lyssavirus, 030304 developmental biology, MESH: Seroepidemiologic Studies, MESH: Cambodia, lcsh:R, MESH: Rhabdoviridae Infections, Serum samples, biology.organism_classification, Virology, Lyssavirus infection, biology.protein, MESH: Antibodies, Viral, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; In Cambodia, 1,303 bats of 16 species were tested for lyssavirus. No lyssavirus nucleocapsid was detected in 1,283 brains tested by immunofluorescence assay. Antibodies against lyssaviruses were detected by enzyme-linked immunosorbent assay in 144 (14.7%) of 981 serum samples. Thirty of 187 serum samples contained neutralizing antibodies against different lyssaviruses.
Published: 2004

39. Arctic ecosystem structure and functioning shaped by climate and herbivore body size

Author: R. I. G. Morrison, Marie-Christine Cadieux, Dominique Gravel, Charles J. Krebs, Shawn J. Leroux, Donald G. Reid, Joël Bêty, Dominique Berteaux, Michel Loreau, Niels-Martin Schmidt, Nigel G. Yoccoz, Gilles Gauthier, Rolf A. Ims, Pierre Legagneux, Nicolas Lecomte, Université Laval [Québec] (ULaval), Université du Québec à Rimouski (UQAR), University of Tromsø (UiT), University of Moncton, Aarhus University [Aarhus], Wildlife Conservation Society (WCS), University of British Columbia (UBC), Carleton University, Memorial University of Newfoundland [St. John's], Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Herbivore, Ecology, Ecosystem ecology, [SDE.MCG]Environmental Sciences/Global Changes, Arctic ecosystem, Climate change, 15. Life on land, Environmental Science (miscellaneous), Body size, Tundra, Arctic, 13. Climate action, Environmental science, Ecosystem, Terrestrial ecosystem, 14. Life underwater, Social Sciences (miscellaneous)
Abstract: International audience; Significant progress has been made in our understanding of species-level responses to climate change, but upscaling to entire ecosystems remains a challenge. This task is particularly urgent in the Arctic, where global warming is most pronounced. Here we report the results of an international collaboration on the direct and indirect effects of climate on the functioning of Arctic terrestrial ecosystems. Our data from seven terrestrial food webs spread along a wide range of latitudes (∼1,500 km) and climates (Δ mean July temperature = 8.5 °C) across the circumpolar world show the effects of climate on tundra primary production, food-web structure and species interaction strength. The intensity of predation on lower trophic levels increased significantly with temperature, at approximately 4.5% per °C. Temperature also affected trophic interactions through an indirect effect on food-web structure (that is, diversity and number of interactions). Herbivore body size was a major determinant of predator–prey interactions, as interaction strength was positively related to the predator–prey size ratio, with large herbivores mostly escaping predation. There is potential for climate warming to cause a switch from bottom-up to top-down regulation of herbivores. These results are critical to resolving the debate on the regulation of tundra and other terrestrial ecosystems exposed to global change.
Published: 2014

40. Subsampling herbarium collections to assess geographic diversity gradients : a case study with endemic Orchidaceae and Rubiaceae in Cameroon

