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256 results on '"Leibniz Institute for Zoo and Wildlife Research (IZW)"'

1. Studying Species Demography and Distribution in Natural Conditions: Hidden Markov Models

Author: Gimenez, Olivier, Louvrier, Julie, Lauret, Valentin, Santostasi, Nina Luisa, 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)-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, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Nathalie Peyrard, Olivier Gimenez, and ANR-16-CE02-0007,DEMOCOM,Effets de la gestion et du climat sur la dynamique des communautés - Développement d'une démographie multi-espèce.(2016)
Subjects: [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Quantitative Biology::Populations and Evolution, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; This chapter shows how hidden Markov models (HMMs) can be used to develop capture–recapture and occupancy models, traditionally used to study the dynamics of populations and the distribution of species in a context of imperfect detection. It shows how the HMM formulation permits the estimation of hidden variables in two different case studies. These case studies include: estimating the prevalence of dog–wolf hybrids with uncertain individual identification; and estimating the distribution of a wolf population with species identification errors and heterogeneous detection. The hidden variables encountered in the study of animal populations are living/dead; developmental states, which are generally discrete, such as sexual maturity; epidemiological states; or social states. HMM will be used to model species distribution in a case featuring identification errors and heterogeneous detection. The main advantage of the HMM approach lies in the ability to infer the ecological states of individuals and species which are partially observable: these are hidden variables.
Published: 2022
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2. The sperm-interacting proteome in the bovine isthmus and ampulla during the periovulatory period

Author: Coline Mahé, Régis Lavigne, Emmanuelle Com, Charles Pineau, Aleksandra Maria Zlotkowska, Guillaume Tsikis, Pascal Mermillod, Jennifer Schoen, Marie Saint-Dizier, Institut Français du Cheval et de l'Equitation [Saumur] (IFCE), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Proteomics Core Facility (Protim), Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®, Leibniz Institute for Farm Animal Biology (FBN), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, This work was funded by INRAE and Agence Nationale de la Recherche under the grant number ANR-18-CE92-0049. This work was also supported by grants from Biogenouest, Infrastructures en Biologie Santé et Agronomie (IBiSA) and Conseil Régional de Bretagne awarded to Protim proteomics core facility., ANR-18-CE92-0049,DIALOG,Dialoguer pour être fertile : comprendre les interactions spermatozoïdes-oviducte et leurs implications pour l'insémination artificielle chez les bovins laitiers(2018), Jonchère, Laurent, and APPEL À PROJETS GÉNÉRIQUE 2018 - Dialoguer pour être fertile : comprendre les interactions spermatozoïdes-oviducte et leurs implications pour l'insémination artificielle chez les bovins laitiers - - DIALOG2018 - ANR-18-CE92-0049 - AAPG2018 - VALID
Subjects: Ovulation, Proteomics, Interactome, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Oviduct, Pre-ovulatory, Fallopian tube, Biochemistry, Isthmus, Spermatozoa, Ampulla, Post-ovulatory, Animal Science and Zoology, [SDV.BDLR] Life Sciences [q-bio]/Reproductive Biology, Food Science, Biotechnology
Abstract: Background Spermatozoa interact with oviduct secretions before fertilization in vivo but the molecular players of this dialog and underlying dynamics remain largely unknown. Our objectives were to identify an exhaustive list of sperm-interacting proteins (SIPs) in the bovine oviduct fluid and to evaluate the impact of the oviduct anatomical region (isthmus vs. ampulla) and time relative to ovulation (pre-ovulatory vs. post-ovulatory) on SIPs number and abundance. Methods Pools of oviduct fluid (OF) from the pre-ovulatory ampulla, pre-ovulatory isthmus, post-ovulatory ampulla, and post-ovulatory isthmus in the side of ovulation were collected from the slaughterhouse. Frozen-thawed bull sperm were incubated with OF or phosphate-buffered saline (control) for 60 min at 38.5 °C. After protein extraction and digestion, sperm and OF samples were analyzed by nanoLC-MS/MS and label-free protein quantification. Results A quantitative comparison between proteins identified in sperm and OF samples (2333 and 2471 proteins, respectively) allowed for the identification of 245 SIPs. The highest number (187) were found in the pre-ovulatory isthmus, i.e., time and place of the sperm reservoir. In total, 41 SIPs (17%) were differentially abundant between stages in a given region or between regions at a given stage and 76 SIPs (31%) were identified in only one region × stage condition. Functional analysis of SIPs predicted roles in cell response to stress, regulation of cell motility, fertilization, and early embryo development. Conclusion This study provides a comprehensive list of SIPs in the bovine oviduct and evidences dynamic spatio-temporal changes in sperm-oviduct interactions around ovulation time. Moreover, these data provide protein candidates to improve sperm conservation and in vitro fertilization media.
Published: 2023
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3. A species-level trait dataset of bats in Europe and beyond

Author: Jérémy S. P. Froidevaux, Nia Toshkova, Luc Barbaro, Ana Benítez-López, Christian Kerbiriou, Isabelle Le Viol, Michela Pacifici, Luca Santini, Clare Stawski, Danilo Russo, Jasja Dekker, Antton Alberdi, Francisco Amorim, Leonardo Ancillotto, Kévin Barré, Yves Bas, Lisette Cantú-Salazar, Dina K. N. Dechmann, Tiphaine Devaux, Katrine Eldegard, Sasan Fereidouni, Joanna Furmankiewicz, Daniela Hamidovic, Davina L. Hill, Carlos Ibáñez, Jean-François Julien, Javier Juste, Peter Kaňuch, Carmi Korine, Alexis Laforge, Gaëlle Legras, Camille Leroux, Grzegorz Lesiński, Léa Mariton, Julie Marmet, Vanessa A. Mata, Clare M. Mifsud, Victoria Nistreanu, Roberto Novella-Fernandez, Hugo Rebelo, Niamh Roche, Charlotte Roemer, Ireneusz Ruczyński, Rune Sørås, Marcel Uhrin, Adriana Vella, Christian C. Voigt, Orly Razgour, University of Stirling, Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Bristol [Bristol], National Museum of Natural History, Sofia, Bulgaria (NMNHS), Bulgarian Academy of Sciences (BAS), Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad de Granada = University of Granada (UGR), Dipartimento INFOCOM [Roma], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Norwegian University of Science and Technology (NTNU), University of the Sunshine Coast (USC), University of Naples Federico II = Università degli studi di Napoli Federico II, Auteur indépendant, IT University of Copenhagen (ITU), Centro de Investigação em Biodiversidade e Recursos Genéticos [Vairao] (CIBIO), Universidade do Porto = University of Porto, 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)-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, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Luxembourg Institute of Science and Technology (LIST), Max Planck Institute of Animal Behavior, University of Konstanz, Office français de la biodiversité (OFB), Norwegian University of Life Sciences (NMBU), University of Veterinary Medicine [Vienna] (Vetmeduni), University of Wrocław [Poland] (UWr), Croatian Biospeleological Society, University of Glasgow, CIBER de Epidemiología y Salud Pública (CIBERESP), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), University of Southampton, School of Biological Sciences, University of P. J. Safarik in Kosice, University of Malta [Malta], Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, University of Exeter, and Jeremy Froidevaux was funded by the Région Bretagne (SAD grant number 19041) and the Leverhulme Trust (grant number: ECF-2020-571). Nia Toshkova was funded by the Bulgarian National Science Fund (CP-06-COST/15from 16.12.2020) and а PhD Fellowship from Karoll Knowledge Foundation.
Subjects: Statistics and Probability, [SDV]Life Sciences [q-bio], ddc:570, Library and Information Sciences, Statistics, Probability and Uncertainty, Computer Science Applications, Education, Information Systems
Abstract: Knowledge of species’ functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.
Published: 2023
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4. Genomic and ecologic characteristics of the airway microbial-mucosal complex

Author: Leah Cuthbertson, Ulrike Löber, Jonathan S. Ish-Horowicz, Claire N. McBrien, Colin Churchward, Jeremy C. Parker, Michael T. Olanipekun, Conor Burke, Orla O’Carroll, John Faul, Gwyneth A. Davies, Keir E. Lewis, Julian M. Hopkin, Joy Creaser-Thomas, Robin Goshal, Kian Fan Chung, Stefan Piatek, Saffron A.G. Willis-Owen, Theda U. P. Bartolomaeus, Till Birkner, Sarah Dwyer, Nitin Kumar, Elena M. Turek, A. William Musk, Jenni Hui, Michael Hunter, Alan James, Marc-Emmanuel Dumas, Sarah Filippi, Michael J. Cox, Trevor D. Lawley, Sofia K. Forslund, Miriam F. Moffatt, William O.C. Cookson, Royal Brompton and Harefield NHS Foundation Trust, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Imperial College London, Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Institut Pasteur de Lille, and 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 National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: Summary paragraphLung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide1-4. Microbial communities at the airway mucosal barrier are conserved and highly ordered5, reflecting symbiosis and co-evolution with human host factors6. Freed of selection to digest nutrients for the host, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species, identifying abundant novel organisms within the genera Streptococcus, Pauljensenia, Neisseria and Gemella. Bacterial genomes were enriched for genes encoding antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. RNA-targeting CRISPR elements in some taxa suggest the potential to prevent or treat specific viral infections. Homologues of human RO60 present in Neisseria spp. provide a possible respiratory primer for autoimmunity in systemic lupus erythematosus (SLE) and Sjögren syndrome. We interpret the structure and biogeography of airway microbial communities from clinical surveys in the context of whole-genome content, identifying features of airway dysbiosis that may presage breakdown of homeostasis during acute attacks of asthma and chronic obstructive pulmonary disease (COPD). We match the gene content of isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.
Published: 2022

5. Protected area personnel and ranger numbers are insufficient to deliver global expectations

Author: Michael R. Appleton, Alexandre Courtiol, Lucy Emerton, James L. Slade, Andrew Tilker, Lauren C. Warr, Mónica Álvarez Malvido, James R. Barborak, Louise de Bruin, Rosalie Chapple, Jennifer C. Daltry, Nina P. Hadley, Christopher A. Jordan, François Rousset, Rohit Singh, Eleanor J. Sterling, Erin G. Wessling, Barney Long, Re:Wild, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Colorado State University [Fort Collins] (CSU), Fauna and Flora International [Cambridge, UK], Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), World Wide Fund (WWF), Hawai'i Institute of Marine Biology (HIMB), Department of Human Evolutionary Biology, and Harvard University
Subjects: Urban Studies, Global and Planetary Change, Ecology, Renewable Energy, Sustainability and the Environment, Geography, Planning and Development, Management, Monitoring, Policy and Law, [SDE.ES]Environmental Sciences/Environmental and Society, Nature and Landscape Conservation, Food Science, Ecosystem services, Interdisciplinary studies, Sustainability, Conservation biology
Abstract: The 2020 global spatial targets for protected areas set by the Convention on Biological Diversity have almost been achieved, but management effectiveness remains deficient. Personnel shortages are widely cited as major contributing factors but have not previously been quantified. Using data from 176 countries and territories, we estimate a current maximum of 555,000 terrestrial protected area personnel worldwide (one per 37 km2), including 286,000 rangers (one per 72 km2), far short of published guidance on required densities. Expansion by 2030 to 30% coverage of protected areas and other effective area-based conservation measures is widely agreed as a minimum for safeguarding biodiversity and ecosystem services. We project that effective management of this expanded system will require approximately 3 million personnel (one per 13 km2), including more than 1.5 million rangers or equivalents (one per 26 km2). Parallel improvements in resourcing, working conditions and capacity are required for effective, equitable and sustainable management.
Published: 2022
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6. Sex and dominance

Author: Peter M. Kappeler, Elise Huchard, Alice Baniel, Charlotte Canteloup, Marie J. E. Charpentier, Leveda Cheng, Eve Davidian, Julie Duboscq, Claudia Fichtel, Charlotte K. Hemelrijk, Oliver P. Höner, Lee Koren, Jérôme Micheletta, Lea Prox, Tommaso Saccà, Lauren Seex, Nikolaos Smit, Martin Surbeck, Erica van de Waal, Cédric Girard-Buttoz, Theoretical Research in Evolutionary Life Sciences, Hemelrijk group, Leibniz Institute for Primate Research, German Primate Centre, Johann-Friedrich Blumenbach Institut für Zoologie und Anthropologie, Georg-August-University = Georg-August-Universität Göttingen, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Arizona State University [Tempe] (ASU), Université de Lausanne = University of Lausanne (UNIL), Mawana Game Reserve, Harvard University, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Université Paris Diderot - Paris 7 (UPD7), Muséum national d'Histoire naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Bar-Ilan University [Israël], University of Portsmouth, Institut des sciences cognitives Marc Jeannerod - Centre de neuroscience cognitive - UMR5229 (ISC-MJ), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: Ecology, Ecology, Evolution, Behavior and Systematics, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, mammals, hierarchy, methodology, dominance, sex, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The causes and consequences of being in a particular dominance position have been illuminated in various animal species, and new methods to assess dominance relationships and to describe the structure of dominance hierarchies have been developed in recent years. Most research has focused on same-sex relationships, however, so that intersexual dominance relationships and hierarchies including both sexes have remained much less studied. In particular, different methods continue to be employed to rank males and females along a dominance hierarchy, and sex biases in dominance are still widely regarded as simple byproducts of sexual size dimorphism. However, males and females regularly compete over similar resources when living in the same group, and sexual conflict takes a variety of forms across Frontiers in Ecology and Evolution 01 frontiersin.org Kappeler et al. 10.3389/fevo.2022.918773 societies. These processes affect the fitness of both sexes, and are mitigated by intersexual hierarchies. In this study, we draw on data from free-ranging populations of nine species of mammals that vary in the degree to which members of one sex dominate members of the other sex to explore the consequences of using different criteria and procedures for describing intraand intersexual dominance relationships in these societies. Our analyses confirmed a continuum in patterns of intersexual dominance, from strictly male-dominated species to strictly female-dominated species. All indices of the degree of female dominance were well correlated with each other. The rank order among same-sex individuals was highly correlated between the intra-and intersexual hierarchies, and such correlation was not affected by the degree of female dominance. The relative prevalence of aggression and submission was sensitive to variation in the degree of female dominance across species, with more submissive signals and fewer aggressive acts being used in societies where female dominance prevails. Thus, this study provides important insights and key methodological tools to study intersexual dominance relationships in mammals.
Published: 2022
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7. Spatiotemporal profiling of the bovine oviduct fluid proteome around the time of ovulation

Author: Mahé, Coline, Lavigne, Régis, Com, Emmanuelle, Pineau, Charles, Locatelli, Yann, Zlotkowska, Aleksandra Maria, Almiñana, Carmen, Tsikis, Guillaume, Mermillod, Pascal, Schoen, Jennifer, Saint-Dizier, Marie, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biosit : biologie, santé, innovation technologique (SFR UMS CNRS 3480 - INSERM 018), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Universität Zürich [Zürich] = University of Zurich (UZH), ANR-18-CE92-0049,DIALOG,Dialoguer pour être fertile : comprendre les interactions spermatozoïdes-oviducte et leurs implications pour l'insémination artificielle chez les bovins laitiers(2018), Chard-Hutchinson, Xavier, APPEL À PROJETS GÉNÉRIQUE 2018 - Dialoguer pour être fertile : comprendre les interactions spermatozoïdes-oviducte et leurs implications pour l'insémination artificielle chez les bovins laitiers - - DIALOG2018 - ANR-18-CE92-0049 - AAPG2018 - VALID, University of Zurich, and Mahé, Coline
Subjects: Ovulation, 1000 Multidisciplinary, Multidisciplinary, animal structures, Proteome, 10077 Institute of Veterinary Anatomy, [SDV]Life Sciences [q-bio], Oviducts, [SDV] Life Sciences [q-bio], Tandem Mass Spectrometry, 570 Life sciences, biology, Female [MeSH], Molecular biology, Tandem Mass Spectrometry [MeSH], Proteome/metabolism [MeSH], Ovulation/physiology [MeSH], Oviducts/metabolism [MeSH], Developmental biology, Cattle [MeSH], Animals [MeSH], Fallopian Tubes/metabolism [MeSH], Animals, Cattle, Female, Fallopian Tubes
Abstract: Understanding the composition of the oviduct fluid (OF) is crucial to better comprehend the microenvironment in which sperm capacitation, fertilization and early embryo development take place. Therefore, our aim was to determine the spatiotemporal changes in the OF proteome according to the anatomical region of the oviduct (ampulla vs. isthmus), the proximity of the ovulating ovary (ipsilateral vs. contralateral side) and the peri-ovulatory stage (pre-ovulatory or Pre-ov vs. post-ovulatory or Post-ov). Oviducts from adult cyclic cows were collected at a local slaughterhouse and pools of OF were analyzed by nanoLC-MS/MS and label-free protein quantification (n = 32 OF pools for all region × stage × side conditions). A total of 3760 proteins were identified in the OF, of which 65% were predicted to be potentially secreted. The oviduct region was the major source of variation in protein abundance, followed by the proximity of the ovulating ovary and finally the peri-ovulatory stage. Differentially abundant proteins between regions, stages and sides were involved in a broad variety of biological functions, including protein binding, response to stress, cell-to-cell adhesion, calcium homeostasis and the immune system. This work highlights the dynamic regulation of oviduct secretions and provides new protein candidates for interactions between the maternal environment, the gametes and the early embryo.
Published: 2022
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8. Temperature synchronizes temporal variation in laying dates across European hole-nesting passerines

