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109 results on '"The Department of Organismic and Evolutionary Biology"'

1. Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

Author: Pringle, Anne [Harvard Univ., Cambridge, MA (United States). Department of Organismic and Evolutionary Biology]
Published: 2014
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2. The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)

Author: Laura P. Lagomarsino, Alexandre Antonelli, Fabien L. Condamine, Charles C. Davis, Andreas Mulch, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University, University of Gothenburg (GU), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Goethe-University Frankfurt am Main, We thank members of the Davis and Antonelli research groups for helpful feedback, and Suzette Flantua, Elisabeth Forrestel, Carina Hoorn, Daniel Santamaría‐Aguilar, and Zhenxiang Xi for insightful conversations. The directors and curators at the following herbaria provided important access to their collections: BOLV, CR, GB, GH, INB, LPB, MO, MOL, NY, PMA, SCZ, SMF and USZ (acronyms follow the Index Herbariorum, Theirs et al., 2013 (continuously updated)). We are also very thankful for the detailed and insightful comments from two anonymous reviewers and the editors. Funding was provided by a National Science Foundation Doctoral Dissertation Improvement Grant DEB‐1210401 to L.P.L. and C.C.D., by the Swedish Research Council (B05 69601), the European Research Council under the European Union's Seventh Framework Programme (FP/2007‐2013, ERC Grant Agreement no. 331024), and a Wallenberg Academy Fellowship to A.A., by the Carl Tryggers Stiftelse (CTS 12:14) and a Marie Curie Actions (BIOMME project, IOF‐627684) to F.L.C., and by the Department of Organismic and Evolutionary Biology, the Botanical Society of America, the American Society of Plant Taxonomists, the Arnold Arboretum's Deland Award, the Explorer's Club, and the Rockefeller Center for Latin American Studies to L.P.L., European Project: ERC FP/2007‐2013, Harvard University [Cambridge], and Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
Subjects: 0106 biological sciences, 0301 basic medicine, biodiversity hotspot, Neotropics, diversification, Physiology, [SDV]Life Sciences [q-bio], Climate, Climate Change, Biodiversity, Climate change, Andes, Flowers, Plant Science, Biology, Pollination syndrome, 010603 evolutionary biology, 01 natural sciences, Lobelioideae, 03 medical and health sciences, Pollination, Phylogeny, Abiotic component, Plant evolution, Codonopsis, Extinction, Biotic component, rapid radiation, Ecology, Geology, South America, Biological Evolution, Biodiversity hotspot, 030104 developmental biology, ddc:580, pollination syndromes
Abstract: International audience; The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in driving diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 million yr. Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world's biodiversity.
Published: 2016
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3. Landscape of somatic mutations in 560 breast cancer whole-genome sequences

Author: John W.M. Martens, Sandrine Boyault, David Jones, Stefania Tommasi, Jeong-Yeon Lee, Germán Fg Rodríguez-González, Inigo Martincorena, Sung-Min Ahn, Alastair M Thompson, Manasa Ramakrishna, Gilles Thomas, Helen Davies, Savitri Krishnamurthy, Stian Knappskog, Steven Van Laere, Lucy Stebbings, Andrea L. Richardson, Andrew Tutt, Anne Lise Børresen-Dale, Olafur Oa Stefansson, Sunil R. Lakhani, Michiel M. Smid, Gerrit Gk Hooijer, Young Seok Ju, Tari Ta King, Rebecca Shepherd, Luc Dirix, Xavier Pivot, Adam Butler, Aquila Fatima, Peter Pt Simpson, Serena Nik-Zainal, Sancha Martin, Hyung-Yong Kim, Hendrik G. Stunnenberg, Jos Jonkers, Michael R. Stratton, Jon W. Teague, Se Jin Jang, Sandro Morganella, Ville Mustonen, Moritz Gerstung, Gu Kong, Carlos Caldas, Anne Vincent-Salomon, Anieta