Author: Droissart, Vincent, Hardy, Olivier J., Sonké, Bonaventure, Dahdouh-Guebas, Farid, Stévart, Tariq, Équipe 1 - Diversité des Plantes et des Communautés Végétales, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Laboratoire de Complexité Dynamique des Systèmes Tropicaux (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Herbarieum et Bibliothèque de Botanique africaine, Université libre de Bruxelles (ULB), Service Evolution Biologique et Ecologie -Faculté des Sciences, Laboratoire de Botanique et Ecologie, Université de Yaoundé I, Laboratoire de Complexité Dynamique des Systèmes Tropicaux (ULB), Herbarieum et Bibliothèque de Botanique africaine, ECOFAC Program (EC-DG8°, DIVEAC (CUD-ULB), Wildlife Conservation Society (WCS), Fonds de la Recherche Scientifique (F.R.S.-F.N.R.S.), American Orchid Society, Sud Expert Plant (France - Ministère des Affaires Etrangères), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Laboratoire de Complexité Dynamique des Systèmes Tropicaux (ULB), Université Libre de Bruxelles [Bruxelles] (ULB)-Université Libre de Bruxelles [Bruxelles] (ULB)-Herbarieum et Bibliothèque de Botanique africaine, Université Libre de Bruxelles [Bruxelles] (ULB), and Université de Yaoundé I [Yaoundé]
Subjects: Effective number of species, Similarity index, Central Africa, effective number of species, BiodivR, diversity patterns, Herbarium collections, herbarium collections, Diversity patterns, similarity index, Subsampling procedure, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, central Africa, subsampling procedure, rarefaction principles, Rarefaction principles, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities
Abstract: ACL-12-04; International audience; We compiled herbarium specimen data to provide an improved characterization of geographic patterns of diversity using indices of species diversity and floristic similarity based on rarefaction principles. A dataset of 3650 georeferenced plant specimens belonging to Orchidaceae and Rubiaceae endemic to Atlantic Central Africa was assembled to assess species composition per half-degree or one-degree grid cells. Local diversity was measured by the expected number of species (Sk) per grid cell found in subsamples of increasing size and compared with raw species richness (SR). A nearly unbiased estimator of the effective number of species per grid cell was also used, allowing quantification of ratios of 'true diversity' between grid cells. Species turnover was measured using a presence/absence-based similarity index (Sørensen) and an abundance-based index that corrects for sampling bias (NNESS). Our results confirm that the coastal region of Cameroon is more diverse in endemic species than those more inland. The southern part of this coastal forest is, however, as diverse as the more intensively inventoried northern part, and should also be recognized as an important center of endemism. A strong congruence between Sørensen and NNESS similarity matrices lead to similar delimitations of floristic units. Hence, heterogeneous sampling seems to confer more bias when measuring patterns of local diversity using raw species richness than species turnover using Sørensen index. Overall, we argue that subsampling methods represent a useful way to assess diversity gradients using herbarium specimens while correcting for heterogeneous sampling effort.
Published: 2012

41. Nipah virus in Lyle's flying foxes, Cambodia

Author: Dorian Counor, Sophie Molia, Joe Walston, Vansay Seng, Jean-Marc Reynes, Caroline Faure, Jean-Louis Sarthou, Marie Claude Georges-Courbot, Vincent Deubel, Sivuth Ong, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), 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)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), 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)-Institut Pasteur [Paris] (IP), Wildlife Conservation Society [Phnom Penh, Cambodia], Wildlife Conservation Society (WCS), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Veterinary medicine, Cynopterus sphinx, Epidemiology, lcsh:Medicine, MESH: Henipavirus Infections, Nipah virus, L73 - Maladies des animaux, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chiroptera, Immunologie, MESH: Animals, MESH: Nipah Virus, MESH: Phylogeny, Phylogeny, Henipavirus Infections, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, MESH: Chiroptera, 3. Good health, Pteropus, Infectious Diseases, Paramyxoviridae, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taphozous melanopogon, Cambodia, Pteropus lylei, Henipavirus, Microbiology (medical), zoonose, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Animals, Humans, Hendra Virus, lcsh:RC109-216, Surveillance épidémiologique, Transmission des maladies, 030304 developmental biology, MESH: Humans, 030306 microbiology, Research, MESH: Cambodia, lcsh:R, Hipposideros larvatus, biology.organism_classification, Virology, Scotophilus kuhlii, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Keywords: Cambodia
Abstract: International audience; We conducted a survey in Cambodia in 2000 on henipavirus infection among several bat species, including flying foxes, and persons exposed to these animals. Among 1,072 bat serum samples tested by enzyme-linked immunosorbent assay, antibodies reactive to Nipah virus (NiV) antigen were detected only in Pteropus lylei species; Cynopterus sphinx, Hipposideros larvatus, Scotophilus kuhlii, Chaerephon plicata, Taphozous melanopogon, and T. theobaldi species were negative. Seroneutralization applied on a subset of 156 serum samples confirmed these results. None of the 8 human serum samples was NiV seropositive with the seroneutralization test. One virus isolate exhibiting cytopathic effect with syncytia was obtained from 769 urine samples collected at roosts of P. lylei specimens. Partial molecular characterization of this isolate demonstrated that it was closely related to NiV. These results strengthen the hypothesis that flying foxes could be the natural host of NiV. Surveillance of human cases should be implemented.
Published: 2005