Author: Stefan J. G. Vriend, Vidar Grøtan, Marlène Gamelon, Frank Adriaensen, Markus P. Ahola, Elena Álvarez, Liam D. Bailey, Emilio Barba, Jean‐Charles Bouvier, Malcolm D. Burgess, Andrey Bushuev, Carlos Camacho, David Canal, Anne Charmantier, Ella F. Cole, Camillo Cusimano, Blandine F. Doligez, Szymon M. Drobniak, Anna Dubiec, Marcel Eens, Tapio Eeva, Kjell Einar Erikstad, Peter N. Ferns, Anne E. Goodenough, Ian R. Hartley, Shelley A. Hinsley, Elena Ivankina, Rimvydas Juškaitis, Bart Kempenaers, Anvar B. Kerimov, John Atle Kålås, Claire Lavigne, Agu Leivits, Mark C. Mainwaring, Jesús Martínez‐Padilla, Erik Matthysen, Kees van Oers, Markku Orell, Rianne Pinxten, Tone Kristin Reiertsen, Seppo Rytkönen, Juan Carlos Senar, Ben C. Sheldon, Alberto Sorace, János Török, Emma Vatka, Marcel E. Visser, Bernt‐Erik Sæther, Animal Ecology (AnE), Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Department of Biology [Trondheim] (IBI NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), University of Antwerp (UA), Swedish Museum of Natural History (NRM), Unidad de Investigación, Fundación Hospital de Jove, Universitad Politecnica de Valencia, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Bedfordshire, 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)-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, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Oxford [Oxford], Università degli studi di Palermo - University of Palermo, University of New South Wales [Sydney] (UNSW), Polish Academy of Sciences (PAN), Behavioural Ecology & Ecophysiology Group, University of Turku, High North Research Centre for Climate and the Environment, Norwegian Polar Institute, Centre for Conservation Biology, University of Gloucestershire (Cheltenham, GB), Lancaster University, Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Centre de Recherche en Informatique de Paris 1 (CRI), Université Paris 1 Panthéon-Sorbonne (UP1), Nature Research Centre, Institute of Ecology, Akademijos str. 2, LT-08412, Vilnius, Lithuania., Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Evolutionary Ecology Group, Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València (UV), University of Exeter, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Oxford, Department of Agriculture and Forest Sciences, Centre National de la Recherche Scientifique (CNRS), Museum and Institute of Zoology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Department of Biology (Ethology), Cardiff University, University of Gloucestershire [Gloucester], Institute of Ecology of Nature Research Centre, University of Montana, Instituto Pirenaico de Ecologia = Pyrenean Institute of Ecology (IPE), Netherlands Institute of Ecology (NIOO-KNAW), Department of Ecology, University of Oulu, Norwegian Institute for Nature Research (NINA), Museu de Ciències Naturals de Barcelona, and SROPU
Subjects: Ekologi, clutch size, Evolutionary Biology, comparative analysis, Ecology, [SDV]Life Sciences [q-bio], weather, passerines, timing of breeding, phenology, Ecology and Environment, Evolutionsbiologi, spatial synchrony, Chemistry, fledgling number, birds, 1181 Ecology, evolutionary biology, clutch, fitness-related traits, Biology, climate, Ecology, Evolution, Behavior and Systematics
Abstract: Identifying the environmental drivers of variation in fitness-related traits is a central objective in ecology and evolutionary biology. Temporal fluctuations of these environmental drivers are often synchronized at large spatial scales. Yet, whether synchronous environmental conditions can generate spatial synchrony in fitness-related trait values (i.e., correlated temporal trait fluctuations across populations) is poorly understood. Using data from long-term monitored populations of blue tits (Cyanistes caeruleus, n = 31), great tits (Parus major, n = 35), and pied flycatchers (Ficedula hypoleuca, n = 20) across Europe, we assessed the influence of two local climatic variables (mean temperature and mean precipitation in February–May) on spatial synchrony in three fitness-related traits: laying date, clutch size, and fledgling number. We found a high degree of spatial synchrony in laying date but a lower degree in clutch size and fledgling number for each species. Temperature strongly influenced spatial synchrony in laying date for resident blue tits and great tits but not for migratory pied flycatchers. This is a relevant finding in the context of environmental impacts on populations because spatial synchrony in fitness-related trait values among populations may influence fluctuations in vital rates or population abundances. If environmentally induced spatial synchrony in fitness-related traits increases the spatial synchrony in vital rates or population abundances, this will ultimately increase the risk of extinction for populations and species. Assessing how environmental conditions influence spatiotemporal variation in trait values improves our mechanistic understanding of environmental impacts on populations. birds, climate, clutch size, comparative analysis, fitness-related traits, fledgling number, phenology, spatial synchrony, timing of breeding, weather
Published: 2022
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9. Connecting the data landscape of long‐term ecological studies: the SPI‐Birds data hub

Author: Culina, Antica, Adriaensen, Frank, Bailey, Liam, Burgess, Malcolm, Charmantier, Anne, Cole, Ella, Eeva, Tapio, Matthysen, Erik, Nater, Chloé, Sheldon, Ben, Sæther, Bernt‐erik, Vriend, Stefan J.G., Zajkova, Zuzana, Adamík, Peter, Aplin, Lucy, Angulo, Elena, Artemyev, Alexandr, Barba, Emilio, Barišić, Sanja, Belda, Eduardo, Can Bilgin, C., Bleu, Josefa, Both, Christiaan, Bouwhuis, Sandra, Branston, Claire, Broggi, Juli, Burke, Terry, Bushuev, Andrey, Camacho, Carlos, Campobello, Daniela, Canal, David, Cantarero, Alejandro, Caro, Samuel, Cauchoix, Maxime, Chaine, Alexis, Cichoń, Mariusz, Ćiković, Davor, Cusimano, Camillo, Deimel, Caroline, Dhondt, André, Dingemanse, Niels, Doligez, Blandine, Dominoni, Davide, Doutrelant, Claire, Drobniak, Szymon, Dubiec, Anna, Eens, Marcel, Erikstad, Kjell Einar, Espín, Silvia, Farine, Damien, Figuerola, Jordi, Kavak Gülbeyaz, Pinar, Grégoire, Arnaud, Hartley, Ian, Hau, Michaela, Hegyi, Gergely, Hille, Sabine, Hinde, Camilla, Holtmann, Benedikt, Ilyina, Tatyana, Isaksson, Caroline, Iserbyt, Arne, Ivankina, Elena, Kania, Wojciech, Kempenaers, Bart, Kerimov, Anvar, Komdeur, Jan, Korsten, Peter, Král, Miroslav, Krist, Miloš, Lambrechts, Marcel, Lara, Carlos, Leivits, Agu, Liker, András, Lodjak, Jaanis, Mägi, Marko, Mainwaring, Mark, Mänd, Raivo, Massa, Bruno, Massemin, Sylvie, Martínez‐padilla, Jesús, Mazgajski, Tomasz, Mennerat, Adele, Moreno, Juan, Mouchet, Alexia, Nakagawa, Shinichi, Nilsson, Jan‐åke, Nilsson, Johan, Norte, Ana Cláudia, Oers, Kees Van, Orell, Markku, Potti, Jaime, Quinn, John, Réale, Denis, Reiertsen, Tone Kristin, Rosivall, Balázs, Russel, Andrew, Rytkönen, Seppo, Sánchez‐virosta, Pablo, Santos, Eduardo S.A., Schroeder, Julia, Senar, Juan Carlos, Seress, Gábor, Slagsvold, Tore, Szulkin, Marta, Teplitsky, Céline, Tilgar, Vallo, Tolstoguzov, Andrey, Török, János, Valcu, Mihai, Vatka, Emma, Verhulst, Simon, Visser, Marcel, Watson, Hannah, Yuta, Teru, Zamora‐marín, José, Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), University of Antwerp (UA), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, University of Exeter, 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), University of Oxford, University of Turku, Trondheim University, Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), 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: FAIR data, long-term studies, MESH: animals, meta-data standards, research network, birds, MESH: birds, [SDE]Environmental Sciences, MESH: databases, factual, MESH: metadata, data standards, database
Abstract: International audience; The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change).To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)—a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting.SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language).The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.
Published: 2021
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10. Mothers with higher twinning propensity had lower fertility in pre-industrial Europe

Author: Ian J. Rickard, Colin Vullioud, François Rousset, Erik Postma, Samuli Helle, Virpi Lummaa, Ritva Kylli, Jenni E. Pettay, Eivin Røskaft, Gine R. Skjærvø, Charlotte Störmer, Eckart Voland, Dominique Waldvogel, Alexandre Courtiol, Department of Anthropology [Durham University], Durham University, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), University of Exeter, University of Turku, Université d'Oulu, Trondheim University, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), and Universität Zürich [Zürich] = University of Zurich (UZH)
Subjects: Adult, Female [MeSH], General Chemistry, Adult [MeSH], Multidisciplinary, Humans [MeSH], Parturition [MeSH], Behavioural ecology, Fertility [MeSH], Twins [MeSH], Middle Aged [MeSH], General Biochemistry, Genetics and Molecular Biology, Europe/epidemiology [MeSH], Maternal Age [MeSH], Human behaviour, Biological anthropology, Young Adult [MeSH], Mothers [MeSH], Statistical methods, Pregnancy [MeSH], General Physics and Astronomy, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Parturition, Twins, Mothers, [SHS.DEMO]Humanities and Social Sciences/Demography, Middle Aged, Europe, Young Adult, Fertility, Pregnancy, Humans, Female, Maternal Age
Abstract: Historically, mothers producing twins gave birth, on average, more often than non-twinners. This observation has been interpreted as twinners having higher intrinsic fertility – a tendency to conceive easily irrespective of age and other factors – which has shaped both hypotheses about why twinning persists and varies across populations, and the design of medical studies on female fertility. Here we show in >20k pre-industrial European mothers that this interpretation results from an ecological fallacy: twinners had more births not due to higher intrinsic fertility, but because mothers that gave birth more accumulated more opportunities to produce twins. Controlling for variation in the exposure to the risk of twinning reveals that mothers with higher twinning propensity – a physiological predisposition to producing twins – had fewer births, and when twin mortality was high, fewer offspring reaching adulthood. Twinning rates may thus be driven by variation in its mortality costs, rather than variation in intrinsic fertility.
Published: 2021
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11. Impacts of land use on an insectivorous tropical bat: The importance of mercury, physio-immunology and trophic position

Author: Gábor Á. Czirják, David Costantini, Christian C. Voigt, Sara Bumrungsri, Paco Bustamante, Department of Biology (University of Antwerp), University of Antwerp (UA), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Muséum national d'Histoire naturelle (MNHN), Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Leibniz Institute for Zoo and Wildlife Research, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Prince of Songkla University (PSU), and Freie Universität Berlin
Subjects: Environmental Engineering, 010504 meteorology & atmospheric sciences, Population, Wildlife, Biodiversity, 010501 environmental sciences, Biology, Southeast asian, 01 natural sciences, Antioxidants, Deforestation, Environmental Chemistry, education, Waste Management and Disposal, Stable isotopes, 0105 earth and related environmental sciences, Trophic level, education.field_of_study, Ecology, Agriculture, Insectivore, 15. Life on land, Pollution, Chemistry, Habitat, Oxidative stress, Rice, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology
Abstract: Deforestation, agricultural intensification, and habitat homogenization are critical threats to biodiversity in Southeast Asia. Limited information is available on the trophic and physiological responses of tropical animals to these environmental changes. The wrinkle-lipped free-tailed bat Chaerephon plicatus is a cave roosting species that is experiencing population declines across Southeast Asia, where landscapes have been drastically modified. In our study site in central Thailand, we tested the hypothesis that wrinkle-lipped free-tailed bats living in landscapes that contrast in heterogeneity and land-use differed in mercury contamination, trophic position and physio-immunological status. Bats from less heterogeneous landscapes (dominated by rice crops, absence of large forest patches) occupied a lower trophic position than conspecifics from more heterogeneous landscapes (including large forest patches). Additionally, bats from these habitats had lower concentrations of mercury in erythrocytes, lower body mass, higher antioxidant superoxide dismutase (SOD), lower antioxidant glutathione peroxidase (GPx) and lower values of the GPx/SOD ratio than bats from more heterogeneous landscapes. Individual bat mercury concentrations were positively correlated with body mass and two immune markers (lysozyme and immunoglobulin) but were negatively correlated with plasma non-enzymatic antioxidant capacity. Our results suggest various links among landscape heterogeneity, mercury exposure/accumulation, and health status of wildlife in Southeast Asian countries. (C) 2019 Elsevier B.V. All rights reserved.
Published: 2019
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12. Productivity and Change in Fish and Squid in the Southern Ocean

Author: Jilda Alicia Caccavo, Henrik Christiansen, Andrew J. Constable, Laura Ghigliotti, Rowan Trebilco, Cassandra M. Brooks, Cédric Cotte, Thomas Desvignes, Tracey Dornan, Christopher D. Jones, Philippe Koubbi, Ryan A. Saunders, Anneli Strobel, Marino Vacchi, Anton P. van de Putte, Andrea Walters, Claire M. Waluda, Briannyn L. Woods, José C. Xavier, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Laboratory of Biodiversity and Evolutionary Genomics, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Institute for Marine and Antarctic Studies and Centre for Marine Socioecology, University of Tasmania [Hobart, Australia] (UTAS), Institute for the Study of the Anthropic Impacts and the Sustainability in the Marine Environment (IAS), Consiglio Nazionale delle Ricerche (CNR), CISRO Oceans and Atmosphere, Environmental Studies Program, University of Colorado [Boulder], Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), 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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-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)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), University of Oregon [Eugene], School of Biological Sciences [Bristol], University of Bristol [Bristol], Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Biotechnologies et Ressources Marines (IFREMER BRM), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Alfred Wegener Institute for Polar and Marine Research (AWI), Royal Belgian Institute of Natural Sciences (RBINS), Marine and Environmental Sciences Centre (MARE UC), Universidade de Coimbra [Coimbra], National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Biotechnologies et Ressources Marines (BRM), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: 0106 biological sciences, Environmental change, TOOTHFISH DISSOSTICHUS-MAWSONI, TERRA-NOVA BAY, 01 natural sciences, LIFE-HISTORY CONNECTIVITY, QH540-549.5, education.field_of_study, Biomass (ecology), biology, Ecology, Fisheries and climate change, SPECIES NOTOTHENIA-ROSSII, climate change, DUMONT DURVILLE SEA, marine ecosystem assessment, PATAGONIAN TOOTHFISH, SPATIAL-DISTRIBUTION, Life Sciences & Biomedicine, notothenioids, POPULATION GENETIC-STRUCTURE, squid, Krill, Evolution, Population, Climate change, Environmental Sciences & Ecology, 010603 evolutionary biology, fisheries, conservation management, myctophids, Antarctic, QH359-425, Ecosystem, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Science & Technology, ICEFISH CHAENOCEPHALUS-ACERATUS, 010604 marine biology & hydrobiology, Global warming, 15. Life on land, biology.organism_classification, Fishery, 13. Climate action, PLEURAGRAMMA-ANTARCTICUM PISCES, Environmental science, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Southern Ocean ecosystems are globally important and vulnerable to global drivers of change, yet they remain challenging to study. Fish and squid make up a significant portion of the biomass within the Southern Ocean, filling key roles in food webs from forage to mid-trophic species and top predators. They comprise a diverse array of species uniquely adapted to the extreme habitats of the region. Adaptations such as antifreeze glycoproteins, lipid-retention, extended larval phases, delayed senescence, and energy-conserving life strategies equip Antarctic fish and squid to withstand the dark winters and yearlong subzero temperatures experienced in much of the Southern Ocean. In addition to krill exploitation, the comparatively high commercial value of Antarctic fish, particularly the lucrative toothfish, drives fisheries interests, which has included illegal fishing. Uncertainty about the population dynamics of target species and ecosystem structure and function more broadly has necessitated a precautionary, ecosystem approach to managing these stocks and enabling the recovery of depleted species. Fisheries currently remain the major local driver of change in Southern Ocean fish productivity, but global climate change presents an even greater challenge to assessing future changes. Parts of the Southern Ocean are experiencing ocean-warming, such as the West Antarctic Peninsula, while other areas, such as the Ross Sea shelf, have undergone cooling in recent years. These trends are expected to result in a redistribution of species based on their tolerances to different temperature regimes. Climate variability may impair the migratory response of these species to environmental change, while imposing increased pressures on recruitment. Fisheries and climate change, coupled with related local and global drivers such as pollution and sea ice change, have the potential to produce synergistic impacts that compound the risks to Antarctic fish and squid species. The uncertainty surrounding how different species will respond to these challenges, given their varying life histories, environmental dependencies, and resiliencies, necessitates regular assessment to inform conservation and management decisions. Urgent attention is needed to determine whether the current management strategies are suitably precautionary to achieve conservation objectives in light of the impending changes to the ecosystem.
Published: 2021
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13. Sex‐specific spatial variation in fitness in the highly dimorphic Leucadendron rubrum

Author: Ophélie Ronce, Isabelle Olivieri, Sylvie Oddou-Muratorio, Jeanne Tonnabel, Etienne K. Klein, Alexandre Courtiol, Agnès Mignot, François Rousset, 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, Université de Lausanne (UNIL), Department of Ecology and Evolution (UNIL-SORGE), Biostatistique et Processus Spatiaux (BioSP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of British Columbia (UBC), Ecologie des Forêts Méditerranéennes (URFM), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, This work was supported by a grant from the FRB to I.O. and A.M., from the ANR Evorange, ANR-09-PEXT-011 to O.R. and from the ANR MeCC, ANR-13-ADAP-006 to O.R., E.K.K. and S.O.M. J.T. was supported by a grant to John Pannell from the Swiss National Science Foundation (SNSF) 31003A_163384. O.R. acknowledges support from the Peter Wall Institute of Advanced Studies, UBC, and from CNRS.31003A_163384, ANR-09-PEXT-0011,EVORANGE,Comment l'évolution affecte-t-elle la dynamique d'extinction et de changements d'aire dans le contexte des changements globaux ? Implications pour les projections écologiques(2009), ANR-13-ADAP-0006,MeCC,Mécanismes de l'adaptation au Changement Climatique: comment plasticité phénotypique, micro-évolution et migration affecteront-elles la phénologie des arbres forestiers ?(2013), 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), and Université de Lausanne = University of Lausanne (UNIL)
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Seed dispersal, Zoology, Wind, Biology, Spatial distribution, 010603 evolutionary biology, 01 natural sciences, Proteaceae, cost of reproduction, 03 medical and health sciences, Genetics, Animals, sexual selection, dispersal kernels, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Sex Characteristics, selection gradients, Directional selection, spatial structure, Fecundity, Sexual dimorphism, 030104 developmental biology, Fertility, Phenotype, Sexual selection, sexual dimorphism, Biological dispersal, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: We dedicate this manuscript to I.O. who passed away before the completion of this study, which she initiated. She inspired and is still inspiring our research in many ways.; International audience; Sexual dimorphism in plants may emerge as a result of sex-specific selection on traits enhancing access to nutritive resources and/or to sexual partners. Here we investigated sex-specific differences in selection of sexually dimorphic traits and in the spatial distribution of effective fecundity (our fitness proxy) in a highly dimorphic dioecious wind-pollinated shrub, Leucadendron rubrum. In particular, we tested for the effect of density on male and female effective fecundity. We used spatial and genotypic data of parent and offspring cohorts to jointly estimate individual male and female effective fecundity on the one hand and pollen and seed dispersal kernels on the other hand. This methodology was adapted to the case of dioecious species. Explicitly modelling dispersal avoids the confounding effects of heterogeneous spatial distribution of mates and sampled seedlings on the estimation of effective fecundity. We also estimated selection gradients on plant traits while modelling sex-specific spatial autocorrelation in fecundity. Males exhibited spatial autocorrelation in effective fecundity at a smaller scale than females. A higher local density of plants was associated with lower effective fecundity in males but was not related to female effective fecundity. These results suggest sex-specific sensitivities to environmental heterogeneity in L. rubrum. Despite these sexual differences, we found directional selection for wider canopies and smaller leaves in both sexes, and no sexually antagonistic selection on strongly dimorphic traits in L. rubrum. Many empirical studies in animals similarly failed to detect sexually antagonistic selection in species expressing strong sexual dimorphism, and we discuss reasons explaining this common pattern.
Published: 2021
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14. General statistical scaling laws for stability in ecological systems