M. Sieuwerts, Lucy R. Yates, Sarah O’Meara, Peter B. Vermeulen, Dominik Glodzik, Peter Van Loo, Naoto T. Ueno, Arie B. Brinkman, Stuart McLaren, Yang Li, Marc J. van de Vijver, Laura Van't Veer, P. Andrew Futreal, Markus Ringnér, Christos Sotiriou, Ewan Birney, Kamna Ramakrishnan, Miriam Ragle Aure, Johan Staaf, Jane E. Brock, Benita Kiat Tee Bk Tan, Alain Viari, Xueqing Zou, Anita Langerød, David C. Wedge, Hee Jin Lee, Christine Desmedt, Gilles Romieu, Paul N. Span, Jorunn E. Eyfjord, Annegien Broeks, Isabelle Treilleux, Åke Borg, Colin Ca Purdie, Ole Christian Lingjærde, Gert Van den Eynden, John A. Foekens, Serge Dronov, Andrew Menzies, Peter J. Campbell, Iris Pauporté, Ludmil B. Alexandrov, Keiran Raine, The Wellcome Trust Sanger Institute [Cambridge], Lund University [Lund], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Radboud university [Nijmegen], Oslo University Hospital Radiumhospitalet, University of Oslo (UiO), Gachon University Hospital, Génomique Fonctionnelle des Tumeurs Solides (U1162), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Brigham and Women's Hospital [Boston], Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, Breast Cancer Translational Research Laboratory, Institut Jules Bordet [Bruxelles], Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Algemeen Ziekenhuis St Augustinus Oncology, Dana-Farber Cancer Institute [Boston], Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA), University of Ulsan, NASA Johnson Space Center (JSC), NASA, University of Stuttgart, Esso UK Ltd, Department of Exploration, Esso UK Ltd, Department of Computer Science & Engineering [Riverside] (CSE), University of California [Riverside] (UCR), University of California-University of California, Department of Geriatric Medicine [Singapore] (Alexandra Hospital), Institut national du cancer [Boulogne] (INCA), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Department of Pathology [Dundee], Ninewells Hospital and Medical School [Dundee], Canary Institute for Cancer Research (ICIC), Department of Biochemistry and Physiology, Faculty of Health Sciences, University of Las Palmas de Gran Canaria (ULPGC), Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Department of Medical Oncology [Rotterdam], Cancer Genomics Centre, University of Queensland [Brisbane], University of Iceland [Reykjavik], Beckman Research Institute [Duarte, CA], Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Antwerp (UA), European Central Bank (ECB), European Central Bank, Unité de génétique et biologie des cancers (U830), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Tumor Biology, Institut Curie [Paris], University of Cambridge [UK] (CAM), Division of Diagnostic Oncology, Netherlands Cancer Institute, Agendia BV, Breakthrough Breast Cancer Centre, London Institute of Cancer, University of Bergen (UiB), National Cancer Centre Singapore (NCCS), National Cancer Centre Singapore, Division of Molecular Biology, National Institutes of Natural Sciences, The Graduate University for Advanced Studies, Baobab, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), 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), Department of Radiation Oncology 874, Radboud University Medical Center [Nijmegen], Department of Laboratory Medicine, Department Medical Oncology, Department of Pathology, Ospedale 'Mater Salutis', Goddard Earth Sciences and Technology and Research (GESTAR), NASA-Universities Space Research Association (USRA), Department of Molecular Biology [Nijmegen], Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Department of Computing [London], Biomedical Image Analysis Group [London] (BioMedIA), Imperial College London-Imperial College London, Synergie Lyon Cancer [Lyon], Centre Léon Bérard [Lyon], Sagot, Marie-France, Radboud University [Nijmegen], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Nik-Zainal, Serena [0000-0001-5054-1727], Zou, Xueqing [0000-0003-1143-1028], Caldas, Carlos [0000-0003-3547-1489], Apollo - University of Cambridge Repository, Medical Oncology, Harvard University, Fondation Synergie Lyon Cancer [Lyon], CCA -Cancer Center Amsterdam, Pathology, Erasmus University Medical Center [Rotterdam], University of Oslo ( UiO ), Genomique Fonctionnelle des Tumeurs Solides, Université Paris Diderot - Paris 7 ( UPD7 ) -IFR105-Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Netherlands Cancer Institute ( NKI ), Institut Jules Bordet, Academic Medical Center [Amsterdam] ( AMC ), University of Amsterdam [Amsterdam] ( UvA ), NASA Johnson Space Center ( JSC ), Department of Computer Science & Engineering [Riverside] ( CSE ), University of California [Riverside] ( UCR ), Institut national du cancer [Boulogne] ( INCA ), Hôpital Jean Minjoz, Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ), Department of Medical Oncology, Erasmus Medical Center Rotterdam, Josephine Nefkens Institute and Cancer Genomics Centre, University of Las Palmas de Gran Canaria ( ULPGC ), Institut de Recherche en Cancérologie de Montpellier ( IRCM - U1194 Inserm - UM ), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ), Erasmus MC, Beckman Research Institute, Centre de Recherche en Cancérologie de Lyon ( CRCL ), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), University of Antwerp ( UA ), European Central Bank ( ECB ), U 830, Institut National de la Santé et de la Recherche Médicale, Institut Curie, University of Cambridge [UK] ( CAM ), University of Bergen ( UIB ), National Cancer Centre Singapore ( NCCS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale ( ERABLE ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ), Goddard Earth Sciences and Technology and Research ( GESTAR ), NASA-Universities Space Research Association ( USRA ), Department of Organismic and Evolutionary Biology ( OEB ), and Biomedical Image Analysis Group [London] ( BioMedIA )
Subjects: 0301 basic medicine, DNA Replication, Male, Mutation rate, DNA repair, [SDV]Life Sciences [q-bio], DNA Mutational Analysis, Genes, BRCA2, Genes, BRCA1, Breast Neoplasms, Biology, medicine.disease_cause, Genome, Cohort Studies, 03 medical and health sciences, Germline mutation, SDG 3 - Good Health and Well-being, Mutation Rate, medicine, Humans, Gene, Molecular Biology, Genetics, Mutation, Multidisciplinary, [ SDV ] Life Sciences [q-bio], Genome, Human, Recombinational DNA Repair, DNA, Neoplasm, Genomics, Oncogenes, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, Mutagenesis, Human genome, Female, Engineering sciences. Technology
Abstract: Item does not contain fulltext We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
Published: 2016
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4. Etude des notifications à la Maison départementale des personnes handicapées chez les enfants placés à l’Aide sociale àl’enfance dans les Bouches-du-Rhoˆne

Author: L de Montaigne, E. Bosdure, M Soffer, Olivier Bernard, Brigitte Chabrol, D. Da Fonseca, Jean-Christophe Dubus, A. Richardson, Jean Gaudart, Service de Neurologie Pédiatrique, Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Centre de Référence des Maladies Héréditaires du Métabolisme, Génétique des tumeurs (U985), Institut Gustave Roussy (IGR)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Pédopsychiatrie, Hôpital Sainte-Marguerite [CHU - APHM] (Hôpitaux Sud ), Aix Marseille Université (AMU), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U912 INSERM - Aix Marseille Univ - IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University, Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Harvard University [Cambridge], Gaudart, Jean, Assistance Publique - Hôpitaux de Marseille ( APHM ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ) -Centre de Référence des Maladies Héréditaires du Métabolisme, Génétique des tumeurs ( U985 ), Institut Gustave Roussy ( IGR ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpital Sainte-Marguerite [CHU - APHM] ( Hôpitaux Sud ), Aix Marseille Université ( AMU ), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale ( SESSTIM - U912 INSERM - AMU - IRD ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), and Department of Organismic and Evolutionary Biology ( OEB )