42. Local genetic adaptation to habitat in wild chimpanzees.

Author: Ostridge HJ, Fontsere C, Lizano E, Soto DC, Schmidt JM, Saxena V, Alvarez-Estape M, Barratt CD, Gratton P, Bocksberger G, Lester JD, Dieguez P, Agbor A, Angedakin S, Assumang AK, Bailey E, Barubiyo D, Bessone M, Brazzola G, Chancellor R, Cohen H, Coupland C, Danquah E, Deschner T, Dotras L, Dupain J, Egbe VE, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kambere M, Kienast I, Kujirakwinja D, Langergraber KE, Lapuente J, Larson B, Laudisoit A, Lee KC, Llana M, Maretti G, Martín R, Meier A, Morgan D, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Orume R, Pacheco L, Preece J, Regnaut S, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, van Schijndel J, Vendras E, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Vigilant L, Piel A, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic M, and Andrés AM
Abstract: How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees., Competing Interests: Competing interests: The authors declare no competing interests.
Published: 2024
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43. Vulnerability of Eastern Tropical Pacific chondrichthyan fish to climate change.

Author: Cerutti-Pereyra F, Drenkard EJ, Espinoza M, Finucci B, Galván-Magaña F, Hacohen-Domené A, Hearn A, Hoyos-Padilla ME, Ketchum JT, Mejía-Falla PA, Moya-Serrano AV, Navia AF, Pazmiño DA, Ramírez-Macías D, Rummer JL, Salinas-de-León P, Sosa-Nishizaki O, Stock C, and Chin A
Subjects: Animals, Pacific Ocean, Risk Assessment, Ecosystem, Fishes physiology, Climate Change
Abstract: Climate change is an environmental emergency threatening species and ecosystems globally. Oceans have absorbed about 90% of anthropogenic heat and 20%-30% of the carbon emissions, resulting in ocean warming, acidification, deoxygenation, changes in ocean stratification and nutrient availability, and more severe extreme events. Given predictions of further changes, there is a critical need to understand how marine species will be affected. Here, we used an integrated risk assessment framework to evaluate the vulnerability of 132 chondrichthyans in the Eastern Tropical Pacific (ETP) to the impacts of climate change. Taking a precautionary view, we found that almost a quarter (23%) of the ETP chondrichthyan species evaluated were highly vulnerable to climate change, and much of the rest (76%) were moderately vulnerable. Most of the highly vulnerable species are batoids (77%), and a large proportion (90%) are coastal or pelagic species that use coastal habitats as nurseries. Six species of batoids were highly vulnerable in all three components of the assessment (exposure, sensitivity and adaptive capacity). This assessment indicates that coastal species, particularly those relying on inshore nursery areas are the most vulnerable to climate change. Ocean warming, in combination with acidification and potential deoxygenation, will likely have widespread effects on ETP chondrichthyan species, but coastal species may also contend with changes in freshwater inputs, salinity, and sea level rise. This climate-related vulnerability is compounded by other anthropogenic factors, such as overfishing and habitat degradation already occurring in the region. Mitigating the impacts of climate change on ETP chondrichthyans involves a range of approaches that include addressing habitat degradation, sustainability of exploitation, and species-specific actions may be required for species at higher risk. The assessment also highlighted the need to further understand climate change's impacts on key ETP habitats and processes and identified knowledge gaps on ETP chondrichthyan species., (© 2024 The Author(s). Global Change Biology published by John Wiley & Sons Ltd.)
Published: 2024
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44. Upper thermal tolerance and population implications for the Magdalena River stingray Potamotrygon magdalenae.

Author: Gómez-Martínez D, Londoño-Cruz E, and Mejía-Falla PA
Subjects: Animals, Male, Female, Rivers, Thermotolerance, Temperature, Hot Temperature, Behavior, Animal, Acclimatization, Skates, Fish physiology
Abstract: Knowledge of thermal tolerance limits provides important clues to the capacity of a species to withstand acute and chronic thermal changes. Climate models predict the increase and intensification of events such as heat waves, therefore understanding the upper thermal limits that a species can tolerate has become of utmost importance. We measured the upper thermal tolerance of the endemic Magdalena river stingray Potamotrygon magdalenae acclimated to experimental conditions, and then used critical thermal methodology to find the temperature at which an organism reaches a critical endpoint where locomotory activity becomes disorganized and the animal loses its ability to escape from conditions that will promptly lead to its death. We also describe the behavioral response of individuals to acute thermal stress and infer the possible consequences of temperature increases in the habitats of P. magdalenae populations. There were no significant differences between sexes in temperature tolerance or behavior. The critical thermal maximum (39°C) was 5.9°C above the maximum recorded temperature for the study area. Although P. magdalenae was tolerant to high temperature and currently is not living at its upper thermal limit, its survival in Guarinocito Pond will be threatened if temperatures continue to increase, considering the warming scenarios predicted for tropical regions due to climate change, even including short-term climate phenomena such as El Niño., (© 2024 Fisheries Society of the British Isles.)
Published: 2024
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45. Fishing for oil and meat drives irreversible defaunation of deepwater sharks and rays.