Author: Yuval R. Zelnik, Lauren G. Shoemaker, Claire Jacquet, Ian Donohue, Adam Thomas Clark, Shaopeng Wang, Stanley Harpole, Andrea Mentges, Canan Karakoç, Thorsten Wiegand, Viktoriia Radchuk, Jean-François Arnoldi, Andreas Huth, Michel Loreau, Franziska Taubert, Jonathan M. Chase, Sara König, Dorian Nothaaß, György Barabás, Claire de Mazancourt, Dorothee Hodapp, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Karl-Franzens-Universität Graz, German Centre for Integrative Biodiversity Research (iDiv), Trinity College Dublin, Swedish University of Agricultural Sciences (SLU), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Linköping University (LIU), Helmholtz Institute Ulm (HIU), Alfred Wegener Institute for Polar and Marine Research (AWI), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Universität Zürich [Zürich] = University of Zurich (UZH), Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland and ETH Zürich, Universitätstrasse 16, CH-8092 Zürich, Switzerland, Martin-Luther-University Halle-Wittenberg, University of Wyoming (UW), Peking University [Beijing], ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), and European Project: 666971,H2020,ERC-2014-ADG,BIOSTASES(2015)
Subjects: 0106 biological sciences, Dynamical systems theory, Computer science, Population, population, Context (language use), invariability, Ecological systems theory, 010603 evolutionary biology, 01 natural sciences, Stability (probability), diversity, resistance, Econometrics, invariance, education, resilience, community, disturbance, temporal, spatial, Scaling, Ecology, Evolution, Behavior and Systematics, Ecosystem, Ecological stability, Ekologi, education.field_of_study, Resistance (ecology), Ecology, 010604 marine biology & hydrobiology, Research Design, [SDE]Environmental Sciences
Abstract: Ecological stability refers to a family of concepts used to describe how systems of interacting species vary through time and respond to disturbances. Because observed ecological stability depends on sampling scales and environmental context, it is notoriously difficult to compare measurements across sites and systems. Here, we apply stochastic dynamical systems theory to derive general statistical scaling relationships across time, space, and ecological level of organisation for three fundamental stability aspects: resilience, resistance, and invariance. These relationships can be calibrated using random or representative samples measured at individual scales, and projected to predict average stability at other scales across a wide range of contexts. Moreover deviations between observed vs. extrapolated scaling relationships can reveal information about unobserved heterogeneity across time, space, or species. We anticipate that these methods will be useful for cross-study synthesis of stability data, extrapolating measurements to unobserved scales, and identifying underlying causes and consequences of heterogeneity. Funding Agencies|TULIP French Laboratory of Excellence [ANR-10-LABX-41, ANR-11-IDEX-0002-02]; Swedish Research CouncilSwedish Research CouncilEuropean Commission [VR 2017-05245]; Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [FZT 118]; NSFNational Science Foundation (NSF) [EPS-1655726]; Horizon 2020 Framework Programme [666971]
Published: 2021
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15. Keeping modelling notebooks with TRACE

Author: J. Gareth Polhill, Romina Martin, Julita Stadnicka-Michalak, Amelie Schmolke, Pernille Thorbek, Hans Baveco, Thomas G. Preuss, E. Emiel van Loon, Cyril Piou, Cara A. Gallagher, Volker Grimm, Andreas Focks, Sandrine Charles, Daniel Ayllón, Chun Liu, Jacob Nabe-Nielsen, Nika Galic, Uta Berger, Jacqueline Augusiak, Viktoriia Radchuk, Steven F. Railsback, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Lang Railsback & Associates, Department of Bioscience [Aarhus], Charles River Laboratories Den Bosch B.V. (CRIVER), Wageningen University and Research [Wageningen] (WUR), Wageningen Environmental Research (Alterra), Technische Universität Dresden = Dresden University of Technology (TU Dresden), Dresden University of Technology - Institute of Soil Science and Site Ecology, Tharandt, Allemagne, Partenaires INRAE, 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), Stockholm University, Syngenta Crop Protection LLC, Jealott’s Hill International Research Centre, Syngenta, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), The James Hutton Institute, Bayer Pharma AG [Berlin], Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Waterborne Environmental Inc., Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), BASF SE, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), University of Potsdam = Universität Potsdam, D. Ayllon was financially supported by the Spanish Ministry of Economy, Industry and Competitiveness through the research project CGL 2017-84269-P. S. Charles is participating under the umbrella of the Graduate School H2O'Lyon (ANR-17-EURE-0018) and 'Université de Lyon' (UdL), as part of the program 'Investissements d'Avenir' run by 'Agence Nationale de la Recherche' (ANR). C. Piou participated under the funding from ANR-JCJC PEPPER (ANR-18-CE32-0010-01). J. G. Polhill receives funding from the Scottish Government Rural Affairs Food and Environment Strategic Research Programme., ANR-17-EURE-0018,H2O'LYON,School of Integrated Watershed Sciences(2017), ANR-18-CE32-0010,PEPPER,Etude de l'émergence du polyphénisme de phase et des risques associés(2018), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Potsdam, and Theoretical and Computational Ecology (IBED, FNWI)
Subjects: Environmental Risk Assessment, 0106 biological sciences, Standards, Environmental Engineering, Process (engineering), Computer science, [SDV]Life Sciences [q-bio], Environmental modelling, Documentation, Reuse, Modelling cycle, 010603 evolutionary biology, 01 natural sciences, Norme, Reproducible research, Terminology, 03 medical and health sciences, Scientific communication, Model documentation, Diffusion de la recherche, Modélisation environnementale, Reliability (statistics), 030304 developmental biology, TRACE (psycholinguistics), Structure (mathematical logic), 0303 health sciences, WIMEK, U10 - Informatique, mathématiques et statistiques, Ecological Modeling, Modèle de simulation, Transparency (behavior), Data science, Modélisation, Diffusion de l'information, U30 - Méthodes de recherche, système d'aide à la décision, Software, Gestion de l'environnement
Abstract: International audience; The acceptance and usefulness of simulation models are often limited by the efficiency, transparency, reproducibility, and reliability of the modelling process. We address these issues by suggesting that modellers (1) "trace" the iterative modelling process by keeping a modelling notebook corresponding to the laboratory notebooks used by empirical researchers, (2) use a standardized notebook structure and terminology based on the existing TRACE documentation framework, and (3) use their notebooks to compile TRACE documents that supplement publications and reports. These practices have benefits for model developers, users, and stakeholders: improved and efficient model design, analysis, testing, and application; increased model acceptance and reuse; and replicability and reproducibility of the model and the simulation experiments. Using TRACE terminology and structure in modelling notebooks facilitates production of TRACE documents. We explain the rationale of TRACE, provide example TRACE documents, and suggest strategies for keeping "TRACE Modelling Notebooks."Highlights:• The quality and reproducibility of modelling would be increased by keeping modelling notebooks.• Simulation modellers have not yet developed a strong culture of keeping notebooks.• We propose a standard format for notebooks based on the TRACE document framework.• We make recommendations about the type of information to be included in the notebooks.• We describe existing tools to keep notebooks.
Published: 2021
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16. Amino acids activate mTORC1 to release roe deer embryos from decelerated proliferation during diapause

Author: van der Weijden, Vera A, Bick, Jochen T, Bauersachs, Stefan, Rüegg, Anna B, Hildebrandt, Thomas B, Goeritz, Frank, Jewgenow, Katarina, Giesbertz, Pieter, Daniel, Hannelore, Derisoud, Emilie, Chavatte-Palmer, Pascale, Bruckmaier, Rupert M, Drews, Barbara, Ulbrich, Susanne E, University of Zurich, Ulbrich, Susanne E, Animal Physiology, Institute of Agricultural sciences, ETH, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Universität Zürich [Zürich] = University of Zurich (UZH), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Technische Universität München [München] (TUM), Biologie de la Reproduction, Environnement, Epigénétique & Développement (BREED), École nationale vétérinaire d'Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Veterinary Physiology, Vetsuisse Faculty, and Zurich Center for Integrative Human Physiology (ZIHP), Swiss National Science Foundation (31003A_159734 and 310030_185026), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), and Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École nationale vétérinaire d'Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)
Subjects: Physiology, 10077 Institute of Veterinary Anatomy, gamete, embryo, Embryonic Development, Mechanistic Target of Rapamycin Complex 1, embryonic diapause, gonad, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Pregnancy, Animals, roe deer, Amino Acids, European roe deer (Capreolus capreolus), Cell Proliferation, 1000 Multidisciplinary, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, 630 Agriculture, embryo development, Deer, Gene Expression Profiling, Uterus, Biological Sciences, Embryo, Mammalian, Diapause, Blastocyst, Cellular Microenvironment, 570 Life sciences, biology, Female
Abstract: Significance In mammals, embryo development can halt at the hatched blastocyst stage. Uniquely, proliferation of diapausing embryonic roe deer cells decelerates to a doubling time of 2 to 3 wk over a period of 4 mo. We highlight nutrient sensing as an important factor regulating embryonic developmental pace. The resumption of embryo development is characterized by an increase in uterine fluid mTORC1-activating amino acids, embryonic mTORC1 activity, and expression of metabolism and cell cycle genes. We propose selective mTORC1 inhibition via reduced estrogen signaling and high let-7 levels as mechanisms for slow cell cycle progression. We hypothesize that it is the lack of embryonic mTORC2 inhibition during embryonic diapause in the roe deer that enables the continuous decelerated rate of proliferation., Embryonic diapause in mammals leads to a reversible developmental arrest. While completely halted in many species, European roe deer (Capreolus capreolus) embryos display a continuous deceleration of proliferation. During a 4-mo period, the cell doubling time is 2 to 3 wk. During this period, the preimplantation blastocyst reaches a diameter of 4 mm, after which it resumes a fast developmental pace to subsequently implant. The mechanisms regulating this notable deceleration and reacceleration upon developmental resumption are unclear. We propose that amino acids of maternal origin drive the embryonic developmental pace. A pronounced change in the abundance of uterine fluid mTORC1-activating amino acids coincided with an increase in embryonic mTORC1 activity prior to the resumption of development. Concurrently, genes related to the glycolytic and phosphate pentose pathway, the TCA cycle, and one carbon metabolism were up-regulated. Furthermore, the uterine luminal epithelial transcriptome indicated increased estradiol-17β signaling, which likely regulates the endometrial secretions adapting to the embryonic needs. While mTORC1 was predicted to be inactive during diapause, the residual embryonic mTORC2 activity may indicate its involvement in maintaining the low yet continuous proliferation rate during diapause. Collectively, we emphasize the role of nutrient signaling in preimplantation embryo development. We propose selective mTORC1 inhibition via uterine catecholestrogens and let-7 as a mechanism regulating slow stem cell cycle progression.
Published: 2021
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17. Intravital dynamic and correlative imaging reveals diffusion‐dominated canalicular and flow‐augmented ductular bile flux

Author: Vartak, Nachiket, Guenther, Georgia, Joly, Florian, Damle-Vartak, Amruta, Wibbelt, Gudrun, Fickel, Jörns, Jörs, Simone, Begher-Tibbe, Brigitte, Friebel, Adrian, Wansing, Kasimir, Ghallab, Ahmed, Rosselin, Marie, Boissier, Noemie, Vignon-Clementel, Irene, Hedberg, Christian, Geisler, Fabian, Hofer, Heribert, Jansen, Peter, Hoehme, Stefan, Drasdo, Dirk, Hengstler, Jan, Leibniz Research Centre for Working Environment and Human Factors [Dortmund] (IFADO), Technische Universität Dortmund [Dortmund] (TU), Modelling and Analysis for Medical and Biological Applications (MAMBA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, University of Potsdam, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Institut für Informatik [Leipzig], Universität Leipzig [Leipzig], South Valley University [Qena], Umeå University, Numerical simulation of biological flows (REO), Sorbonne Université (SU)-Inria de Paris, Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Freie Universität Berlin, University of Amsterdam [Amsterdam] (UvA), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Potsdam = Universität Potsdam, Universität Leipzig, SImulations en Médecine, BIOtechnologie et ToXicologie de systèmes multicellulaires (SIMBIOTX ), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and ANR-16-RHUS-0005,iLite,iLite(2016)
Subjects: [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.MHEP.AHA]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Bile flux proceeds by diffusion in canaliculi, Augmented by advection in ducts, digestive system
Abstract: International audience; Small-molecule flux in tissue-microdomains is essential for organ function, but knowledge of this process is scant due to the lack of suitable methods. We developed two independent techniques that allow the quantification of advection (flow) and diffusion in individual bile canaliculi and in interlobular bile ducts of intact livers in living mice, namely Fluorescence Loss After Photoactivation (FLAP) and Intravital Arbitrary Region Image Correlation Spectroscopy (IVARICS). The results challenge the prevailing 'mechano-osmotic' theory of canalicular bile flow. After active transport across hepatocyte membranes bile acids are transported in the canaliculi primarily by diffusion. Only in the interlobular ducts, diffusion is augmented by regulatable advection. Photoactivation of fluorescein bis-(5-carboxymethoxy-2-nitrobenzyl)-ether (CMNB-caged fluorescein) in entire lobules demonstrated the establishment of diffusive gradients in the bile canalicular network and the sink function of interlobular ducts. In contrast to the bile canalicular network, vectorial transport was detected and quantified in the mesh of interlobular bile ducts. In conclusion, the liver consists of a diffusion dominated canalicular domain, where hepatocytes secrete small molecules and generate a concentration gradient and a flow-augmented ductular domain, where regulated water influx creates unidirectional advection that augments the diffusive flux.
Published: 2020
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18. Reproductive capacity of an endangered and recovering population of humpback whales in the Southern Hemisphere

Author: Chero, Guillaume, Pradel, Roger, Derville, Solène, Bonneville, Claire, Gimenez, Olivier, Garrigue, Claire, Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC), 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), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Kélonia - Observatoire des tortues marines, Laboratoire d'Astrophysique de Marseille (LAM), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Université de la Nouvelle-Calédonie (UNC), 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), 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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: New Caledonia, Pacific population, Humpback whales, Recovery, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Calving rate, Calving interval, Sexual maturity, population, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Pacific
Abstract: International audience; Estimating demographic parameters is essential to assessing the recovery potential of severely depleted populations of marine mammal species such as the baleen whales, which were decimated by commercial whaling of the past century. The Oceania humpback whale Megaptera novaeangliae population is classified as endangered by the IUCN because of low numbers and a slow recovery rate. Nevertheless, an anomalously strong increase has recently been detected in the New Caledonia breeding population. To determine the drivers of population growth, reproductive parameters were estimated for the first time for a humpback whale population of Oceania. Based on an extensive monitoring program (1995-2018), recapture histories were reconstructed for 607 females and incorporated in multi-event capture-recapture models. As the females’ ages were generally unknown (87%), 2 models with contrasting age scenarios were investigated. For females of unknown age, the mature scenario assumed maturity at the first encounter, while the immature scenario assumed immaturity within 7 yr after the first encounter, unless the female was encountered breeding. These models respectively resulted in a calving interval of 1.49 yr (95% CI: 1.21-2.08) or 2.83 yr (95% CI: 2.28-3.56) and a calving rate of 0.67 or 0.35. The relatively high calving rate modelled by the mature model is consistent with high pregnancy rates recently observed in the migratory corridors of the Kermadec Islands and on the feeding grounds of the Antarctic Peninsula. Therefore, our results suggest that the recovery of the New Caledonia humpback whale population from past exploitation may be partially driven by an increased reproductive capacity.
Published: 2020
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19. Truly sedentary? The multi-range tactic as a response to resource heterogeneity and unpredictability in a large herbivore

Author: Benedikt Gehr, Atle Mysterud, Francesca Cagnacci, Marco Heurich, Petter Kjellander, A. J. Mark Hewison, Max Kroeschel, Pavel Sustr, Sandro Nicoloso, Ferdinando Urbano, Leif Soennichsen, John D. C. Linnell, Wibke Peters, Anne Berger, Simon Chamaillé-Jammes, Robin Sandfort, Nicolas Morellet, Ophélie Couriot, Sonia Saïd, Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Office National de la Chasse et de la Faune Sauvage (ONCFS), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Norwegian Institute for Nature Research (NINA), Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), LWF BAVARIAN STATE INSTITUTE OF FORESTRY FREISING DEU, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Independent Consultant, Bavarian Forest National Park, University of Freiburg [Freiburg], Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Research, Ecology and Environment Dimension ((D.R.E.Am. Italia)), Research, Ecology and Environment Dimension, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Czech Academy of Sciences [Prague] (CAS), National Park Sumava, Department of Soil and Environment, Forest Research Institute of Baden-Wuerttemberg, Polish Academy of Sciences (PAN), University of Natural Resources and Life Sciences (BOKU), Department of Evolutionary Biology and Environmental Studies, Universität Zürich [Zürich] = University of Zurich (UZH), CNERA Cervidés Sanglier (ONCFS), Office National de la Chasse et de la Faune Sauvage, Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), Department of Ecosystem and Conservation Science, Wildlife Biology Program, University of Montana, Dipartimento delle Arti e del Disegno Industriale [Venice], IUAV University Venice, Nationalparkverwaltung Bayerischer Wald, Swedish University of Agricultural Science (SLU), Service d'oncologie médicale [CHU HEGP], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Laboratoire de Comportement et d'Ecologie de la Faune Sauvage, INRA, 31326 Castanet-Tolosan cedex, France, University of Zurich, and Couriot, Ophélie
Subjects: 0106 biological sciences, Resource (biology), Range (biology), Resource distribution, migration, 010603 evolutionary biology, 01 natural sciences, 10127 Institute of Evolutionary Biology and Environmental Studies, Homing Behavior, Capreolus, Settore BIO/07 - ECOLOGIA, biology.animal, Animals, roe deer, Herbivory, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Herbivore, biology, Ecology, Deer, 010604 marine biology & hydrobiology, sub-seasonal functional home range, 15. Life on land, biology.organism_classification, Europe, Roe deer, 1105 Ecology, Evolution, Behavior and Systematics, plasticity, 570 Life sciences, 590 Animals (Zoology), Local environment, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, residency
Abstract: Much research on large herbivore movement has focused on the annual scale to distinguish between resident and migratory tactics, commonly assuming that individuals are sedentary at the within-season scale. However, apparently sedentary animals may occupy a number of sub-seasonal functional home ranges (sfHR), particularly when the environment is spatially heterogeneous and/or temporally unpredictable. The roe deer (Capreolus capreolus) experiences sharply contrasting environmental conditions due to its widespread distribution, but appears markedly sedentary over much of its range. Using GPS monitoring from 15 populations across Europe, we evaluated the propensity of this large herbivore to be truly sedentary at the seasonal scale in relation to variation in environmental conditions. We studied movement using net square displacement to identify the possible use of sfHR. We expected that roe deer should be less sedentary within seasons in heterogeneous and unpredictable environments, while migratory individuals should be seasonally more sedentary than residents. Our analyses revealed that, across the 15 populations, all individuals adopted a multi-range tactic, occupying between two and nine sfHR during a given season. In addition, we showed that (i) the number of sfHR was only marginally influenced by variation in resource distribution, but decreased with increasing sfHR size; and (ii) the distance between sfHR increased with increasing heterogeneity and predictability in resource distribution, as well as with increasing sfHR size. We suggest that the multirange tactic is likely widespread among large herbivores, allowing animals to track spatio-temporal variation in resource distribution and, thereby, to cope with changes in their local environment. Migration · Residency · Sub-seasonal functional home range · Plasticity · Roe deer
Published: 2018
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20. Progress on bringing together raptor collections in Europe for contaminant research and monitoring in relation to chemicals regulation