Subjects: [ SDV.MP.PAR ] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [MATH.MATH-PR] Mathematics [math]/Probability [math.PR], [ MATH.MATH-DS ] Mathematics [math]/Dynamical Systems [math.DS], [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [MATH.MATH-DS] Mathematics [math]/Dynamical Systems [math.DS], [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 050906 social work, 03 medical and health sciences, 0302 clinical medicine, [STAT.AP] Statistics [stat]/Applications [stat.AP], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, 030225 pediatrics, Political science, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [ MATH.MATH-ST ] Mathematics [math]/Statistics [math.ST], [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, [STAT.AP]Statistics [stat]/Applications [stat.AP], [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [STAT.ME] Statistics [stat]/Methodology [stat.ME], [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [ STAT.AP ] Statistics [stat]/Applications [stat.AP], 05 social sciences, [ SDV.SPEE ] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDE.ES]Environmental Sciences/Environmental and Society, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [ STAT.ME ] Statistics [stat]/Methodology [stat.ME], [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Pediatrics, Perinatology and Child Health, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDE.ES] Environmental Sciences/Environmental and Society, 0509 other social sciences, [ MATH.MATH-PR ] Mathematics [math]/Probability [math.PR], Humanities, [STAT.ME]Statistics [stat]/Methodology [stat.ME], [ SDE.ES ] Environmental Sciences/Environmental and Society, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
Abstract: Resume Introduction Il existe peu d’etudes concernant les problemes medicaux rencontres chez les enfants places a l’Aide sociale a l’enfance (ASE). L’objectif de notre etude etait de decrire la population des mineurs places a l’ASE et ayant fait l’objet d’une notification a la MDPH (Maison departementale des personnes handicapees) des Bouches-du-Rhone au 1er janvier 2014. Patients et methodes Le registre informatique de l’ASE et celui de la MDPH ont ete croises afin d’en extraire les donnees administratives. Apres une analyse des dossiers medicaux MDPH, les informations sur les enfants places (âge gestationnel, deficiences, pathologies) ont ete codees. Resultats Parmi les 2965 mineurs places (0,7 % des mineurs de notre region), 506 (17 %) avaient une notification a la MDPH, contre 2,5 % en population generale. Parmi eux, 80,2 % avaient ete confies suite a une mesure de placement et 50 % des notifications MDPH concernaient les orientations vers un etablissement scolaire et medico-social. On a note 2,1 deficiences par enfant, dont 35,9 % etaient des deficiences du psychisme, 26,4 % des deficiences du langage et de la parole et 21,6 % des deficiences intellectuelles cognitives. Les pathologies rencontrees etaient pour 71 % des troubles mentaux et du comportement. Les enfants les plus jeunes et places en famille d’accueil presentaient plus de pathologies et de deficiences d’organe et peu d’atteintes du psychisme. Les enfants presentant des troubles du comportement etaient en general plus âges et places en foyer. Discussion Le taux de notification MDPH est 7 fois plus eleve parmi les enfants places qu’en population generale. Ce lien entre enfance en danger et handicap est difficile a expliquer, et la psychopathologie des enfants places complexe. Ces resultats illustrent la necessite d’un suivi adapte aux besoins specifiques de ces enfants.
