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100 results on '"University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences"'

1. Mass-independent and mass-dependent Cr isotopic composition of the Rumuruti (R) chondrites: Implications for their origin and planet formation

Author: Martin Schiller, Jean-Alix Barrat, Frédéric Moynier, Conel M. O'd. Alexander, Martin Bizzarro, Addi Bischoff, Ke Zhu, Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Carnegie Institution for Science, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut für Planetologie [Münster], Westfälische Wilhelms-Universität Münster = University of Münster (WWU), F. M. acknowledges funding from the European Research Council under the H2020 framework program/ERC grant agreement (ERC starting grant, #637503-PRISTINE) and financial support of the UnivEarthS Labex program at Université de Paris (#ANR-10-LABX-0023 and #ANR-11-IDEX-0005-02), and the IPGP platform PARI, and the Region Île-de-France Sesame grant no. 12015908. M. S. acknowledges funding from the Villum Fonden (#00025333). M. B. acknowledges funding from the Carlsberg Foundation (#CF18-1105), the Danish National Research Foundation (#DNRF97) and the European Research Council (ERC Advanced Grant Agreement, #833275-DEEPTIME). A. B. thanks the support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, #263649064) – TRR 170 (subproject B05). This is TRR170 Publication No. 116. K. Z. thanks the China Scholarship Council (CSC) for the PhD fellowship (#201706340161) and IPGP for the funding support of traveling, 'Aide à la MOBILITE INTERNATIONALE des doctorants de l’IPGP' (2019), to visit Earth and Planetary Laboratory, Carnegie Institution for Science., ANR-10-LABX-0023,UnivEarthS,Earth - Planets - Universe: observation, modeling, transfer(2010), ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011), European Project: 637503,H2020,ERC-2014-STG,PRISTINE(2015), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Carnegie Institution for Science [Washington], Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Westfälische Wilhelms-Universität Münster (WWU)
Subjects: chondrules, cr-54, 010504 meteorology & atmospheric sciences, oxygen-isotope, Geochemistry, EARLY SOLAR-SYSTEM, earth, Ureilite, engineering.material, CHEMICAL-COMPOSITION, 010502 geochemistry & geophysics, 01 natural sciences, Cosmochemistry, CR-54, Geochemistry and Petrology, Chondrite, Cr stable isotopes, QUANTITATIVE MODELS, EARTH, fractionation, UBO, 0105 earth and related environmental sciences, Isotope, Chemistry, FRACTIONATION, ACL, METEORITE, Chondrule, Cr-54 nucleosynthetic anomalies, CHONDRULES, Rumuruti Chondrites, meteorite, OXYGEN-ISOTOPE, Mn-53-Cr-53 chronometry, Planetary science, 13. Climate action, DISCOVERY, Enstatite, engineering, Chondritic clast, quantitative models, chemical-composition, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, early solar-system, Planetary differentiation
Abstract: WOS:000600550100030; International audience; Chromium (Cr) isotopes play an important role in cosmochemistry and planetary science because they are powerful tools for dating (Mn-53-Cr-53 short-lived chronometry), tracing (Cr-54 nucleosynthetic anomalies) the origins of the materials, and studying the processes involved in volatile element fractionation and planetary differentiation (Cr stable isotopic fractionation). To use Cr isotopes for these purposes, it is essential to precisely know the compositions of the various chondritic reservoirs. However, the Cr isotope composition of Rumuruti (R) chondrites remains unknown. Here, we report high-precision mass-independent (average 2SE uncertainty of similar to 0.02 and similar to 0.06 for epsilon Cr-53 and epsilon Cr-54, respectively; epsilon indicates 10,000 deviation) and mass-dependent (uncertainty of average 0.03 parts per thousand for delta Cr-53; .delta indicates 1000 deviation) Cr isotope data for 12 bulk R chondrites of petrologic types 3-6 (including R chondrite breccias), and one R chondrite-like clast (MS-CH) in the Almahata Sitta polymict ureilite. All the R chondrites show homogeneous bulk epsilon Cr-54 values, -0.06 +/- 0.08 (2SD), similar only to those of the Earth-Moon system and enstatite chondrites. This first epsilon Cr-54 dataset for R chondrites provides significant addition to the epsilon Cr-54-A, Delta O-17 diagram, and positions them as a potential endmember for planetary precursors. The R chondrites possess a higher Mn-55/Cr-52 of 0.68 +/- 0.04 relative to most of carbonaceous chondrites and higher epsilon Cr-53 values 0.23 +/- 0.05 (2SD) relative to most of chondrite groups. This likely results from the lower chondrule abundance in R chondrites compared to that of ordinary and enstatite chondrites. The stable Cr isotope composition of R chondrites is homogeneous with a delta Cr-53 = -0.12 +/- 0.03%e (2SD). Combined with previous data of other groups of chondrites, we show that the stable Cr isotopic composition of all the chondrites is homogeneous with delta Cr-53 of -0.12 +/- 0.04%e (2SD, N = 42) and is independent of the petrologic type and redox conditions. The lack of mass-dependent fractionation between all groups of chondrites suggests that the average chondrite delta Cr-53 value is also representative for the initial composition of all differentiated planets in the Solar System. Finally, the MS-CH clast in Almahata Sitta has a Cr isotopic composition (epsilon Cr-53 = 0.18 +/- 0.04, epsilon Cr-54 = 0.16 +/- 0.07, and delta Cr-53 = -0.11 +/- 0.05%e) that is consistent (within error) with it being an R chondrite-like clast. (C) 2020 Elsevier Ltd. All rights reserved.
Published: 2021

2. Origin of hydrogen isotopic variations in chondritic water and organics

Author: Laurette Piani, Hisayoshi Yurimoto, Lionel G. Vacher, Martin Bizzarro, Yves Marrocchi, Centre de Recherches Pétrographiques et Géochimiques (CRPG), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Washington University in Saint Louis (WUSTL), Hokkaido University [Sapporo, Japan], Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), and ANR-19-CE31-0027,HYDRaTE,Distribution of HYdrogen in the protoplanetary Disk and deliveRy to the Terrestrial planEts(2019)
Subjects: Solar System, molecular cloud, 010504 meteorology & atmospheric sciences, Hydrogen, water, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], chemistry.chemical_element, FOS: Physical sciences, 010502 geochemistry & geophysics, Protoplanetary disk, 01 natural sciences, Parent body, Astrobiology, Physics - Geophysics, Geochemistry and Petrology, Chondrite, Earth and Planetary Sciences (miscellaneous), 0105 earth and related environmental sciences, organic matter, Earth and Planetary Astrophysics (astro-ph.EP), Mineral hydration, Molecular cloud, disk, Geophysics (physics.geo-ph), hydrogen isotopes, Geophysics, chemistry, 13. Climate action, Space and Planetary Science, Sublimation (phase transition), chondrite, Geology, Astrophysics - Earth and Planetary Astrophysics
Abstract: International audience; Chondrites are rocky fragments of asteroids that formed at different times and heliocentric distances in the early solar system. Most chondrite groups contain water-bearing minerals, attesting that both water-ice and dust were accreted on their parent asteroids. Nonetheless, the hydrogen isotopic composition (D/H) of water in the different chondrite groups remains poorly constrained, due to the intimate mixture of hydrated minerals and organic compounds, the other main H-bearing phase in chondrites. Building on our recent works using in situ secondary ion mass spectrometry analyses, we determined the H isotopic composition of water in a large set of chondritic samples (CI, CM, CO, CR, CY, and C-ungrouped carbonaceous chondrites) and report that water in each group shows a distinct and unique D/H signature. Based on a comparison with literature data on bulk chondrites and their water and organics, our data do not support a preponderant role of parent-body processes in controlling the D/H variations among chondrites. Instead, we propose that the water and organic D/H signatures were mostly shaped by interactions between the protoplanetary disk and the molecular cloud that episodically fed the disk over several million years. Because the 2 preservation of D-rich interstellar water and/or organics in chondritic materials is only possible below their respective sublimation temperatures (160 and 350-450 K), the H isotopic signatures of chondritic materials depend on both the timing and location at which their parent body formed.
Published: 2021

3. AMBITION – comet nucleus cryogenic sample return

Author: Hervé Cottin, Carsten Güttler, Stavro Ivanoski, Colin Snodgrass, Claudio Codella, Jean-Baptiste Vincent, Kelly E. Miller, Pierre Henri, Maria Drozdovskaya, Alain Herique, Gianrico Filacchione, Kathrin Altwegg, Nicolas Thomas, Martin Bizzarro, Maria Cristina De Sanctis, Rosita Kokotanekova, E. Bianchi, Björn Davidsson, Lydie Bonal, Stefan Ulamec, Cécile Engrand, Cecilia Tubiana, Dominique Bockelée-Morvan, Mathieu Choukroun, Anny Chantal Levasseur-Regourd, Marina Galand, Alessandra Rotundi, Jürgen Blum, M. Schönbächler, Fabrizio Capaccioni, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Istituto di Astrofisica e Planetologia Spaziali - INAF (IAPS), Istituto Nazionale di Astrofisica (INAF), Physikalisches Institut [Bern], Universität Bern [Bern] (UNIBE), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France, Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Natural History Museum of Denmark, Faculty of Science [Copenhagen], Institut für Geophysik und Extraterrestrische Physik [Braunschweig] (IGEP), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), INAF - Osservatorio Astrofisico di Arcetri (OAA), Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA (UMR_7583)), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Center for Space and Habitability (CSH), University of Bern, Laboratoire de Physique des 2 Infinis Irène Joliot-Curie (IJCLab), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Imperial College London], Imperial College London, Max-Planck-Institut für Sonnensystemforschung (MPS), Max-Planck-Gesellschaft, Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Joseph Louis LAGRANGE (LAGRANGE), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), INAF - Osservatorio Astronomico di Trieste (OAT), European Southern Observatory (ESO), PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Southwest Research Institute [San Antonio] (SwRI), Dipartimento di Scienze e Tecnologie [Napoli] (DIST), Università degli Studi di Napoli 'Parthenope' = University of Naples (PARTHENOPE), Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute for Astronomy [Edinburgh] (IfA), University of Edinburgh, German Aerospace Center (DLR), DLR Institut für Planetenforschung, Deutsches Zentrum für Luft- und Raumfahrt [Berlin] (DLR), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Universität Bern [Bern], Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Paris (UP)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National d’Études Spatiales [Paris] (CNES), Université Nice Sophia Antipolis (... - 2019) (UNS), Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Universita degli studi di Napoli 'Parthenope' [Napoli], Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Centre de Sciences Nucléaires et de Sciences de la Matière (CSNSM), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Space and Atmospheric Physics Group [London], Blackett Laboratory, and Imperial College London-Imperial College London
Subjects: Solar System, 010504 meteorology & atmospheric sciences, Comet, Context (language use), 01 natural sciences, Space missions, Space exploration, Astrobiology, Comet nucleus, 0103 physical sciences, Comets, 010303 astronomy & astrophysics, 0105 earth and related environmental sciences, Solar system, 520 Astronomy, Giant planet, Astronomy and Astrophysics, 620 Engineering, 13. Climate action, Space and Planetary Science, Asteroid, [SDU]Sciences of the Universe [physics], Formation and evolution of the Solar System, Geology
Abstract: We describe the AMBITION project, a mission to return the first-ever cryogenically-stored sample of a cometary nucleus, that has been proposed for the ESA Science Programme Voyage 2050. Comets are the leftover building blocks of giant planet cores and other planetary bodies, and fingerprints of Solar System’s formation processes. We summarise some of the most important questions still open in cometary science and Solar System formation after the successful Rosetta mission. We show that many of these scientific questions require sample analysis using techniques that are only possible in laboratories on Earth. We summarize measurements, instrumentation and mission scenarios that can address these questions. We emphasize the need for returning a sample collected at depth or, still more challenging, at cryogenic temperatures while preserving the stratigraphy of the comet nucleus surface layers. We provide requirements for the next generation of landers, for cryogenic sample acquisition and storage during the return to Earth. Rendezvous missions to the main belt comets and Centaurs, expanding our knowledge by exploring new classes of comets, are also discussed. The AMBITION project is discussed in the international context of comet and asteroid space exploration.
Published: 2021

4. Germanium and silicon isotope investigations in Main-Group and Eagle Station pallasites

Author: Zhengbin Deng, Johan Villeneuve, Damien Cividini, Béatrice Luais, Centre de Recherches Pétrographiques et Géochimiques (CRPG), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut de Physique du Globe de Paris (IPGP), and Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)
Subjects: Eagle, Materials science, chemistry, biology, Group (periodic table), [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, biology.animal, Radiochemistry, chemistry.chemical_element, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Germanium, Isotopes of silicon, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

5. Ecological networks: Pursuing the shortest path, however narrow and crooked

Author: Costa, Martin Gonzalez, A. M., Guizien, Doglioli, Gómez, J. M., Petrenko, A. A. Allesina, Korea Institute of Science and Technology, Marie Curie Fellows Association, Danish National Research Foundation, IBS Center for Climate Physics, Pusan National University, Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Departament Electronica, Universitat de Barcelona (UB), Department of Ecology and Evolutionary Biology, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, and University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)
Subjects: 0106 biological sciences, Multidisciplinary, Theoretical computer science, Computer science, 010604 marine biology & hydrobiology, lcsh:R, lcsh:Medicine, 010603 evolutionary biology, 01 natural sciences, Replication (computing), Article, Ecological network, Identification (information), [SDE]Environmental Sciences, Shortest path problem, Ecological networks, lcsh:Q, Enhanced Data Rates for GSM Evolution, Theoretical ecology, Centrality, Representation (mathematics), lcsh:Science, Network analysis
Abstract: Representing data as networks cuts across all sub-disciplines in ecology and evolutionary biology. Besides providing a compact representation of the interconnections between agents, network analysis allows the identification of especially important nodes, according to various metrics that often rely on the calculation of the shortest paths connecting any two nodes. While the interpretation of a shortest paths is straightforward in binary, unweighted networks, whenever weights are reported, the calculation could yield unexpected results. We analyzed 129 studies of ecological networks published in the last decade that use shortest paths, and discovered a methodological inaccuracy related to the edge weights used to calculate shortest paths (and related centrality measures), particularly in interaction networks. Specifically, 49% of the studies do not report sufficient information on the calculation to allow their replication, and 61% of the studies on weighted networks may contain errors in how shortest paths are calculated. Using toy models and empirical ecological data, we show how to transform the data prior to calculation and illustrate the pitfalls that need to be avoided. We conclude by proposing a five-point check-list to foster best-practices in the calculation and reporting of centrality measures in ecology and evolution studies., This work was supported by the Institute for Basic Science (IBS), Republic of Korea, under IBS-R028-D1. AMMG is supported through a Marie Skłodowska-Curie Individual Fellowship (H2020-MSCA-IF-2015-704409), and thanks the Danish National Research Foundation for its support of the Center for Macroecology, Evolution and Climate (Grant number DNRF96)
Published: 2019

6. Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

Author: Anders J. Hansen, Aurore Val, Marnie Potgieter, Simon J. Underdown, Stephan Woodborne, Jessica E. Koopman, Guillaume Porraz, Grant Hall, Eske Willerslev, Tina B. Brand, Riaan F. Rifkin, Yves Van de Peer, Surendra Vikram, Don A. Cowan, Matthieu Le Bailly, Jean-Baptiste Ramond, Alba Rey-Iglesia, Apollo - University of Cambridge Repository, Willerslev, Eske [0000-0002-7081-6748], Centre National de la Recherche Scientifique (CNRS), Laboratoire méditerranéen de préhistoire Europe-Afrique (LAMPEA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), University of the Witwatersrand [Johannesburg] (WITS), Centre d'Études Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), University of Tübingen, 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 Plant Systems Biology, Flanders Institute for Biotechnology, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: IMPACT, DIVERSITY, Bantu languages, [SHS]Humanities and Social Sciences, Taxonomic composition, Feces, ComputingMilieux_MISCELLANEOUS, History, 15th Century, Human evolution, DAMAGE, 0303 health sciences, Ancient DNA, GUT MICROBIOTA, Intestinal microbiome, Geography, Archaeology, Metabolic capacity, Intestinal Microbiome, lcsh:QR100-130, Enterotype, Molecular ecology, Microbiology (medical), Sub saharan, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Zoology, Biology, Microbiology, ENTEROTYPES, lcsh:Microbial ecology, 03 medical and health sciences, DYSBIOSIS, Iceman, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Africa South of the Sahara, 030304 developmental biology, 030306 microbiology, Research, Biology and Life Sciences, DNA, Gastrointestinal Microbiome, Metagenomics, PATTERNS, Multi proxy, RESISTANCE, Rock shelter, CHAIN CHLORINATED PARAFFINS [KeyWords Plus]
Abstract: Funder: Ministère des Affaires Etrangères; doi: http://dx.doi.org/10.13039/501100003763, Background: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. Methods: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. Results: Our results indicate that the distal IM of the Neolithic ‘Middle Iron Age’ (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to ‘Western’ diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. Conclusions: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. E_CXsNG9ctE_c_B9sn31A9Video Abtract.
Published: 2021
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7. Voluminous Silica Precipitated from Martian Waters during Late-stage Aqueous Alteration

Author: Lu Pan, M. Pineau, Boris Chauviré, C. Quantin-Nataf, John Carter, Laetitia Le Deit, Nicolas Mangold, Benjamin Rondeau, Vincent Chevrier, Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Institut d'astrophysique spatiale (IAS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Laboratoire de Planétologie et Géodynamique [UMR 6112] (LPG), Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de la Terre (ISTerre), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Gustave Eiffel-Université Grenoble Alpes (UGA), Arkansas Center for Space and Planetary Sciences, University of Arkansas [Fayetteville], ANR-16-CE31-0012,MARS-PRIME,Environnement Primitif de Mars(2016), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010504 meteorology & atmospheric sciences, Amazonian, Geochemistry, FOS: Physical sciences, 010502 geochemistry & geophysics, 01 natural sciences, chemistry.chemical_compound, [SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology, Martian surface, Earth and Planetary Sciences (miscellaneous), ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Earth and Planetary Astrophysics (astro-ph.EP), Martian, geography, geography.geographical_feature_category, Hydrated silica, Alluvial fan, Astronomy and Astrophysics, Mars Exploration Program, 15. Life on land, CRISM, Geophysics, chemistry, 13. Climate action, Space and Planetary Science, Hesperian, Geology, Astrophysics - Earth and Planetary Astrophysics
Abstract: Mars’ transition from an early “warm and wet” to a “cold and dry” environment left fingerprints on the geological record of fluvial activity on Mars. The morphological and mineralogical observations of aqueous activity provided varying constraints on the condition and duration of liquid water on the Martian surface. In this study, we surveyed the mineralogy of Martian alluvial fans and deltas and investigated the hydrated silica-bearing deposits associated with some of these landforms. Using CRISM data, we identified 35 locations across Mars with hydrated silica in proximity to fans/deltas, where the spectral characteristics are consistent with immature or dehydrated opal-A. In a few stepped fans/deltas, we find hydrated silica occurs within the bulk fan deposits and form sedimentary layers correlated with elevation. Meanwhile, in the older fans/deltas, silica mostly occurs at distal locations, and the relation to primary sedimentary deposits is more complex. We propose that the hydrated silica-bearing deposits in stepped fans/deltas likely formed authigenically from Martian surface waters, mainly during the Late Hesperian and Early Amazonian. These silica-bearing deposits could be a tracer for the temperature or duration of water involved in the formation of these deposits, given more precise and detailed observations of the sedimentary context, accessory minerals, the concentration of hydrated silica, and sediment-to-water ratio. Therefore, we consider that silica-bearing deposits should be among the most critical samples to investigate for future Mars missions, which are accessible in the landing sites of Mars 2020 and ExoMars 2022 missions.
Published: 2021