Author: Finucci B, Pacoureau N, Rigby CL, Matsushiba JH, Faure-Beaulieu N, Sherman CS, VanderWright WJ, Jabado RW, Charvet P, Mejía-Falla PA, Navia AF, Derrick DH, Kyne PM, Pollom RA, Walls RHL, Herman KB, Kinattumkara B, Cotton CF, Cuevas JM, Daley RK, Dharmadi, Ebert DA, Fernando D, Fernando SMC, Francis MP, Huveneers C, Ishihara H, Kulka DW, Leslie RW, Neat F, Orlov AM, Rincon G, Sant GJ, Volvenko IV, Walker TI, Simpfendorfer CA, and Dulvy NK
Subjects: Animals, Humans, Conservation of Natural Resources, Commerce, Internationality, Meat, Fisheries, Sharks physiology
Abstract: The deep ocean is the last natural biodiversity refuge from the reach of human activities. Deepwater sharks and rays are among the most sensitive marine vertebrates to overexploitation. One-third of threatened deepwater sharks are targeted, and half the species targeted for the international liver-oil trade are threatened with extinction. Steep population declines cannot be easily reversed owing to long generation lengths, low recovery potentials, and the near absence of management. Depth and spatial limits to fishing activity could improve conservation when implemented alongside catch regulations, bycatch mitigation, and international trade regulation. Deepwater sharks and rays require immediate trade and fishing regulations to prevent irreversible defaunation and promote recovery of this threatened megafauna group.
Published: 2024
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46. Border fences reduce potential for transboundary migration of Marco Polo Sheep (Ovis ammon polii) in the Pamir Plateau.

Author: Zhuo Y, Wang M, Liu Z, Xu W, Abdulnazar A, Rajabi AM, Davletbakov A, Haider J, Khan MZ, Loik N, Faryabi SP, Michel S, Ostrowski S, Moheb Z, Ruckstuhl K, da Silva AA, Alves J, and Yang W
Subjects: Animals, Sheep, China, Afghanistan, Kyrgyzstan, Conservation of Natural Resources, Ecosystem, Mammals
Abstract: Border fences have severely impeded the transboundary migration of a number of large mammals worldwide, with central Asia being one of the most impacted. The Marco Polo sheep (Ovis ammon polii), an iconic species of Pamir, is threatened in its transboundary movement by increasing border fencing among their five distributed countries, including Tajikistan, Kyrgyzstan, China, Afghanistan, and Pakistan. In this study, by building ensemble species distribution models, we found that eastern Tajikistan had the largest suitable Macro Polo sheep habitat (about 42 % of the total suitable habitat), followed by China (about 32 %). We used least-cost paths to identify 51 ecological corridors including 5 transboundary ecological corridors, which may be important to maintain connectivity in both domestic and transboundary regions. To assess the potential barrier effect of border fences, we assessed four scenarios (30, 40, 50 and 60°) corresponding to the upper limit of the slope for the construction of fences. In areas too steep for fencing, these could be used by wild sheep to cross barriers or borders and may represent migration or movement routes, defined as natural passages. In the most pessimistic Scenario 60, only 25 migratory passages along the border fences were identified, compared to 997 in the most optimistic scenario (Scenario 30), indicating a strong negative effect of intensive border fencing on the transboundary movement of Marco Polo sheep. The establishment of transnational conservation parks, and ensuring permeability is maintained in key areas, could have a positive impact on the connectivity and persistence of Marco Polo sheep populations, and provide important lessons for other large migratory mammals in transboundary regions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)
Published: 2024
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47. Mapping density, diversity and species-richness of the Amazon tree flora.