Author: Michel Guiraud, Guy Duke, Maria-Christina Nika, Veerle L.B. Jaspers, Alexander Badry, Fausto Barbagli, Burkhard Knopf, Koos Biesmeijer, Sylke Frahnert, Tibor I. Fuiz, Jan Koschorreck, Marcel Eens, Christian Sonne, Oliver Krone, Natalia Glowacka, Peter A. Hosner, Igor Eulaers, Didier Vangeluwe, Paola Movalli, Marco Pavia, Silvia Espín, Rui Lourenço, Rafael Mateo, Alessandra Cincinelli, Till Töpfer, Nikolaos S. Thomaidis, Eero Kubin, Georgios Gkotsis, Sabrina Lo Brutto, René W. R. J. Dekker, Pilar Gómez-Ramírez, Pepijn Kamminga, Gloria Ramello, Risto Väinölä, Andreia Dias, Nikiforos A. Alygizakis, Jari Valkama, Chris V. Wernham, Sara Danielsson, Daniel Osborn, Emma Martínez-López, Yael Choresh, Al Vrezec, Friederike Woog, M. Glória Pereira, Olivier S. G. Pauwels, Heinz Rüdel, Richard F. Shore, Tania Martellini, Steven van der Mije, Alexander L. Bond, Gabriele Treu, Giovanni Boano, Marco Grotti, Antonio J. García-Fernández, Jaroslav Slobodnik, Varvara Nikolopoulou, Pablo Sánchez-Virosta, Ben H. Warren, Ulf S. Johansson, Jan Bolding Christensen, Rune Dietz, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Museo Civico di Storia Naturale, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), National Environmental Research Institute (NERI), University of Antwerp (UA), Department of Bioscience [Aarhus], 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), University College of Borås, Instituto de Engenharia de Sistemas e Computadores (INESC), Instituto de Investigación en Recursos Cinegéticos (IREC), Institut Royal des Sciences Naturelles de Belgique (IRSNB), Dipartimento di Scienze della Terra, Università degli studi di Torino (UNITO), Environmental Institute, Department of Arctic Environment [Rockilde], National Environmental Research Institute [Danmark] (NERI)-Aarhus University [Aarhus], Department of Chemistry, Finnish Museum of Natural History (LUOMUS), University of Helsinki, 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), Staatliches Museum für Naturkunde Stuttgart (SMNS), Movalli P., Duke G., Ramello G., Dekker R., Vrezec A., Shore R.F., Garcia-Fernandez A., Wernham C., Krone O., Alygizakis N., Badry A., Barbagli F., Biesmeijer K., Boano G., Bond A.L., Choresh Y., Christensen J.B., Cincinelli A., Danielsson S., Dias A., Dietz R., Eens M., Espin S., Eulaers I., Frahnert S., Fuiz T.I., Gkotsis G., Glowacka N., Gomez-Ramirez P., Grotti M., Guiraud M., Hosner P., Johansson U., Jaspers V.L.B., Kamminga P., Koschorreck J., Knopf B., Kubin E., LoBrutto S., Lourenco R., Martellini T., Martinez-Lopez E., Mateo R., Nika M.-C., Nikolopoulou V., Osborn D., Pauwels O., Pavia M., Pereira M.G., Rudel H., Sanchez-Virosta P., Slobodnik J., Sonne C., Thomaidis N., Topfer T., Treu G., Vainola R., Valkama J., van der Mije S., Vangeluwe D., Warren B.H., Woog F., Publica, University of Helsinki, Zoology, and European Commission
Subjects: 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, Settore BIO/05 - Zoologia, 010501 environmental sciences, natural history museum, 01 natural sciences, Environmental monitoring, collection, ComputingMilieux_MISCELLANEOUS, chemicals regulation, environmental specimen bank, Ecology, Published Erratum, Environmental resource management, Environmental exposure, General Medicine, Pollution, Europe, Chemistry, Geography, Specimen collection, raptor, [SDV.TOX]Life Sciences [q-bio]/Toxicology, 1181 Ecology, evolutionary biology, Environmental Pollutants, contaminant, Environmental Monitoring, Resource (biology), Relation (database), MEDLINE, chemicals management, Chemical management, Environmental Chemistry, Ecotoxicology, Animals, collections, Biology, Environmental planning, 0105 earth and related environmental sciences, Raptors, business.industry, apex predator, [SDE.ES]Environmental Sciences/Environmental and Society, monitoring, biomonitoring, Specimen Handling, REACH, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental specimen, business
Abstract: Paola Movalli et al., European Raptor Biomonitoring Facility COST Action (CA16224) is supported by COST (European Cooperation in Science and Technology) and funded by the Horizon 2020 Framework Programme of the European Union. Life APEX is financed by the European Union through the program LIFE17ENV/SK/000355‘Systematic use ofcontaminant data from apex predators and their prey in chemicals management’.
Published: 2019
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21. Fear of the dark? Contrasting impacts of humans versus lynx on diel activity of roe deer across Europe

Author: Nicolas Morellet, Leif Sönnichsen, Francesca Cagnacci, Ophélie Couriot, Benedikt Gehr, Johannes De Groeve, Max Kröschel, Nadège C. Bonnot, A. J. Mark Hewison, Anne Berger, Petter Kjellander, Marco Heurich, Simone Ciuti, University of Zurich, Vander Wal, Eric, Bonnot, Nadège C, Ecosystèmes forestiers (UR EFNO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Fondazione Edmund Mach [San Michele all'Adige], University College Dublin [Dublin] (UCD), Polish Academy of Sciences (PAN), Universität Zürich [Zürich] = University of Zurich (UZH), University of Freiburg [Freiburg], Bavarian Forest National Park, Forest Research Institute Baden-Württemberg - Forstliche Versuchs- und Forschungsanstalt Baden-Württemberg, ANR-16-CE02-0010-02, N N304172536, Mammal Research Institute - Polish Academy of Sciences, Leibniz-Institut fur Zoo-und Wildtierforschung, Marie Claire Cronstedts Stiftelse, Polish Mammal Research Institute - Polish Academy of Sciences, Leibniz-Institut für Zoo- und Wildtierforschung, Agence Nationale de la Recherche, Grant/Award Number: ANR-16-CE02-0010-02, Marie-Claire Cronstedts Stiftelse, Polish Ministry of Science and Higher Education, Grant/Award Number: N N304172536, and ANR-16-CE02-0010,Mov-It,Le mouvement des ongulés au sein de paysages hétérogènes: identification des processus comportementaux reliant les changements globaux aux performances démographiques et à la gestion spatialement explicite(2016)
Subjects: 0106 biological sciences, REPARTITION TEMPORELLE DE L'ACTIVITE, NOCTURNALITY, 01 natural sciences, Predation, ACCELEROMETRES, DIURNALITE, biology, Ecology, INTERACTION PREDATEURS PROIES, CREPUSCULARITY, URBANIZATION, Fear, HUMAN FOOTPRINT, Predator– prey interaction, Roe deer, Europe, TEMPORAL PARTITIONING, [SDE]Environmental Sciences, Lynx, 590 Animals (Zoology), NOCTURNALITE, PAYSAGE DE LA PEUR, Ungulate, Evolution, LANDSCAPE OF FEAR, Context (language use), PREDATOR-PREY INTERACTION, 010603 evolutionary biology, Hunting season, 10127 Institute of Evolutionary Biology and Environmental Studies, Capreolus, EMPREINTE HUMAINE, Behavior and Systematics, Settore BIO/07 - ECOLOGIA, biology.animal, Hunting, Animals, Humans, ACCELEROMETERS, Diurnality, CREPUSCULARITE, Diel vertical migration, Ecology, Evolution, Behavior and Systematics, Ecosystem, 010604 marine biology & hydrobiology, Deer, 15. Life on land, biology.organism_classification, 1105 Ecology, Evolution, Behavior and Systematics, DIURNALITY, Predatory Behavior, 570 Life sciences, Animal Science and Zoology, 1103 Animal Science and Zoology, URBANISATION
Abstract: Humans, as super predators, can have strong effects on wildlife behaviour, including profound modifications of diel activity patterns. Subsequent to the return of large carnivores to human-modified ecosystems, many prey species have adjusted their spatial behaviour to the contrasting landscapes of fear generated by both their natural predators and anthropogenic pressures. The effects of predation risk on temporal shifts in diel activity of prey, however, remain largely unexplored in human-dominated landscapes. We investigated the influence of the density of lynx Lynx lynx, a nocturnal predator, on the diel activity patterns of their main prey, the roe deer Capreolus capreolus, across a gradient of human disturbance and hunting at the European scale. Based on 11 million activity records from 431 individually GPS-monitored roe deer in 12 populations within the EURODEER network (http://eurodeer.org), we investigated how lynx predation risk in combination with both lethal and non-lethal human activities affected the diurnality of deer. We demonstrated marked plasticity in roe deer diel activity patterns in response to spatio-temporal variations in risk, mostly due to human activities. In particular, roe deer decreased their level of diurnality by a factor of 1.37 when the background level of general human disturbance was high. Hunting exacerbated this effect, as during the hunting season deer switched most of their activity to night-time and, to a lesser extent, to dawn, although this pattern varied noticeably in relation to lynx density. Indeed, in the presence of lynx, their main natural predator, roe deer were relatively more diurnal. Overall, our results revealed a strong influence of human activities and the presence of lynx on diel shifts in roe deer activity. In the context of the recovery of large carnivores across Europe, we provide important insights about the effects of predators on the behavioural responses of their prey in human-dominated ecosystems. Modifications in the temporal partitioning of ungulate activity as a response to human activities may facilitate human-wildlife coexistence, but likely also have knock-on effects for predator-prey interactions, with cascading effects on ecosystem functioning.Résumé Les humains, en tant que ‘super-prédateurs’, peuvent avoir des effets importants sur le comportement de la faune sauvage, y compris des modifications profondes de leurs rythmes circadiens d'activité. A la suite du retour des grands carnivores dans les écosystèmes anthropisés, de nombreuses espèces proies ont ajusté leur comportement spatial à ces paysages de la peur contrastés, générés à la fois par les pressions liées aux risques anthropiques et à la présence de leurs prédateurs naturels. Les effets du risque de prédation sur les modifications temporelles des rythmes circadiens d'activité des proies restent cependant largement inconnus dans les écosystèmes dominés par l'homme. Ici, nous avons étudié l'influence de la densité de lynx Lynx lynx, un prédateur nocturne, sur les rythmes circadiens d'activité de leur proie principale, le chevreuil Capreolus capreolus, à travers un gradient de pressions anthropiques à l’échelle Européenne. Sur la base de plus de 11 million de données d'activité issues de 431 suivis individuels de chevreuils équipés de colliers GPS provenant de 12 populations au sein du réseau EURODEER (http://eurodeer.org), nous avons analysé comment le risque de prédation par le lynx, associé aux risques létaux et non-létaux des activités humaines, influence la diurnalité des chevreuils. Nous avons démontré une forte plasticité des rythmes circadiens d'activité des chevreuils en réponse aux variations spatio-temporelles du risque, et notamment face aux activités humaines. Plus particulièrement, les chevreuils diminuent leur degré de diurnalité d'un facteur de 1.37 lorsque le dérangement humain est important. La chasse accentue cet effet, puisque durant la saison de chasse les chevreuils basculent la plupart de leur activité de nuit, et dans une moindre mesure, durant l'aube également, bien que ce patron soit essentiellement variable en fonction de la densité de lynx. En effet, en présence de lynx, leur principal prédateur, les chevreuils sont relativement plus diurnes. Globalement, nos résultats révèlent une forte influence des activités humaines et de la présence de lynx sur l'ajustement des rythmes circadiens d'activité des chevreuils. Dans le contexte du retour des grands carnivores en Europe, notre étude apporte de nouvelles connaissances sur les effets des prédateurs sur la réponse comportementale de leur proie dans des écosystèmes anthropisés. La modification de la répartition temporelle de l'activité des ongulés en réponse aux activités humaines pourrait être un facteur facilitant la coexistence homme-faune sauvage, avec toutefois des conséquences autres sur les interactions prédateurs-proies et leurs effets en cascade sur le fonctionnement des écosystèmes.
Published: 2019
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22. Leukocyte Profiles Reflect Geographic Range Limits in a Widespread Neotropical Bat

Author: Becker, DJ, Nachtmann, C, Argibay, HD, Botto, G, Escalera-Zamudio, M, Carrera, JE, Tello, C, Winiarski, E, Greenwood, AD, Méndez-Ojeda, ML, Loza-Rubio, E, Lavergne, A, de Thoisy, B, Czirják, GÁ, Plowright, RK, Altizer, S, Streicker, DG, Universidad Nacional de la Plata [Argentine] (UNLP), Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, and University of Georgia [USA]
Subjects: blood, vertebrates, expression, vampire bats, ecological immunology, parasite infection, disease, stress, responses, immune function, S2 The scale of sickness: how immune variation across space and species affects infectious disease dynamics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Chiroptera, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Leukocytes, Animals, Animal Distribution, ComputingMilieux_MISCELLANEOUS, Ecosystem, Immunity, Innate
Abstract: Quantifying how the environment shapes host immune defense is important for understanding which wild populations may be more susceptible or resistant to pathogens. Spatial variation in parasite risk, food and predator abundance, and abiotic conditions can each affect immunity, and these factors can also manifest at both local and biogeographic scales. Yet identifying predictors and the spatial scale of their effects is limited by the rarity of studies that measure immunity across many populations of broadly distributed species. We analyzed leukocyte profiles from 39 wild populations of the common vampire bat (Desmodus rotundus) across its wide geographic range throughout the Neotropics. White blood cell differentials varied spatially, with proportions of neutrophils and lymphocytes varying up to six-fold across sites. Leukocyte profiles were spatially autocorrelated at small and very large distances, suggesting that local environment and large-scale biogeographic factors influence cellular immunity. Generalized additive models showed that bat populations closer to the northern and southern limits of the species range had more neutrophils, monocytes, and basophils, but fewer lymphocytes and eosinophils, than bats sampled at the core of their distribution. Habitats with access to more livestock also showed similar patterns in leukocyte profiles, but large-scale patterns were partly confounded by time between capture and sampling across sites. Our findings suggest that populations at the edge of their range experience physiologically limiting conditions that predict higher chronic stress and greater investment in cellular innate immunity. High food abundance in livestock-dense habitats may exacerbate such conditions by increasing bat density or diet homogenization, although future spatially and temporally coordinated field studies with common protocols are needed to limit sampling artifacts. Systematically assessing immune function and response over space will elucidate how environmental conditions influence traits relevant to epidemiology and help predict disease risks with anthropogenic disturbance, land conversion, and climate change.
Published: 2019
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23. Large herbivore migration plasticity along environmental gradients in Europe:life-history traits modulate forage effects

Author: Atle Mysterud, Max Kröschel, Nicolas Morellet, Ferdinando Urbano, Robin Sandfort, Johannes De Groeve, Peter Sunde, Leif Sönnichsen, Anders Jarnemo, Mark Hebblewhite, Daniel R. Eacker, John D. C. Linnell, Luca Pedrotti, Benedikt Gehr, Horst Reinecke, Marco Heurich, A. J. Mark Hewison, Stefano Focardi, Petter Kjellander, Francesca Cagnacci, Wibke Peters, Bavarian State Institute of Forestry, University of Montana, University of Oslo (UiO), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Norwegian Institute for Nature Research (NINA), Consiglio Nazionale delle Ricerche (CNR), Universiteit Gent = Ghent University [Belgium] (UGENT), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), 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]), Department of Evolutionary Biology and Environmental Studies, University of Zurich, Department of Conservation and Research, Bavarian Forest National Park, Halmstad University, Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), University of Freiburg [Freiburg], Forest Research Institute Baden-Württemberg - Forstliche Versuchs- und Forschungsanstalt Baden-Württemberg, Parco Nazionale dello Stelvio, Partenaires INRAE, Georg-August-University [Göttingen], Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Polish Academy of Sciences (PAN), Aarhus University [Aarhus], Harvard University [Cambridge], Vectronic Aerospace GmbH, Autonomous Province of Trento (BECOCERWI) [3479], EU-programme INTERREG IV (EFRE Ziel 3), 'Marie Claire Cronstedts Stiftelse' foundation, Swedish Environmental Protection Agency, Swedish Association for Hunting and Wildlife Management, Region Skane, Stiftelsen Skanska Landskap, Hogestads and Christinehofs Fideikommiss, Ittur Jakt AB, Vira Bruk AB, Holmen Skog AB, Sveaskog, Karl-Erik Onnesjos stiftelse for vetenskaplig forskning och utveckling, Stiftelsen Oscar och Lili Lamms mine, Ericsbergs Fideikommis AB, Agerup and Elsagardens Sateri AB, Kolmardens insamlingsstiftelse/Taby Allmanning, Norwegian Environment Agency, Research Council of Norway [212919, 251112], Buskerud county, Centre for Advanced Study Oslo, Norway, Institute for Zoo and Wildlife Research (IZW), Mammal Research Institute - Polish Academy of Sciences, Polish Ministry of Science and Higher Education [N N304172536], and NASA [NNX11AO47G]
Subjects: 0106 biological sciences, Ungulate, Foraging, Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 [VDP], Biology, 010603 evolutionary biology, 01 natural sciences, Life history theory, behavioral plasticity, Capreolus, biology.animal, Settore BIO/07 - ECOLOGIA, Ecology, Evolution, Behavior and Systematics, Herbivore, partial migration, Ecology, 010604 marine biology & hydrobiology, 15. Life on land, biology.organism_classification, Mating system, herbivores, Behavioural plasticity, Roe deer, Sympatric speciation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, forage maturation hypothesis
Abstract: The most common framework under which ungulate migration is studied predicts that it is driven by spatio–temporal variation in plant phenology, yet other hypotheses may explain differences within and between species. To disentangle more complex patterns than those based on single species/ single populations, we quantified migration vari-ability using two sympatric ungulate species differing in their foraging strategy, mating system and physiological constraints due to body size. We related observed variation to a set of hypotheses. We used GPS-collar data from 537 individuals in 10 roe Capreolus capreolus and 12 red deer Cervus elaphus populations spanning environmental gra-dients across Europe to assess variation in migration propensity, distance and tim-ing. Using time-to-event models, we explored how the probability of migration varied in relation to sex, landscape (e.g. topography, forest cover) and temporally-varying environmental factors (e.g. plant green-up, snow cover). Migration propensity varied across study areas. Red deer were, on average, three times more migratory than roe deer (56% versus 18%). This relationship was mainly driven by red deer males which were twice as migratory as females (82% versus 38%). The probability of roe deer migration was similar between sexes. Roe deer (both sexes) migrated earliest in spring. While territorial male roe deer migrated last in autumn, male and female red deer migrated around the same time in autumn, likely due to their polygynous mating system. Plant productivity determined the onset of spring migration in both species, but if plant productivity on winter ranges was sufficiently high, roe deer were less likely to leave. In autumn, migration coincided with reduced plant productivity for both species. This relationship was stronger for red deer. Our results confirm that ungulate migration is influenced by plant phenology, but in a novel way, that these effects appear to be modulated by species-specific traits, especially mating strategies.
Published: 2019
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24. Sex and species differences of stress markers in sympatric cheetahs and leopards in Namibia