8. AMBITION, the Comet Nucleus Cryogenic Sample Return mission for ESA Voyage 2050 program

Author: Filacchione, Gianrico, Bockelée-Morvan, Dominique, Altwegg, Kathrin, Bianchi, Eleonora, Bizzarro, Martin, Blum, Jürgen, Bonal, Lydie, Capaccioni, Fabrizio, Codella, Claudio, Choukroun, Mathieu, Cottin, Hervé, Davidsson, Björn, De Sanctis, Maria Cristina, Drozdovskaya, Maria, Engrand, Cécile, Galand, Marina, Güttler, Carsten, Henri, Pierre, Hérique, Alain, Ivanovski, Stavro L., Kokotanekova, Rosita, Levasseur-Regourd, Anny Chantal, Miller, Kelly E., Rotundi, Alessandra, Schönbächler, Maria, Snodgrass, Colin, Thomas, Nicolas, Tubiana, Cécilia, Ulamec, Stefan, Vincent, Jean-Baptiste, Istituto di Astrofisica e Planetologia Spaziali - INAF (IAPS), Istituto Nazionale di Astrofisica (INAF), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Physikalisches Institut [Bern], Universität Bern [Bern] (UNIBE), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France, Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Institut für Geophysik und Extraterrestrische Physik [Braunschweig] (IGEP), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], INAF - Osservatorio Astrofisico di Arcetri (OAA), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA (UMR_7583)), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Center for Space and Habitability (CSH), University of Bern, Centre de Sciences Nucléaires et de Sciences de la Matière (CSNSM), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Imperial College London], Imperial College London, Max-Planck-Institut für Sonnensystemforschung (MPS), Max-Planck-Gesellschaft, Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), INAF - Osservatorio Astronomico di Trieste (OAT), European Southern Observatory [Garching], PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Southwest Research Institute [San Antonio] (SwRI), Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute for Astronomy [Edinburgh] (IfA), University of Edinburgh, Deutsches Zentrum für Luft- und Raumfahrt [Köln] (DLR), DLR Institut für Planetenforschung, Deutsches Zentrum für Luft- und Raumfahrt [Berlin] (DLR), Cardon, Catherine, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Universität Bern [Bern], Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), California Institute of Technology (CALTECH)-NASA, Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National d’Études Spatiales [Paris] (CNES), and Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)
Subjects: [SDU] Sciences of the Universe [physics], [SDU]Sciences of the Universe [physics], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

9. Two decades of forest-related legislation changes in European countries analysed from a property rights perspective

Author: Nichiforel, Liviu, Deuffic, Philippe, Thorsen, Bo Jellesmark, Weiss, Gerhard, Hujala, Teppo, Keary, Kevin, Lawrence, Anna, Avdibegović, Mersudin, Dobšinská, Zuzana, Feliciano, Diana, Gorriz-Mifsud, Elena, Hoogstra-Klein, Marjanke, Hrib, Michal, Jarský, Vilém, Jodłowski, Krzysztof, Lukmine, Diana, Pezdevšek Malovrh, Špela, Nedeljković, Jelena, Nonić, Dragan, Krajter Ostoić, Silvija, Pukall, Klaus, Rondeux, Jacques, Samara, Theano, Sarvašová, Zuzana, Scriban, Ramona Elena, Šilingienė, Rita, Sinko, Milan, Stojanovska, Makedonka, Stojanovski, Vladimir, Stoyanov, Todor, Teder, Meelis, Vennesland, Birger, Wilhelmsson, Erik, Wilkes-Allemann, Jerylee, Živojinović, Ivana, Bouriaud, Laura, Universitatea Stefan cel Mare Suceava (USU), Environnement, territoires et infrastructures (UR ETBX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Natural Resources Institute Finland (LUKE), University of Joensuu, Department of Agriculture Food and the Marine, Dublin, University of the Highlands and Islands (UHI), University of Sarajevo, UNIVERZITET U SARAJEVU, Faculty of Forestry, Zvolen, School of Biological Sciences, University of Aberdeen, Aberdeen, UK, European Forest Institute = Institut Européen de la Forêt = Euroopan metsäinstituutti (EFI), Wageningen University and Research [Wageningen] (WUR), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CZU), Forest Research Institute, Sekocin Stary, Institut of Forestry, Girionys, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia, University of Belgrade [Belgrade], Croatian Forest Research Institute, Jastrebarsko, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Gestion des ressources forestières et des milieux naturels, Faculté Universitaire des Sciences Agronomiques de Gembloux, Forest Research Institute of Thessaloniki, Vassilika, National Forest Centre, Zvolen, University Stefan cel Mare of Suceava (USU), Institute of Forestry, Girionys, University of Ljubljana, University of Skopje, Bulgarian Academy of Sciences (BAS), Estonian University of Life Sciences (EMU), Swedish University of Agricultural Sciences (SLU), European Forest Inst Cent East & South East Europ, and University of Vienna [Vienna]
Subjects: Private ownership, Economics, Forest Science, Institutional changes, Forest governance, Property rights, PRIF, [SHS.SCIPO]Humanities and Social Sciences/Political science, [SHS]Humanities and Social Sciences, Law (excluding Law and Society)
Abstract: In the last two decades, attention on forests and ownership rights has increased in different domains of international policy, particularly in relation to achieving the global sustainable development goals. This paper looks at the changes in forest-specific legislation applicable to regular productive forests, across 28 European countries. We compare the legal framework applicable in the mid-1990s with that applicable in 2015, using the Property Rights Index in Forestry (PRIF) to measure changes across time and space. The paper shows that forest owners in most western European countries already had high decision-making power in the mid-1990s, following deregulation trends from the 1980s; and for the next two decades, distribution of rights remained largely stable. For these countries, the content and direction of changes indicate that the main pressure on forest-focused legislation comes from environmental discourses (e.g. biodiversity and climate change policies). In contrast, former socialist countries in the mid-1990s gave lower decision-making powers to forest owners than in any of the Western Europe countries; over the next 20 years these show remarkable changes in management, exclusion and withdrawal rights. Nevertheless, with the exception of Baltic countries which have moved towards the western forest governance system, most of the former socialist countries still maintain a state-centred approach in private forest management. Despite this diverse setting of property rights, there is no longer a clear line between western and former socialist countries with respect to the national governance systems used to address private forest ownership. Overall, most of the changes we identified in the last two decades across Europe were recorded in the categories of management rights and exclusion rights. These changes reflect the general trend in European forest policies to expand and reinforce the landowners’ individual rights, while preserving minimal rights for other categories of forest users; and to make use of financial instruments when targeting policy goals related to the environmental discourse.
Published: 2020

10. A mouse ear skin model to study the dynamics of innate immune Running title: Biofilm-dependent modulation of physiological inflammation

Author: Abdul Hamid, Aizat, Nakusi, Laurence, Givskov, Mickael, Chang, Young-Tae, Marquès, Claire, Gueirard, Pascale, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Costerton Biofilm Center [Copenhagen], Department of Immunology and Microbiology [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Chemistry [Pohang, Corée du Sud], Pohang University of Science and Technology (POSTECH), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), and Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, biochemical phenomena, metabolism, and nutrition, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract: International audience; Background: Staphylococcus aureus is a human pathogen that is a common cause of nosocomial infections and infections on indwelling medical devices, mainly due to its ability to shift between the planktonic and the biofilm/sessile lifestyle. Biofilm infections present a serious problem in human medicine as they often lead to bacterial persistence and thus to chronic infections. The immune responses elicited by biofilms have been described as specific and ineffective. In the few experiments performed in vivo, the importance of neutrophils and macrophages as a first line of defence against biofilm infections was clearly established. However, the bilateral interactions between biofilms and myeloid cells remain poorly studied and analysis of the dynamic processes at the cellular level in tissues inoculated with biofilm bacteria is still an unexplored field. It is urgent, therefore, to develop biologically sound experimental approaches in vivo designed to extract specific immune signatures from the planktonic and biofilm forms of bacteria. Results: We propose an in vivo transgenic mouse model, used in conjunction with intravital confocal microscopy to study the dynamics of host inflammatory responses to bacteria. Culture conditions were created to prepare calibrated inocula of fluorescent planktonic and biofilm forms of bacteria. A confocal imaging acquisition and analysis protocol was then drawn up to study the recruitment of innate immune cells in the skin of LysM-EGFP transgenic mice. Using the mouse ear pinna model, we showed that inflammatory responses to S. aureus can be quantified over time and that the dynamics of innate immune cells after injection of either the planktonic or biofilm form can be characterized. First results showed that the ability of phagocytic cells to infiltrate the injection site and their motility is not the same in planktonic and biofilm forms of bacteria despite the cells being considerably recruited in both cases. Conclusion: We developed a mouse model of infection to compare 42 the dynamics of the inflammatory responses to planktonic and biofilm bacteria at the tissue and cellular levels. The mouse ear pinna model is a powerful imaging system to analyse the mechanisms of biofilm tolerance to immune attacks.
Published: 2020

11. Chemical and kinematic structure of extremely high-velocity molecular jets in the Serpens Main star-forming region

Author: Ewine F. van Dishoeck, Lars E. Kristensen, Łukasz Tychoniec, Valentin J. M. Le Gouellec, John J. Tobin, Charles L. H. Hull, Leiden Observatory [Leiden], Universiteit Leiden [Leiden], National Astronomical Observatory of Japan (NAOJ), Joint ALMA Observatory (JAO), National Radio Astronomy Observatory (NRAO)-European Southern Observatory (ESO), Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), National Radio Astronomy Observatory [Charlottesville] (NRAO), National Radio Astronomy Observatory (NRAO), European Southern Observatory (ESO), Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Max-Planck-Institut für Extraterrestrische Physik (MPE), European Project: 291141,EC:FP7:ERC,ERC-2011-ADG_20110209,CHEMPLAN(2012), Universiteit Leiden, European Southern Observatory (ESO)-National Radio Astronomy Observatory (NRAO), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010504 meteorology & atmospheric sciences, Serpens, FOS: Physical sciences, Kinematics, Astrophysics, Star (graph theory), 01 natural sciences, 0103 physical sciences, profiles [line], Protostar, ISM [submillimeter], 010303 astronomy & astrophysics, Chemical composition, Solar and Stellar Astrophysics (astro-ph.SR), protostars [stars], 0105 earth and related environmental sciences, Physics, Jet (fluid), Momentum (technical analysis), stars: protostars, jets and outflows [ISM], astrochemistry, Astronomy and Astrophysics, line: profiles, Astrophysics - Astrophysics of Galaxies, interferometric [techniques], ISM: jets and outflows, Astrophysics - Solar and Stellar Astrophysics, Space and Planetary Science, techniques: interferometric, Astrophysics of Galaxies (astro-ph.GA), submillimeter: ISM, Outflow, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph]
Abstract: The fastest molecular component to the protostellar outflows -- extremely high-velocity (EHV) molecular jets -- are still puzzling since they are seen only rarely. The first aim is to analyze the interaction between the EHV jet and the slow outflow by comparing their outflow force content. The second aim is to analyze the chemical composition of the different outflow velocity components and to reveal the spatial location of molecules. ALMA 3 mm and 1.3 mm observations of five outflow sources at 130 -- 260 au resolution in the Serpens Main cloud are presented. Observations of CO, SiO, H$_2$CO and HCN reveal the kinematic and chemical structure of those flows. Three velocity components are distinguished: the slow and the fast wing, and the EHV jet. Out of five sources, three have the EHV component. Comparison of outflow forces reveals that only the EHV jet in the youngest source Ser-emb 8 (N) has enough momentum to power the slow outflow. The SiO abundance is generally enhanced with velocity, while HCN is present in the slow and the fast wing, but disappears in the EHV jet. For Ser-emb 8 (N), HCN and SiO show a bow-shock shaped structure surrounding one of the EHV peaks suggesting sideways ejection creating secondary shocks upon interaction with the surroundings. Also, the SiO abundance in the EHV gas decreases with distance from this protostar, whereas that in the fast wing increases. H$_2$CO is mostly associated with low-velocity gas but also appears surprisingly in one of the bullets in the Ser-emb~8~(N) EHV jet. The high detection rate suggests that the presence of the EHV jet may be more common than previously expected. The origin and temporal evolution of the abundances of SiO, HCN and H$_2$CO through high-temperature chemistry are discussed. The data are consistent with a low C/O ratio in the EHV gas versus high C/O ratio in the fast and slow wings., Comment: 25 pages, 20 figures, Accepted for publication in the Astronomy & Astrophysics
Published: 2019

12. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic

Author: Catherine F. West, James Haile, Åslaug Midtdal, Ramona Harrison, Anders J. Hansen, Martin Appelt, Ophélie Lebrasseur, Benjamin N. Sacks, James Woollett, Audrey T. Lin, Olga I. Goriunova, John Darwent, Mikkel-Holger S. Sinding, Lutz Bachmann, Morten Meldgaard, Rick Knecht, Matthew W. Betts, Kate Britton, Robert J. Losey, Rune Dietz, Laurent A. F. Frantz, Mitya Vasyukov, Ardern Hulme-Beaman, Love Dalén, Keith Dobney, M. Thomas P. Gilbert, Tatiana R. Feuerborn, Iurii G. Nikitin, Zachary T. Lounsberry, Scott Shirar, Mikhail Sablin, Christian Sonne, Konrad Smiarowski, Øystein Wiig, Shyam Gopalakrishnan, Mary C. Stiner, Edouard Masson-MacLean, Sarah K. Brown, Jón Hallsteinn Hallsson, Thomas H. McGovern, Mads Peter Heide-Jørgensen, Christyann M. Darwent, Merete Fredholm, Madonna L. Moss, Carly Ameen, Anna Linderholm, Sanne Eline Wennerberg, Bjarne Grønnow, Ellen McManus-Fry, Gro Birgit Ween, Anne Lisbeth Schmidt, Joshua D. Reuther, Albína Hulda Pálsdóttir, Greger Larson, Tatiana Nomokonova, Allowen Evin, Angela R. Perri, Aleksandr N. Popov, Lisa Rankin, Texas A&M University [College Station], University of Oxford, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Department of Arctic Environment [Rockilde], Aarhus University [Aarhus]-National Environmental Research Institute [Danmark] (NERI), IT University of Copenhagen (ITU), Irkutsk State University (ISU), Agricultural University of Iceland, University of Aberdeen, University of Alberta, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Zoological Institute, Russian Academy of Sciences [Moscow] (RAS), Natural History Museum [Oslo], University of Oslo (UiO), Department of Archaeology, University of Aberdeen, 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), University of Oxford [Oxford], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), IT University of Copenhagen, 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: Sledge dogs, Canis lupus familiaris, osteology, [SDV]Life Sciences [q-bio], Greenland, migration, Medical and Health Sciences, [SHS]Humanities and Social Sciences, Naturvetenskap, 0601 history and archaeology, ComputingMilieux_MISCELLANEOUS, General Environmental Science, 0303 health sciences, education.field_of_study, Genome, palaeontology archaeology, 060102 archaeology, Human migration, Arctic Regions, 06 humanities and the arts, General Medicine, circumpolar, Biological Sciences, Mitochondrial, Geography, Phenotype, Humanities and the Arts, Humaniora och konst, Palaeobiology, [SDE]Environmental Sciences, General Agricultural and Biological Sciences, Natural Sciences, geographic locations, Research Article, aDNA, Canada, Human Migration, Population, Zoology, DNA, Mitochondrial, General Biochemistry, Genetics and Molecular Biology, Ancient, 03 medical and health sciences, Dogs, evolution, Genetics, genomics, Animals, DNA, Ancient, Domestication, education, geometric morphometrics, ancient DNA, 030304 developmental biology, General Immunology and Microbiology, Osteology, Agricultural and Veterinary Sciences, business.industry, archaeology, Circumpolar star, DNA, [SDE.ES]Environmental Sciences/Environmental and Society, Ancient DNA, Arctic, Genome, Mitochondrial, Biological dispersal, business, Animal Distribution, Alaska
Abstract: Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP. Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
Published: 2019

13. EPAS1 Gain-of-Function Mutation Contributes to High-Altitude Adaptation in Tibetan Horses

Author: Weijun Guan, Weihuang Chen, Yuehui Ma, Qianjun Zhao, Xuexue Liu, Jianfei Pan, Ludovic Orlando, Zhang Yanli, Lin Jiang, Yabin Pu, Jian-Lin Han, Zhuqing Zheng, Yefang Li, Dandan Wang, Xiaohong He, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), and Shanghai Jiao Tong University [Shanghai]
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Locus (genetics), Biology, 010603 evolutionary biology, 01 natural sciences, Genome, hypoxia adaptation, 03 medical and health sciences, EPAS1, Convergent evolution, Genetics, Missense mutation, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, Discoveries, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, convergence, EPAS1 Gene, Evolutionary biology, Tibetan horse, Mammal, metabolism, respiration
Abstract: High altitude represents some of the most extreme environments worldwide. The genetic changes underlying adaptation to such environments have been recently identified in multiple animals but remain unknown in horses. Here, we sequence the complete genome of 138 domestic horses encompassing a whole altitudinal range across China to uncover the genetic basis for adaptation to high-altitude hypoxia. Our genome data set includes 65 lowland animals across ten Chinese native breeds, 61 horses living at least 3,300 m above sea level across seven locations along Qinghai-Tibetan Plateau, as well as 7 Thoroughbred and 5 Przewalski’s horses added for comparison. We find that Tibetan horses do not descend from Przewalski’s horses but were most likely introduced from a distinct horse lineage, following the emergence of pastoral nomadism in Northwestern China ∼3,700 years ago. We identify that the endothelial PAS domain protein 1 gene (EPAS1, also HIF2A) shows the strongest signature for positive selection in the Tibetan horse genome. Two missense mutations at this locus appear strongly associated with blood physiological parameters facilitating blood circulation as well as oxygen transportation and consumption in hypoxic conditions. Functional validation through protein mutagenesis shows that these mutations increase EPAS1 stability and its hetero dimerization affinity to ARNT (HIF1B). Our study demonstrates that missense mutations in the EPAS1 gene provided key evolutionary molecular adaptation to Tibetan horses living in high-altitude hypoxic environments. It reveals possible targets for genomic selection programs aimed at increasing hypoxia tolerance in livestock and provides a textbook example of evolutionary convergence across independent mammal lineages.
Published: 2019

14. Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition

Author: Ian T. Fiddes, Carrie J. Finno, Michael S. DePriest, Alisa O. Vershinina, Jessica L. Petersen, Edward S. Rice, Richard E. Green, Rebecca R. Bellone, Douglas F. Antczak, Samantha A. Brooks, Nedda F. Saremi, Matthew S. Hestand, Ludovic Orlando, Brian P. Walenz, Theodore S. Kalbfleisch, Brendan O'Connell, James N. MacLeod, Molly E. McCue, Donald Miller, Joris Vermeesch, Ernest Bailey, Department of Population Health and Reproduction and the Veterinary Genetics Laboratory, University of California [Davis] (UC Davis), University of California-University of California, College of Veterinary Medicine, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Mathematics, University of Colorado, and University of Colorado [Boulder]
Subjects: [SDV]Life Sciences [q-bio], Contiguity, Medicine (miscellaneous), Genome informatics, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Bellone, Author Correction, lcsh:QH301-705.5, Composition (language), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, biology, Agriculture, Genomics, 16. Peace & justice, biology.organism_classification, lcsh:Biology (General), 030220 oncology & carcinogenesis, Next-generation sequencing, General Agricultural and Biological Sciences, Humanities, Reference genome
Abstract: Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.
Published: 2019

15. Thermal evolution of hydrated asteroids inferred from oxygen isotopes

Author: Lionel G. Vacher, Maxime Piralla, Martin Bizzarro, Matthieu Gounelle, Yves Marrocchi, Centre de Recherches Pétrographiques et Géochimiques (CRPG), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), ANR-14-CE33-0002,SAPINS,Processus d'altération secondaire dans le système solaire(2014), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)
Subjects: Physics, Solar System, 010504 meteorology & atmospheric sciences, Meteoroid, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], protoplanetary disks, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Astronomy and Astrophysics, Protoplanetary disk, 01 natural sciences, Accretion (astrophysics), Isotopes of oxygen, Astrobiology, meteorites, meteors, meteoroids, Meteorite, 13. Climate action, Space and Planetary Science, Chondrite, Asteroid, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, 0103 physical sciences, 010303 astronomy & astrophysics, general [minor planets, asteroids], 0105 earth and related environmental sciences
Abstract: International audience; Chondrites are fragments of unmelted asteroids that formed due to gravitational instabilities in turbulent regions of the Solar protoplanetary disk. Hydrated chondrites are common among meteorites, indicating that a substantial fraction of the rocky bodies that formed early in the Solar System accreted water ice grains that subsequently melted due to heat released by the radioactive decay of 26Al. However, the thermal histories of asteroids are still largely unknown whereas it would bring fundamental information on their timing of accretion and their physical characteristics. Here we show that hydrated meteorites (CM chondrites) contain previously uncharacterized calcium carbonates with peculiar oxygen isotopic compositions (Δ17O ≈ -2.5 ‰), which artificially produce the mass-independent trend previously reported for carbonates. Based on these isotopic data, we propose a new model to quantitatively estimate the precipitation temperatures of secondary phases (carbonates and serpentine). It reveals that chondritic secondary phases recorded a gradual increase of the temperature during the extent of aqueous alteration, from –10 °C to maximum 250 °C. We also show that the thermal path of C-type asteroids is independent of the initial oxygen isotopic composition of the primordial water ice grains that they accreted. Our estimated temperatures for hydrated asteroids remain lower than those experienced by other carbonaceous chondrites, providing strong constraints for modelling the formation conditions and size-distribution of water-rich asteroids, especially in anticipation of the return of samples of water-rich asteroids to Earth by the OSIRIS-REx and Hayabusa2 missions.
Published: 2019