Published: 2015
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5. Differences in xylem and leaf hydraulic traits explain differences in drought tolerance among mature Amazon rainforest trees

Author: Moorcroft, Paul [Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA USA]
Published: 2017
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6. Confronting model predictions of carbon fluxes with measurements of Amazon forests subjected to experimental drought

Author: POWELL, T. I., GALBRAITH, D. R., CHRISTOFFERSEN, B. O., HARPER, A., IMBUZEIRO, H. M. A., ROWLAND, L., ALMEIDA, S., BRANDO, P. M., COSTA, A. C. L. da, COSTA, M. H., LEVINE, N. M., MALHI, Y., SALESKA, S. R., SOTTA, E., WILLIAMS, M., MEIR, P., MOORCROFT, P. R., Thomas L. Powell, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA, Patrick Meir, School of GeoSciences, University of Edinburgh, Edinburgh, EH8 9XP, UK, Paul R. Moorcroft, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA., Paulo M. Brando, Instituto de Pesquisa Ambiental da Amazônia, CEP 71503-505, Brasilia, Distrito Federal, Brazil, Naomi M. Levine, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA, David R. Galbraith, School of Geography, University of Leeds, Leeds, LS2 9JT, UK, Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK, Bradley O. Christoffersen, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, Anna Harper, College of Engineering, Mathematics, and Physical Science, University of Exeter, Exeter, EX4 4QF, UK, Department of Atmospheric Science, Colorado State University, Fort Collins, CO 80523, USA, Antonio Carlos Lola da Costa, Centro de Geociências, Universidade Federal do Para, Belem, CEP 66017-970, Para, Brazil, Hewlley M. A. Imbuzeiro, Grupo de Pesquisas em Interação Atmosfera-Biosfera, Universidade Federal de Vicosa, Vicosa, CEP 36570-000, Minas Gerias, Brazil, Marcos Heil Costa, Grupo de Pesquisas em Interac~ao Atmosfera-Biosfera, Universidade Federal de Vicosa, Vicosa, CEP 36570-000, Minas Gerias, Brazil, Samuel Almeida, Museu Paraense Emilio Goeldi, Belem, CEP 66077-530, Para, Brazil, Yadvinder Malhi, Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK, Scott R. Saleska, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, ELENEIDE DOFF SOTTA, CPAF-AP, Lucy Rowland, School of GeoSciences, University of Edinburgh, Edinburgh, EH8 9XP, UK, and Mathew Williams, School of GeoSciences, University of Edinburgh, Edinburgh, EH8 9XP, UK
Subjects: Tropical rainforest, Terrestrial biosphere model, carbon cycle, Ciclo do cabono, Modelo de biosfera terrestre, Floresta tropical
Abstract: Considerable uncertainty surrounds the fate of Amazon rainforests in response to climate change. Here, carbon (C) flux predictions of five terrestrial biosphere models (Community Land Model version 3.5 (CLM3.5), Ecosystem Demography model version 2.1 (ED2), Integrated BIosphere Simulator version 2.6.4 (IBIS), Joint UK Land Environment Simulator version 2.1 (JULES) and Simple Biosphere model version 3 (SiB3)) and a hydrodynamic terrestrial ecosystem model (the Soil?Plant?Atmosphere (SPA) model) were evaluated against measurements from two large-scale Amazon drought experiments. Model predictions agreed with the observed C fluxes in the control plots of both experiments, but poorly replicated the responses to the drought treatments. Most notably, with the exception of ED2, the models predicted negligible reductions in aboveground biomass in response to the drought treatments, which was in contrast to an observed c. 20% reduction at both sites. For ED2, the timing of the decline in aboveground biomass was accurate, but the magnitude was too high for one site and too low for the other. Three key findings indicate critical areas for future research and model development. First, the models predicted declines in autotrophic respiration under prolonged drought in contrast to measured increases at one of the sites. Secondly, models lacking a phenological response to drought introduced bias in the sensitivity of canopy productivity and respiration to drought. Thirdly, the phenomenological water-stress functions used by the terrestrial biosphere models to represent the effects of soil moisture on stomatal conductance yielded unrealistic diurnal and seasonal responses to drought.
Published: 2013

7. Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life

Author: Raquel López-Antoñanzas, Jonathan Mitchell, Tiago R. Simões, Fabien L. Condamine, Robin Aguilée, Pablo Peláez-Campomanes, Sabrina Renaud, Jonathan Rolland, Philip C. J. Donoghue, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), West Virginia University [Morgantown], Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), School of Earth Sciences [Bristol], University of Bristol [Bristol], ANR-22-CE02-0022,RoMa,Macroévolution des rongeurs dans le contexte des changements environnementaux majeurs du Miocène(2022), Ministerio de Ciencia e Innovación (España), and National Research Council of Canada
Subjects: macroevolution, General Immunology and Microbiology, morphometrics, Evolution, molecular clock, Biodiversity, [SDV.BID]Life Sciences [q-bio]/Biodiversity, phylogeny, morphological clock, General Biochemistry, Genetics and Molecular Biology, Palaeobiogeography, taxonomy, palaeobiogeography, evolution, Morphological clock, Macroevolution, Morphometrics, General Agricultural and Biological Sciences, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Phylogeny, Taxonomy, biodiversity
Abstract: The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms., ANR-AAPG 2022. PGC2018-094122-B-100 (MICU/AEI/FEDER, EU). National Science and Engineering Research Council of Canada (NSERC) postdoctoral fellowship to T.R.S.