Author: Vera Menges, David Costantini, Joerg Melzheimer, Bettina Wachter, Gábor Á. Czirják, Muséum national d'Histoire naturelle (MNHN), University of Glasgow, Department of Biology (University of Antwerp), University of Antwerp (UA), Leibniz Institute for Zoo and Wildlife Research (IZW), and Leibniz Association
Subjects: Male, 0106 biological sciences, 0301 basic medicine, Felidae, Physiology, Endangered species, Zoology, Biology, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Biochemistry, Antioxidants, 03 medical and health sciences, Sex Factors, Species Specificity, Felines, biology.animal, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, medicine, Animals, Acinonyx jubatus, Molecular Biology, chemistry.chemical_classification, Mammals, Glutathione peroxidase, Leopard, Reproduction, Cheetah, 15. Life on land, Chemistry, 030104 developmental biology, chemistry, Sympatric speciation, Oxidative stress, Carnivores, Threatened species, Female, Human medicine, Acinonyx, Panthera, Biomarkers
Abstract: International audience; Physiological stress markers may provide valuable insight for our understanding of costs of given life-history strategies or of wildlife health condition, most importantly in case of threatened species. In the last decade, there has been growing interest in the ecological relevance of cellular oxidative stress, which would provide complimentary information to that obtained by the classic analyses of glucocorticoid hormones. In this study, we analysed the sex and species variation of five blood-based markers of oxidative status, both molecular oxidative damage and antioxidant protection, in sympatric cheetahs (Acinonyx jubatus) and leopards (Panthera pardus) living on Namibian farmlands. Both these terrestrial carnivores are classified as vulnerable by the International Union for Conservation of Nature. We found that female cheetahs had significantly higher serum reactive oxygen metabolites of non-protein origin and lower glutathione peroxidase activity in whole blood than both male and female leopards and male cheetahs. We also found that cheetahs and leopards differed in the association between the two antioxidant enzymes glutathione peroxidase and superoxide dismutase. Correlations among oxidative status markers were stronger in female cheetahs than leopards or male cheetahs. Our results suggest that female cheetahs are more sensitive to local sources of stress. Our work did not corroborate the assumption that two species with different life histories consistently differ in key physiological traits.
Published: 2019
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25. Modeling the emergence of migratory corridors and foraging hot spots of the green sea turtle

Author: Gilles Lajoie, Yassine Gangat, Volker Grimm, Jerome Bourjea, Mayeul Dalleau, Stephanie Kramer-Schadt, Kélonia - Observatoire des tortues marines, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Technical University of Berlin / Technische Universität Berlin (TU), Laboratoire d'Informatique et de Mathématiques (LIM), Université de La Réunion (UR), 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), UMR 228 Espace-Dev, Espace pour le développement, 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)-Université de Guyane (UG)-Université des Antilles (UA), Department of Ecological Modelling [UFZ Leipzig], Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), University of Potsdam = Universität Potsdam, German Centre for Integrative Biodiversity Research (iDiv), Technische Universität Berlin (TU), 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), 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), University of Potsdam, and Germany, German Centre for Integrative Biodiversity Research (iDiv)
Subjects: 0106 biological sciences, Foraging, Endangered species, Spatial distribution, migration, 010603 evolutionary biology, 01 natural sciences, corridors, movement, individual‐based model, sea turtle, connectivity, 03 medical and health sciences, lcsh:QH540-549.5, ddc:550, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Nature and Landscape Conservation, Original Research, Green sea turtle, 0303 health sciences, Ecology, biology, 15. Life on land, biology.organism_classification, Sea turtle, Habitat, Spatial ecology, Nesting (computing), Institut für Geowissenschaften, lcsh:Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, individual-based model
Abstract: Environmental factors shape the spatial distribution and dynamics of populations. Understanding how these factors interact with movement behavior is critical for efficient conservation, in particular for migratory species. Adult female green sea turtles, Chelonia mydas, migrate between foraging and nesting sites that are generally separated by thousands of kilometers. As an emblematic endangered species, green turtles have been intensively studied, with a focus on nesting, migration, and foraging. Nevertheless, few attempts integrated these behaviors and their trade‐offs by considering the spatial configurations of foraging and nesting grounds as well as environmental heterogeneity like oceanic currents and food distribution. We developed an individual‐based model to investigate the impact of local environmental conditions on emerging migratory corridors and reproductive output and to thereby identify conservation priority sites. The model integrates movement, nesting, and foraging behavior. Despite being largely conceptual, the model captured realistic movement patterns which confirm field studies. The spatial distribution of migratory corridors and foraging hot spots was mostly constrained by features of the regional landscape, such as nesting site locations, distribution of feeding patches, and oceanic currents. These constraints also explained the mixing patterns in regional forager communities. By implementing alternative decision strategies of the turtles, we found that foraging site fidelity and nesting investment, two characteristics of green turtles' biology, are favorable strategies under unpredictable environmental conditions affecting their habitats. Based on our results, we propose specific guidelines for the regional conservation of green turtles as well as future research suggestions advancing spatial ecology of sea turtles. Being implemented in an easy to learn open‐source software, our model can coevolve with the collection and analysis of new data on energy budget and movement into a generic tool for sea turtle research and conservation. Our modeling approach could also be useful for supporting the conservation of other migratory marine animals., Our model represents the migration of green sea turtles in the southwest Indian Ocean between nesting and foraging sites. It can cover thousands of km and is contratined by the regional landscape and oceanic currents. Emerging migration corridors were identified, which can be used for identifying priority sites for conservation.
Published: 2019
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26. The dimensionality of stability depends on disturbance type

Author: Jens-Christian Svenning, Frederik De Laender, Michael Crawford, Jonathan De Raedt, Viktoriia Radchuk, Cédric Scherer, Kirsten Thonicke, Friedrich J. Bohn, Stephanie Kramer-Schadt, Juliano Sarmento Cabral, Frank M. Schurr, Volker Grimm, Isabelle Boulangeat, IZW LEIBNIZ INSTITUTE FOR ZOO AND WILDLIFE RESEARCH DEU, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Université de Namur [Namur] (UNamur), UNIVERSITY OF WURZBURG DEU, Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), UNIVERSITY OF POSTDAM DEU, UFZ HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH HALLE DEU, Aarhus University [Aarhus], PIK POTSDAM INSTITUTE FOR CLIMATE IMPACT RESEARCH POSTDAM DEU, UNIVERSITY OF HOHENHEIM DEU, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Institute of Life, Earth and Environment, Evolutionary Genomics Center for Computational and Theoretical Biology (CCTB), Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Aarhus, Denmark, Institute of Biochemistry and Biology University of Potsdam, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Karlsruhe Institute of Technology (KIT), Laboratory of Environmental Toxicology and Aquatic Ecology, Universiteit Gent = Ghent University [Belgium] (UGENT), Potsdam Institute for Climate Impact Research (PIK), Institute of Landscape and Plant Ecology, Universität Hohenheim, German Centre for Integrative Biodiversity Research (iDiv), University of Berlin, BioMove Research Training Group of the German Research Foundation : DFG-GRK 2118/1, DFG Priority Program 1374, 'Infrastructure-Biodiversity-Exploratories' : DFG-JE 207/5-1, FWO : FWO14/ASP/075, Fonds de la Recherche Scientifique - FNRS : PDR T.0048.16, and VILLUM FONDEN : 16549
Subjects: 0106 biological sciences, Disturbance (geology), [SDV]Life Sciences [q-bio], Population Dynamics, Population, invariability, 010603 evolutionary biology, 01 natural sciences, Stability (probability), disturbance intensity, resistance, recovery, ddc:570, disturbance type, education, Ecosystem, Ecology, Evolution, Behavior and Systematics, Institut für Biochemie und Biologie, Mathematics, Trophic level, Ecological stability, education.field_of_study, Ecology, Resistance (ecology), extinction, 010604 marine biology & hydrobiology, Community model, persistence, 15. Life on land, [SDE]Environmental Sciences, Species richness, Biological system, individual-based model, Curse of dimensionality
Abstract: International audience; Ecosystems respond in various ways to disturbances. Quantifying ecological stability therefore requires inspecting multiple stability properties, such as resistance, recovery, persistence and invariability. Correlations among these properties can reduce the dimensionality of stability, simplifying the study of environmental effects on ecosystems. A key question is how the kind of disturbance affects these correlations. We here investigated the effect of three disturbance types (random, species-speciﬁc, local) applied at four intensity levels, on the dimensionality of stability at the population and community level. We used previously parameterized models that represent ﬁve natural communities, varying in species richness and the number of trophic levels. We found that disturbance type but not intensity affected the dimensionality of stability and only at the population level. The dimensionality of stability also varied greatly among species and communities. Therefore, studying stability cannot be simpliﬁed to using a single metric and multi-dimensionalassessments are still to be recommended.
Published: 2019
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27. Social support drives female dominance in the spotted hyaena

Author: Alexandre Courtiol, Oliver P. Höner, Bettina Wachter, Eve Davidian, François Rousset, Colin Vullioud, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226
Subjects: 0106 biological sciences, Male, Behavioural ecology, Biology, Crocuta crocuta, Evolutionary ecology, 010603 evolutionary biology, 01 natural sciences, Social group, Sexual conflict, 03 medical and health sciences, 5. Gender equality, Animals, 10. No inequality, Social Behavior, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Sex Characteristics, Ecology, Female dominance, Behavior, Animal, Evolutionary theory, biology.organism_classification, Sexual dimorphism, Dominance (ethology), Sexual selection, Female, Hyaenidae, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Demography, Sex characteristics
Abstract: International audience; Identifying how dominance within and between the sexes is established is pivotal to understanding sexual selection and sexual conflict. In many species, members of one sex dominate those of the other in one-on-one interactions. Whether this results from a disparity in intrinsic attributes, such as strength and aggressiveness, or in extrinsic factors, such as social support, is currently unknown. We assessed the effects of both mechanisms on dominance in the spotted hyaena (Crocuta crocuta), a species where sexual size dimorphism is low and females often dominate males. We found that individuals with greater potential social support dominated one-on-one interactions in all social contexts, irrespective of their body mass and sex. Female dominance emerged from a disparity in social support in favour of females. This disparity was a direct consequence of male-biased dispersal and the disruptive effect of dispersal on social bonds. Accordingly, the degree of female dominance varied with the demographic and kin structure of the social groups, ranging from male and female co-dominance to complete female dominance. Our study shows that social support can drive sex-biased dominance and provides empirical evidence that a sex-role-defining trait can emerge without the direct effect of sex.
Published: 2019
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28. Characterization of early embryonic cellular defects after somatic cell nuclear transfer in goldfish

Author: Rouillon, Charlène, ProdInra, Migration, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Leibniz Institute for Zoo and Wildlife Research (IZW). DEU.
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [INFO] Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

29. Migratory flight imposes oxidative stress in bats

Author: Gunārs Pētersons, Oliver Lindecke, David Costantini, Christian C. Voigt, University of Antwerp (UA), Physiologie moléculaire et adaptation (PhyMA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Freie Universität Berlin, and University of Latvia (LU)
Subjects: 0106 biological sciences, Zoology, Oxidative phosphorylation, oxidative damage, Biology, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Oxidative damage, stress, Pipistrellus nathusii, Animal migration, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, medicine, 0501 psychology and cognitive sciences, mammals, 050102 behavioral science & comparative psychology, Animal species, chemistry.chemical_classification, Glutathione peroxidase, 05 social sciences, stopover, antioxidants, Articles, biology.organism_classification, chemistry, Animal Science and Zoology, Body condition, Oxidative stress
Abstract: International audience; Many animal species migrate over long distances, but the physiological challenges of migration are poorly understood. It has recently been suggested that increased molecular oxidative damage might be one important challenge for migratory animals. We tested the hypothesis that autumn migration imposes an oxidative challenge to bats by comparing values of 4 blood-based markers of oxidative status (oxidative damage and both enzymatic and nonenzymatic antioxidants) between Nathusius' bats Pipistrellus nathusii that were caught during migration flights with those measured in conspecifics after resting for 18 or 24 h. Experiments were carried out at Pape Ornithological Station in Pape (Latvia) in 2016 and 2017. Our results show that flying bats have a blood oxidative status different from that of resting bats due to higher oxidative damage and different expression of both nonenzymatic and en-zymatic antioxidants (glutathione peroxidase). The differences in oxidative status markers varied between sampling years and were independent from individual body condition or sex. Our work provides evidence that migratory flight might impose acute oxidative stress to bats and that resting helps animals to recover from oxidative damage accrued en route. Our data suggest that migrating bats and birds might share similar strategies of mitigating and recovering from oxidative stress.
Published: 2019
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30. Slow recovery from a disease epidemic in the spotted hyena, a keystone social carnivore

Author: Marion L. East, Lucile Marescot, Sarah Benhaiem, Stephanie Kramer-Schadt, Heribert Hofer, Olivier Gimenez, Jean-Dominique Lebreton, 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]), Institute of Zoo & Wildlife Research, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, 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), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Population, Wildlife, Medicine (miscellaneous), Zoology, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, biology.animal, medicine, 14. Life underwater, Carnivore, education, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, education.field_of_study, Canine distemper, Population size, Outbreak, 15. Life on land, medicine.disease, 030104 developmental biology, Hyena, Population model, lcsh:Biology (General), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences
Abstract: Predicting the impact of disease epidemics on wildlife populations is one of the twenty-first century’s main conservation challenges. The long-term demographic responses of wildlife populations to epidemics and the life history and social traits modulating these responses are generally unknown, particularly for K-selected social species. Here we develop a stage-structured matrix population model to provide a long-term projection of demographic responses by a keystone social predator, the spotted hyena, to a virulent epidemic of canine distemper virus (CDV) in the Serengeti ecosystem in 1993/1994 and predict the recovery time for the population following the epidemic. Using two decades of longitudinal data from 625 known hyenas, we demonstrate that although the reduction in population size was moderate, i.e., the population showed high ecological ‘resistance’ to the novel CDV genotype present, recovery was slow. Interestingly, high-ranking females accelerated the population’s recovery, thereby lessening the impact of the epidemic on the population., Sarah Benhaiem et al. present a model of demographic responses by the spotted hyena to an epidemic of canine distemper virus in 1993–1994.They find that recovery from the outbreak was slow despite initial moderate mortality, and that high-ranking females sped up recovery by increasing the ecological resistance of the population.
Published: 2018
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31. Vocal tract modelling in fallow deer: are male groans nasalized?