16. AMBITION Comet Nucleus Cryogenic Sample Return

Author: Bockelée-Morvan, D., Filacchione, Gianrico, Altwegg, Kathrin, Bianchi, Eleonora, Bizzarro, Martin, Blum, Jürgen, Bonal, Lydie, Capaccioni, Fabrizio, Codella, Claudio, Choukroun, Mathieu, Cottin, Hervé, Davidsson, Björn, De Sanctis, Maria Cristina, Drozdovskaya, Maria, Engrand, Cécile, Galand, Marina, Güttler, Carsten, Henri, Pierre, Herique, Alain, Ivanoski, Stavro, Kokotanekova, Rosita, Levasseur-Regourd, Anny Chantal, Miller, Kelly E., Rotundi, Alessandra, Schönbächler, Maria, Snodgrass, Colin, Thomas, Nicolas, Tubiana, Cecilia, Ulamec, Stefan, Vincent, Jean-Baptiste, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Istituto di Astrofisica e Planetologia Spaziali - INAF (IAPS), Istituto Nazionale di Astrofisica (INAF), Physikalisches Institut [Bern], Universität Bern [Bern], Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Centre National d'Études Spatiales [Toulouse] (CNES)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Natural History Museum of Denmark, Faculty of Science [Copenhagen], Institut für Geophysik und Extraterrestrische Physik [Braunschweig] (IGEP), Technische Universität Braunschweig [Braunschweig], INAF - Osservatorio Astrofisico di Arcetri (OAA), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA (UMR_7583)), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Center for Space and Habitability (CSH), University of Bern, Centre de Sciences Nucléaires et de Sciences de la Matière (CSNSM), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Space and Atmospheric Physics Group [London], Blackett Laboratory, Imperial College London-Imperial College London, Department of Physics [Imperial College London], Imperial College London, Max-Planck-Institut für Sonnensystemforschung (MPS), Max-Planck-Gesellschaft, Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Centre National d’Études Spatiales [Paris] (CNES), Joseph Louis LAGRANGE (LAGRANGE), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), INAF - Osservatorio Astronomico di Trieste (OAT), European Southern Observatory (ESO), IMPEC - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Southwest Research Institute [San Antonio] (SwRI), Department of Earth Sciences [ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Institute for Astronomy [Edinburgh] (IfA), University of Edinburgh, German Aerospace Center (DLR), DLR Institut für Planetenforschung, Deutsches Zentrum für Luft- und Raumfahrt [Berlin] (DLR), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National d’Études Spatiales [Paris] (CNES), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), PLANETO - LATMOS, Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), California Institute of Technology (CALTECH)-NASA, Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut national des sciences de l'Univers (INSU - CNRS), PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Observatoire de la Côte d'Azur, and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Earth and Planetary Astrophysics (astro-ph.EP), [SDU]Sciences of the Universe [physics], FOS: Physical sciences, Astrophysics - Instrumentation and Methods for Astrophysics, Instrumentation and Methods for Astrophysics (astro-ph.IM), Astrophysics - Earth and Planetary Astrophysics
Abstract: This white paper proposes that AMBITION, a Comet Nucleus Sample Return mission, be a cornerstone of ESA's Voyage 2050 programme. We summarise some of the most important questions still open in cometary science after the successes of the Rosetta mission, many of which require sample analysis using techniques that are only possible in laboratories on Earth. We then summarise measurements, instrumentation and mission scenarios that can address these questions, with a recommendation that ESA select an ambitious cryogenic sample return mission. Rendezvous missions to Main Belt comets and Centaurs are compelling cases for M-class missions, expanding our knowledge by exploring new classes of comets. AMBITION would engage a wide community, drawing expertise from a vast range of disciplines within planetary science and astrophysics. With AMBITION, Europe will continue its leadership in the exploration of the most primitive Solar System bodies., 8 figures, 26 pages
Published: 2019

17. Two FtsH Proteases Contribute to Fitness and Adaptation of Pseudomonas aeruginosa Clone C Strains

Author: Shady Mansour Kamal, Morten Levin Rybtke, Manfred Nimtz, Stefanie Sperlein, Christian Giske, Janja Trček, Julien Deschamps, Romain Briandet, Luciana Dini, Lothar Jänsch, Tim Tolker-Nielsen, Changhan Lee, Ute Römling, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Microbiology, Tumor and Cell Biology, Ajouter cet établissement, Future University in Egypt, Costerton Biofilm Center [Copenhagen], Department of Immunology and Microbiology [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Cellular Proteomics, Helmholtz Centre for Infection Research (HZI), Division of Clinical Microbiology - Department of Laboratory Medicine, Karolinska Institute, Department of Biology - Faculty of Natural Sciences and Mathematics, University of Maribor, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COMUE), Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Università del Salento, and Römling, Ute
Subjects: Microbiology (medical), FtsH protease, Proteases, [SDV]Life Sciences [q-bio], Mutant, lcsh:QR1-502, Virulence, secondary metabolite, autolysis, Biology, medicine.disease_cause, heat shock factor RpoH, Microbiology, lcsh:Microbiology, Secondary metabolite, 03 medical and health sciences, Genomic island, Protein biosynthesis, medicine, Phenazine, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Original Research, clone C strains, Genetics, 0303 health sciences, 030306 microbiology, Pseudomonas aeruginosa, phenazine, Clone C strains, Heat shock factor, virulence, phenazine,secondary metabolite, Heat shock factor RpoH, Autolysis
Abstract: Pseudomonas aeruginosa is an environmental bacterium and a nosocomial pathogen with clone C one of the most prevalent clonal groups. The P. aeruginosa clone C specific genomic island PACGI-1 harbors a xenolog of ftsH encoding a functionally diverse membrane-spanning ATP-dependent metalloprotease on the core genome. In the aquatic isolate P. aeruginosa SG17M, the core genome copy ftsH1 significantly affects growth and dominantly mediates a broad range of phenotypes, such as secretion of secondary metabolites, swimming and twitching motility and resistance to aminoglycosides, while the PACGI-1 xenolog ftsH2 backs up the phenotypes in the ftsH1 mutant background. The two proteins, with conserved motifs for disaggregase and protease activity present in FtsH1 and FtsH2, have the ability to form homo- and hetero-oligomers with ftsH2 distinctively expressed in the late stationary phase of growth. However, mainly FtsH1 degrades a major substrate, the heat shock transcription factor RpoH. Pull-down experiments with substrate trap-variants inactive in proteolytic activity indicate both FtsH1 and FtsH2 to interact with the inhibitory protein HflC, while the phenazine biosynthesis protein PhzC was identified as a substrate of FtsH1. In summary, as an exception in P. aeruginosa, clone C harbors two copies of the ftsH metallo-protease, which cumulatively are required for the expression of a diversity of phenotypes.
Published: 2019

18. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

Author: Inger Greve Alsos, Lucie Zinger, Gentile Francesco Ficetola, Aurélie Bonin, Frédéric Boyer, Marta De Barba, Simon N. Jarman, M. Thomas P. Gilbert, Ian A. Dickie, Leho Tedersoo, Anthony A. Chariton, Bruce E. Deagle, Philip Francis Thomsen, Johan Pansu, Alex J. Dumbrell, Ari Jumpponen, Håvard Kauserud, Holly M. Bik, Eske Willerslev, Pierre Taberlet, Luca Fumagalli, Simon Creer, Eric Coissac, Miklós Bálint, Jan Pawlowski, Ludovic Orlando, Noah Fierer, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Biogéosciences [UMR 6282] [Dijon] (BGS), 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, New York University [New York] (NYU), NYU System (NYU), Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, emlyon business school, Politecnico di Milano [Milan] (POLIMI), University of Copenhagen = Københavns Universitet (KU), Microbial Evolution Research Group (MERG), Department of Biology [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), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Genetics and Evolution, Université de Genève (UNIGE), University of Tartu, JP was supported by the Marie Skłodowska-Curie actions (TEAM-Coast project, MSCA-GF 750570), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), 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), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Robotique Et Vivant (ReV), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques
Subjects: 0106 biological sciences, replication, Ecology (disciplines), [SDV]Life Sciences [q-bio], experimental controls, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Dna genetics, Replication (statistics), Genetics, DNA Barcoding, Taxonomic, data quality, Environmental DNA, Ecology, Evolution, Behavior and Systematics, Sound (geography), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, geography, geography.geographical_feature_category, Ecology, Biodiversity, DNA, environmental DNA, chemistry, Evolutionary biology, [SDE]Environmental Sciences
Abstract: International audience
Published: 2019

19. Authentication and Assessment of Contamination in Ancient DNA

Author: Gabriel Renaud, Mikkel Schubert, Susanna Sawyer, Ludovic Orlando, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, University of Copenhagen = Københavns Universitet (KU), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Shapiro, Beth, Barlow, Axel, Heintzman, Peter D., Hofreiter, Michael, Paijmans, Johanna L. A., and Soares, André E. R.
Subjects: DICE, Postmortem damage, Computer science, [SDV]Life Sciences [q-bio], Computational biology, DNA, Mitochondrial, 03 medical and health sciences, 0302 clinical medicine, Contamination, mapDamage2.0, Humans, DNA, Ancient, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Sequence (medicine), Cell Nucleus, 0303 health sciences, Authentication, [SDV.GEN]Life Sciences [q-bio]/Genetics, Ancient DNA, Schmutzi, Sequence Analysis, DNA, DNA Contamination, Genome, Mitochondrial, 030217 neurology & neurosurgery
Abstract: Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.
Published: 2019

20. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Author: Raquel Matoso Silva, Eric Barrey, Marjan Mashkour, Eske Willerslev, Carlos Fernández-Rodríguez, Khaled A. S. Al-Rasheid, Maria do Mar Oom, Pavel Kuznetsov, Pavel A. Kosintsev, Eloísa Bernáldez-Sánchez, Sonia Shidrang, Michael Hofreiter, Konstantin Pitskhelauri, Silvia Valenzuela-Lamas, Sabine Felkel, Ali A. Vahdati, Cristina Luís, Emma Usmanova, Sainbileg Undrakhbold, Jón Hallsteinn Hallsson, Jamsranjav Bayarsaikhan, Victor Zaibert, Irina Shevnina, Silvia Albizuri, Haeedeh Laleh, Anna Dohr, Ahmed H. Alfarhan, Sanne Boessenkool, Morten E. Allentoft, Homa Fathi, Cleia Detry, Petra Rajic Sikanjic, Oleg Monchalov, Heidi Nistelberger, Alireza Sardari, Jennifer A. Leonard, Jaco Weinstock, Christian McCrory Constantz, Andaine Seguin-Orlando, Johanna Lhuillier, Wolf-Rüdiger Teegen, Naveed Khan, Sébastien Lepetz, Linas Daugnora, Bazartseren Boldgiv, Helmut Hemmer, Peter Barros de Damgaard, Lembi Lõugas, Victor Merz, Lukas F. K. Kuderna, Vedat Onar, Angela Schlumbaum, Barbara Wallner, Esteban García-Viñas, Enkhbayar Mijiddorj, Nadine Dill, Fereidoun Biglari, Eric Crubézy, Bastiaan Star, Albína Hulda Pálsdóttir, José D. Granado, Tabaldiev Kubatbek, John Southon, Alan K. Outram, Corina Liesau von Lettow-Vorbeck, Anita Rapan Papeša, Norbert Benecke, Amelie Scheu, Simon Trixl, Agnar Helgason, Dorcas Brown, Hossein Davoudi, Cristina Gamba, Jörg Schibler, Renate Schafberg, James H. Barrett, Dashzeveg Tumen, Ludovic Orlando, Nurbol Baimukhanov, Ana Margarida Arruda, William Timothy Treal Taylor, Fatemeh Azadeh Mohaseb, Mutalib Khasanov, Sabine Deschler-Erb, Kari Stefansson, Charleen Gaunitz, Mélanie Pruvost, Arturo Morales, Roya Khazaeli, Tomas Marques-Bonet, David W. Anthony, Aitor Serres-Armero, Benoît Clavel, Kamal Taheri, Kristian Hanghøj, Beth Shapiro, Arne Ludwig, Saleh A. Alquraishi, Andrey Logvin, Gottfried Brem, Kristian Kristiansen, Natalia Roslyakova, Shiva Sheikhi Seno, Naomi Sykes, María los Ángeles Chorro y de de de Villa-Ceballos, Joachim Burger, Eberhard Sauer, Catarina Viegas, Mietje Germonpré, Michela Leonardi, Antoine Fages, Nathalie Serrand, Diimaajav Erdenebaatar, Aleksei Kasparov, Tajana Trbojević Vukičević, Vladimir V. Pitulko, Bryan K. Miller, Pablo Librado, Sturla Ellingvåg, Ariadna Nieto-Espinet, Luis Berrocal-Rangel, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (KU), Abdul Wali Khan University, Université Fédérale Toulouse Midi-Pyrénées, Department of Zoology, University of Cambridge, Cambridge, United Kingdom, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), King Saud University [Riyadh] (KSU), SERP, université de Barcelone, Universitat de Barcelona (UB), Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia, Anthropology Department - Hartwick College, Shejire DNA project, McDonald Institute for Archaeological Research, University of Cambridge [UK] (CAM), National Center of Mental Health of Mongolia, Deutsches Archäologisches Institut (DAI), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine [Vienna] (Vetmeduni), Tarbiat Modares University [Tehran], UNIARQ, Universidade de Lisboa (ULISBOA), Universidad de León [León], Department of Palaeontology, Royal Belgian Institue of Natural Sciences, Department of Evolutianory Genetics, Max-Planck-Institut, Institut d'Archéologie de l'Académie des Sciences d'Ouzbékistan, Académie des Sciences, Institut de France-Institut de France, ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut-Leibniz Institute for Zoo and Wildlife Research Berlin (IZW), Institució Catalana de Recerca i Estudis Avançats (ICREA), University of Basel (Unibas), Institut national de recherches archéologiques préventives (Inrap), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Center for Palaeolithic Research, National Museum of Iran, Department of Earth System Science [Irvine] (ESS), University of California [Irvine] (UCI), University of California-University of California, Institución Milá y Fontanals de investigación en Humanidades (IMF), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), New University of Lisbon, Muséum national d'Histoire naturelle (MNHN), deCODE Genetics, deCODE genetics [Reykjavik], Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Eco-Anthropologie et Ethnobiologie (EAE), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Muséum national d'Histoire naturelle (MNHN), Zoology Department, College of Science, King Saud University, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Academie des Sciences, Institución Milá i Fontanals (IMF), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Repositório da Universidade de Lisboa, and İÜC, Veteriner Fakültesi, Veteriner Hekimliği Temel Bilimler Bölümü
Subjects: Male, Range (biology), Biología, Breeding horses, Breeding, Genome, Domestication, 0302 clinical medicine, Paleobiología, ComputingMilieux_MISCELLANEOUS, History, Ancient, Phylogeny, horses, 0303 health sciences, Diversity, Ancient DNA, animal breeding, Biological Evolution, mules, humanities, Management, Europe, Domestication animal, Equestrian civilizations, Ethnology, Female, management, equestrian civilizations, Extinct lineages, Asia, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, selection, Multiple alleles, Caballos, Biology, Mules, Article, General Biochemistry, Genetics and Molecular Biology, diversity, 03 medical and health sciences, domestication, Caballo de Przewalski, ddc:570, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Genetic variation, Horses, DNA, Ancient, Selection, ancient DNA, Institut für Biochemie und Biologie, 030304 developmental biology, Animal breeding, Series (stratigraphy), Genetic diversity, Genetic Variation, Equidae, Genética, extinct lineages, Análisis, 030217 neurology & neurosurgery
Abstract: Summary Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management., Graphical Abstract, Highlights • Two now-extinct horse lineages lived in Iberia and Siberia some 5,000 years ago • Iberian and Siberian horses contributed limited ancestry to modern domesticates • Oriental horses have had a strong genetic influence within the last millennium • Modern breeding practices were accompanied by a significant drop in genetic diversity, Genome-wide data from 278 ancient equids provide insights into how ancient equestrian civilizations managed, exchanged, and bred horses and indicate vast loss of genetic diversity as well as the existence of two extinct lineages of horses that failed to contribute to modern domestic animals.
Published: 2019