Published: 2022
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8. Testing the Münch hypothesis of long distance phloem transport in plants

Author: Holbrook, N. [Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States]
Published: 2016
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9. Understanding the uncertainty in global forest carbon turnover

Author: T. A. M. Pugh, T. Rademacher, S. L. Shafer, J. Steinkamp, J. Barichivich, B. Beckage, V. Haverd, A. Harper, J. Heinke, K. Nishina, A. Rammig, H. Sato, A. Arneth, S. Hantson, T. Hickler, M. Kautz, B. Quesada, B. Smith, K. Thonicke, School of Geography, Earth and Environmental Sciences [Birmingham], University of Birmingham [Birmingham], Birmingham Institute of Forest Research (BIFoR), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University [Flagstaff], Center for Ecosystem Science and Society (ECOSS), Geosciences and Environmental Climate Change Science Center, United States Geological Survey [Reston] (USGS), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Universidad Austral de Chile, University of Vermont [Burlington], CSIRO Oceans and Atmosphere, CISRO Oceans and Atmosphere, College of Engineering, Mathematics and Physical Sciences [Exeter] (EMPS), University of Exeter, Potsdam Institute for Climate Impact Research (PIK), National Institute for Environmental Studies (NIES), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), DEPARTMENT OF EARTH SYSTEM SCIENCES UNIVERSITY OF CALIFORNIA IRVINE CA USA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Forest Research Institute Baden-Württemberg - Forstliche Versuchs- und Forschungsanstalt Baden-Württemberg, Universidad del Rosario [Bogota], DEPARTMENT OF PHYSICAL GEOGRAPHY AND ECOSYSTEM SCIENCE LUND UNIVERSITY SWE, Western Sydney University, Seventh Framework Programme, FP7: 50 603542 European Research Council, ERC: 758873 Centre National de la Recherche Scientifique, CNRS Svenska ForskningsrÃ¥det Formas: 211-2009-1682 Helmholtz Association Centre National de la Recherche Scientifique, CNRS, Financial support. This research has been supported by the Euro, pean Commission, European Research Council (TreeMort – grant no. 758873), Seventh Framework Programme (LUC4C – grant no. 50 603542), the Svenska Forskningsrådet Formas (Dnr. 211-2009-1682 and the strategic research areas BECC and MERGE), the Helmholtz Association ATMO programme, the Centre National de la Recherche Scientifique (CNRS) of France through the programme 'Make Our Planet Great Again', the U.S. Geological Survey Land Change Science Program, and the Helmholtz Alliance 'Remote Sensing and Earth System Dynamics'., Harvard University, and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Environmental change, lcsh:Life, 01 natural sciences, Carbon cycle, lcsh:QH540-549.5, ddc:550, Baseline (configuration management), Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Earth-Surface Processes, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Biomass (ecology), lcsh:QE1-996.5, Biosphere, Soil carbon, 15. Life on land, Plant functional type, lcsh:Geology, Earth sciences, lcsh:QH501-531, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, 13. Climate action, Turnover, lcsh:Ecology, Physical geography, 010606 plant biology & botany
Abstract: The length of time that carbon remains in forest biomass is one of the largest uncertainties in the global carbon cycle, with both recent historical baselines and future responses to environmental change poorly constrained by available observations. In the absence of large-scale observations, models used for global assessments tend to fall back on simplified assumptions of the turnover rates of biomass and soil carbon pools. In this study, the biomass carbon turnover times calculated by an ensemble of contemporary terrestrial biosphere models (TBMs) are analysed to assess their current capability to accurately estimate biomass carbon turnover times in forests and how these times are anticipated to change in the future. Modelled baseline 1985–2014 global average forest biomass turnover times vary from 12.2 to 23.5 years between TBMs. TBM differences in phenological processes, which control allocation to, and turnover rate of, leaves and fine roots, are as important as tree mortality with regard to explaining the variation in total turnover among TBMs. The different governing mechanisms exhibited by each TBM result in a wide range of plausible turnover time projections for the end of the century. Based on these simulations, it is not possible to draw robust conclusions regarding likely future changes in turnover time, and thus biomass change, for different regions. Both spatial and temporal uncertainty in turnover time are strongly linked to model assumptions concerning plant functional type distributions and their controls. Thirteen model-based hypotheses of controls on turnover time are identified, along with recommendations for pragmatic steps to test them using existing and novel observations. Efforts to resolve uncertainty in turnover time, and thus its impacts on the future evolution of biomass carbon stocks across the world's forests, will need to address both mortality and establishment components of forest demography, as well as allocation of carbon to woody versus non-woody biomass growth.