Author: Roland Frey, Megan T. Wyman, Jean-Pierre Dalmont, Benjamin D. Charlton, David Reby, Joël Gilbert, University of Sussex, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, San Diego Zoo Global Institute for Conservation Research, Laboratoire d'Acoustique de l'Université du Mans (LAUM), and Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Larynx, Male, Call production, Adult male, Physiology, Oropharynx, Acoustic variation, Vocal tract shape, Aquatic Science, Biology, Call nasalization, 010603 evolutionary biology, 01 natural sciences, Models, Biological, Mammal, Nasalization, Vocalization, Nasopharynx, Mobile larynx, 0103 physical sciences, medicine, otorhinolaryngologic diseases, Animals, Vocal tract resonance, Head and neck, 010301 acoustics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Mouth, Deer, Anatomy, respiratory system, [PHYS.MECA.ACOU]Physics [physics]/Mechanics [physics]/Acoustics [physics.class-ph], Formant, medicine.anatomical_structure, Insect Science, Animal Science and Zoology, Nasal Cavity, Vocalization, Animal, Tomography, X-Ray Computed, Vocal tract, Quarter wavelength resonator
Abstract: International audience; Males of several species of deer have a descended and mobile larynx, resulting in an unusually long vocal tract, which can be further extended by lowering the larynx during call production. Formant frequencies are lowered as the vocal tract is extended, as predicted when approximating the vocal tract as a uniform quarter wavelength resonator. However, formant frequencies in polygynous deer follow uneven distribution patterns, indicating that the vocal tract configuration may in fact be rather complex. We CT-scanned the head and neck region of two adultmale fallowdeer specimens with artificially extended vocal tracts and measured the cross-sectional areas of the supralaryngeal vocal tract along the oral and nasal tracts. The CT data were then used to predict the resonances produced by three possible configurations, including the oral vocal tract only, the nasal vocal tract only, or combining the two. We found that the area functions from the combined oral and nasal vocal tracts produced resonances more closely matching the formant pattern and scaling observed in fallow deer groans than those predicted by the area functions of the oral vocal tract only or of the nasal vocal tract only. This indicates that the nasal and oral vocal tracts are both simultaneously involved in the production of a non-human mammal vocalization, and suggests that the potential for nasalization in putative oral loud calls should be carefully considered.
Published: 2018
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32. Social status mediates the fitness costs of infection with canine distemper virus in Serengeti spotted hyenas

Author: Heribert Hofer, Olivier Gimenez, Sarah Benhaiem, Lucile Marescot, Jean-Dominique Lebreton, Ximena A. Olarte-Castillo, Marion L. East, Stephanie Kramer-Schadt, 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]), Institute of Zoo & Wildlife Research, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Infection risk, resource allocation, 010603 evolutionary biology, 01 natural sciences, Virus, 03 medical and health sciences, biology.animal, medicine, canine distemper virus, infection risk, Carnivore, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Behavioural Ecology, biology, Individual heterogeneity, Canine distemper, medicine.disease, social status, fitness costs, multi‐event capture–mark–recapture model, 030104 developmental biology, Hyena, exposure, Negative relationship, spotted hyena, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Research Article, Demography, Social status
Abstract: The extent to which the fitness costs of infection are mediated by key life‐history traits such as age or social status is still unclear. Within populations, individual heterogeneity in the outcome of infection is the result of two successive processes; the degree of contact with the pathogen (exposure) and the immune response to infection. In social mammals, because individuals holding high social status typically interact more frequently with group members, they should be more often in contact with infected individuals than those of low social status. However, when access to resources is determined by social status, individuals with a high social status are often better nourished, have a greater opportunity to allocate resources to immune processes and therefore should have a smaller chance of succumbing to infection than individuals with low social status.We investigated the risk and fitness costs of infection during a virulent epidemic of canine distemper virus (CDV) in a social carnivore, the spotted hyena, in the Serengeti National Park. We analysed two decades of detailed life‐history data from 625 females and 816 males using a multi‐event capture–mark–recapture model that accounts for uncertainty in the assignment of individual infection states.Cubs of mothers with a high social status had a lower probability of CDV infection and were more likely to survive infection than those with low social status. Subadult and adult females with high social status had a higher infection probability than those with low social status. Subadult females and pre‐breeder males that had recovered from CDV infection had a lower survival than susceptible ones.Our study disentangles the relative importance of individual exposure and resource allocation to immune processes, demonstrates fitness costs of infection for juveniles, particularly for those with low social status, shows that patterns of infection can be driven by different mechanisms among juveniles and adults and establishes a negative relationship between infection and fitness in a free‐ranging mammal. A http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13059/suppinfo is available for this article., http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13059/suppinfo
Published: 2018
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33. Cat preantral follicle survival after prolonged cooled storage followed by vitrification

Author: Katarina Jewgenow, Maria Denise Lopes, Jorge Luis Araújo Martins, Fabiana Ferreira de Souza, Fábio Sossai Possebon, Gudrun Wibbelt, Universidade Estadual Paulista (Unesp), and Leibniz-Institute for Zoo and Wildlife Research (IZW)
Subjects: 0301 basic medicine, Neutral red, Ovarian Cortex, H&E stain, Ovary, Tissue Banks, General Biochemistry, Genetics and Molecular Biology, Andrology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Ovarian Follicle, medicine, Animals, Vitrification, Cryopreservation, 030219 obstetrics & reproductive medicine, Chemistry, Histology, General Medicine, Cold Temperature, 030104 developmental biology, medicine.anatomical_structure, Ultrastructure, Cats, Gamete, Female, General Agricultural and Biological Sciences
Abstract: Made available in DSpace on 2018-12-11T17:18:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-04-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) The aim of this study was to investigate the impact of prolonged storage at 4 °C on survival of cat preantral follicles (PAFs) pre- and post-vitrification. Ovaries were obtained from 12 queens and transported at 4 ºC within 2–6 h. Parts of the ovaries were stored for an additional 24 h or 72 h. The ovarian cortex was dissected, analyzed for viability (neutral red - NR) and morphology (histology - HE and ultrastructural analysis by TEM) and vitrified. We used 2 mm biopsy punches to obtain equal size pieces as the experimental units. After NR assessment, each sample was fixed and embedded in paraffin for HE staining to determine the number of morphologically intact follicles. Another 2 mm piece of ovary was subjected to TEM. NR viability assessment and HE results showed a similar tendency with PAF survival postvitrification even after prolonged cooling at 24 h and 72 h. With TEM, integrity of mitochondria, plasma and basal membranes as well as the presence of pre-granulose cells of PAFs were documented postvitrification for the control group and 24 h prolonged storage group, but not after 72 h storage. Our results showed that cat PAFs can survive prolonged storage followed by vitrification. The described set of techniques are applicable towards creating a gamete bank for endangered feline species. Laboratory of Small and Wild Animals Reproduction Department of Animal Reproduction and Veterinary Radiology FMVZ UNESP Department of Veterinary Hygiene and Public Health FMVZ UNESP Department of Reproductive Biology Leibniz-Institute for Zoo and Wildlife Research (IZW) Laboratory of Small and Wild Animals Reproduction Department of Animal Reproduction and Veterinary Radiology FMVZ UNESP Department of Veterinary Hygiene and Public Health FMVZ UNESP
Published: 2018

34. Two Novel, Distantly Related Papillomaviruses Isolated from Healthy Skin of the Timor Deer ( Rusa timorensis )

Author: Mengual-Chuliá, Beatriz, Wibbelt, Gudrun, Gottschling, Marc, Bravo, Ignacio G., Catalan Institute of Oncology, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Ludwig-Maximilians-Universität München (LMU), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Virostyle (MIVEGEC-Virostyle), Perturbations, Evolution, Virulence (PEV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; We report the complete genome sequences of Rusa timorensis papillo-mavirus 1 (RtimPV1) and Rusa timorensis papillomavirus 2 (RtimPV2), isolated from hair follicles of asymptomatic skin from the same Timor deer specimen. RtimPV1 and RtimPV2 are evolutionarily only distantly related. RtimPV1 lacks a canonical E2-binding site, and RtimPV2 does not carry an E6 gene. T he genome of papillomaviruses (PVs) is a single double-stranded DNA (dsDNA) circular molecule of approximately 8 kbp, carrying genes involved in cell replication, viral replication, and viral encapsidation. Most PVs cause epithelial asymptomatic infections in amniotes and probably also in bony fishes, while some of them induce proliferative benign lesions and different cancers (1, 2). The Timor deer Rusa timorensis (de Blainvillee, 1822) is native to the island of Java and is classified as "vulnerable" by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species (http://www.iucnredlist.org) (3). A biopsy specimen from asymptomatic skin (isolate IZW 39/08) was collected from a female deer, about 19 years old, living in captivity in a zoo in Berlin, Germany. The animal did not present papilloma-like lesions and was euthanized because of a severe internal infection that was unrelated to any PV infection. Total DNA was extracted from hair bulbs and PCR tested for the presence of PV DNA using broad-spectrum primers targeting the E1 and L1 genes (4). Using this partial information, we designed tail-to-tail primers to amplify the full-length genomes using long-range PCR, which were then Sanger sequenced in both strands through primer walking and cloned. Phylogenetic relationships for the E1E2, L2L1, and E1E2L2L1 gene concatenates were inferred under a maximum-likelihood framework (5). We retrieved two complete PV genomes from the same skin sample of the R. timorensis individual, here named Rusa timorensis papillomavirus 1 (RtimPV1) (isolate IZW 39/08) and Rusa timorensis papillomavirus 2 (RtimPV2) (isolate IZW 39/08). Both viral genomes display the standard features of PVs, with a long control region; the early genes E7, E1, and E2; and the late genes L2 and L1. Remarkably, RtimPV2 does not carry an E6 gene. This gene may have been lost independently in several PV lineages through time (6, 7). The RtimPV1 L1 gene displays maximum nucleotide similarity values around 65% with very divergent PVs, while RtimPV2 L1 displays identity values around 65% with divergent PVs in the 5= end, and only above 50% in the 3= end. Therefore, this criterion alone does not suffice for taxonomic assignment following the current rules (8), which need to be revised (7, 9). Phylogenetic reconstruction confidently places RtimPV1 as a sister lineage to Capra hircus papillomavirus 1 (ChPV1), isolated from healthy skin of a female goat (10), a Phipapillomavirus in the Beta Xi PV supergroup
Published: 2018
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35. Mate choice intensifies motor signalling in Drosophila

Author: Rhonda R. Snook, Michael G. Ritchie, Alexandre Courtiol, Allan Debelle, Department of Animal and Plant Sciences [Sheffield], University of Sheffield [Sheffield], University of Sussex, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, University of St Andrews [Scotland], This work was funded by the Marie Curie Initial Training Network 'Understanding the evolutionary origin of biological diversity' (ITN-2008-213780 SPECIATION, M.G.R.), and by a US National Science Foundation grant (R.R.S.) (DEB-0093149) and NERC grants (R.R.S. and M.G.R., NE/B504065/1, NE/D003741/1, NE/I014632/1)., European Project: 213780,EC:FP7:PEOPLE,FP7-PEOPLE-2007-1-1-ITN,SPECIATION(2008), 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), European Commission, NERC, University of St Andrews. School of Biology, University of St Andrews. Centre for Biological Diversity, and University of St Andrews. Institute of Behavioural and Neural Sciences
Subjects: Interpulse interval, 0106 biological sciences, 0301 basic medicine, Mate choice, animal structures, QH301 Biology, media_common.quotation_subject, [SDV]Life Sciences [q-bio], NDAS, Courtship song, 010603 evolutionary biology, 01 natural sciences, Courtship, Drosophila pseudoobscura, Motor performance, QH301, 03 medical and health sciences, interpulse interval, sexual selection, experimental evolution, mate choice, Drosophila, Ecology, Evolution, Behavior and Systematics, media_common, Experimental evolution, Communication, biology, courtship song, business.industry, biology.organism_classification, 030104 developmental biology, Signalling, Sexual selection, Evolutionary biology, motor performance, [SDE]Environmental Sciences, behavior and behavior mechanisms, Animal Science and Zoology, business, psychological phenomena and processes, Production rate
Abstract: International audience; Mate choice has the potential to act on the evolution of motor performance via its direct influence on motor sexual signals. However, studies demonstrating this are rare. Here, we performed an in-depth analysis of Drosophila pseudoobscura courtship song rate, a motor signal under mate choice in this species, and analysed the response of this signal to sexual selection manipulation using experimental evolution. We show that manipulating the opportunity for sexual selection led to changes in song production rate and singing endurance, with males from the polyandrous populations producing faster song rates over longer time periods than males from monogamous populations. We also show that song rate was correlated with estimates of overall courtship vigour. Our results suggest that the action of mate choice on a motor signal has affected male motor performance displayed during courtship. We consider potential selective benefits associated with changes in motor performance, including condition-dependent signalling, and discuss the implications of these results for the study of motor signals under sexual selection. (C) 2017 The Association for the Study of Animal Behaviour.Highlights• We experimentally increased or decreased sexual selection in Drosophila populations.• We perform an in-depth analysis of the response of a motor signal (pulse rate).• Polyandrous males sing at a faster rate and do so for longer than monogamous males.• Fast song rates are associated with overall increased male motor performance.• Increasing the opportunity for mate choice increased male motor performance.
Published: 2017
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36. Does chromosomal change restrict gene flow between house mouse populations (Mus musculus domesticus)? Evidence from microsatellite polymorphisms

Author: Marie Pagès, Pierre Caminade, Eve Davidian, Janice Britton-Davidian, 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, Leibniz Institute for Zoo and Wildlife Research (IZW), and Leibniz Association
Subjects: 0106 biological sciences, 0301 basic medicine, introgression, Robertsonian translocation, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, House mouse, Loss of heterozygosity, 03 medical and health sciences, Hybrid zone, Meiosis, medicine, genetic structure, Ecology, Evolution, Behavior and Systematics, Genetics, biology, Karyotype, biology.organism_classification, chromosomal speciation, recombination, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Microsatellite, Underdominance, divergence
Abstract: International audience; Chromosomal change is recognized as an important force in speciation-with-gene-flow models. Although Robertsonian (Rb) translocations contribute to hybrid unfitness and modify recombination patterns, they are generally not considered as efficient as inversions in reducing gene flow. The present study analyses two hybridizing chromosomal races of the house mouse (Mus musculus domesticus), one carrying nine Rb fusions (2n = 22) and the other carrying the ancestral karyotype (2n = 40). Chromosomal heterozygosity involves simple meiotic configurations, the underdominance of which is not as efficient in promoting speciation as more complex chromosomal differences. The pattern of divergence between these races was investigated using 32 microsatellite loci distributed over all autosomes. The results highlighted a relatively large differentiation between the two chromosomal races. The contribution of variation in recombination patterns to this differentiation was supported by the contrasting levels of divergence between proximal vs. non-proximal microsatellite loci. Clinal analyses of the Rb fusions through the hybrid zone uncovered differences in steepness between metacentrics, suggesting associated differences in selection which did not involve linked genic incompatibilities. This study illustrates the significant role of Rb-associated changes in recombination in promoting or maintaining divergence between chromosomal races of the house mouse.
Published: 2017
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37. Phylogeography of the small Indian civet and origin of introductions to western Indian Ocean islands

Author: Philippe Gaubert, André Lourenço, Steven M. Goodman, Andreas Wilting, Fabienne Justy, Jörns Fickel, Marie Sigaud, Riddhi P. Patel, Bheem Dutt Joshi, Raquel Vasconcelos, Maraike Willsch, Géraldine Veron, 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, Freie Universität Berlin, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, 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), Field Museum of Natural History [Chicago, USA], Association Vahatra [Antananarivo, Madagascar], Museum für Naturkunde [Berlin], Institut de Biologia Evolutiva [Barcelona] (IBE / UPF - CSIC), Universitat Pompeu Fabra [Barcelona] (UPF), Universidade do Porto, Office National de la Chasse et de la Faune Sauvage (ONCFS), University of Potsdam, 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), 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), Universidade do Porto = University of Porto, and University of Potsdam = Universität Potsdam
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Gene Frequency, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, Phylogeny, Genetics (clinical), MESH: Evolution, Molecular, biology, Ecology, mtDNA, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Plio-Pleistocene, Cytochromes b, MESH: Cytochromes b, Phylogeography, MESH: Phylogeography, Civet, MESH: Genome, Mitochondrial, Viverridae, Viverricula indica, Biotechnology, Asia, Biogeography, DNA, Mitochondrial, 010603 evolutionary biology, Evolution, Molecular, 03 medical and health sciences, MESH: Viverridae, Indian Ocean Islands, ddc:570, biology.animal, Genetics, MESH: Gene Frequency, Animals, East Asia, 14. Life underwater, Endemism, Molecular Biology, Institut für Biochemie und Biologie, biogeography, MESH: Indian Ocean Islands, MESH: DNA, Mitochondrial, Genetic Variation, MESH: Haplotypes, 15. Life on land, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Haplotypes, Genome, Mitochondrial, civet oil
Abstract: International audience; The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (1) establish a time-calibrated phylogeography across the species' native range and (2) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified 3 geographic lineages (East Asia, sister-group to Southeast Asia and the Indian subcontinent + northern Indochina) diverging 3.2-2.3 million years ago (Mya), with no clear signature of past demographic expansion. Within Southeast Asia, Balinese populations separated from the rest 2.6-1.3 Mya. Western Indian Ocean populations were assigned to the Indian subcontinent + northern Indochina lineage and had the lowest mitochondrial diversity. Approximate Bayesian computation did not distinguish between single versus multiple introduction scenarios. The early diversification of the small Indian civet was likely shaped by humid periods in the Late Pliocene-Early Pleistocene that created evergreen rainforest barriers, generating areas of intra-specific endemism in the Indian subcontinent, East, and Southeast Asia. Later, Pleistocene dispersals through drier conditions in South and Southeast Asia were likely, giving rise to the species' current natural distribution. Our molecular data supported the delineation of only 4 subspecies in V. indica, including an endemic Balinese lineage. Our study also highlighted the influence of prefirst millennium AD introductions to western Indian Ocean islands, with Indian and/or Arab traders probably introducing the species for its civet oil.
Published: 2017
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38. Plastic response by a small cervid to supplemental feeding in winter across a wide environmental gradient

Author: Nathan Ranc, Leif Soennichsen, Pavel Sustr, John D. C. Linnell, Michele Rocca, Atle Mysterud, Marco Heurich, Mark Hebblewhite, Anne Berger, Nicolas Morellet, Jean-Michel Gaillard, Ferdinando Urbano, Francesca Cagnacci, Federico Ossi, Petter Kjellander, Robin Sandfort, Max Kroeschel, Biodémographie évolutive, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), 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), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), University of Freiburg [Freiburg], Swedish University of Agricultural Sciences (SLU), University of Oslo (UiO), Norwegian Institute for Nature Research (NINA), Bavarian Forest National Park, Mammal Research Institute, Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa]-University of Pretoria [South Africa], Global Change Research Centre (CzechGlobe), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Associazione Cacciatori Trentina = Trentino hunters association, Università Iuav di Venezia = Iuav University of Venice (IUAV), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Harvard University, and Ossi, Federico
Subjects: 0106 biological sciences, Ungulate, Range (biology), winter severity, Climate behavioural responses, alimentation artificielle, [SDV]Life Sciences [q-bio], Context (language use), capreolus capreolus, 010603 evolutionary biology, 01 natural sciences, comportement animal, facteur biotique, Capreolus, Settore BIO/07 - ECOLOGIA, biology.animal, Ecology, Evolution, Behavior and Systematics, climate behavioral responses, Roe deer, Environmental gradient, 2. Zero hunger, roe deer, artificial feeding, ungulate management, climate change, Biotic component, Ecology, biology, 15. Life on land, roe, deer, biology.organism_classification, faune sauvage, 010601 ecology, 13. Climate action, Spatial ecology, adaptation au changement climatique
Abstract: International audience; Supplemental feeding for ungulates is a widespread practice in many human-dominated landscapes across Europe and North America, mainly intended to seasonally support populations. Surprisingly, little consideration was given so far to the effect of supplemental feeding on ungulate spatial ecology at a large scale, in management and conservation studies. Analyses of the main ecological drivers influencing the use of supplemental feeding sites by ungulates across a gradient of abiotic and biotic factors are currently lacking. We conducted a large-scale assessment of ecological and management drivers of use of feeding station sites in roe deer (Capreolus capreolus), a small cervid widely distributed across Europe that is particularly sensitive to winter severity. We tested four competing hypotheses by comparing the time spent at feeding station sites by 180 individual Global Positioning System-collared roe deer from nine populations spanning a wide latitudinal and altitudinal gradient. We found that roe deer used feeding station sites highly opportunistically in response to winter severity across its range. The harshest weather conditions at the northern range limit or the highest elevations provoked an intense use of feeding station sites, which typically peaked at the end of winter, in accordance with the adverse weather and nutritional condition hypotheses. Consistently, milder winters corresponded to a reduced and/or more homogeneous use of supplemental feeding. In general, intensively used feeding station sites heavily conditioned spatial behavior of roe deer. Importantly, biotic factors such as the presence of competitors decreased roe deer use of supplemental feeding station sites. Our results emphasize the importance of this human-induced alteration to resource distribution, especially in the context of the rapidly occurring climate change that is modifying resource availability for ungulate populations.
Published: 2017
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39. Evolutionary history of ssDNA bacilladnaviruses features horizontal acquisition of the capsid gene from ssRNA nodaviruses