21. High-coverage genomes to elucidate the evolution of penguins

Author: Kim Labuschagne, Melanie J. Young, M. Thomas P. Gilbert, Pablo García Borboroglu, Mikkel-Holger S. Sinding, Guojie Zhang, Zhengtao Yang, Ursula Ellenberg, Tom Hart, Richard A. Phillips, X. J. Bi, Charles-André Bost, Chengran Zhou, Stefanie Grosser, Theresa L. Cole, Lisa S. Argilla, Gary Miller, Thomas Mattern, Petra Quillfeldt, Juan F. Masello, Lisa J. Nupen, George Pacheco, Daniel T. Ksepka, David M. Houston, Peter G. Ryan, Pauline Howard, Bruce McKinlay, Juan L. Bouzat, Martin R. Ellegaard, Lara D. Shepherd, Patricia G. Parker, Peter Dann, Miaoquan Fang, Andrew Hart Reeve, De Xing Zhang, David R. Thompson, P. Dee Boersma, Yves Cherel, Steven R. Fiddaman, Kathryn Johnson, Hailin Pan, Mads F. Bertelsen, Helen Taylor, Emily Kay, Thomas Stracke, Alan J. D. Tennyson, Beijing Genomics Institute [Shenzhen] (BGI), Manaaki Whenua – Landcare Research [Lincoln], Bruce Museum [USA], Department of Zoology [Oxford], University of Oxford [Oxford], Department of Biological Sciences [OH, USA], Bowling Green State University (BGSU), The Wildlife Hospital Dunedin [New Zealand], Otago Polytechnic [New Zealand], Copenhagen Zoo, Center for Ecosystem Sentinels [Seattle, USA], University of Washington [Seattle], 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), Research Department, Phillip Island Nature Parks [Australia], Phillip Island Nature Parks [Australia], Department of Zoology, Peter Medawar Building for Pathogen Research [UK], Hornby Veterinary Centre [New Zealand], National Zoological Gardens of South Africa, Department of Zoology, University of Otago [Dunedin, Nouvelle-Zélande], Division of Pathology and Laboratory Medicine [Australia], The University of Western Australia (UWA), Department of Biology, University of Missouri [USA], University of Missouri [USA], British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Justus-Liebig-Universität Giessen [Germany], Universität Giessen [Germany], FitzPatrick Institute of African Ornithology, University of Cape Town-DST-NRF Centre of Excellence, Vet Services Hawkes Bay Ltd [New Zealand], National Institute of Water and Atmospheric Research [Auckland] (NIWA), Department of Zoology, University of Otago [New Zealand], Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], Museum of New Zealand - Te Papa Tongarewa, Wildbase, Massey University [New Zealand], Massey University [New Zealand], Global Penguin Society and Department of Ecology [Australia], La Trobe University [Melbourne], Biodiversity Group, Department of Conservation [New Zealand], Section for Ecology and Evolution [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], South Island Wildlife Hospital [New Zealand], Global Penguin Society and Center for Ecosystem Sentinels [USA], Center for Computational and Evolutionary Biology [China], and Institute of Zoology, Chinese Academy of Sciences [China]
Subjects: 0106 biological sciences, demography, Range (biology), Biogeography, AcademicSubjects/SCI02254, Climate change, Health Informatics, Data Note, 01 natural sciences, Ciencias Biológicas, purl.org/becyt/ford/1 [https], Evolution, Molecular, Genética y Herencia, 03 medical and health sciences, comparative evolution, evolution, genomics, Animals, 14. Life underwater, Sphenisciformes, purl.org/becyt/ford/1.6 [https], Southern Hemisphere, Phylogeny, biogeography, 030304 developmental biology, 0303 health sciences, Genome, biology, Ecology, 15. Life on land, biology.organism_classification, Spheniscidae, Computer Science Applications, phylogenetics, Geography, Procellariiformes, climate change, speciation, [SDE]Environmental Sciences, AcademicSubjects/SCI00960, Antarctica, Adaptation, Corrigendum, Temperate rainforest, CIENCIAS NATURALES Y EXACTAS, 010606 plant biology & botany
Abstract: Background: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. Results: Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. Conclusions: We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage. Fil: Pan, Hailin. Bgi-shenzhen; China Fil: Cole, Theresa L. University Of Otago; Canadá Fil: Bi, Xupeng. Bgi-shenzhen; China Fil: Fang, Miaoquan. Bgi-shenzhen; China Fil: Zhou, Chengran. Bgi-shenzhen; China Fil: Yang, Zhengtao. Bgi-shenzhen; China Fil: Ksepka, Daniel T. Bruce Museum; Estados Unidos Fil: Hart, Tom. University of Oxford; Reino Unido Fil: Bouzat, Juan L.. Bowling Green State University; Estados Unidos Fil: Boersma, P. Dee. University of Washington; Estados Unidos Fil: Bost, Charles-André. Centre Detudes Biologiques de Chizé; Francia Fil: Cherel, Yves. Centre Detudes Biologiques de Chizé; Francia Fil: Dann, Peter. Phillip Island Nature Parks; Australia Fil: Mattern, Thomas. University of Otago; Nueva Zelanda Fil: Ellenberg, Ursula. Global Penguin Society; Estados Unidos. La Trobe University; Australia Fil: Garcia Borboroglu, Jorge Pablo. University of Washington; Estados Unidos. Global Penguin Society; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Argilla, Lisa S.. Otago Polytechnic; Nueva Zelanda Fil: Bertelsen, Mads F.. Copenhagen Zoo; Dinamarca. University of Copenhagen; Dinamarca Fil: Fiddaman, Steven R.. University of Oxford; Reino Unido Fil: Howard, Pauline. Hornby Veterinary Centre; Nueva Zelanda. South Island Wildlife Hospital; Nueva Zelanda Fil: Labuschagne, Kim. National Zoological Garden; Sudáfrica Fil: Miller, Gary. University of Western Australia; Australia. University of Tasmania; Australia Fil: Parker, Patricia. University of Missouri St. Louis; Estados Unidos Fil: Phillips, Richard A.. Natural Environment Research Council; Reino Unido Fil: Quillfeldt, Petra. Justus-Liebig-Universit ̈ at Giessen; Alemania Fil: Ryan, Peter G.. University of Cape Town; Sudáfrica Fil: Taylor, Helen. Vet Services Hawkes Bay Ltd; Nueva Zelanda. Wairoa Farm Vets; Nueva Zelanda Fil: Zhang, De-Xing. Chinese Academy of Sciences; República de China Fil: Zhang, Guojie. BGI-Shenzhen; China. Chinese Academy of Sciences; República de China. University of Copenhagen; Dinamarca Fil: McKinlay, Bruce. Department of Conservation; Nueva Zelanda
Published: 2019
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22. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Author: M. Thomas P. Gilbert, Ralf Dietrich Kahlke, Senthilvel K. S. S. Nathan, Yoshan Moodley, Bienvenido Martínez-Navarro, Lorenzo Rook, Luca Pandolfi, Jesper V. Olsen, Marc R. Dickinson, Reid Ferring, Jordi Agustí, Beth Shapiro, David Lyon, Christian D. Kelstrup, Jazmín Ramos-Madrigal, Morten E. Allentoft, Patrick Rüther, Mikkel-Holger S. Sinding, Anna K. Fotakis, David Lordkipanidze, Meaghan Mackie, Rosa Rakownikow Jersie-Christensen, Love Dalén, Eske Willerslev, Marcela Sandoval Velasco, Joshua D. Kapp, Gocha Kiladze, Aurélien Ginolhac, Frido Welker, Irina V. Kirillova, Peter D. Heintzman, J. Víctor Moreno-Mayar, Kirsty Penkman, Maia Bukhsianidze, Thomas W. Stafford, Ludovic Orlando, Diana Samodova, Enrico Cappellini, Martha Tappen, Shanlin Liu, Yvonne L. Chan, Anders Götherström, Eleftheria Palkopoulou, University of Copenhagen = Københavns Universitet (KU), The National Museum of Georgia, LibraGen, industriel, Stockholm Univ, Dept Biochem & Biophys, S-10691 Stockholm, Sweden, Department of Zoology, University of Venda [South Africa], University of Venda, Institució Catalana de Recerca i Estudis Avançats (ICREA), Área de Prehistoria, URV-IPHES, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Georgian State Museum, Geology Paleontology and Paleoanthropology, and Musée de Géorgie
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Proteomics, History, Early Pleistocene, Proteome, Lineage (evolution), [SDV]Life Sciences [q-bio], Amino Acid Motifs, 01 natural sciences, Woolly rhinoceros, Naturvetenskap, Phosphorylation, ComputingMilieux_MISCELLANEOUS, History, Ancient, Phylogeny, Paleoproteomics, Stephanorhinus, Phylogeny, Dmanisi, Early Pleistocene, Stephanorhinus, Multidisciplinary, Fossils, Coelodonta, DNA, Ancient/analysis, Sister group, VDP::Mathematics and natural science: 400::Geosciences: 450::Stratigraphy and paleontology: 461, Natural Sciences, Biotechnology, General Science & Technology, Dental Enamel/metabolism, Perissodactyla/classification, Biology, 010603 evolutionary biology, Article, Ancient, 03 medical and health sciences, stomatognathic system, Phylogenetics, Genetics, Proteome/analysis, Animals, Humans, Amino Acid Sequence, DNA, Ancient, Dental Enamel, Perissodactyla, VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Stratigrafi og paleontologi: 461, Bayes Theorem, DNA, 15. Life on land, biology.organism_classification, 030104 developmental biology, Ancient DNA, Evolutionary biology, Phosphorylation/genetics
Abstract: The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5—although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7–9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck’s rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel—which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record—can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation. Palaeoproteomic analysis of dental enamel from an Early Pleistocene Stephanorhinus resolves the phylogeny of Eurasian Rhinocerotidae, by enabling the reconstruction of molecular evolution beyond the limits of ancient DNA preservation.
Published: 2019

23. DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage

Author: Gabriel Renaud, Anders Albrechtsen, Kristian Hanghøj, Ludovic Orlando, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Section of Biostatistics [Copenhagen], Department of Public Health [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Section for GeoGenetics, and Globe Institute
Subjects: Epigenomics, DNA damage, [SDV]Life Sciences [q-bio], Bisulfite sequencing, Health Informatics, Accounting, high-throughput DNA sequencing, Biology, methylome, 010402 general chemistry, 01 natural sciences, Genome, 03 medical and health sciences, Technical Note, Humans, Epigenetics, ancient DNA, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, epigenetics, business.industry, Gene Expression Profiling, Computational Biology, High-Throughput Nucleotide Sequencing, Methylation, CpG dinucleotide, DNA Methylation, 0104 chemical sciences, Computer Science Applications, Ancient DNA, CpG site, DNA methylation, CpG Islands, Autopsy, business, Algorithms, Software, DNA Damage
Abstract: BACKGROUND: Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons.FINDINGS: Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues.CONCLUSIONS: DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial.
Published: 2019
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24. Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

Author: Eske Willerslev, Karl-Göran Sjögren, Simon Rasmussen, Christelle Desnues, Kristian Kristiansen, Rasmus Nielsen, Nicolás Rascovan, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Gothenburg (GU), Dept Integrat Biol, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), and University of Copenhagen = Københavns Universitet (KU)
Subjects: DNA, Bacterial, Yersinia pestis, mega settlements, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Plague (disease), General Biochemistry, Genetics and Molecular Biology, Prehistory, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, Humans, Molecular clock, Pandemics, ancient DNA, History, Ancient, Phylogeny, 030304 developmental biology, 0303 health sciences, metagenomics, biology, Phylogenetic tree, Human migration, business.industry, pathogen evolution, emergence and spread of infectious diseases, biology.organism_classification, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, plague, 3. Good health, Europe, Neolithic decline, Ancient DNA, 13. Climate action, Evolutionary biology, business, 030217 neurology & neurosurgery, Genome, Bacterial
Abstract: Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.
Published: 2019

25. Open access solutions for biodiversity journals: Do not replace one problem with another

Author: Janine Bolliger, Núria Roura-Pascual, Wilfried Thuiller, David S. Schoeman, Christopher P. Burridge, Petr Pyšek, Sara Varela, Anna Traveset, Jorge M. Lobo, Evan Knop, Enrique Martínez-Meyer, José J. Lahoz-Monfort, Andrés Lira-Noriega, Jane Elith, Ingolf Kühn, A. Townsend Peterson, Marlon E. Cobos, Lluís Brotons, Michael A. McCarthy, Rafael Loyola, Brendan A. Wintle, Ralph Charles Mac Nally, Daniel Jiménez-García, Luis Osorio-Olvera, Franz Essl, Damaris Zurell, Marcel Rejmánek, Javier Nori, Daniel Romero-Alvarez, Tomáš Václavík, Boris Schröder, Clare B. Embling, Carlos Yañez-Arenas, Enrico Di Minin, Laura Jiménez, Jorge Soberón, Luis E. Escobar, Fernando Machado-Stredel, Yolanda F. Wiersma, Octavio Rojas Soto, Erik A. Treml, Lucy A. Hawkes, Mark P. Robertson, Claudia Nuñez-Penichet, Jeffrey M. Diez, Angela P. Cuervo-Robayo, Maria Beger, Cory Merow, Diederik Strubbe, James E. M. Watson, David M. Green, Luca Santini, Anthony Ricciardi, Kenneth J. Feeley, Robert P. Anderson, University of Kansas [Lawrence] (KU), Centre for Automotive Safety Research, University of Adelaide, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Tasmania [Hobart, Australia] (UTAS), Umweltbundesamt, University of California [Los Angeles] (UCLA), University of California, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), University of Coimbra, Smithsonian Environmental Research Center, Czech Academy of Sciences [Prague] (CAS), Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Humboldt-Universität zu Berlin, Department of Geosciences and Geography, Digital Geography Lab, and Helsinki Lab of Interdisciplinary Conservation Science
Subjects: 0106 biological sciences, 0303 health sciences, Ecology, Agroforestry, Comercialization, Ecology (disciplines), Science, [SDE.MCG]Environmental Sciences/Global Changes, education, 518 Media and communications, Biodiversity, 010603 evolutionary biology, 01 natural sciences, purl.org/becyt/ford/1 [https], 03 medical and health sciences, Biodiversity conservation, Open Access, 1181 Ecology, evolutionary biology, Business, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, purl.org/becyt/ford/1.6 [https], Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: For much of the twentieth century, many or most scholarly journals in biodiversity, ecology, biogeography and conservation were owned and published by scientific societies and made available to the broader scientific community at relatively low cost. However, the past several decades have seen a dominant process of commercialization of the publication process in this field, either by commercial publishing firms taking over publication of journals owned by a society (e.g., Evolution), or by commercial publishers starting new journals to fill “niches” that were until then empty in the scholarly publishing ecosystem. Diversity and Distributions is an example of this latter category of journals, having been created by Wiley Publishers in 1993 (as Biodiversity Letters). Being a journal owned by a commercial publisher, it has always been accessed by readers via subscription, but the publication process has been free to potential authors whose work has passed peer review.
Published: 2019

26. La cueva de Can Sadurní (Begues, Barcelona) : El episodio funerario del neolítico antiguo cardial pleno. Estado actual de la cuestión

Author: Edo, Manuel, Antolín, Ferran, Martinez, Pablo, Josefa, Maria, Fullola, Josep Maria, Mercè, Maria, Saña Seguí, Maria, Verdun, Esther, Fernandez Dominguez, Eva, Gamba, Cristina, Arroyo-Pardo, Eduardo, Ache, Mireia, Gibaja, Juan Francesco, Palomo, Antoni, Clop Garcia, Xavier, Manen, Claire, Convertini, Fabien, University of Basel (Unibas), Universitat Autònoma de Barcelona (UAB), Duke University [Durham], Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Archéologie des Sociétés Méditerranéennes (ASM), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Gibaja JF, Subirà M.E, Martín A, Mozota M, Roig J, SERP-Universitat de Barcelona, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Musée d’Archeologie de Catalogne, Prehistory Department, SGR SAPPO, Facultat de Filosofia i Lletres, Barcelona, Ministère de la Culture et de la Communication (MCC)-École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UPVM)-Ministère de la Culture (MC), Juan Francisco Gibaja, Millan Mozoto, Maria Eulalia Subira, and Araceli Martin
Subjects: [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

27. 2019 ARIA Care pathways for allergen immunotherapy

Author: Dana Wallace, Karin C. Lødrup Carlsen, M. T. Ventura, Igor Kaidashev, Stephen R. Durham, Motohiro Ebisawa, Oliver Pfaar, Hae-Sim Park, Daniel Laune, Wytske Fokkens, Antonella Muraro, Moises A. Calderon, Torsten Zuberbier, Mohamed H. Shamji, Mark S. Dykewicz, Roy Gerth van Wijk, Josep M. Antó, Samantha Walker, Petr Panzner, Giorgio Walter Canonica, Nelson Rosario, Juan Carlos Ivancevich, Holger J. Schünemann, Susanne Halken, Lorenzo Cecchi, Sinthia Bosnic-Anticevich, Violeta Kvedariene, Stefania La Grutta, João Fonseca, Marek L Kowalski, Tari Haahtela, Aziz Sheikh, Montserrat Fernandez-Rivas, Nhan Pham-Thi, Isabelle Bosse, Jean Bousquet, Lan Le, Despo Ierodiakonou, Tomohisa Iinuma, Lars Jacobsen, Christine Rolland, Gert Marien, Wienczyslawa Czarlewski, Glenis Scadding, Ioana Agache, Bolesław Samoliński, Olga Lourenço, Ludger Klimek, Yoshitaka Okamoto, Ulrich Wahn, Joaquim Mullol, Erkka Valovirta, Luigi Caraballo, Sanna Toppila-Salmi, Ioanna Tsiligianni, Derek K. Chu, Ruby Pawankar, Jean Luc Fauquert, Musa Khaitov, Jorg Kleine Tebbe, Jean-François Fontaine, Victoria Cardona, Désirée Larenas-Linemann, Thomas B. Casale, Omer Kalayci, Alvaro A. Cruz, Arunas Valiulis, Anna Bedbrook, Susanne Lau, Alkis Togias, H.-J. Malling, Claus Bachert, Dermot Ryan, Elísio Costa, Giovanni Passalacqua, Ignacio J. Ansotegui, Ana Todo Bom, Marek Jutel, Enrica Menditto, Piotr Kuna, Nikolaos G. Papadopoulos, Gregoire Mercier, Mario Sánchez-Borges, Karl-Christian Bergmann, Susan Waserman, Gunter J. Sturm, Maryline Valentin-Rostan, Arzu Yorgancioglu, Giovanni Battista Pajno, Jan Brozek, George Du Toit, Robyn E O'Hehir, Peter Hellings, Graham Roberts, uBibliorum, Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon (MACVIA-LR), Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire de Nîmes (CHU Nîmes)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-European Innovation Partnership on Active and Healthy Ageing Reference Site (EIP on AHA), Commission Européenne-Commission Européenne-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Center for Rhinology and Allergology, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Clinical Epidemiology and Biostatistics and Medicine, McMaster University [Hamilton, Ontario], Department of Allergy and Immunology, Hospital Quiròn Bizkaia Erandio, UPC Research Laboratories, Allergy Department, University of Crete [Heraklion] (UOC), Department of Allergy and Clinical Immunology, Transylvania University of Brasov, Universitat Pompeu Fabra [Barcelona] (UPF), Ghent University Hospital, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Department of Dermatology and Allergy [Berlin, Allemagne], Comprehensive Allergy Center [Berlin, Allemagne], Berlin Institute of Health (BIH)-Berlin Institute of Health (BIH), The University of Sydney, Woolcock Institute of Medical Research [Sydney], CHU Montpellier, Departments of Clinical Epidemiology and Biostatistics and Medicine [Ontario], Section of Allergy and Clinical Immunology [London, UK], Imperial College London-Royal Brompton Hospital-National Heart and Lung Institute, Humanitas Clinical and Research Center [Rozzano, Milan, Italy], Institute for Immunological Research (University of Cartagena), University of Cartagena, Allergy Section, Department of Internal Medicine, Vall d'Hebron University Hospital [Barcelona], Division of Allergy and Immunology, Department of Medicine, Creighton University, Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON, Canada, Universidade do Porto, Instituto de Biologia Molecular e Celular (IBMC), Universidade Federal da Bahia (UFBA), UCB Pharma, Colombes, Section of Allergy and Clinical Immunology, Imperial College London-Royal Brompton Hospital-National Heart and Lung Institute [UK], King‘s College London, Saint Louis University School of Medicine [St Louis], Sagamihara National Hospital, CHU Estaing [Clermont-Ferrand], CHU Clermont-Ferrand, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos [Madrid, Spain] (IdISSC), European Forum for Research and Education in Allergy and Airway Diseases (EUFOREA), Center of Research in Health Technologies and Information Systems (CINTESIS), Department of Allergology, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Helsinki University Hospital, Odense University Hospital, University Hospitals Leuven [Leuven], Chiba University Hospital, Servicio de Alergia e ImmunologiaBuenos Aires (Clinica Santa Isabel), Research Centre for Prevention and Health (RCPH), Department of Public Health [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Capital Region of Denmark, Department of Clinical Immunology, Wroclaw Medical University, Ukrainina Medical Stomatological Academy [Poltava, Ukraine], Laboratory of Molecular Immunology [Moscow, Russian Federation] (National Research Center), Institute of Immunology [Moscow, Russian Federation]-Federal Medicobiological Agency [Moscow, Russian Federation], Hacettepe University = Hacettepe Üniversitesi, Allergy & Asthma Center Westend, Outpatient Clinic Hanf, Department of Immunology, Rheumatology and Allergy, Division of Internal Medicine, Asthma and Allergy, Medical University of Łódź (MUL)-Barlicki University Hospital, Vilnius University [Vilnius], CNR-IBIM : National Research Council-Institute of Biomedicine and Molecular Immunology, Department of Pediatric Pneumology and Immunology, Ho Chi Minh City University of Technology (HCMUT), University of Oslo (UiO), Faculty of Health Sciences and CICS-UB (Health Sciences Research Centre), 'Federico II' University of Naples Medical School, Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CIBERES), Food Allergy Referral Centre Veneto Region [Padua, Italy], Universita degli Studi di Padova, Monash University [Melbourne], Department of Otorhinolaryngology, Department of Pediatrics, Allergy Unit, University of Messina, Ajou University School of Medicine, Department of Allergology and Clinical Immunology, Medical Faculty in Pilsen-Charles University in Prague - the First Faculty of Medicine, Allergy and Respiratory Diseases, University of Genoa (UNIGE), Saint Mary's Hospital [London], St Mary's Hospital [London], Department of Pediatrics, Nippon Medical School, Pediatrics, Universidade Federal do Paraná (UFPR), Medical Centre, Woodbrook Medical Centre, Medical University of Warsaw - Poland, Department of Prevention of Environmental Hazards and Allergology, Medical University of Warsaw - Poland-Faculté de Pharmacie de Paris, Department of Allergy and Clinical Immunology [Caracas, Venezuela], Centro Medico-Docente La Trinidad, The Royal National Throat, Nose and Ear Hospital, Imperial College London, Centre for Population Health Sciences, University of Edinburgh, Medical University Graz, University of Coimbra [Portugal] (UC), Vilnius University Clinic of Children's Diseases, Suomen Terveystalo Allergy Clinic, Università degli studi di Bari Aldo Moro (UNIBA), Department for Pediatric Pneumology and Immunology, Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, (MRC), Guy's Hospital [London], Nova Southeastern University (NSU), Department of Pulmonology, Manisa Celal Bayar University, Department of Dermatology, Medical School-Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Association Asthme et Allergie, Internal Medicine, Bousquet, J., Pfaar, O., Togias, A., Schunemann, H. J., Ansotegui, I., Papadopoulos, N. G., Tsiligianni, I., Agache, I., Anto, J. M., Bachert, C., Bedbrook, A., Bergmann, K. -C., Bosnic-Anticevich, S., Bosse, I., Brozek, J., Calderon, M. A., Canonica, G. W., Caraballo, L., Cardona, V., Casale, T., Cecchi, L., Chu, D., Costa, E., Cruz, A. A., Czarlewski, W., Durham, S. R., Du Toit, G., Dykewicz, M., Ebisawa, M., Fauquert, J. L., Fernandez-Rivas, M., Fokkens, W. J., Fonseca, J., Fontaine, J. -F., Gerth van Wijk, R., Haahtela, T., Halken, S., Hellings, P. W., Ierodiakonou, D., Iinuma, T., Ivancevich, J. C., Jacobsen, L., Jutel, M., Kaidashev, I., Khaitov, M., Kalayci, O., Kleine Tebbe, J., Klimek, L., Kowalski, M. L., Kuna, P., Kvedariene, V., La Grutta, S., Larenas-Linemann, D., Lau, S., Laune, D., Le, L., Lodrup Carlsen, K., Lourenco, O., Malling, H. -J., Marien, G., Menditto, E., Mercier, G., Mullol, J., Muraro, A., O'Hehir, R., Okamoto, Y., Pajno, G. B., Park, H. -S., Panzner, P., Passalacqua, G., Pham-Thi, N., Roberts, G., Pawankar, R., Rolland, C., Rosario, N., Ryan, D., Samolinski, B., Sanchez-Borges, M., Scadding, G., Shamji, M. H., Sheikh, A., Sturm, G. J., Todo Bom, A., Toppila-Salmi, S., Valentin-Rostan, M., Valiulis, A., Valovirta, E., Ventura, M. -T., Wahn, U., Walker, S., CORBO UGULINO, Wallace, Waserman, S., Yorgancioglu, A., Zuberbier, T., Hospital Quirónsalud Bizkaia [Bilbao], Sagamihara National Hospital [Kanagawa, Japan], Universidade do Porto = University of Porto, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Capital Region of Denmark, Wrocław Medical University, Università degli Studi di Padova = University of Padua (Unipd), Charles University [Prague] (CU)-Medical Faculty in Pilsen, Università degli studi di Genova = University of Genoa (UniGe), Centro Médico Docente La Trinidad, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), and Hibade, Monique
Subjects: Cost effectiveness, [SDV]Life Sciences [q-bio], Cost-Benefit Analysis, Comorbidity, medicine.disease_cause, 0302 clinical medicine, Allergen, Cost of Illness, Immunology and Allergy, Medicine, 030212 general & internal medicine, [SDV.IMM.ALL]Life Sciences [q-bio]/Immunology/Allergology, Precision Medicine, mHealth, Children, media_common, Allergen immunotherapy, Rhinitis, Disease Management, 3. Good health, [SDV] Life Sciences [q-bio], rhiniti, Treatment Outcome, Practice Guidelines as Topic, Critical Pathways, [SDV.IMM]Life Sciences [q-bio]/Immunology, Disease Susceptibility, [SDV.IMM.ALL] Life Sciences [q-bio]/Immunology/Allergology, medicine.medical_specialty, [SDV.IMM] Life Sciences [q-bio]/Immunology, Attitude of Health Personnel, Immunology, Clinical Decision-Making, 03 medical and health sciences, Pharmacotherapy, rhinitis, stratification, children, media_common.cataloged_instance, Animals, Humans, European union, Intensive care medicine, allergen immunotherapy, asthma, children, mHealth, rhinitis, stratification, Asthma, business.industry, Allergens, asthma, medicine.disease, Rhinitis, Allergic, Review article, 030228 respiratory system, Desensitization, Immunologic, allergen immunotherapy, Stratification, business, Biomarkers
Abstract: Allergen immunotherapy (AIT) is a proven therapeutic option for the treatment of allergic rhinitis and/or asthma. Many guidelines or national practice guidelines have been produced but the evidence-based method varies, many are complex and none propose care pathways. This paper reviews care pathways for AIT using strict criteria and provides simple recommendations that can be used by all stakeholders including health professionals. The decision to prescribe AIT for the patient should be individualized and based on the relevance of the allergens, the persistence of symptoms despite appropriate medications according to guidelines as well as on the availability of good-quality and efficacious extracts. Allergen extracts cannot be regarded as generics. Immunotherapy is selected by specialists for stratified patients. There are no currently available validated biomarkers that can predict AIT success. In adolescents and adults, AIT should be reserved for patients with moderate/severe rhinitis or for those with moderate asthma who, despite appropriate pharmacotherapy and adherence, continue to exhibit exacerbations that appear to be related to allergen exposure, except in some specific cases. Immunotherapy may be even more advantageous in patients with multimorbidity. In children, AIT may prevent asthma onset in patients with rhinitis. mHealth tools are promising for the stratification and follow up of patients. This article is protected by copyright. All rights reserved.
Published: 2019