Author: Ter Steege H, Pitman NCA, do Amaral IL, de Souza Coelho L, de Almeida Matos FD, de Andrade Lima Filho D, Salomão RP, Wittmann F, Castilho CV, Guevara JE, Veiga Carim MJ, Phillips OL, Magnusson WE, Sabatier D, Revilla JDC, Molino JF, Irume MV, Martins MP, da Silva Guimarães JR, Ramos JF, Bánki OS, Piedade MTF, Cárdenas López D, Rodrigues DJ, Demarchi LO, Schöngart J, Almeida EJ, Barbosa LF, Cavalheiro L, Dos Santos MCV, Luize BG, de Leão Novo EMM, Vargas PN, Silva TSF, Venticinque EM, Manzatto AG, Reis NFC, Terborgh J, Casula KR, Honorio Coronado EN, Monteagudo Mendoza A, Montero JC, Costa FRC, Feldpausch TR, Quaresma AC, Castaño Arboleda N, Zartman CE, Killeen TJ, Marimon BS, Marimon-Junior BH, Vasquez R, Mostacedo B, Assis RL, Baraloto C, do Amaral DD, Engel J, Petronelli P, Castellanos H, de Medeiros MB, Simon MF, Andrade A, Camargo JL, Laurance WF, Laurance SGW, Maniguaje Rincón L, Schietti J, Sousa TR, de Sousa Farias E, Lopes MA, Magalhães JLL, Nascimento HEM, de Queiroz HL, Aymard C GA, Brienen R, Stevenson PR, Araujo-Murakami A, Baker TR, Cintra BBL, Feitosa YO, Mogollón HF, Duivenvoorden JF, Peres CA, Silman MR, Ferreira LV, Lozada JR, Comiskey JA, Draper FC, de Toledo JJ, Damasco G, García-Villacorta R, Lopes A, Vicentini A, Cornejo Valverde F, Alonso A, Arroyo L, Dallmeier F, Gomes VHF, Jimenez EM, Neill D, Peñuela Mora MC, Noronha JC, de Aguiar DPP, Barbosa FR, Bredin YK, de Sá Carpanedo R, Carvalho FA, de Souza FC, Feeley KJ, Gribel R, Haugaasen T, Hawes JE, Pansonato MP, Ríos Paredes M, Barlow J, Berenguer E, da Silva IB, Ferreira MJ, Ferreira J, Fine PVA, Guedes MC, Levis C, Licona JC, Villa Zegarra BE, Vos VA, Cerón C, Durgante FM, Fonty É, Henkel TW, Householder JE, Huamantupa-Chuquimaco I, Pos E, Silveira M, Stropp J, Thomas R, Daly D, Dexter KG, Milliken W, Molina GP, Pennington T, Vieira ICG, Weiss Albuquerque B, Campelo W, Fuentes A, Klitgaard B, Pena JLM, Tello JS, Vriesendorp C, Chave J, Di Fiore A, Hilário RR, de Oliveira Pereira L, Phillips JF, Rivas-Torres G, van Andel TR, von Hildebrand P, Balee W, Barbosa EM, de Matos Bonates LC, Dávila Doza HP, Zárate Gómez R, Gonzales T, Gallardo Gonzales GP, Hoffman B, Junqueira AB, Malhi Y, de Andrade Miranda IP, Pinto LFM, Prieto A, Rudas A, Ruschel AR, Silva N, Vela CIA, Zent EL, Zent S, Cano A, Carrero Márquez YA, Correa DF, Costa JBP, Flores BM, Galbraith D, Holmgren M, Kalamandeen M, Lobo G, Torres Montenegro L, Nascimento MT, Oliveira AA, Pombo MM, Ramirez-Angulo H, Rocha M, Scudeller VV, Sierra R, Tirado M, Umaña MN, van der Heijden G, Vilanova Torre E, Reategui MAA, Baider C, Balslev H, Cárdenas S, Casas LF, Endara MJ, Farfan-Rios W, Ferreira C, Linares-Palomino R, Mendoza C, Mesones I, Parada GA, Torres-Lezama A, Urrego Giraldo LE, Villarroel D, Zagt R, Alexiades MN, de Oliveira EA, Garcia-Cabrera K, Hernandez L, Cuenca WP, Pansini S, Pauletto D, Ramirez Arevalo F, Sampaio AF, Valderrama Sandoval EH, Gamarra LV, Levesley A, Pickavance G, and Melgaço K
Subjects: Forests, Soil, Temperature, Trees, RNA, Long Noncoding
Abstract: Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution., (© 2023. The Author(s).)
Published: 2023
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48. High-resolution assessment of the carrying capacity and utilization intensity in mountain rangelands with remote sensing and field data.