Author: Arvind Varsani, Mart Krupovic, Sharyn J. Goldstien, Anisha Dayaram, Simona Kraberger, Darius Kazlauskas, Vilnius University [Vilnius], University of Canterbury [Christchurch], Colorado State University [Fort Collins] (CSU), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Arizona State University [Tempe] (ASU), University of Cape Town, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], DK was supported by an EMBO short term fellowship (ASTF 82–2016). The molecular work was supported by a grant (UC-E6007) from the American New Zealand Association (USA) awarded to AV., and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, Capsid protein, Gastropoda, CRESS DNA viruses, DNA, Single-Stranded, Bacilladnavirus, Genome, Viral, Biology, Virus Replication, Genome, Homology (biology), Evolution, Molecular, 03 medical and health sciences, Monophyly, MESH: New Zealand, Virology, Animals, Nodaviridae, MESH: Animals, MESH: Genetic Variation, Clade, Gene, MESH: Capsid Proteins, MESH: Evolution, Molecular, Genetics, MESH: Gastropoda, Phylogenetic tree, MESH: Virus Replication, DNA Viruses, Genetic Variation, biology.organism_classification, Amphibola crenata, ssDNA viruses, MESH: DNA Viruses, MESH: DNA, Viral, 030104 developmental biology, MESH: DNA, Single-Stranded, MESH: Nodaviridae, DNA, Viral, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: DNA, Circular, Capsid Proteins, DNA, Circular, MESH: Genome, Viral, New Zealand
Abstract: International audience; Bacilladnaviruses have single-stranded (ss) DNA genomes and infect diatoms, a major group of unicellular algae widespread in aquatic habitats. Despite their ecological importance, the provenance and relationships of bacilladnaviruses to other eukaryotic viruses remain unclear. Accordingly, they are currently classified into the 'floating' genus Bacilladnavirus. Here we present three new bacilladnavirus genomes recovered from a mollusc Amphibola crenata and benthic sediments from the Avon-Heathcote estuary in New Zealand. Our analysis shows that the rolling-circle replication-initiation proteins of bacilladnaviruses display unique conserved motifs and in phylogenetic trees form a monophyletic clade separated from other groups of ssDNA viruses. Unexpectedly, distant homology detection combined with structural modeling indicates that bacilladnavirus capsid proteins are homologous to those of ssRNA viruses from the Nodaviridae family. Considering the sequence diversity within the expanding Bacilladnavirus genus, we argue that classification of these viruses has to be revised and the current genus upgraded to the family level.
Published: 2017
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40. Species undersampling in tropical bat surveys: effects on emerging biodiversity patterns

Author: Luis F. Aguirre, Thomas H. Kunz, Erica M. Sampaio, Deborah Faria, Mickaël Henry, Sergio Estrada Villegas, Dietrich von Staden, Isabel Moya, Ludmilla M. S. Aguiar, Elisabeth K. V. Kalko, Paul A. Racey, Jean-Marc Pons, Neil M. Furey, M. Cristina Mac-Swiney González, Jean-François Cosson, Frank M. Clarke, Christa D. Weise, Christoph F. J. Meyer, Katja Rex, Julio Baumgarten, Christian C. Voigt, Jakob Fahr, Kathryn E. Stoner, Richard K. B. Jenkins, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Institute of Experimental Ecology, Universität Ulm - Ulm University [Ulm, Allemagne], Universidade de Brasília (UnB), Universidad Mayor de San Simón [Cochabamba, Bolivie] (UMSS), Programa Conservac Murcielagos Bolivia, Partenaires INRAE, Universidade Estadual de Santa Cruz (UESC), Institute of Biological and Environmental Sciences, University of Aberdeen, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), School of Freshwater Sciences, University of Wisconsin - Milwaukee, Department of Migration and Immuno-ecology, Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Technical University Braunschweig, Abeilles & Environnement (UR 406 ), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Madagasikara Voakajy, School of Anthropology and Conservation, University of Kent [Canterbury], School of Environment, Natural Resources and Geography, Bangor University, Boston University [Boston] (BU), Universidad Veracruzana, Muséum national d'Histoire naturelle (MNHN), Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, New Mexico State University, United States Fish and Wildlife Service (USFWS), and Smithsonian Tropical Research Institute
Subjects: 0106 biological sciences, Conservation of Natural Resources, Cost effectiveness, [SDV]Life Sciences [q-bio], Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, species subsamples, Chiroptera, Animals, Assemblage (archaeology), cost-effectiveness, Ecology, Evolution, Behavior and Systematics, Tropical Climate, Ecology, 010604 marine biology & hydrobiology, Biodiversity surveys, species rarity, Sampling (statistics), Tropics, 15. Life on land, Taxon, representative sampling, Animal Science and Zoology, Species richness, Bioindicator
Abstract: International audience; 1. Undersampling is commonplace in biodiversity surveys of species-rich tropical assemblages in which rare taxa abound, with possible repercussions for our ability to implement surveys and monitoring programmes in a cost-effective way. 2. We investigated the consequences of information loss due to species undersampling (missing subsets of species from the full species pool) in tropical bat surveys for the emerging patterns of species richness (SR) and compositional variation across sites. 3. For 27 bat assemblage data sets from across the tropics, we used correlations between original data sets and subsets with different numbers of species deleted either at random, or according to their rarity in the assemblage, to assess to what extent patterns in SR and composition in data subsets are congruent with those in the initial data set. We then examined to what degree high sample representativeness (r ≥ 0 8) was influenced by biogeographic region, sampling method, sampling effort or structural assemblage characteristics. 4. For SR, correlations between random subsets and original data sets were strong (r ≥ 0 8) with moderate (ca. 20%) species loss. Bias associated with information loss was greater for species composition; on average ca. 90% of species in random subsets had to be retained to adequately capture among-site variation. For non random subsets, removing only the rarest species (on average c. 10% of the full data set) yielded strong correlations (r > 0 95) for both SR and composition. Eliminating greater proportions of rare species resulted in weaker correlations and large variation in the magnitude of observed correlations among data sets. 5. Species subsets that comprised ca. 85% of the original set can be considered reliable surrogates, capable of adequately revealing patterns of SR and temporal or spatial turnover in many tropical bat assemblages. Our analyses thus demonstrate the potential as well as limitations for reducing survey effort and streamlining sampling protocols, and consequently for increasing the cost-effectiveness in tropical bat surveys or monitoring programmes. The dependence of the performance of species subsets on structural assemblage characteristics (total assemblage abundance, proportion of rare species), however, underscores the importance of adaptive monitoring schemes and of establishing surrogate performance on a site by site basis based on pilot surveys.
Published: 2014
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41. Using individual-based movement models to assess inter-patch connectivity for large carnivores in fragmented landscapes

Author: Surendra Prakash Goyal, Thorsten Wiegand, Rajapandian Kanagaraj, Stephanie Kramer-Schadt, Institut Français de Pondichéry (IFP), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Leibniz Institute for Zoo and Wildlife Research (IZW), and Leibniz Association
Subjects: 0106 biological sciences, biology, Tiger, Range (biology), Ecology, 010604 marine biology & hydrobiology, Endangered species, Small population size, Context (language use), 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Geography, Habitat, biology.animal, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Panthera, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract: Most rare and endangered large carnivores such as tiger ( Panthera tigris ) exist in human-dominated landscapes as small, fragmented and isolated populations across their range. Connectivity between the remaining populations in the habitat fragments is essential for their long-term persistence and focus of management initiatives. We describe an individual-based, spatially explicit model of tiger movement behavior based on previously developed habitat models to (i) quantify inter-patch connectivity among major (protected) habitat patches in the Terai Arc Landscape of India and Nepal and (ii) investigate the effect of potential management initiatives, e.g. restoring corridors, on enhancing connectivity among fragmented protected habitats. Connectivity was not solely a function of distance between patches, but an outcome of the interplay between movement behavior and landscape composition, with asymmetric connectivity explained by canalizing or diffusing effects of the landscape, and depending on the landscape context of the starting patch. Patch connectivity was mostly determined by autocorrelation in tiger movement, the daily movement capacity, landscape structure, and the amount of matrix habitat. Several habitat patches were likely to be island-like and already effectively isolated. However, simulating scenarios of corridor restoration showed that most habitat patches in India and between India and Nepal could recover connectivity, which may mitigate negative genetic consequences of small population size and effective isolation on tiger populations in this landscape. Combining habitat models with individual-based models is a powerful and robust approach that could be widely applied to delineate dispersal corridors of large carnivores and quantify patch connectivity even if data are scarce.
Published: 2013
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42. Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia)

Author: Niccolò Alfano, Gono Semiadi, Kristofer M. Helgen, Johan Michaux, Pierre-Henri Fabre, Yuli Sulistya Fitriana, Serge Morand, Kyriakos Tsangaras, Yasuko Ishida, Maribeth V. Eiden, Alfred L. Roca, Ken Aplin, Ulrike Löber, Alex D. Greenwood, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Université de Liège, Smithsonian Institution, 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, Indonesian Institute of Sciences (LIPI), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, and National Institute of Mental Health (NIMH)
Subjects: 0301 basic medicine, viruses, [SDV]Life Sciences [q-bio], Immunology, Subspecies, L73 - Maladies des animaux, Southeast asian, Microbiology, Rodent Diseases, 03 medical and health sciences, Retrovirus, Proviruses, Virology, Animals, 030102 biochemistry & molecular biology, biology, Phylogenetic tree, High-Throughput Nucleotide Sequencing, Nucleic Acid Hybridization, Murinae, Melomys burtoni, Sequence Analysis, DNA, Provirus, biology.organism_classification, 030104 developmental biology, Genetic Diversity and Evolution, Evolutionary biology, Indonesia, Insect Science, Leukemia Virus, Gibbon Ape, Koala retrovirus, Retroviridae Infections
Abstract: Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent ( Melomys burtoni ) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies of Melomys burtoni from Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the Indonesian M. burtoni subsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV in M. burtoni provides further evidence that M. burtoni , and potentially other lineages within the widespread subfamily Murinae , may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution of M. burtoni , specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents. IMPORTANCE Gibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only a Melomys burtoni subspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize that Melomys burtoni , and potentially related lineages with an Australo-Papuan distribution, may have played a key role in cross-species transmission to other taxa.
Published: 2016
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43. Tracking pan-continental trends in environmental contamination using sentinel raptors—what types of samples should we use?

Author: Paola Movalli, Antonio J. García-Fernández, Silvia Espín, Michael Coeurdassier, Oliver Krone, Richard F. Shore, B. van Hattum, Veerle L.B. Jaspers, Christian Sonne, Emma Martínez-López, N.W. van den Brink, Pilar Gómez-Ramírez, Igor Eulaers, Clémentine Fritsch, Dorte Herzke, Rafael Mateo, Björn Helander, Guy Duke, European Science Foundation, Section of Ecology, Department of Biology, University of Turku, Department of Toxicology, Faculty of Veterinary Medicine, University of Murcia, FRAM—High North Research Centre for Climate and the Environment, Norwegian Institute for Air Research (NILU), NERC Centre for Ecology and Hydrology, Natural Environment Research Council (NERC), Institute for Environmental Studies, VU University, Vrije Universiteit Amsterdam [Amsterdam] (VU), DELTARES - Marine and Coastal Systems, Deltares system, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Department of Bioscience, Artic Research Centre (ARC), Aarhus University [Aarhus], Behavioural Ecology and Ecophysiology Group, Department of Biology, UA, University of Antwerp (UA), Department of Biology [Trondheim] (IBI NTNU), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Centre for the Environment, Oxford University Environmental Change Institute, University of Oxford [Oxford], Environmental Research & Monitoring, Swedish Museum of Natural History, Swedish Museum of Natural History (NRM), Instituto de Investigación en Recursos Cinegéticos (IREC), Department of Collections, Naturalis Biodiversity Center, Naturalis Biodiversity Center [Leiden], Division of Toxicology, Wageningen University, Wageningen University and Research [Wageningen] (WUR), Research Networking Programme funded through European Science Foundation (ESF), Norwegian Institute for Air Research ( NILU ), NERC Centre for Ecology and Hydrology Lancaster Environment Centre, Centre for Ecology and Hydrology ( NERC ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Deltares system (NETHERLANDS), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Department of Bioscience, Artic Research Centre ( ARC ), University of Antwerp ( UA ), Department of Biology ( Norwegian University of Science and Technology ), Norwegian University of Science and Technology [Trondheim] ( NTNU ), Leibniz Institute for Zoo and Wildlife Research, Oxford University, Swedish Museum of Natural History, Instituto de Investigacion en Recursos Cinegeticos ( IREC CSIC UCLM JCCM ), and Wageningen University and Research Centre [Wageningen] ( WUR )
Subjects: 010504 meteorology & atmospheric sciences, Health, Toxicology and Mutagenesis, Environmental pollution, 010501 environmental sciences, Toxicology, 01 natural sciences, Diagnostics & Crisis Organization, Environmental monitoring, Biomonitoring, media_common, Trophic level, Diagnostiek & Crisisorganisatie, Ecology, Pharmacology. Therapy, Contaminación, Environmental resource management, General Medicine, Bird of prey, Matrix, Sample type, Contaminant, Monitoring, Contamination, Europe, Chemistry, Dierecologie, Environmental Pollutants, Animal Ecology, Environmental Monitoring, Sentinel species, Biology, Management, Monitoring, Policy and Law, Article, Ecology and Environment, media_common.cataloged_instance, Animals, European Union, European union, Toxicologie, 0105 earth and related environmental sciences, WIMEK, Raptors, business.industry, Ave de rapiña, Feathers, [SDE.ES]Environmental Sciences/Environmental and Society, 13. Climate action, business, Environmental Pollution, Zoology, [ SDE.ES ] Environmental Sciences/Environmental and Society, Bird of prey, Contaminant, Monitoring, Sample type, Matrix
Abstract: This article is an output from a workshop on Setting Best Practices on Raptor Contaminant Monitoring Activities in Europe, one of the activities of the EURAPMON network (http:// www.eurapmon.net) hosted in Murcia in May–June 2013.-- et al., Biomonitoring using birds of prey as sentinel species has been mooted as a way to evaluate the success of European Union directives that are designed to protect people and the environment across Europe from industrial contaminants and pesticides. No such pan-European evaluation currently exists. Coordination of such large scale monitoring would require harmonisation across multiple countries of the types of samples collected and analysed-matrices vary in the ease with which they can be collected and the information they provide. We report the first ever pan-European assessment of which raptor samples are collected across Europe and review their suitability for biomonitoring. Currently, some 182 monitoring programmes across 33 European countries collect a variety of raptor samples, and we discuss the relative merits of each for monitoring current priority and emerging compounds. Of the matrices collected, blood and liver are used most extensively for quantifying trends in recent and longer-term contaminant exposure, respectively. These matrices are potentially the most effective for pan-European biomonitoring but are not so widely and frequently collected as others. We found that failed eggs and feathers are the most widely collected samples. Because of this ubiquity, they may provide the best opportunities for widescale biomonitoring, although neither is suitable for all compounds. We advocate piloting pan-European monitoring of selected priority compounds using these matrices and developing read-across approaches to accommodate any effects that trophic pathway and species differences in accumulation may have on our ability to track environmental trends in contaminants., The work undertaken for this review was also supported by EURAPMON.
Published: 2016
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44. The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats

Author: Gager, Yann, Tarland, Emilia, Lieckfeldt, Dietmar, Ménage, Matthieu, Botero-Castro, Fidel, Rossiter, Stephen J., Kraus, Robert, Ludwig, Arne, Dechmann, Dina K. N., Department of Migration and Immuno-ecology, Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, International Max Planck Research School for Organismal Biology (IMPRS), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft-University of Konstanz, Swedish University of Agricultural Sciences (SLU), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, University of Konstanz, 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, School of Biological and Chemical Sciences, Queen Mary University of London (QMUL), Smithsonian Tropical Research Institute, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and 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)
Subjects: Male, Sound Spectrography, Physiology, Sensory Physiology, lcsh:Medicine, Skin Pigmentation, Biochemistry, MESH: Wings, Animal, Chiroptera, Wings, Bats, Medicine and Health Sciences, Wings, Animal, MESH: Animals, Animal Anatomy, MESH: Phylogeny, lcsh:Science, Musculoskeletal System, Animal Signaling and Communication, Energy-Producing Organelles, Phylogeny, MESH: Sympatry, Forearms, Mammals, Principal Component Analysis, Animal Behavior, [SDV.BA]Life Sciences [q-bio]/Animal biology, MESH: Chiroptera, Phylogenetic Analysis, Sensory Systems, Mitochondria, Arms, Sympatry, Auditory System, Multigene Family, Vertebrates, Female, MESH: Skin Pigmentation, MESH: Sound Spectrography, Anatomy, Cellular Structures and Organelles, MESH: Echolocation, Sequence Analysis, Research Article, Animal Navigation, Bioenergetics, Research and Analysis Methods, MESH: Genetic Loci, Gentic loci, Phylogenetic analysis, Taxonomy, Sequence alignment, Species Specificity, ddc:570, Genetics, Animals, MESH: Species Specificity, Molecular Biology Techniques, Sequencing Techniques, Molecular Biology, MESH: Sample Size, MESH: Principal Component Analysis, Molecular Biology Assays and Analysis Techniques, Behavior, Limbs (Anatomy), Body Weight, lcsh:R, Organisms, Biology and Life Sciences, Extremities, Cell Biology, Acoustics, MESH: Male, MESH: Body Weight, Genetic Loci, MESH: Acoustics, Echolocation, Sample Size, MESH: Multigene Family, Animal Migration, lcsh:Q, MESH: Extremities, MESH: Microsatellite Repeats, Zoology, Sequence Alignment, MESH: Female, Neuroscience, Microsatellite Repeats
Abstract: International audience; A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative.
Published: 2016
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45. R2d2 drives selfish sweeps in the house mouse