28. Convergent genomic signatures of domestication in sheep and goats

Author: Alberto, Florian J., Boyer, Frédéric, Orozco-terWengel, Pablo, Streeter, Ian, Servin, Bertrand, de Villemereuil, Pierre, Benjelloun, Badr, Librado, Pablo, Biscarini, Filippo, Colli, Licia, Barbato, Mario, Zamani, Wahid, Alberti, Adriana, Engelen, Stefan, Stella, Alessandra, Joost, Stéphane, Ajmone-Marsan, Paolo, Negrini, Riccardo, Orlando, Ludovic, Rezaei, Hamid Reza, Naderi, Saeid, Clarke, Laura, Flicek, Paul, Wincker, Patrick, Coissac, Eric, Kijas, James, Tosser-Klopp, Gwenola, Chikhi, Abdelkader, Bruford, Michael W., Taberlet, Pierre, Pompanon, François, Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), School of Biosciences [Cardiff], Cardiff University, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), PTP Science Park, Institute of Zootechnics [Piacenza], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, Department of Environmental Sciences [Tarbiat], Faculty of Natural Resources and Marine Sciences [Tarbiat], Tarbiat Modaras University-Tarbiat Modaras University, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratory of Geographical Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Research Center on Biodiversity and Ancient DNA [Piacenza] (BioDNA), Environmental Sciences Department [Gorgan], Gorgan University of Agricultural Sciences and Natural Resources, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), CSIRO Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Institut national de la recherche agronomique [Maroc] (INRA Maroc), ANR-14-JFAC-0002,ClimGen,Climate Genomics for farm animal adaptation(2014), ANR10 LABX56,ANR10 LABX56, European Project: 244356,EC:FP7:KBBE,FP7-KBBE-2009-3,NEXTGEN(2010), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Tarbiat Modares University [Tehran]-Tarbiat Modares University [Tehran], Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), FACCE ERA-NET Plus project CLIMGEN ANR-14-JFAC-0002-01 / LabEx OSUG (Investissements d'avenir) ANR10LABX56 / Wellcome Trust WT108749/Z/15/Z, ANR-10-LABX-0056,OSUG@2020,Innovative strategies for observing and modelling natural systems(2010), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: sheep, Science, [SDV]Life Sciences [q-bio], selection signature, selection, Article, domestication, evolution, genomics, Animals, dna-sequencing data, animal domestication, population history, analysis toolkit, gene, discovery, reveals, association, Selection, Genetic, lcsh:Science, Phylogeny, Sheep, Domestic, Genome, Settore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICO, Whole Genome Sequencing, Goats, goat, evolutionary basis of domestication, Genetic Variation, Biological Evolution, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Phenotype, Haplotypes, Animals, Domestic, lcsh:Q
Abstract: The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species., The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.
Published: 2018

29. A large impact crater beneath Hiawatha Glacier in northwest Greenland

Author: Shfaqat Abbas Khan, Olaf Eisen, Tod E. Waight, Tobias Binder, Svend Funder, Joseph A. MacGregor, Michael Houmark-Nielsen, John Paden, Iain McDonald, Veit Helm, Henning Haack, Anders A. Bjørk, Mathieu Morlighem, Horst Machguth, Jeremie Mouginot, Eske Willerslev, Adam A. Garde, Mark Fahnestock, Christian Weikusat, Nicolaj K. Larsen, Kristian K. Kjeldsen, Kurt H. Kjær, Abteilung Klinische Sozialmedizin, Berufs- und Umweltdermatologie, Universität Heidelberg [Heidelberg], Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Jodrell Bank Centre for Astrophysics (JBCA), University of Manchester [Manchester], Institut des Géosciences de l’Environnement (IGE), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut de Recherche pour le Développement (IRD)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), University of California [Irvine] (UCI), University of California, Center for Remote Sensing of Ice Sheets (CReSIS), University of Kansas [Lawrence] (KU), Section for GeoGenetics, Institute for Geophysics, University of Texas at Dallas [Richardson] (UT Dallas), Kjær, Kurt H [0000-0002-8871-5179], Larsen, Nicolaj K [0000-0002-0117-1106], Binder, Tobias [0000-0002-9826-8835], Bjørk, Anders A [0000-0002-4919-792X], Eisen, Olaf [0000-0002-6380-962X], Fahnestock, Mark A [0000-0002-5896-6858], Garde, Adam A [0000-0002-0410-3547], Haack, Henning [0000-0002-4618-3178], Helm, Veit [0000-0001-7788-9328], Kjeldsen, Kristian K [0000-0002-8557-5131], Khan, Shfaqat A [0000-0002-2689-8563], Machguth, Horst [0000-0001-5924-0998], McDonald, Iain [0000-0001-9066-7244], Morlighem, Mathieu [0000-0001-5219-1310], Mouginot, Jérémie [0000-0001-9155-5455], Paden, John D [0000-0003-0775-6284], Waight, Tod E [0000-0003-2601-1202], Weikusat, Christian [0000-0002-3812-6325], Willerslev, Eske [0000-0002-7081-6748], MacGregor, Joseph A [0000-0002-5517-2235], Apollo - University of Cambridge Repository, University of Zurich, Kjær, Kurt H, Universität Heidelberg [Heidelberg] = Heidelberg University, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Institut de Recherche pour le Développement (IRD)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), University of California [Irvine] (UC Irvine), and University of California (UC)
Subjects: 010506 paleontology, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Greenland ice sheet, 010502 geochemistry & geophysics, 01 natural sciences, Paleontology, Impact crater, Shocked quartz, 910 Geography & travel, Foreland basin, Holocene, Research Articles, 0105 earth and related environmental sciences, 1000 Multidisciplinary, geography, Multidisciplinary, geography.geographical_feature_category, Bedrock, SciAdv r-articles, Glacier, Geology, Debris, 10122 Institute of Geography, Geophysics, [SDE]Environmental Sciences, 0406 Physical Geography and Environmental Geoscience, Research Article
Abstract: Researchers present the first unambiguous discovery of a 31-km-wide impact crater buried beneath the Greenland Ice Sheet., We report the discovery of a large impact crater beneath Hiawatha Glacier in northwest Greenland. From airborne radar surveys, we identify a 31-kilometer-wide, circular bedrock depression beneath up to a kilometer of ice. This depression has an elevated rim that cross-cuts tributary subglacial channels and a subdued central uplift that appears to be actively eroding. From ground investigations of the deglaciated foreland, we identify overprinted structures within Precambrian bedrock along the ice margin that strike tangent to the subglacial rim. Glaciofluvial sediment from the largest river draining the crater contains shocked quartz and other impact-related grains. Geochemical analysis of this sediment indicates that the impactor was a fractionated iron asteroid, which must have been more than a kilometer wide to produce the identified crater. Radiostratigraphy of the ice in the crater shows that the Holocene ice is continuous and conformable, but all deeper and older ice appears to be debris rich or heavily disturbed. The age of this impact crater is presently unknown, but from our geological and geophysical evidence, we conclude that it is unlikely to predate the Pleistocene inception of the Greenland Ice Sheet.
Published: 2018

30. The prehistoric peopling of Southeast Asia

Author: Hsiao-chun Hung, Tadayuki Masuyama, Christophe Pottier, Farhang Aghakhanian, Thi Minh Tran, Anne-Marie Bacon, Lasse Vinner, Andaine Seguin-Orlando, Laura L. Shackelford, Thi Mai Huong Nguyen, Tsunehiko Hanihara, Anh Nguyen, Hajime Ishida, Ashot Margaryan, Yasuhiro Yamada, Thongsa Sayavongkhamdy, Hiroki Shibata, Constanza de la Fuente Castro, Rasmi Shoocongdej, Eske Willerslev, Silas Anselm Rasmussen, Peter de Barros Damgaard, Patcharee Lertrit, Nobuo Shigehara, Marta Mirazón Lahr, Jean Christophe Galipaud, Jean Luc Ponche, Thomas Higham, Shigeki Nakagome, Sally Wasef, Uffe Gram Wilken, David M. Lambert, Thibaut Devièse, Takashi Gakuhari, Robert Foley, George van Driem, Atsushi Tajima, Ludovic Orlando, Bérénice Bellina-Pryce, Morten E. Allentoft, Charles Higham, Hiroki Oota, J. Víctor Moreno-Mayar, Anna-Sapfo Malaspinas, Huu Nghia Truong, Giang Hai Nguyen, Maude E. Phipps, Fernando Racimo, Rebecca Kinaston, Elise Patole-Edoumba, Supannee Kaewsutthi, Ketut Wiradnyana, Ana Prohaska, Fabrice Demeter, Viengkeo Souksavatdy, Shaiful Shahidan, Hugh McColl, Mokhtar Saidin, Hallie R. Buckley, Thorfinn Sand Korneliussen, Minoru Yoneda, Atsushi Toyoda, Takehiro Sato, Hiromi Matsumae, Philippe Duringer, Martin Sikora, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Préhistoire et Technologie (PréTech), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Université Silpakorn, Department of Museums, Historic Buildings and Archaeology, Ministry of Information and Culture, Département des musées et de l'archéologie, Ministère de la Culture et de l?Information, Kyoto University [Kyoto], Dynamique de l'évolution humaine : individus, populations, espèces [Paris] (DEHIPE), Centre National de la Recherche Scientifique (CNRS), Centre de géochimie de la surface (CGS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de chimie et procédés pour l'énergie, l'environnement et la santé (ICPEES), Université de Strasbourg (UNISTRA)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Illinois at Urbana Champaign (UIUC), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Museum d'Histoire Naturelle de La Rochelle, Service d'Anatomo-Cyto-Pathologie et de NeuroPathologie [Hôpital de la Timone - APHM] (ACPNP), Aix Marseille Université (AMU)- Hôpital de la Timone [CHU - APHM] (TIMONE), Patrimoines Locaux et Gouvernance (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Anatomy, University of Otago, Dunedin, University of Otago [Dunedin, Nouvelle-Zélande], École française d'Extrême-Orient (EFEO), Ctr Biol Sequence Anal, Technical University of Denmark [Lyngby] (DTU), Research Laboratory for Archaeology and the History of Art, University of Oxford [Oxford], Institut de Biologia Evolutiva (UPF-CSIC), Max-Planck-Institut für evolutionäre Anthropologie (MPI-EVA), Max-Planck-Gesellschaft, Silpakorn University [Bangkok, Thaïlande], Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Analyse et de Mathématiques Appliquées (LAMA), Université Paris-Est Marne-la-Vallée (UPEM)-Fédération de Recherche Bézout-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-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 la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-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 la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Illinois System, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Oxford, Kyoto University, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), McColl, Hugh [0000-0002-7568-4270], Racimo, Fernando [0000-0002-5025-2607], Demeter, Fabrice [0000-0002-1288-5534], Gakuhari, Takashi [0000-0003-1855-8371], Gram Wilken, Uffe [0000-0003-3434-7312], Seguin-Orlando, Andaine [0000-0002-8265-3229], de la Fuente Castro, Constanza [0000-0002-2857-3615], Wasef, Sally [0000-0002-7207-7395], Sayavongkhamdy, Thongsa [0000-0001-9467-0811], Korneliussen, Thorfinn [0000-0001-7576-5380], Prohaska, Ana [0000-0001-5459-6186], Margaryan, Ashot [0000-0002-2576-2429], Kaewsutthi, Supannee [0000-0002-3959-8420], Lertrit, Patcharee [0000-0002-4801-3834], Hung, Hsiao-Chun [0000-0001-5794-3040], Minh Tran, Thi [0000-0001-8833-693X], Nghia Truong, Huu [0000-0003-3291-5646], Shahidan, Shaiful [0000-0002-8367-3539], Matsumae, Hiromi [0000-0003-1858-3833], Ishida, Hajime [0000-0002-5781-7914], Tajima, Atsushi [0000-0001-6808-5491], Toyoda, Atsushi [0000-0002-0728-7548], Nakagome, Shigeki [0000-0001-9613-975X], Deviese, Thibaut [0000-0003-0495-7398], Duringer, Philippe [0000-0001-6213-5726], Patole-Edoumba, Elise [0000-0002-9378-2202], Bellina-Pryce, Bérénice [0000-0001-8790-1394], Galipaud, Jean-Christophe [0000-0003-3546-5265], Kinaston, Rebecca [0000-0001-7697-4950], Higham, Tom [0000-0002-5949-598X], Foley, Robert A [0000-0003-0479-3039], Lahr, Marta Mirazón [0000-0001-5752-5770], Orlando, Ludovic [0000-0003-3936-1850], Sikora, Martin [0000-0003-2818-8319], Lambert, David M [0000-0002-5821-3637], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Human Migration, Population, Southeast asian, Indigenous, Prehistory, 03 medical and health sciences, 0302 clinical medicine, Asian People, Humans, East Asia, 14. Life underwater, DNA, Ancient, education, Asia, Southeastern, History, Ancient, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Genome, Human, business.industry, Human migration, Genetic Variation, Sequence Analysis, DNA, Hoabinhian, 030104 developmental biology, Agriculture, Ethnology, [SHS.HIST]Humanities and Social Sciences/History, business, 030217 neurology & neurosurgery
Abstract: Ancient migrations in Southeast AsiaThe past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipsonet al.generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McCollet al.sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations.Science, this issue p.92, p.88; see also p.31
Published: 2018

31. 137 ancient human genomes from across the Eurasian steppes

Author: Karl-Göran Sjögren, Nina Lau, Nikolay N. Kradin, Igor Kukushkin, Arman Beisenov, Kadicha Tashbaeva, Andrey Logvin, Peter de Barros Damgaard, Irina Shevnina, Viktor K. Mertz, Ilya V. Mertz, Alexander Tkachev, Amy Goldberg, Zaruhi Khachatryan, Vyacheslav Moiyesev, Nina Marchi, Valeriy Evdokimov, Gabit Baimbetov, Valeriy Loman, Turaly Tulegenov, Evgeniy Dmitriev, Kasper Nielsen, Diimaajav Erdenebaatar, Lotte Hedeager, Levon Yepiskoposyan, Almaz Aldashev, Egor Kitov, Evelyne Heyer, Kristian Kristiansen, Victor Varfolomeev, Nurbol Baimukhanov, Enkhbayar Mijiddorj, Tereza Štolcová, Melissa A. Wilson Sayres, Sturla Ellingvåg, Dmitriy Voyakin, Gennady Afanasiev, Simon Rasmussen, Anders Gorm Pedersen, Ashyk Alpaslan, Mikkel Winther Pedersen, Ashot Margaryan, Sainbileg Undrakhbold, Z. Orozbekova, Bekmukhanbet Nurmukhanbetov, Tabaldiev Kubatbek, Eske Willerslev, Andrey Gromov, Ruslan Khaskhanov, Hakon Hakonarson, Alina Kolbina, Václav Smrčka, Rasmus Nielsen, Morten E. Allentoft, Gulmira Mukhtarova, Martin Sikora, Gabriel Renaud, J. Víctor Moreno-Mayar, Bazartseren Boldgiv, Angela M. Taravella, Tatyana Hegay, Choduraa Dorzhu, Emma Usmanova, Karol Pieta, Inga Merkyte, Alexey Kukushkin, Michaël Peyrot, Kunbolot Akmatov, Karin Margarita Frei, Vladimir I. Bazaliiskii, Thorfinn Sand Korneliussen, Alexander Goryachev, Ludovic Orlando, Andrzej W. Weber, Irina P. Panyushkina, Rana Dajani, Bazartseren Boldbaatar, Eco-Anthropologie et Ethnobiologie (EAE), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Muséum national d'Histoire naturelle (MNHN), Ctr Biol Sequence Anal, Technical University of Denmark [Lyngby] (DTU), Max Planck Institute for Evolutionary Anthropology, Max-Planck-Gesellschaft, Institute of Molecular Biology and Medicine, Irkutsk State University (ISU), The Center for Applied Genomics, Children’s Hospital of Philadelphia (CHOP ), Institute of Immunology, Uzbekistan Academy of Sciences, Laboratory for Tree-Ring Research, University of Arizona, University of Copenhagen = Københavns Universitet (KU), Dept Integrat Biol, Institut de Biologia Evolutiva (UPF-CSIC), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Max Planck Institute for Evolutionary Anthropology [Leipzig], Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7), Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Asia, Steppe, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Ancient history, Plague (disease), White People, 03 medical and health sciences, Asian People, Bronze Age, Humans, Middle Ages, East Asia, education, History, Ancient, Phylogeny, geography, education.field_of_study, Farmers, Multidisciplinary, geography.geographical_feature_category, Genome, Human, Human migration, business.industry, Grassland, Europe, 030104 developmental biology, Iron Age, business
Abstract: For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century bc, forming the Hun traditions in the fourth–fifth century ad, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry. Sequences of 137 ancient and 502 modern human genomes illuminate the population history of the Eurasian steppes after the Bronze Age and document the replacement of Indo-European speakers of West Eurasian ancestry by Turkic-speaking groups of East Asian ancestry.
Published: 2018