Author: Zandler H, Vanselow KA, Poya Faryabi S, Rajabi AM, and Ostrowski S
Abstract: Dry rangelands provide resources for half of the world's livestock, but degradation due to overgrazing is a major threat to system sustainability. Existing carrying capacity assessments are limited by low spatiotemporal resolution and high generalization, which hampers applied ecological management decisions. This paper provides an example for deriving the carrying capacity and utilization levels for cold drylands at a new level of detail by including major parts of the transhumance system. We combined field data on vegetation biomass and communities, forage quality, productivity, livestock species and quantities, grazing areas and their spatiotemporal variations with Sentinel-2 and MODIS snow cover satellite imagery to develop maps of forage requirements and availability. These products were used to calculate carrying capacity and grazing potential in the Pamir-Hindukush Mountains. Results showed high spatial variability of utilization rates between 5% and 77%. About 30% of the area showed unsustainable grazing above the carrying capacity. Utilization rates displayed strong spatial differences with unsustainable grazing in winter pastures and at lower elevations, and low rates at higher altitudes. The forage requirements of wild herbivores (ungulates and marmots) were estimated to be negligible compared to livestock, with one tenth of the biomass consumption and no increase in unsustainably grazed pastures due to the wider distribution of animals. The assessment was sensitive to model parameterization of forage requirements and demand, whereby conservative scenarios, i.e. lower fodder availability or higher fodder requirements of livestock due to climate and altitude effects, increased the area with unsustainable grazing practices to 50%. The presented approach enables an in-depth evaluation of the carrying capacity and corresponding management actions. It includes new variables relevant for transhumance systems, such as the combination of forage quantity and quality or accessibility restrictions due to snow, and shows utilization patterns at high spatial resolutions. Regional maps allow the identification of unsustainable utilization areas, such as winter pastures in this study., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)
Published: 2023
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49. More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia.