Author: David W. Threadgill, Wesley J. Jolley, Maria da Graça Ramalhinho, James Holt, Amanda J. Chunco, Lydia Ortiz de Solorzano, Daniel W. Förster, Daniel Pomp, Andrew Holmes, Fernando Pardo-Manuel de Villena, Sofia A. Grize, Leonard McMillan, Sofia I. Gabriel, Mabel D. Giménez, John P. Didion, Jeremy S. Herman, Jeremy B. Searle, George M. Weinstock, Riccardo Castiglia, İslam Gündüz, Kunjie Hua, Timothy A. Bell, Karl J. Campbell, John E. French, Janice Britton-Davidian, Karen L. Svenson, Andrew P. Morgan, Elissa J. Chesler, Carol J. Bult, Maria da Luz Mathias, Daniel M. Gatti, George P. Mitsainas, James J. Crowley, Rachel C. McMullan, Pat Thomas-Laemont, Heidi C. Hauffe, Yung-Hao Ching, Meng Shin Shiao, Stephan P. Rosshart, Liran Yadgary, María José López-Fuster, Emanuela Solano, Barbara Rehermann, Gary A. Churchill, Jacint Ventura Queija, Eva B. Giagia-Athanasopoulou, Theodore Garland, Anna K. Lindholm, University of Zurich, de Villena, Fernando Pardo-Manuel, Lineberger Comprehensive Cancer Center (UNC Lineberger), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Carolina Center for Genome Sciences, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), The Jackson Laboratory [Bar Harbor] (JAX), Island Conservation, University of Queensland [Brisbane], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Elon University [NC, USA], University of North Carolina System (UNC), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, National Institute of Environmental Health Sciences [Durham] (NIEHS-NIH), National Institutes of Health [Bethesda] (NIH), Centre for Environmental and Marine Studies [Aveiro] (CESAM), Universidade de Aveiro, Universidade de Lisboa = University of Lisbon (ULISBOA), University of California [Riverside] (UC Riverside), University of California (UC), Department of Biology [Patras], University of Patras, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Universidad Nacional de Misiones, Universität Zürich [Zürich] = University of Zurich (UZH), Ondokuz Mayis University (OMU), National Institute on Alcohol Abuse and Alcoholism (NIAAA), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Department of Computer Science [Chapel Hill], Universitat de Barcelona (UB), National Institute of Diabetes and Digestive and Kidney Diseases [Bethesda], Department of Ecology and Evolutionary Biology [Ithaca], Cornell University [New York], Mahidol University [Bangkok], Texas A&M University [College Station], Universitat Autònoma de Barcelona (UAB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Universidade de Lisboa (ULISBOA), University of California [Riverside] (UCR), University of California, University of Patras [Patras], Ondokuz Mayis University, and OMÜ
Subjects: Male, 0301 basic medicine, MESH: Selection, Genetic, Meiotic Drive, House Mouse, purl.org/becyt/ford/1 [https], Mice, Settore BIO/05 - ZOOLOGIA, 0302 clinical medicine, Darwinian Fitness, MUS MUSCULUS DOMESTICUS, MESH: Animals, MESH: Genetic Variation, MESH: Models, Genetic, Selective sweep, MESH: Evolution, Molecular, 2. Zero hunger, Genetics, Selfish Genes, education.field_of_study, Nuclear Proteins, RNA-Binding Proteins, Meiotic drive, Adaptation, Physiological, Biological Evolution, Fixation (population genetics), Fast Track, 590 Animals (Zoology), Female, MESH: DNA Copy Number Variations, CIENCIAS NATURALES Y EXACTAS, Selective Sweep, Selfish genes, MESH: Mutation, DNA Copy Number Variations, Otras Ciencias Biológicas, Population, MESH: Genetics, Population, MESH: Biological Evolution, Biology, R2d2, Evolution, Molecular, Ciencias Biológicas, 03 medical and health sciences, 10127 Institute of Evolutionary Biology and Environmental Studies, Genetic drift, 1311 Genetics, Genetic variation, 1312 Molecular Biology, Animals, Selection, Genetic, purl.org/becyt/ford/1.6 [https], education, Molecular Biology, MESH: Mice, Alleles, Ecology, Evolution, Behavior and Systematics, Repetitive Sequences, Nucleic Acid, MESH: Repetitive Sequences, Nucleic Acid, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Models, Genetic, MESH: Alleles, Genetic Variation, MESH: Adaptation, Physiological, MESH: Male, House mouse, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genetics, Population, 030104 developmental biology, MESH: RNA-Binding Proteins, 1105 Ecology, Evolution, Behavior and Systematics, Mutation, 570 Life sciences, biology, MESH: Nuclear Proteins, MESH: Female, 030217 neurology & neurosurgery
Abstract: Mitsainas, George/0000-0003-4976-8275; Lindholm, Anna K/0000-0001-8460-9769; Mathias, Maria da Luz/0000-0003-3876-958X; Foerster, Daniel/0000-0002-6934-0404; Hauffe, Heidi Christine C/0000-0003-3098-8964; Threadgill, David W/0000-0003-3538-1635; Gabriel, Sofia I/0000-0003-3702-4631; Chesler, Elissa/0000-0002-5642-5062; Didion, John/0000-0002-8111-6261; solano, emanuela/0000-0001-8482-9243; Weinstock, George/0000-0002-2997-4592; McMullan, Rachel/0000-0003-0297-4549; Holt, James/0000-0001-6411-9236; Rehermann, Barbara/0000-0001-6832-9951 WOS: 000376170300001 PubMed: 26882987 A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether "selfish" genes are capable of fixation-thereby leaving signatures identical to classical selective sweeps-despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2(HC)) in natural populations. We replicate this finding inmultiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2(HC) rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2(HC) is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [T32GM067553, F30MH103925, P50GM076468, K01MH094406, DK-076050, DK-056350, AG038070]; National Science FoundationNational Science Foundation (NSF) [IOS-1121273]; Vaadia-BARD Postdoctoral Fellowship AwardUS-Israel Binational Science Foundation [FI-478-13]; U.S. Army Medical Research and Materiel CommandU.S. Army Medical Research & Materiel Command (USAMRMC) [W81XWH-11-1-0762]; Jackson Laboratory new investigator funds; National Center for Scientific Research, France [ISEM 2016-002]; University of Rome "La Sapienza"; Claraz-Stiftung; Natural Environment Research Council (UK)NERC Natural Environment Research Council; EU Human Capital and Mobility Programme [CHRX-CT93-0192]; Foundation for Science and Technology, PortugalPortuguese Foundation for Science and Technology [PTDC/BIA-EVF/116884/2010, UID/AMB/50017/2013]; Spanish "Ministerio de Ciencia y Tecnologia"Spanish Government [CGL2007-62111]; "Ministerio de Economia y Competitividad"Spanish Government [CGL2010-15243]; School of Medicine at University of North Carolina We wish to thank all the scientists and research personnel who collected and processed the samples used in this study. In particular we acknowledge Luanne Peters and Alex Hong-Tsen Yu for providing critical samples; Ryan Buus and T. Justin Gooch for isolating DNA for high-density genotyping of wild-caught mice; and Vicki Cappa, A. Cerveira, Guila Ganem, Ron and Annabelle Lesher, K. Said, Toni Schelts, Dan Small, and J. Tapisso for aiding in mouse trapping. We thank Muriel Davisson at the Jackson Laboratory for maintaining, for several decades, tissue samples from breeding colonies used to generate wild-derived inbred strains. We also thank Francis Collins, Jim Evans, Matthew Hahn, and Corbin Jones for comments on an earlier version of this manuscript. This work was supported by the National Institutes of Health T32GM067553 to J.P.D. and A.P.M., F30MH103925 to A.P.M., P50GM076468 to E.J.C., G.A.C., and F.P.M.V., K01MH094406 to J.J.C., DK-076050 and DK-056350 to D.P., AG038070 to G.A.C, and the intramural research program to B.R. and S.P.R.; National Science Foundation IOS-1121273 to T.G.; Vaadia-BARD Postdoctoral Fellowship Award FI-478-13 to L.Y.; U.S. Army Medical Research and Materiel Command W81XWH-11-1-0762 to C.J.B.; The Jackson Laboratory new investigator funds to E.J.C.; The National Center for Scientific Research, France to J.B.D. (this is contribution no ISEM 2016-002); the University of Rome "La Sapienza" to R.C. and E.S.; Claraz-Stiftung to S.G. and A.L.; Natural Environment Research Council (UK) to M.D.G., H.C.H., and J.B.S.; EU Human Capital and Mobility Programme (CHRX-CT93-0192) to H.C.H. and J.B.S.; Foundation for Science and Technology, Portugal PTDC/BIA-EVF/116884/2010 and UID/AMB/50017/2013 to S.I.G., M.L.M., and J.B.S.; Spanish "Ministerio de Ciencia y Tecnologia" CGL2007-62111 and "Ministerio de Economia y Competitividad" CGL2010-15243 to J.V.;and the Oliver Smithies Investigator funds provided by the School of Medicine at University of North Carolina to F.P.M.V. All data are made available at http://csbio.unc.edu/r2d2/. The authors declare no competing financial interests. Correspondence and requests for materials should be addressed to F.P.M.V. (fernando@med.unc.edu).
Published: 2016
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46. Investigations on the aetiology of pinching off syndrome in four white-tailed sea eagles (Haliaeetus albicilla) from Germany

Author: Kerstin Müller, Elvira Schettler, Dörte Lueschow, Reimar Johne, Leo Brunnberg, Rainer Kollmann, Oliver Krone, Kai Frölich, Michael Lierz, Rüdiger Raue, Annette Mankertz, Kim Hattermann, Dirk Soike, Hermann J. Müller, Sonja Linke, Petra Wolf, Helga Gerlach, Stephanie Speck, Hafez M. Hafez, Christina Prusas, Freie Universität Berlin, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Wildlife Park Eekholt, Robert Koch Institute [Berlin] (RKI), Faculty of Veterinary Medicine, University of Leipzig, Institute for Virology, Project Group for the Protection of the White-tailed Sea Eagle, Landesamt für Verbraucherschutz und Landwirtschaft, University of Veterinary Medicine Hannover, and Department of Animal Nutrition
Subjects: Male, Pathology, medicine.medical_specialty, animal structures, 040301 veterinary sciences, Eagles, Lipofuscin, 0403 veterinary science, 03 medical and health sciences, Follicle, Cytokeratin, Food Animals, Islet cells, biology.animal, medicine, Animals, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, integumentary system, General Immunology and Microbiology, biology, Bird Diseases, Haliaeetus albicilla, Life Sciences, Syndrome, 04 agricultural and veterinary sciences, Feathers, White (mutation), Thyroxine, Feather, visual_art, visual_art.visual_art_medium, Etiology, Female, Animal Science and Zoology
Abstract: The purpose of this study was to investigate the aetiology of the pinching off syndrome (POS), a generalized feather abnormality affecting free-living nestling of the white-tailed sea eagle (Haliaeetus albicilla) in Europe. For the first time, extensive clinical, haematological, biochemical, virological, bacteriological, nutritional, histopathological, parasitological and electron microscopical examinations were performed on three females and one male suffering from POS. Early and increased cytokeratin formation at the base of regenerating feathers and their follicle was observed in affected birds. Ultrathin sections of the feather papillae revealed an extended stratum transitivum and a compact, thickened keratinized stratum corneum. The transitional cells in POS feathers contained vacuoles often associated with the nucleus. Lipofuscin accumulations in neurons, glial cells and islet cells of the pancreas were found in all examined birds. It was not clear whether there is an association between the occurrence of lipofuscin and POS. No evidence was found to suggest that infectious agents (parasites, bacteria, fungi or viruses), malnutrition or hormonal imbalances are involved in the aetiology of POS in white-tailed sea eagles. It remains unclear whether there is a genetic background of POS.
Published: 2007
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47. Corticosterone, inflammation, immune status and telomere length in frigatebird nestlings facing a severe herpesvirus infection

Author: Sebastiano, Manrico, Eens, Marcel, Angelier, Frederic, Pineau, Kévin, Chastel, Olivier, Costantini, David, Pineau, Kevin, Behavioural Ecology & Ecophysiology Group, University of Antwerp (UA), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), 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), Groupe d’Etude et de Protection des Oiseaux en Guyane (GEPOG), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Evolution des régulations endocriniennes (ERE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Inflammation, Disease, Management, Monitoring, Policy and Law, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Immune system, herpesvirus, Corticosterone, immunocompetance, telomere length, medicine, Nature and Landscape Conservation, Innate immune system, Ecological Modeling, Haptoglobin, Outbreak, biology.organism_classification, 3. Good health, Chemistry, 030104 developmental biology, chemistry, [SDE]Environmental Sciences, Immunology, biology.protein, Human medicine, medicine.symptom, Frigatebird, Research Article
Abstract: In this study, we examined the pathophysiological consequences likely to be attributable to a herpesvirus infection for immune function, corticosterone, telomere length and inflammation. We found that the plasma concentration of haptoglobin was strongly associated with the observable clinical manifestation of disease and could predict probabilities of survival., Herpesvirus outbreaks are common in natural animal populations, but little is known about factors that favour the infection and its consequences for the organism. In this study, we examined the pathophysiological consequences of a disease probably attributable to herpesvirus infection for several markers of immune function, corticosterone, telomere length and inflammation. In addition, we assessed whether any markers used in this study might be associated with the occurrence of visible clinical signs of the disease and its impact on short-term survival perspectives. To address our questions, in spring 2015, we collected blood samples from nestlings of the magnificent frigatebird (Fregata magnificens) that were free of any clinical signs or showed visible signs of the disease. We found that the plasma concentration of haptoglobin was strongly associated with the infection status and could predict probabilities of survival. We also found that nestlings with clinical signs had lower baseline corticosterone concentrations and similar telomere length compared with healthy nestlings, whereas we did not find any association of the infection status with innate immune defenses or with nitric oxide concentration. Overall, our results suggest that the plasma concentration of haptoglobin might be a valuable tool to assess survival probabilities of frigatebird nestlings facing a herpesvirus outbreak.
Published: 2017
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48. Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

Author: Johan Michaux, Simon Rasmussen, M. Thomas P. Gilbert, Nathan Wales, Kyriakos Tsangaras, Serge Morand, Alex D. Greenwood, Thomas Sicheritz-Pontén, Yasuko Ishida, Marie-Louise Kampmann, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Technical University of Denmark [Lyngby] (DTU), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, 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, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and 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)
Subjects: 0106 biological sciences, DNA, Bacterial, Molecular Sequence Data, lcsh:Medicine, Genomics, Bacterial genome size, Computational biology, Microbial Genomics, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Polymerase Chain Reaction, DNA sequencing, 03 medical and health sciences, Mice, Escherichia coli, Genetics, Animals, [CHIM]Chemical Sciences, Genomic library, lcsh:Science, Genome Evolution, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Bacterial Genomics, Shotgun sequencing, Oligonucleotide, lcsh:R, Nucleic Acid Hybridization, Biology and Life Sciences, Computational Biology, Genome Analysis, Genomic Libraries, Rats, Animal Genomics, Solution hybridization, lcsh:Q, U30 - Méthodes de recherche, L72 - Organismes nuisibles des animaux, Research Article
Abstract: International audience; Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information.
Published: 2014
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49. Ecologists overestimate the importance of predictor variables in model averaging: a plea for cautious interpretations

Author: Morgan David, Matthias Galipaud, Mark A. F. Gillingham, François-Xavier Dechaume-Moncharmont, Biogéosciences [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 ), Centre de recherche de la Tour du Valat, Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung ( IZW ), Department of Biology-Ethology, University of Antwerp ( UA ), 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), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association-Leibniz Association, University of Antwerp (UA), and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: model selection, Information theory, multimodel inference, Bayesian information criterion, Statistics, Econometrics, Range (statistics), Akaike Information Criterion, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, baseline sum of weights, Set (psychology), Biology, Ecology, Evolution, Behavior and Systematics, Mathematics, information theory, [STAT.AP]Statistics [stat]/Applications [stat.AP], Ecological Modeling, Model selection, [ STAT.AP ] Statistics [stat]/Applications [stat.AP], model averaging, Chemistry, Variable (computer science), Sample size determination, variable importance, Akaike information criterion, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Information-theory procedures are powerful tools for multimodel inference and are now standard methods in ecology. When performing model averaging on a given set of models, the importance of a predictor variable is commonly estimated by summing the weights of models where the variable appears, the so-called sum of weights (SW). However, SWs have received little methodological attention and are frequently misinterpreted. We assessed the reliability of SW by performing model selection and averaging on simulated data sets including variables strongly and weakly correlated to the response variable and a variable unrelated to the response. Our aim was to investigate how useful SWs are to inform about the relative importance of predictor variables. SW can take a wide range of possible values, even for predictor variables unrelated to the response. As a consequence, SW with intermediate values cannot be confidently interpreted as denoting importance for the considered predictor variable. Increasing sample size using an alternative information criterion for model selection or using only a subset of candidate models for model averaging did not qualitatively change our results: a variable of a given effect size can take a wide range of SW values. Contrary to what is assumed in many ecological studies, it seems hazardous to define a threshold for SW above which a variable is considered as having a statistical effect on the response and SW is not a measure of effect size. Although we did not consider every possible condition of analysis, it is likely that in most situations, SW is a poor estimate of variable's importance. 10.1111/(ISSN)2041-210X
Published: 2014
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50. How choosy should I be? The relative searching time predicts evolution of choosiness under direct sexual selection

Author: Alexandre Courtiol, François Rousset, Loïc Etienne, Bernard Godelle, 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, Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and 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)
Subjects: 0106 biological sciences, relative searching time, Theoretical research, Biology, 010603 evolutionary biology, 01 natural sciences, Choice Behavior, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Empirical research, Econometrics, Animals, sexual selection, Mating, Operational sex ratio, mate choice, Research Articles, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, General Environmental Science, 0303 health sciences, General Immunology and Microbiology, Models, Genetic, choosiness, direct benefits, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General Medicine, Mating Preference, Animal, Mating system, Biological Evolution, Variable (computer science), Mate choice, operational sex ratio, Sexual selection, General Agricultural and Biological Sciences, Social psychology
Abstract: Most theoretical research in sexual selection has focused on indirect selection. However, empirical studies have not strongly supported indirect selection. A well-established finding is that direct benefits and costs exert a strong influence on the evolution of mate choice. We present an analytical model in which unilateral mate choice evolves solely by direct sexual selection on choosiness. We show this is sufficient to generate the evolution of all possible levels of choosiness, because of the fundamental trade-off between mating rate and mating benefits. We further identify the relative searching time (RST, i.e. the proportion of lifetime devoted to searching for mates) as a predictor of the effect of any variable affecting the mating rate on the evolution of choosiness. We show that the RST: (i) allows one to make predictions about the evolution of choosiness across a wide variety of mating systems; (ii) encompasses all alternative variables proposed thus far to explain the evolution of choosiness by direct sexual selection; and (iii) can be empirically used to infer qualitative differences in choosiness.
Published: 2014
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