32. Molecular assays for antimalarial drug resistance surveillance:A target product profile

Author: Xavier C. Ding, Eric Legrand, Naomi W. Lucchi, Hans-Peter Beck, Sidsel Nag, Sanjeev Krishna, Sarah K. Volkman, Christian Nsanzabana, Harald Noedl, Cally Roper, Edwin Kamau, Frédéric Ariey, Philip J. Rosenthal, Steve M. Taylor, Iveth J. González, Olivo Miotto, Henk D. F. H. Schallig, Medical Microbiology and Infection Prevention, AII - Infectious diseases, Foundation for Innovative New Diagnostics (FIND), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Service de parasitologie-mycologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Medical Parasitology and Infection Biology [Basel, Suisse] (MPI), Swiss Tropical and Public Health Institute [Basel], University of Basel (Unibas), Walter Reed Army Institute of Research, United States Army Medical Research Directorate [Kenya] (USAMRD-K), Institute for Infection and Immunity [Londres, UK], St George's, University of London, Génétique du paludisme et résistance - Malaria Genetics and Resistance, Institut Pasteur [Paris] (IP), Division of Parasitic Diseases and Malaria [Atlanta, GA, États-Unis] (DPDM), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention-Centers for Disease Control and Prevention, Mahidol Oxford Tropical Medicine Research Unit, University of Oxford-Mahidol University [Bangkok], The Wellcome Trust Sanger Institute [Cambridge], Big Data Institute, University of Oxford, Centre for Medical Parasitology [Copenhagen], Department of Immunology and Microbiology [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Department of Infectious Disease [Copenhague, Danemark], Rigshospitalet [Copenhagen], Copenhagen University Hospital-Copenhagen University Hospital, Institute of Specific Prophylaxis and Tropical Medicine = Institut für Spezifische Prophylaxe und Tropenmedizin [Vienne, Autriche], Medizinische Universität Wien = Medical University of Vienna, London School of Hygiene and Tropical Medicine (LSHTM), Department of Medicine [San Francisco], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Experimental parasitology [Amsterdam, Pays-Bas], Department of Medical Microbiology [Academic Medical Center], Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA)-Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA), Duke University Medical Center, Department of Immunology and Infectious Diseases (IID), Harvard T.H. Chan School of Public Health, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Simmons University [Boston, USA], This study was funded by the by the Department of Foreign Affairs and Trade of the Australian Government. The URL of the funder’s website is https://dfat.gov.au/. Grant number is AUSCORE-02, and the funding was received by the Foundation for Innovative New Diagnostics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Legrand, Eric, Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut Pasteur [Paris], University of Oxford [Oxford]-Mahidol University [Bangkok], University of Oxford [Oxford], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of California [San Francisco] (UCSF), and University of California-University of California
Subjects: 0301 basic medicine, Research Facilities, Molecular biology, DNA hybridization, Electrophoretic techniques, Drug Resistance, DNA electrophoresis, lcsh:Medicine, Drug resistance, Biochemistry, MESH: Biological Assay / economics, 0302 clinical medicine, Medicine and Health Sciences, Artemisinin, lcsh:Science, DNA extraction, MESH: Biological Assay / methods, Multidisciplinary, Drugs, 3. Good health, Nucleic acids, Costs and Cost Analysis, MESH: Drug Resistance, Biological Assay, Research Laboratories, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, medicine.drug, Research Article, Combination therapy, MESH: Antimalarials / pharmacology, 030231 tropical medicine, 030106 microbiology, Early detection, Computational biology, Microbiology, MESH: Costs and Cost Analysis, 03 medical and health sciences, Antimalarials, Antibiotic resistance, Extraction techniques, Microbial Control, parasitic diseases, medicine, Genetics, Parasitic Diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Temporal information, Pharmacology, Molecular probe techniques, business.industry, Product profile, lcsh:R, Biology and Life Sciences, DNA, medicine.disease, Tropical Diseases, Probe hybridization, Malaria, Research and analysis methods, Molecular biology techniques, lcsh:Q, Antimicrobial Resistance, business, Government Laboratories
Abstract: International audience; Antimalarial drug resistance is a major constraint for malaria control and elimination efforts. Artemisinin-based combination therapy is now the mainstay for malaria treatment. However, delayed parasite clearance following treatment with artemisinin derivatives has now spread in the Greater Mekong Sub region and may emerge or spread to other malaria endemic regions. This spread is of great concern for malaria control programmes, as no alternatives to artemisinin-based combination therapies are expected to be available in the near future. There is a need to strengthen surveillance systems for early detection and response to the antimalarial drug resistance threat. Current surveillance is mainly done through therapeutic efficacy studies; however these studies are complex and both time- and resource-intensive. For multiple common antimalarials, parasite drug resistance has been correlated with specific genetic mutations, and the molecular markers associated with antimalarial drug resistance offer a simple and powerful tool to monitor the emergence and spread of resistant parasites. Different techniques to analyse molecular markers associated with antimalarial drug resistance are available, each with advantages and disadvantages. However, procedures are not adequately harmonized to facilitate comparisons between sites. Here we describe the target product profiles for tests to analyse molecular markers associated with antimalarial drug resistance, discuss how use of current techniques can be standardised, and identify the requirements for an ideal product that would allow malaria endemic countries to provide useful spatial and temporal information on the spread of resistance.
Published: 2018

33. Dynamic Species Distribution Models reveal spatiotemporal habitat shifts in native range-expanding versus non-native invasive birds in an urban area

Author: Magali Deschamps-Cottin, Philippe Clergeau, Marine Le Louarn, Diederik Strubbe, Laboratoire Population-Environnement-Développement (LPED), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium, Terrestrial Ecology Unit, Ghent University, KL Ledeganckstraat 32, 9000 Ghent, Belgium, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Antwerp (UA), and Universiteit Gent = Ghent University (UGENT)
Subjects: 0106 biological sciences, Extinction, Ecology, Range (biology), 010604 marine biology & hydrobiology, Species distribution, Introduced species, Parakeet, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Habitat, Abundance (ecology), biology.animal, Biological dispersal, Animal Science and Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS
Abstract: Urbanisation as a major driver of changes leads to the extinction of some species while others increase in abundance, especially non-native species. Spatiotemporal distribution patterns of these successful species are likely to be shaped by their response and tolerance to urban features. This study assesses the anthropo-ecological requirements of two co-occurring bird species, the native range-shifting jackdaw Corvus monedula and the non-native invasive ring-necked parakeet Psittacula krameri. We built yearly models over an eight-year period using an ensemble modelling approach assessing response differences through time and between species. Predictors describing human-made structures, socio-ecological proxies and resources availability were extracted from temporally coincident databases. Dispersal and habitat constraints were implemented in final models to provide more realistic forecasts of species future distributions. Ensemble models evaluated with a random partition of the training dataset showed a higher accuracy than those evaluated with an independent dataset from another time period. Our results highlight temporal variations in the relative importance of predictors for both studied species. Single-season occurrence data may thus be insufficient to characterize species ecological requirements. The ring-necked parakeet and the jackdaw showed different responses to urban features. Jackdaws preferred the more urbanized part of the city while the distribution of parakeets was strongly positively associated with the density of exotic ornamental trees. We concluded that ring-necked parakeet range expansion is likely to be driven by its effective ability to exploit urban resources which native species do not or under exploit, suggesting an open window of foraging opportunities. However, the jackdaw may be misled by a high cavity availability and a large amount of low-quality anthropogenic food in the urban core. We suggest that dynamic SDMs are a critical tool not only to forecast the future expansion of invasive species but also for a better understanding of processes driving urban biodiversity persistence.
Published: 2018

34. Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs

Author: Dias, Graciela M., Bidault, Adeline, Le Chevalier, Patrick, Choquet, Gwenaëlle, Der Sarkissian, Clio, Orlando, Ludovic, Medigue, Claudine, Barbe, Valerie, Mangenot, Sophie, Thompson, Cristiane C., Thompson, Fabiano L., Jacq, Annick, Pichereau, Vianney, Paillard, Christine, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Interactions cellulaires et moléculaires (ICM), Centre National de la Recherche Scientifique (CNRS)-IFR140-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut des sciences biologiques (INSB), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Signalisation et Réseaux de Régulations Bactériens (SRRB), Département Biologie des Génomes (DBG), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 266157, Seventh Framework Programme, 678589, Horizon 2020 Framework Programme, ANR-10-LABX-19, Agence Nationale de la Recherche, 4002- 659 00152B, Natur og Univers, Det Frie Forskningsråd, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal Rural do Rio de Janeiro (UFRRJ), Laboratoire de Biotechnologie et Chimie Marine (LBCM), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), European Project: 266157,EC:FP7:KBBE,FP7-KBBE-2010-4,BIVALIFE(2011), European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Vibrio tapetis, T4SS, core genome, pangenome, ACL, [SDV]Life Sciences [q-bio], pathogenicity, comparative genomics, Venerupis philippinarum, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microbiology, Original Research
Abstract: The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam Venerupis philippinarum introduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium, Vibrio tapetis, which is also pathogenic to fish. Here we report the first assembly of the complete genome of V. tapetis CECT4600T, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan- and core genomes and to identify putative virulence factors. The V. tapetis core genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I restriction modification system, GGDEF domain proteins, several conjugative plasmids, and a Type IV secretion system. Future research on the coevolutionary arms race between V. tapetis virulence factors and host resistance mechanisms will improve our understanding of how pathogenicity develops in this emerging pathogen.
Published: 2018

35. Oral health status in historic population: Macroscopic and metagenomic evidence

Author: Pierre Chevet, Claire Willmann, Xavier Mata, Catherine Thèves, Elodie Cabot, Lenka Tisseyre, Céline Jeziorski, Ludovic Orlando, Rémi Esclassan, Kristian Hanghoej, Laure Tonasso, Eric Crubézy, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), CHU Toulouse [Toulouse], Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Animal Biology and Genetics, University of Florence (UNIFI), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR: 10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2011), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: Male, Rural Population, 0301 basic medicine, Teeth, Physiology, Health Status, Digestive Physiology, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Rothia dentocariosa, lcsh:Medicine, Oral Health, History, 18th Century, Pathology and Laboratory Medicine, Diagnostic Radiology, Streptococcus mutans, 0302 clinical medicine, Oral Diseases, Medicine and Health Sciences, Tannerella forsythia, lcsh:Science, rothia-dentocariosa, ancient dna, dental-caries, streptococcus-mutan, pseudoramibacter-alactolyticus, tannerella-forsythia, periodontal-disease, treponema-denticola, parvimonas-micra, teeth, ComputingMilieux_MISCELLANEOUS, education.field_of_study, Multidisciplinary, Calculus, biology, Shotgun sequencing, Microbiota, Radiology and Imaging, Periodontal diseases, Genomics, Bone Imaging, Medical Microbiology, X-ray radiography, Physical Sciences, Female, France, Genomic libraries, Anatomy, Pathogens, Research Article, Autre (Sciences du Vivant), DNA, Bacterial, Imaging Techniques, Oral Medicine, Population, Dental Caries, Research and Analysis Methods, Microbiology, DNA sequencing, 03 medical and health sciences, Diagnostic Medicine, Genetics, Humans, Dentition, DNA, Ancient, Periodontitis, education, Parvimonas micra, Microbial Pathogens, Paleodontology, Bacteria, lcsh:R, Organisms, Biology and Life Sciences, Streptococcus, Computational Biology, 030206 dentistry, Genome Analysis, biology.organism_classification, stomatognathic diseases, 030104 developmental biology, Ancient DNA, Jaw, Metagenomics, lcsh:Q, Bacterial pathogens, Digestive System, Head, Mathematics
Abstract: International audience; Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macro-scopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces visco-sus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olse-nella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or peri-odontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.
Published: 2018

36. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Author: Marjolein Bosch, Laurent Excoffier, Thomas Higham, Ashot Margaryan, Morten E. Allentoft, Sergey Vasilyev, Thibaut Devièse, Gabriel Renaud, Rasmus Nielsen, Amy Ko, Elizaveta Veselovskaya, Ludovic Orlando, Philip R. Nigst, Svetlana B. Borutskaya, Marta Mirazón Lahr, Dan Comeskey, Simon Rasmussen, Andrea Manica, Andaine Seguin-Orlando, Vitor C. Sousa, Thorfinn Sand Korneliussen, Eske Willerslev, David J. Meltzer, Martin Sikora, Isabelle Dupanloup, Robert Foley, Anders Albrechtsen, University of Copenhagen = Københavns Universitet (UCPH), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Institute of Ecology and Evolution, Universität Bern [Bern] (UNIBE), Section of Biostatistics [Copenhagen], Department of Public Health [Copenhagen], University of California [Berkeley] (UC Berkeley), University of California (UC), Ctr Biol Sequence Anal, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Cambridge [UK] (CAM), McDonald Institute for Archaeological Research, Institute of Molecular Biology of the National Academy of Sciences of Armenia (IMB NAS RA), National Academy of Sciences of the Republic of Armenia [Yerevan] (NAS RA), Russian Academy of Science (RAS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Zoology [Cambridge], Dept Integrat Biol, Institute of Ecology and Evolution [Bern, Switzerland], University of Bern, University of Copenhagen = Københavns Universitet (KU), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of Berne, University of California [Berkeley], University of California, Technical University of Denmark [Lyngby] (DTU), Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK, Russian Academy of the Science, and Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)
Subjects: 0301 basic medicine, Genetics, education.field_of_study, Multidisciplinary, Population, Biology, biology.organism_classification, Social group, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Evolutionary biology, Anatomically modern human, [SDE]Environmental Sciences, Upper Paleolithic, Kinship, Mating, 10. No inequality, Social organization, education, Inbreeding, 030217 neurology & neurosurgery
Abstract: Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. Here, we investigate whether the contemporary HG strategy was already present in the Upper Paleolithic (UP), using complete genome sequences from Sunghir, a site dated to ~34 thousand years BP (kya) containing multiple anatomically modern human (AMH) individuals. We demonstrate that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that UP social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.
Published: 2017

37. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Author: Christine Paillard, James D. Scourse, Laurent Chauvaud, Vianney Pichereau, Mickael Perrigault, Clio Der Sarkissian, Ludovic Orlando, Peter Ilsøe, Paul G. Butler, Jón Eiríksson, Catherine Dupont, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Archéologie, Archéosciences, Histoire (CReAAH), Le Mans Université (UM)-Université de Rennes (UR)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), Université de Nantes (UN)-Université de Nantes (UN)-Ministère de la Culture (MC), College of Life and Environmental Sciences [Exeter], University of Exeter, Institute of Earth Sciences [Reykjavik], University of Iceland [Reykjavik], Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la RechercheScientifique, Grant/Award Number:PaleoCOQ, H2020 Marie Skłodowska-CurieActions, Grant/Award Number: FP7-PEOPLE-2013-ITN 604802, LabexMER,Grant/Award Number: ANR-10-LABX-19, Danmarks Grundforskningsfond, Grant/Award Number: DNRF94, UniversiteEuropeenne de Bretagne, Grant/AwardNumber: EPT PROXACHEOBIO, Natur ogUnivers, Det Frie Forskningsrad, Grant/Award Number: 4002-00152B, Chairesd’Attractivite 2014 IDEX, Grant/AwardNumber: OURASI, LabexMER, Grant/AwardNumber: METHOMOL, UK NaturalEnvironment Research Council, Grant/AwardNumber: NE/H023356/1, ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), European Project: 604802,EC:FP7:PEOPLE,FP7-PEOPLE-2013-ITN,ARAMACC(2013), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Nantes Université (NU)-Ministère de la Culture (MC)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Le Mans Université (UM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN)-Le Mans Université (UM)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC)
Subjects: 0106 biological sciences, 0301 basic medicine, DNA, Bacterial, Mitochondrial DNA, Aquatic Organisms, Microbial DNA, Endangered species, high-throughput DNA sequencing, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, DNA sequencing, 03 medical and health sciences, Animal Shells, marine mollusc shells, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Animals, 14. Life underwater, DNA, Ancient, ancient DNA, Ecology, Evolution, Behavior and Systematics, Vibrio, metagenomics, Ecology, ACL, DNA, Sequence Analysis, DNA, DNA extraction, Body Remains, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Ancient DNA, 13. Climate action, Metagenomics, Mollusca, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biotechnology
Abstract: International audience; Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.
Published: 2017

38. Asteroseismology and Gaia : Testing Scaling Relations Using 2200 Kepler Stars with TGAS Parallaxes

Author: Christian L. Sahlholdt, Timothy R. Bedding, William J. Chaplin, Lars A. Buchhave, Jamie Tayar, Savita Mathur, Benoit Mosser, Daniel Huber, Keivan G. Stassun, Aldo Serenelli, Fabienne A. Bastien, Guy R. Davies, Marc H. Pinsonneault, David W. Latham, Mathias Bojsen-Hansen, Rafael A. García, Joel C. Zinn, Dennis Stello, Sanjib Sharma, Victor Silva Aguirre, Sydney Institute for Astronomy (SIfA), The University of Sydney, Department of Astronomy (Ohio State University), Ohio State University [Columbus] (OSU), Department of Physics and Astronomy [Aarhus], Aarhus University [Aarhus], Institute of Space Sciences [Barcelona] (ICE-CSIC), Spanish National Research Council [Madrid] (CSIC), Stellar Astrophysics Centre [Aarhus] (SAC), Department of Astronomy and Astrophysics [PennState], Pennsylvania State University (Penn State), Penn State System-Penn State System, Niels Bohr Institute [Copenhagen] (NBI), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Department of Psychology, St John's University, Research institute of Computer Vision and Robotics [Girona] (VICOROB), Universitat de Girona (UdG), Département d'Astrophysique, de physique des Particules, de physique Nucléaire et de l'Instrumentation Associée (DAPNIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institute for Astronomy [Honolulu], University of Hawai‘i [Mānoa] (UHM), SETI Institute, Vanderbilt University [Nashville], Fisk University, School of Physics [UNSW Sydney] (UNSW), University of New South Wales [Sydney] (UNSW), Center for Exoplanets and Habitable World (CEHW), Space Science Institute [Boulder] (SSI), Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, School of Physics and Astronomy [Birmingham], University of Birmingham [Birmingham], Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Harvard-Smithsonian Center for Astrophysics (CfA), Harvard University-Smithsonian Institution, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Harvard University [Cambridge]-Smithsonian Institution, Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Observatoire de Paris, and PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: oscillations [stars], Infrared, Metallicity, fundamental parameters [stars], FOS: Physical sciences, Astrophysics, 01 natural sciences, Asteroseismology, photometric [techniques], Frequency separation, 0103 physical sciences, distances [stars], 010303 astronomy & astrophysics, Solar and Stellar Astrophysics (astro-ph.SR), ComputingMilieux_MISCELLANEOUS, Earth and Planetary Astrophysics (astro-ph.EP), Physics, [PHYS]Physics [physics], 010308 nuclear & particles physics, Astronomy and Astrophysics, Astrophysics - Astrophysics of Galaxies, Red-giant branch, Stars, Astrophysics - Solar and Stellar Astrophysics, [SDU]Sciences of the Universe [physics], 13. Climate action, Space and Planetary Science, Astrophysics of Galaxies (astro-ph.GA), parallaxes, Orders of magnitude (length), late-type [stars], Parallax, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Astrophysics - Earth and Planetary Astrophysics
Abstract: We present a comparison of parallaxes and radii from asteroseismology and Gaia DR1 (TGAS) for 2200 Kepler stars spanning from the main sequence to the red giant branch. We show that previously identified offsets between TGAS parallaxes and distances derived from asteroseismology and eclipsing binaries have likely been overestimated for parallaxes, Comment: 14 pages, 12 figures, 3 tables, accepted for publication in ApJ. Electronic versions of Tables 1 & 2 are available as ancillary files (sidebar on the right), and source codes are available at https://github.com/danxhuber/isoclassify
Published: 2017