Author: Peripato V, Levis C, Moreira GA, Gamerman D, Ter Steege H, Pitman NCA, de Souza JG, Iriarte J, Robinson M, Junqueira AB, Trindade TB, de Almeida FO, Moraes CP, Lombardo U, Tamanaha EK, Maezumi SY, Ometto JPHB, Braga JRG, Campanharo WA, Cassol HLG, Leal PR, de Assis MLR, da Silva AM, Phillips OL, Costa FRC, Flores BM, Hoffman B, Henkel TW, Umaña MN, Magnusson WE, Valderrama Sandoval EH, Barlow J, Milliken W, Lopes MA, Simon MF, van Andel TR, Laurance SGW, Laurance WF, Torres-Lezama A, Assis RL, Molino JF, Mestre M, Hamblin M, Coelho LS, Lima Filho DA, Wittmann F, Salomão RP, Amaral IL, Guevara JE, de Almeida Matos FD, Castilho CV, Carim MJV, Cárdenas López D, Sabatier D, Irume MV, Martins MP, Guimarães JRDS, Bánki OS, Piedade MTF, Ramos JF, Luize BG, Novo EMML, Núñez Vargas P, Silva TSF, Venticinque EM, Manzatto AG, Reis NFC, Terborgh J, Casula KR, Demarchi LO, Honorio Coronado EN, Monteagudo Mendoza A, Montero JC, Schöngart J, Feldpausch TR, Quaresma AC, Aymard C GA, Baraloto C, Castaño Arboleda N, Engel J, Petronelli P, Zartman CE, Killeen TJ, Marimon BS, Marimon-Junior BH, Schietti J, Sousa TR, Vasquez R, Rincón LM, Berenguer E, Ferreira J, Mostacedo B, do Amaral DD, Castellanos H, de Medeiros MB, Andrade A, Camargo JL, Farias ES, Magalhães JLL, Mendonça Nascimento HE, de Queiroz HL, Brienen R, Cardenas Revilla JD, Stevenson PR, Araujo-Murakami A, Barçante Ladvocat Cintra B, Feitosa YO, Barbosa FR, Carpanedo RS, Duivenvoorden JF, de Noronha JDC, Rodrigues DJ, Mogollón HF, Ferreira LV, Householder JE, Lozada JR, Comiskey JA, Draper FC, de Toledo JJ, Damasco G, Dávila N, García-Villacorta R, Lopes A, Cornejo Valverde F, Alonso A, Dallmeier F, Gomes VHF, Jimenez EM, Neill D, Peñuela Mora MC, de Aguiar DPP, Arroyo L, Antunes Carvalho F, Coelho de Souza F, Feeley KJ, Gribel R, Pansonato MP, Ríos Paredes M, Brasil da Silva I, Ferreira MJ, Fine PVA, Fonty É, Guedes MC, Licona JC, Pennington T, Peres CA, Villa Zegarra BE, Parada GA, Pardo Molina G, Vos VA, Cerón C, Maas P, Silveira M, Stropp J, Thomas R, Baker TR, Daly D, Huamantupa-Chuquimaco I, Vieira ICG, Weiss Albuquerque B, Fuentes A, Klitgaard B, Marcelo-Peña JL, Silman MR, Tello JS, Vriesendorp C, Chave J, Di Fiore A, Hilário RR, Phillips JF, Rivas-Torres G, von Hildebrand P, Pereira LO, Barbosa EM, de Matos Bonates LC, Doza HPD, Zárate Gómez R, Gallardo Gonzales GP, Gonzales T, Malhi Y, de Andrade Miranda IP, Mozombite Pinto LF, Prieto A, Rudas A, Ruschel AR, Silva N, Vela CIA, Zent EL, Zent S, Cano A, Carrero Márquez YA, Correa DF, Costa JBP, Galbraith D, Holmgren M, Kalamandeen M, Lobo G, Nascimento MT, Oliveira AA, Ramirez-Angulo H, Rocha M, Scudeller VV, Sierra R, Tirado M, van der Heijden G, Vilanova Torre E, Ahuite Reategui MA, Baider C, Balslev H, Cárdenas S, Casas LF, Farfan-Rios W, Ferreira C, Linares-Palomino R, Mendoza C, Mesones I, Urrego Giraldo LE, Villarroel D, Zagt R, Alexiades MN, de Oliveira EA, Garcia-Cabrera K, Hernandez L, Palacios Cuenca W, Pansini S, Pauletto D, Ramirez Arevalo F, Sampaio AF, Valenzuela Gamarra L, and Aragão LEOC
Subjects: Humans, Brazil, Forests, Archaeology
Abstract: Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.
Published: 2023
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50. How many species of genus Lernaeopoda Blainville, 1822 (Siphonostomatoida: Lernaeopodidae) are there in the southwestern Atlantic?

Author: Montes MM, Gmez S, Castro RR, Bovcon N, Vettorazzi RI, Serrano CF, Cardarella GFR, Ferrari W, Cuevas JM, and Martorelli SR
Subjects: Animals, DNA, Mitochondrial genetics, Microscopy, Electron, Scanning, Mouth, Phylogeny, Copepoda, Parasites
Abstract: The family Lernaeopodidae includes 14 genera parasitizing elasmobranchs. Fourteen species of this family have been cited from Argentina, four of which were found on chondrichthyans. Schroederichthys bivius Mller and Henle and Galeorhinus galeus (Linnaeus) from Argentina harbored parasitic copepods of the genus Lernaeopoda. The objective of this study was to identify the species using an integrative approach. The morphology was examined by Optical Microscopy and Scanning Electron Microscopy and the molecular analysis was based on partial sequences of the COI mtDNA gene. Despite differences in the antenna, antennule, mandible, maxilliped and maxillae among the specimens, the morphological and molecular analyses revealed that they belonged to Lernaeopoda bivia Leigh-Sharpe, 1930. The species so far reported for Argentina are L. bivia and L. galei Kryer, 1837, which are distinguished by the size (less and greater than 7 mm, respectively). Here, we report partial sequences of the COI mtDNA gene of L. bivia for the first time, obtained from eleven specimens attached to the mouth, fins, anal slit and claspers of the two shark hosts. The COI mtDNA gene tree shows that the Lernaeopoda group forms a sister clade with Pseudocharopinus bicaudatus (Kryer, 1837), while the genus Pseudocharopinus does not appear to be a natural group. We propose that the material described from Argentinean waters as L. galei was misidentified and actually belongs to L. bivia. The wide variability within the specimens of L. bivia emphasizes the importance of using an integrative approach to revise the taxonomy of the Lernaeopoda species from all over the world.
Published: 2023
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