39. Modelling the choice between and the costs of multiple-use vs. specialized forest management

Author: Garcia, Serge, Petucco, Claudio, Thorsen, Bo Jellesmark, Vedel, Suzanne Elizabeth, Laboratoire d'Economie Forestière (LEF), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), European Project: 243950, European Association of Environmental and Resource Economists (EAERE). INT., Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Bureau d'Économie Théorique et Appliquée (BETA), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Luxembourg Institute of Science and Technology (LIST), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), The research leading to these results has received funding from the European Union’s Seventh Framework Program (FP7/2007-2013) under grant agreement NEWFOREX (no.243950)., and ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011)
Subjects: forest, cost function, multiple-use vs. specialized management, [SDV]Life Sciences [q-bio], corner solution, household production model, recursive mixed system
Abstract: International audience; Forests provide ecosystem services jointly with timber production. In some cases, private forest owners implement management actions in order to enhance the provision of such services. They may get direct benefits from this decision such as private amenity values or effects on (e.g., hunting), they may have altruist traits in their utility function for providing public goods (e.g., biodiversity conservation, carbon sequestration), or they may be incited for by a public authority and compensated for the costs. Specifically, this paper focuses on the decision of setting aside forest land. It raises the more general question of the efficiency of multiple-use vs. specialized management of forest lands. Wepropose an econometric analysis to identify factors of the set-aside choice and to measure the impact of this decision on forest management costs. A flexible cost function is modelled and estimated for both types of management. The percentages of old/mature deciduous and old/mature coniferous forests are used as biodiversity and carbon indicators. Results show that the set-aside choice depends on the landowners’ income and on their socio-economic characteristics. Set-aside decision has a significant and positive impact on the managementcosts. This implies that the additional private and public benefits achieved from specialized relative to multiple-use management should exceed this cost premium.
Published: 2017

40. Genetic population structure of harbour seals in the United Kingdom and neighbouring waters

Author: Tange, Olsen Morten, Islas, Valentina, Graves, Jeff A., Onoufriou, Aubrie, Vincent, Cécile, Brasseur, Sophie, Frie, Anne Kirstine, Hall, Ailsa, NERC, University of St Andrews. School of Biology, University of St Andrews. Sea Mammal Research Unit, University of St Andrews. Marine Alliance for Science & Technology Scotland, University of St Andrews. Scottish Oceans Institute, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews [Scotland], Puerto Ángel, Distrito de San Pedro Pochutla, Universidad del Mar, Ciudad Universitaria, School of Biology, Xelect Ltd, Scottish Oceans Institute, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology, IMARES, AD, IMARES, AD, Institute of Marine Research [Norvège], Institute of Marine Research, Sea Mammal Research Unit [University of St Andrews] (SMRU), School of Biology [University of St Andrews], University of St Andrews [Scotland]-University of St Andrews [Scotland]-Natural Environment Research Council (NERC), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), 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), Institute of Marine Research [Bergen] (IMR), and University of Bergen (UiB)
Subjects: GC, QL, QH301 Biology, Seal Management Units, NDAS, coastal, mammal, microsatellite loci, QL Zoology, Mammal, QH301, Onderzoeksformatie, Coastal, Ecosystemen, [SDE]Environmental Sciences, Genetics, genetics, GC Oceanography, Phoca vitulina, Microsatellite loci
Abstract: Natural Environment Research Council (GrantNumber(s): SMRU1001; Grant recipient(s): Ailsa Hall) 1. In the United Kingdom (UK), several harbour seal (Phoca vitulina) populations have been declining over the past decade. In order to understand the effect of these changes in abundance, this study seeks to determine the population structure of harbour seals in the UK, and in Scotland in particular, on a wider and finer spatial scale than has previously been reported. 2. Harbour seals were genotyped from 18 different localities throughout the UK and neighbouring localities in mainland Europe, at 12 microsatellite loci. Results from Bayesian and frequency based tests of population structure suggested an initial structural division into two main groups consisting of localities in northern UK and southern UK-mainland Europe, respectively. 3. These two clusters were further divided into four geographically distinct genetic clusters. 4. An overall agreement between the genetic results and the existing management areas for UK harbour seals was observed, but it is also clear that an adaptive management approach should be adopted, in which the delineation of the current management areas is maintained until further genetic and ecological information has been accumulated and analysed. Publisher PDF
Published: 2017

41. Previously unknown class of metalorganic compounds revealed in meteorites

Author: Régis D. Gougeon, Qing-Zhu Yin, Joshua Wimpenny, Franco Moritz, Alexander Ruf, Zelimir Gabelica, Michael Gonsior, Norbert Hertkorn, Henning Haack, Philippe Schmitt-Kopplin, Marianna Lucio, Mourad Harir, Eric Quirico, Bernhard Michalke, Stefan Ralew, S. N. Shilobreeva, Tomasz Jakubowski, Peter Jenniskens, Vladimir V. Saraykin, Basil Bronsky, Nancy W. Hinman, Basem Kanawati, Chair of Analytical Food Chemistry, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Research Unit Analytical BioGeoChemistry (BGC), Helmholtz-Zentrum München (HZM), University of California Davis, University of California [Davis] (UC Davis), University of California-University of California, Vernadsky Institute of Geochemistry and Analytical Chemistry (GEOKHI), Russian Academy of Sciences [Moscow] (RAS), Moscow Inst Phys & Technol, Dolgoprudnyi, Russia, Ecole Nationale Supérieure de Chimie de Mulhouse, Procédés Alimentaires et Microbiologiques [Dijon] (PAM), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Instytut Matematyki, Wroclaw University of Science and Technology, Centre for Star and Planet Formation (STARPLAN), Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Chesapeake Biological Laboratory (CBL), University of Maryland Center for Environmental Science (UMCES), University of Maryland System-University of Maryland System, SETI Institute, NASA Ames Research Center (ARC), Montana State University (MSU), NASA Cosmochemistry Grant [NNX14AM62G], Emerging Worlds Grant [NNX16AD34D], Technische Universität München [München] (TUM), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre National d'Études Spatiales [Toulouse] (CNES)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Technische Universität München [München] ( TUM ), Research Unit Analytical BioGeoChemistry ( BGC ), Helmholtz-Zentrum München ( HZM ), Vernadsky Institute of Geochemistry and Analytical Chemistry ( GEOKHI ), Russian Academy of Sciences [Moscow] ( RAS ), Procédés Alimentaires et Microbiologiques [Dijon] ( PAM ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Institut de Planétologie et d'Astrophysique de Grenoble ( IPAG ), Observatoire des Sciences de l'Univers de Grenoble ( OSUG ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Centre National de la Recherche Scientifique ( CNRS ), Centre for Star and Planet Formation, University of Copenhagen ( KU ), Chesapeake Biological Laboratory ( CBL ), University of Maryland Center for Environmetal Science, NASA Ames Research Center ( ARC ), and Montana State University ( MSU )
Subjects: Mass-spectrometry, Organic evolution, Mineralogy, 010502 geochemistry & geophysics, 01 natural sciences, meteorites, Astrobiology, Extraterrestrial amino-acids, Molecular level, 0103 physical sciences, Fall, Molecule, metalorganic chemistry, Organic matter, Magnesium, 010303 astronomy & astrophysics, Carbonaceous meteorites, [ SDU.ASTR ] Sciences of the Universe [physics]/Astrophysics [astro-ph], 0105 earth and related environmental sciences, chemistry.chemical_classification, Metalorganic chemistry, Multidisciplinary, Fourier transform ion cyclotron resonance mass spectrometry, astrochemistry, organic evolution, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], Chemistry, Chondrite, Parent body, Meteorite, 13. Climate action, Physical Sciences, Carbon speciation, Organic-matter, Murchison meteorite, Meteorites
Abstract: International audience; The rich diversity and complexity of organic matter found in meteorites is rapidly expanding our knowledge and understanding of extreme environments from which the early solar system emerged and evolved. Here, we report the discovery of a hitherto unknown chemical class, dihydroxymagnesium carboxylates [(OH)(2)MgO2CR](-), in meteoritic soluble organic matter. High collision energies, which are required for fragmentation, suggest substantial thermal stability of these Mg-metalorganics (CHOMg compounds). This was corroborated by their higher abundance in thermally processed meteorites. CHOMg compounds were found to be present in a set of 61 meteorites of diverse petrological classes. The appearance of this CHOMg chemical class extends the previously investigated, diverse set of CHNOS molecules. A connection between the evolution of organic compounds and minerals is made, as Mg released from minerals gets trapped into organic compounds. These CHOMg metalorganic compounds and their relation to thermal processing in meteorites might shed new light on our understanding of carbon speciation at a molecular level in meteorite parent bodies.
Published: 2017

42. Ancient genomic changes associated with domestication of the horse

Author: Christine Keyser, Inna S. Povolotskaya, Antoine Fages, Stefan Rieder, Zainolla Samashev, Ludovic Orlando, Pablo Librado, Markus Neuditschko, Lukas F. K. Kuderna, Bertrand Ludes, Clio Der Sarkissian, Vidhya Jagannathan, Tomas Marques-Bonet, Catherine Thèves, Eske Willerslev, Naveed Khan, Norbert Benecke, Henri-Paul Francfort, Arne Ludwig, Khaled A. S. Al-Rasheid, Saleh A. Alquraishi, Eric Crubézy, Mélanie Pruvost, Mikkel Schubert, Andaine Seguin-Orlando, Cristina Gamba, Tosso Leeb, Sébastien Lepetz, Michael Hofreiter, Ahmed H. Alfarhan, Charleen Gaunitz, Anders Albrechtsen, Aitor Serres-Armero, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Section of Biostatistics [Copenhagen], Department of Public Health [Copenhagen], Institute of Genetics, University of Bern, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Agroscope, Swiss National Stud Farm, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Swiss College of Agriculture, Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Natural Sciences, German Archaeological Institute (DAI), Department of Evolutianory Genetics, Max-Planck-Institut, Max-Planck-Institut-Leibniz Institute for Zoo and Wildlife Research Berlin (IZW), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, Departament de Ciencies Experimentals i de la Salut, Institut Cavanilles de Biodiverstitat i Biologia Evolutiva, University of Copenhagen = Københavns Universitet (KU), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), The German Archaeological Institute, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (UCPH)
Subjects: 0301 basic medicine, Lineage (genetic), [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Breeding, Biology, Quantitative trait locus, DNA, Mitochondrial, Domestication, 03 medical and health sciences, Quantitative Trait, Heritable, Genetic variation, Animals, Horses, DNA, Ancient, Selection, Genetic, 610 Medicine & health, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, Institut für Biochemie und Biologie, Genetic diversity, Genome, Multidisciplinary, 630 Agriculture, Genetic Variation, 030104 developmental biology, Neural Crest, Evolutionary biology, Iron Age, 570 Life sciences, biology, 590 Animals (Zoology), Inbreeding
Abstract: Ancient genomics of horse domestication The domestication of the horse was a seminal event in human cultural evolution. Librado et al. obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestication process. They could also see evidence of admixture with archaic horses and the demography of the domestication process, which included the accumulation of deleterious variants. The horse appears to have undergone a different type of domestication process than animals that were domesticated simply for food. Science , this issue p. 442
Published: 2017

43. Trained-user opinion about welfare quality measures and integrated scoring of dairy cattle welfare

Author: de Graaf, S, Ampe, B., Winckler, C., Radeski, M., Mounier, L., Kirchner, M.K., Haskell, M.J., van Eerdenburg, F J C M, De Boyer Des Roches, A., Andreasen, S.N., Bijttebier, J., Lauwers, L, Verbeke, W., Tuyttens, F.A.M., LS GZ Landbouwhuisdieren, dFAH AVR, Research Institute for Agricultural, Fisheries and Food (ILVO), Department of Agricultural Economic, Faculty of Bioscience Engineering Coupure links, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University Natural Resources et Life Sciences, Faculty of Veterinary Medicine, Animal Welfare Center, University Ss Cyril and Methodius, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Section for Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Scotland's Rural College (SRUC), Department of Farm Animal Health, Utrecht University [Utrecht], Institute for Agricultural and Fisheries Research, Ghent University [Belgium] (UGENT), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Scotland's Rural College (SCUR), Ghent University [Belgium] ( UGENT ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Department of Veterinary and Animal Sciences, ‌Section for Animal Welfare and Disease Control, University of Copenhagen, Scotland’s Rural College, Utrecht University, LS GZ Landbouwhuisdieren, and dFAH AVR
Subjects: Multivariate statistics, bovin, trained-user opinion, media_common.quotation_subject, [SDV]Life Sciences [q-bio], bien-être animal, fiabilité, Logistic regression, computer.software_genre, Sensitivity and Specificity, animal welfare, welfare quality, Animal welfare, Statistics, Genetics, Animals, Welfare Quality, 0501 psychology and cognitive sciences, 050102 behavioral science & comparative psychology, Dairy cattle, Reliability (statistics), media_common, 2. Zero hunger, reliability, [ SDV ] Life Sciences [q-bio], 05 social sciences, 0402 animal and dairy science, Reproducibility of Results, 04 agricultural and veterinary sciences, 040201 dairy & animal science, Dairying, Logistic Models, Ranking, Categorization, welfare assessment, Cattle, Animal Science and Zoology, Data mining, Psychology, Welfare, computer, Food Science
Abstract: The Welfare Quality (WQ) protocol for on-farm dairy cattle welfare assessment describes 27 measures and a stepwise method for integrating values for these measures into 11 criteria scores, grouped further into 4 principle scores and finally into an overall welfare categorization with 4 levels. We conducted an online survey to examine whether trained users' opinions of the WQ protocol for dairy cattle correspond with the integrated scores (criteria, principles, and overall categorization) calculated according to the WQ protocol. First, the trained users' scores (n = 8-15) for reliability and validity and their ranking of the importance of all measures for herd welfare were compared with the degree of actual effect of these measures on the WQ integrated scores. Logistic regression was applied to identify the measures that affected the WQ overall welfare categorization into the "not classified" or "enhanced" categories for a database of 491 European herds. The smallest multivariate model maintaining the highest percentage of both sensitivity and specificity for the "enhanced" category contained 6 measures, whereas the model for "not classified" contained 4 measures. Some of the measures that were ranked as least important by trained users (e.g., measures relating to drinkers) had the highest influence on the WQ overall welfare categorization. Conversely, measures rated as most important by the trained users (e.g., lameness and mortality) had a lower effect on the WQ overall category. In addition, trained users were asked to allocate criterion and overall welfare scores to 7 focal herds selected from the database (n = 491 herds). Data on all WQ measures for these focal herds relative to all other herds in the database were provided. The degree to which expert scores corresponded to each other, the systematic difference, and the correspondence between median trained-user opinion and the WQ criterion scores were then tested. The level of correspondence between expert scoring and WQ scoring for 6 of the 12 criteria and for the overall welfare score was low. The WQ scores of the protocol for dairy cattle thus lacked correspondence with trained users on the importance of several welfare measures.
Published: 2017

44. A test of the hierarchical model of litter decomposition

Author: Aimée T. Classen, Daniel S. Maynard, Thomas W. Crowther, J. Hans C. Cornelissen, Paul Kardol, G F Ciska Veen, David A. Wardle, Mark A. Bradford, Wim H. van der Putten, Anne Bonis, Gregory S. Newman, Grégoire T. Freschet, Stephen A. Wood, Maria Viketoft, Ella M. Bradford, Richard S.P. Logtestijn, William R. Wieder, Marta Manrubia-Freixa, Jonathan R. De Long, Yale University [New Haven], Netherlands Institute of Ecology (NIOO-KNAW), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Rubenstein School Environment and National Resources, University of Vermont [Burlington], Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Vrije Universiteit Amsterdam [Amsterdam] (VU), Institute for Integrative Biology [Zürich] (IBZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), School of Earth and Environmental Sciences [Manchester] (SEES), University of Manchester [Manchester], 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]), Swedish University of Agricultural Sciences (SLU), Yale School Forestry & Environment Studies, Nanyang Technological University [Singapour], National Center for Atmospheric Research [Boulder] (NCAR), The Nature Conservancy, Wageningen University and Research [Wageningen] (WUR), Research was supported by grants to M.A.B. from the US National Science Foundation (DEB-1457614), The Royal Netherlands Academy of Arts and Sciences (Visiting Professors Programme), and the Netherlands Production Ecology & Resource Conservation Programme for Visiting Scientists. G.F.V. was supported by an NWO-VENI from the Netherlands Organisation for Scientific Research (863.14.013). M.M.-F. and W.H.v.d.P. were supported by a European Research Council grant (ERC-Adv 260-55290), and G.T.F. by grant EC2CO-Multivers., Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), 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), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), University of Vermont, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), 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), Wageningen University and Research Centre [Wageningen] (WUR), Terrestrial Ecology (TE), and Systems Ecology
Subjects: 0106 biological sciences, Biogeochemical cycle, Climate, Climate Change, Ecosystem ecology, Climate change, Atmospheric sciences, 010603 evolutionary biology, 01 natural sciences, Hierarchical database model, Decomposer, Carbon cycle, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Decomposition (computer science), SDG 13 - Climate Action, Life Science, Laboratorium voor Nematologie, Ecology, Evolution, Behavior and Systematics, Soil Microbiology, Biomass (ecology), Ecology, 04 agricultural and veterinary sciences, 15. Life on land, Models, Theoretical, PE&RC, Europe, 13. Climate action, international, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, EPS, Laboratory of Nematology
Abstract: International audience; Our basic understanding of plant litter decomposition informs the assumptions underlying widely applied soil biogeochemical models, including those embedded in Earth system models. Confidence in projected carbon cycle-climate feedbacks therefore depends on accurate knowledge about the controls regulating the rate at which plant biomass is decomposed into products such as CO2. Here we test underlying assumptions of the dominant conceptual model of litter decomposition. The model posits that a primary control on the rate of decomposition at regional to global scales is climate (temperature and moisture), with the controlling effects of decomposers negligible at such broad spatial scales. Using a regional-scale litter decomposition experiment at six sites spanning from northern Sweden to southern France-and capturing both within and among site variation in putative controls-we find that contrary to predictions from the hierarchical model, decomposer (microbial) biomass strongly regulates decomposition at regional scales. Furthermore, the size of the microbial biomass dictates the absolute change in decomposition rates with changing climate variables. Our findings suggest the need for revision of the hierarchical model, with decomposers acting as both local- and broad-scale controls on litter decomposition rates, necessitating their explicit consideration in global biogeochemical models.
Published: 2017

45. Less effective selection leads to larger genomes

Author: Tristan Lefébure, Luca Ermini, Lara Konecny-Dupré, Andaine Seguin-Orlando, Cristina Vieira, Clio Der Sarkissian, David Eme, Laurent Guéguen, Ludovic Orlando, Clémentine M. Francois, Florian Mermillod-Blondin, N. Pierre Charrier, Christophe J. Douady, Claire Morvan, Michèle Weiss-Gayet, Laurent Duret, Florian Malard, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Institut National de la Recherche Agronomique (INRA) - Université Claude Bernard Lyon 1 (UCBL) - École Nationale des Travaux Publics de l'État (ENTPE) - Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive (LBBE), Université Claude Bernard Lyon 1 (UCBL) - Institut National de Recherche en Informatique et en Automatique (Inria) - Centre National de la Recherche Scientifique (CNRS), Institut NeuroMyoGène (INMG), Université Claude Bernard Lyon 1 (UCBL) - Université de Lyon - Institut National de la Santé et de la Recherche Médicale (INSERM) - Centre National de la Recherche Scientifique (CNRS), Centre for Geogenetics, Natural History Museum of Denmark - University of Copenhagen (KU), Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria) - Institut National de Recherche en Informatique et en Automatique (Inria), Institut Universitaire de France (IUF), Ministère de l'Éducation nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), 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)-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), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), IN2P3, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Sagot, Marie-France, and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Transposable element, [SDE] Environmental Sciences, Genome size, Genetic Speciation, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Life history theory, 03 medical and health sciences, Negative selection, Effective population size, Phylogenetics, Decapoda, groundwater, Genetics, Asellidae, Animals, Selection, Genetic, Phylogeny, Genetics (clinical), Selection (genetic algorithm), Polymorphism, Genetic, Research, High-Throughput Nucleotide Sequencing, selection efficacy, [SDV] Life Sciences [q-bio], 030104 developmental biology, Mollusca, [SDE]Environmental Sciences, transposable elements, Transcriptome, effective population size, Isopoda, Microsatellite Repeats
Abstract: The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical data sets. Here, we tested this hypothesis using 22 de novo transcriptomes and low-coverage genomes of asellid isopods, which represent 11 independent habitat shifts from surface water to resource-poor groundwater. We show that these habitat shifts are associated with higher transcriptome-wide dN/dS. After ruling out the role of positive selection and pseudogenization, we show that these transcriptome-wide dN/dS increases are the consequence of a reduction in selection efficacy imposed by the smaller effective population size of subterranean species. This reduction is paralleled by an important increase in genome size (25% increase on average), an increase also confirmed in subterranean decapods and mollusks. We also control for an adaptive impact of genome size on life history traits but find no correlation between body size, or growth rate, and genome size. We show instead that the independent increases in genome size measured in subterranean isopods are the direct consequence of increasing invasion rates by repeat elements, which are less efficiently purged out by purifying selection. Contrary to selection efficacy, polymorphism is not correlated to genome size. We propose that recent demographic fluctuations and the difficulty of observing polymorphism variation in polymorphism-poor species can obfuscate the link between effective population size and genome size when polymorphism data are used alone.
Published: 2017

46. Elevation alters ecosystem properties across temperate treelines globally

Author: Maja K. Sundqvist, Jean-Christophe Clément, Aimée T. Classen, Gaku Kudo, Ellen Cieraad, Jordan R. Mayor, Sandra Lavorel, Karl Grigulis, Richard D. Bardgett, Alex Fajardo, Chelsea Chisholm, Ze’ev Gedalof, David A. Wardle, Daniel L. Oberski, Nathan J. Sanders, Michael Bahn, Department Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Rubenstein School Environment and National Resources, University of Vermont, Rocky Mountain Research Station, School of Earth and Environmental Sciences [Manchester] (SEES), University of Manchester [Manchester], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Center Investigation Ecosistemas Patagonia, Universidad Austral de Chile, Umeå University, Institute of Ecology, Technische Universität Berlin (TUB), Landcare Research, Institute Environment Science, Leiden University, Department of Geography, University of Liverpool, Faculty of Environment Earth Science, Hokkaido University, Department of Methodology and Statistic, Utrecht University [Utrecht], Asian School Environment, Nanyang Technological University (NTU), Wallenberg Scholars Award, Fondecyt 1120171, Carlsberg Fund, Danish National Research Foundation, US Department of Energy, Office of Science, Office of Biological and Environmental Research DE-SC0010562, UK Natural Environment Research Council, BiodivERsA project REGARDS ANR-12-EBID-004-01, REGARDS FWF-I-1056, Netherlands Organization for Scientific Research VENI 451-14-017, Natural Sciences and Engineering Research Council of Canada, Department of Forest Ecology and Management, University of Vermont [Burlington], Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Technische Universität Berlin (TU), Manaaki Whenua – Landcare Research [Lincoln], Institute of Environmental Sciences [Leiden] (CML), Hokkaido University [Sapporo, Japan], Asian School of the Environment (ASE), Nanyang Technological University [Singapour], Department of Forest Ecology [Umeå], Rocky Mountain Biological Laboratory, Universität Innsbruck [Innsbruck], Landcare Research, Lincoln, New Zealand, Universiteit Leiden [Leiden], University of Guelph, Leerstoel Klugkist, Methodology and statistics for the behavioural and social sciences, and Laboratoire d'Ecologie Alpine [2016-2019] (LECA [2016-2019])
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Nitrogen, [SDV]Life Sciences [q-bio], Biodiversity, Biology, Forests, 010603 evolutionary biology, 01 natural sciences, Phosphorus metabolism, Trees, Soil, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Taverne, Ecosystem, Nitrogen cycle, Tundra, Soil Microbiology, 0105 earth and related environmental sciences, Multidisciplinary, Ecology, Soil organic matter, Altitude, Temperature, Plant community, Phosphorus, 15. Life on land, Carbon, Plant Leaves, 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem ecology
Abstract: International audience; Temperature is a primary driver of the distribution of biodiversity as well as of ecosystem boundaries. Declining temperature with increasing elevation in montane systems has long been recognized as a major factor shaping plant community biodiversity, metabolic processes, and ecosystem dynamics. Elevational gradients, as thermoclines, also enable prediction of long-term ecological responses to climate warming. One of the most striking manifestations of increasing elevation is the abrupt transitions from forest to treeless alpine tundra However, whether there are globally consistent above-and belowground responses to these transitions remains an open question. To disentangle the direct and indirect effects of temperature on ecosystem properties, here we evaluate replicate treeline ecotones in seven temperate regions of the world. We find that declining temperatures with increasing elevation did not affect tree leaf nutrient concentrations, but did reduce ground-layer community-weighted plant nitrogen, leading to the strong stoichiometric convergence of ground-layer plant community nitrogen to phosphorus ratios across all regions. Further, elevation-driven changes in plant nutrients were associated with changes in soil organic matter content and quality (carbon to nitrogen ratios) and microbial properties. Combined, our identification of direct and indirect temperature controls over plant communities and soil properties in seven contrasting regions suggests that future warming may disrupt the functional properties of montane ecosystems, particularly where plant community reorganization outpaces treeline advance.
Published: 2017

47. Predicting the consequences of species loss using size-structured biodiversity approaches

Author: Brose, Ulrich, Blanchard, Julia L., Eklöf, Anna, Galiana Ibañez, Núria, Hartvig, Martin, Hirt, Myriam R., Kalinkat, Gregor, Nordstrom, Marie C., O'Gorman, Eoin J., Rall, Björn C., Schneider, Florian D., THEBAULT, Elisa, Jacob, Ute, German Centre for Integrative Biodiversity Research (iDiv), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Institute for Marine and Antarctic Studies and Centre for Marine Socioecology, University of Tasmania [Hobart, Australia] (UTAS), Linköping University (LIU), Ecological Networks and Global Change Group, Experimental Ecology Station, 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), 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), Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), National Institute of Aquatic Resources, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Johann-Friedrich Blumenbach Institut für Zoologie und Anthropologie, Georg-August-University = Georg-August-Universität Göttingen, Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Biology and Inland Fisheries, Department of Fish Ecology and Evolution, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Environmental and Marine Biology, Åbo Academy University, Imperial College London, 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), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Institute for Hydrobiology and Fisheries Science, Center for Earth System Research and Sustainability (CEN), University of Hamburg, Research Network Programme of the European Science Foundation on body size and ecosystem dynamics (SIZEMIC), German Centre for integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig - German Research Foundation [FZT 118], Leibniz Competition [SAW-2013-IGB-2], Villum Foundation, Danish National Research Foundation, German Centre for Integrative Biodiversity Research, Faculty of Biology and Pharmacy, Institute of Ecology, Friedrich-Schiller-Universität Jena, University of Tasmania (UTAS), Department of Physics, Chemistry and Biology, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Technical University of Denmark [Lyngby] (DTU), Systemic Conservation Biology Group, J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August-Universität Göttingen, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), École pratique des hautes études (EPHE), Institut de Recherche pour le Développement (IRD [France-Ouest]), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université Paris Diderot - Paris 7 (UPD7), Université Pierre et Marie Curie (Paris 6), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), and Georg-August-University [Göttingen]
Subjects: Food Chain, extinctions, food webs, ecosystem functioning, [SDV]Life Sciences [q-bio], size spectrum, stability, Extinction, Biological, complexity, Ecosystem, global change, allometric scaling, biodiversity
Abstract: Understanding the consequences of species loss in complex ecological communities is one of the great challenges in current biodiversity research. For a long time, this topic has been addressed by traditional biodiversity experiments. Most of these approaches treat species as trait-free, taxonomic units characterizing communities only by species number without accounting for species traits. However, extinctions do not occur at random as there is a clear correlation between extinction risk and species traits. In this review, we assume that large species will be most threatened by extinction and use novel allometric and size-spectrum concepts that include body mass as a primary species trait at the levels of populations and individuals, respectively, to re-assess three classic debates on the relationships between biodiversity and (i) food-web structural complexity, (ii) community dynamic stability, and (iii) ecosystem functioning. Contrasting current expectations, size-structured approaches suggest that the loss of large species, that typically exploit most resource species, may lead to future food webs that are less interwoven and more structured by chains of interactions and compartments. The disruption of natural body-mass distributions maintaining food-web stability may trigger avalanches of secondary extinctions and strong trophic cascades with expected knock-on effects on the functionality of the ecosystems. Therefore, we argue that it is crucial to take into account body size as a species trait when analysing the consequences of biodiversity loss for natural ecosystems. Applying size-structured approaches provides an integrative ecological concept that enables a better understanding of each species' unique role across communities and the causes and consequences of biodiversity loss.
Published: 2017

48. Unveiling information on opportunity costs in REDD: Who obtains the surplus when policy objectives differ?

Author: Charles Palmer, Philippe Delacote, Riyong Kim Bakkegaard, Bo Jellesmark Thorsen, Laboratoire d'Economie Forestière (LEF), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institute of Food and Resource Economics [Copenhagen] (IFRO), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, and FP7 Newforex
Subjects: Economics and Econometrics, Opportunity cost, Asymmetric information, REDD, media_common.quotation_subject, Ecosystem services, Information asymmetry, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q5 - Environmental Economics/Q.Q5.Q56 - Environment and Development • Environment and Trade • Sustainability • Environmental Accounts and Accounting • Environmental Equity • Population Growth, Net income, Economics, deforestation, Opportunity costs, media_common, JEL: H - Public Economics/H.H2 - Taxation, Subsidies, and Revenue/H.H2.H23 - Externalities • Redistributive Effects • Environmental Taxes and Subsidies, Economic rent, 1. No poverty, Redistribution (cultural anthropology), 15. Life on land, Environmental economics, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q5 - Environmental Economics/Q.Q5.Q54 - Climate • Natural Disasters and Their Management • Global Warming, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Payment, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q2 - Renewable Resources and Conservation/Q.Q2.Q23 - Forestry, Payment for environmental services, Welfare, Brazil
Abstract: Improving information about individual opportunity costs of deforestation agents has the potential to increase the efficiency of REDD when it takes the form of a payment for environmental services scheme. However, objectives pursued in REDD projects may vary across policy makers. Within a theoretical framework, this paper explores the impacts of different policy objectives under two opportunity cost settings: asymmetric and full information. For a policy maker aiming to maximize net income from REDD, having full information may not increase the amount of forest conserved but could lead to a redistribution of rents away from agents. By contrast, for an environmental policy maker focused on maximizing the amount of forest conserved under REDD having full information increases the amount of forest conserved while reducing the rents received by agents. For a policy maker pursuing poverty alleviation objectives in REDD-affected communities, having full information makes no difference to overall welfare as rents remain with agents. The amount of deforestation avoided will at least be as high as under asymmetric information. These results are illustrated with data collected on opportunity costs in Amazonas State, Brazil. Improving information about individual opportunity costs of deforestation agents has the potential to increase the efficiency of REDD when it takes the form of a payment for environmental services scheme. However, objectives pursued in REDD projects may vary across policy makers. Within a theoretical framework, this paper explores the impacts of different policy objectives under two opportunity cost settings: asymmetric and full information. For a policy maker aiming to maximize net income from REDD, having full information may not increase the amount of forest conserved but could lead to a redistribution of rents away from agents. By contrast, for an environmental policy maker focused on maximizing the amount of forest conserved under REDD having full information increases the amount of forest conserved while reducing the rents received by agents. For a policy maker pursuing poverty alleviation objectives in REDD-affected communities, having full information makes no difference to overall welfare as rents remain with agents. The amount of deforestation avoided will at least be as high as under asymmetric information. These results are illustrated with data collected on opportunity costs in Amazonas State, Brazil.
Published: 2014

49. The Intracranial Distribution of Gliomas in Relation to Exposure From Mobile Phones: Analyses From the INTERPHONE Study

Author: Per Kragh Andersen, Mary L. McBride, Kirsten Frederiksen, Sarah Fleming, Bruce K. Armstrong, Joachim Schüz, Siegal Sadetzki, Maria Blettner, Maria Feychting, Jack Siemiatycki, Christoffer Johansen, Martine Hours, Kathrine Grell, Alistair Woodward, Anthony J. Swerdlow, Susanna Lagorio, Tore Tynes, Daniel Krewski, Anssi Auvinen, Naohito Yamaguchi, Elisabeth Cardis, Section of Biostatistics [Copenhagen], Department of Public Health [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Aarhus University [Aarhus], Centre International de Recherche contre le Cancer - International Agency for Research on Cancer (CIRC - IARC), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Center for Research in Environmental Epidemiology (CREAL), Universitat Pompeu Fabra [Barcelona] (UPF)-Catalunya ministerio de salud, School of Public Health, University of Sydney, University of Montreal, University of Ottawa [Ottawa], BC Cancer Agency, University of Copenhagen = Københavns Universitet (KU), department of Epidemiology, University of Tampere [Finland], Unité Mixte de Recherche Epidémiologique et de Surveillance Transport Travail Environnement (UMRESTTE UMR T9405), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR), Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), Johannes Gutenberg - Universität Mainz (JGU), Cancer & Radiation Epidemiology Unit, Gertner Institute, Istituto Superiore di Sanità, Tokyo Women's Medical University (TWMU), Epidemiology and Biostatistics, University of Auckland [Auckland], National Institute of Occupational Health (STAMI), National Institute of Occupational Health (STAMI) (STAMI), Institute of Environmental Medicine, Karolinska Institutet [Stockholm], University of Leeds, Epidemiology section, and Institute of Cancer Research in Sutton
Subjects: Adult, Male, medicine.medical_specialty, TELEPHONE, Neoplasms, Radiation-Induced, Time Factors, Epidemiology, Original Contributions, Tumor burden, Brain tumor, Audiology, MOBILE TELEPHONES, 03 medical and health sciences, 0302 clinical medicine, Phone, Risk Factors, Recall bias, EXPOSITION AU RISQUE, CERVEAU, Medicine, Humans, 030212 general & internal medicine, Epidemiologic research, Self report, ONDE, RADIO-FREQUENCY ELECTROMAGNETIC FIELDS, business.industry, Brain Neoplasms, INTERPHONE STUDY, Middle Aged, medicine.disease, Tumor Burden, Mobile phone, 030220 oncology & carcinogenesis, Epidemiologic Research Design, GLIOMA, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, SPATIAL POINT PATTERN, Neoplasm Grading, business, INTRACRANIAL DISTRIBUTION, Cell Phone, TUMEUR
Abstract: When investigating the association between brain tumors and use of mobile telephones, accurate data on tumor position are essential, due to the highly localized absorption of energy in the human brain from the radio-frequency fields emitted. We used a point process model to investigate this association using information that included tumor localization data from the INTERPHONE Study (Australia, Canada, Denmark, Finland, France, Germany, Israel, Italy, Japan, New Zealand, Norway, Sweden, and the United Kingdom). Our main analysis included 792 regular mobile phone users diagnosed with a glioma between 2000 and 2004. Similar to earlier results, we found a statistically significant association between the intracranial distribution of gliomas and the self-reported location of the phone. When we accounted for the preferred side of the head not being exclusively used for all mobile phone calls, the results were similar. The association was independent of the cumulative call time and cumulative number of calls. However, our model used reported side of mobile phone use, which is potentially inuenced by recall bias. The point process method provides an alternative to previously used epidemiologic research designs when one is including localization in the investigation of brain tumors and mobile phone use.; Il s'agit d'explorer la relation entre dose de radiofréquences reçue ds le cerveau lors de l'utilisation de téléphone mobile et la survenue de tumeurs du cerveau.
Published: 2016

50. Early cave art and ancient DNA record the origin of European bison

Author: Frauke Langbein, Joachim Burger, Pere Bover, Vladimir B. Doronichev, Gilles Tosello, Damien A. Fordham, Adam Ben Rohrlach, Jeremy F. Taylor, Kefei Chen, Graham Gower, Ruth Bollongino, Alexander Immel, Federica Fontana, Jared E. Decker, Katerina Douka, Maågorzata Tokarska, David Chivall, Bastien Llamas, Johannes Krause, Michael S. Y. Lee, Thomas Higham, Simon Y. W. Ho, Jan Glimmerveen, Marie-Anne Julien, Colin P. Groves, Antonio Guerreschi, Stephen M. Richards, Robert D. Schnabel, Amelie Scheu, Oleksandra Krotova, Liubov V. Golovanova, Johannes van der Plicht, Gennady F. Baryshnikov, Evelyne Crégut-Bonnoure, Pavel A. Kosintsev, Greger Larson, Rafa Kowalczyk, Ayla L. van Loenen, Ludovic Orlando, Emilia Hofman-Kamińska, Beth Shapiro, Alan Cooper, Julien Soubrier, Kieren J. Mitchell, Carole Fritz, Jean-Denis Vigne, Wolfgang Haak, Oliver Wooley, Isotope Research, Australian Research Council, European Commission, National Science Centre (Poland), Russian Foundation for Basic Research, Danish National Research Foundation, Human Genome Sequencing Center, Baylor College of Medicine (BCM), Baylor University-Baylor University, School of Biological Sciences [Sydney], The University of Sydney, Departament de Biodiversati i Conservacio (IMEDEA, CSIC-UIB), Institut Mediterrani d'Estudis Avançats, Museum Requien, Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), University of Oxford [Oxford], Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Ferrara (UniFE), Research Laboratory for Archaeology and the History of Art, Department of Archaeogenetics [Jena] (DAG), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, University of Southampton, Natl Ukrainian Acad Sci, Inst Archaeol, Dept Stone Age, Kiev, Ukraine, Univ Tubingen, Inst Archaeol Sci Archaeo & Palaeogenet, Tubingen, Germany, Centre for Isotope Research [Groningen] (CIO), University of Groningen [Groningen], Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Faculty of Biomedical and Life Sciences, and University of Glasgow
Subjects: 0301 basic medicine, General Physics and Astronomy, megafauna, Bison priscus, Megafauna, hybridization, Bison bonasus, ComputingMilieux_MISCELLANEOUS, Holocene, Phylogeny, Multidisciplinary, geography.geographical_feature_category, Genome, biology, Bison, Fossils, American Bison, fossil record, Mitochondrial, Pleistocene, Europe, Caves, visual_art, Sequence Analysis, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Evolution, Life on Land, Science, Bison, Pleistocene, fossil record, mitochondrial genome, hybridization, Socio-culturale, Zoology, Steppe bison, DNA, Mitochondrial, Article, General Biochemistry, Genetics and Molecular Biology, Ancient, Evolution, Molecular, 03 medical and health sciences, Paleontology, Cave, Genetics, Pleistocene extinctions, Animals, DNA, Ancient, visual_art.artwork, Cell Nucleus, geography, Human Genome, Molecular, Sequence Analysis, DNA, General Chemistry, DNA, Aurochs, biology.organism_classification, Eurpoean Bison, Bos primigenius, 030104 developmental biology, Ancient DNA, mitochondrial genome, American bison, Genome, Mitochondrial, Commentary, Cattle, Paintings
Abstract: The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (, This research was supported by the Australian Research Council, the European Commission (PIRSES-GA-2009-247652—BIOGEAST), the Polish National Science Centre (N N304 301940 and 2013/11/B/NZ8/00914), the Danish National Research Foundation (DNRF94), the Marie Curie International Outgoing Fellowship (7th European Community Framework Program—MEDITADNA, PIOF-GA-2011-300854, FP7-PEOPLE) and the Russian Foundation for Basic Research (N 15-04-03882).
Published: 2016

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