Published: 2020
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10. Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

Author: Ivana Cvijovic, Alief Moulana, Angela M Phillips, Thomas Dupic, Thierry Mora, Michael M. Desai, Katherine R. Lawrence, Milo S Johnson, Aleksandra M. Walczak, Jeffrey Chang, Laboratoire de physique de l'ENS - ENS Paris (LPENS (UMR_8023)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Université Paris Diderot - Paris 7 (UPD7), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University, Massachusetts Institute of Technology (MIT), Department of Physics [Harvard University], Stanford University, Physique Statistique et Inférence pour la Biologie, Laboratoire de physique de l'ENS - ENS Paris (LPENS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Département de Physique de l'ENS-PSL, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), 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)-Département de Physique de l'ENS-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), and European Project: 724208,STRUGGLE
Subjects: epistasis, [SDV]Life Sciences [q-bio], Antibody Affinity, S. cerevisiae, Antibodies, Viral, 01 natural sciences, Germline, 0302 clinical medicine, antibody, Biology (General), Antigens, Viral, [PHYS]Physics [physics], 0303 health sciences, General Neuroscience, General Medicine, Orthomyxoviridae, 3. Good health, Influenza Vaccines, Medicine, breadth, Antibody, influenza, Research Article, QH301-705.5, Science, Computational biology, Biology, 010402 general chemistry, General Biochemistry, Genetics and Molecular Biology, Cell Line, 03 medical and health sciences, Antigen, CR6261, evolution, Animals, Humans, 030304 developmental biology, Evolutionary Biology, General Immunology and Microbiology, Epistasis, Genetic, landscape, 0104 chemical sciences, Evolutionary biology, Mutation, biology.protein, Epistasis, 030217 neurology & neurosurgery, Broadly Neutralizing Antibodies
Abstract: Over the past two decades, several broadly neutralizing antibodies (bnAbs) that confer protection against diverse influenza strains have been isolated1,2. Structural and biochemical characterization of these bnAbs has provided molecular insight into how they bind distinct antigens1. However, our understanding of the evolutionary pathways leading to bnAbs, and thus how best to elicit them, remains limited. Here, we measure equilibrium dissociation constants of combinatorially complete mutational libraries for two naturally isolated influenza bnAbs3–5 (CR-9114, 16 mutations; CR-6261, 11 mutations), reconstructing all possible intermediates back to the unmutated germline sequences. We find that these two libraries exhibit strikingly different patterns of breadth: while many variants of CR-6261 display moderate affinity to diverse antigens, those of CR-9114 display appreciable affinity only in specific, nested combinations. By examining the extensive pairwise and higher-order epistasis between mutations, we find key sites with strong synergistic interactions that are highly similar across antigens for CR-6261 and different for CR-9114. Together, these features of the binding affinity landscapes strongly favor sequential acquisition of affinity to diverse antigens for CR-9114, while the acquisition of breadth to more similar antigens for CR-6261 is less constrained. These results, if generalizable to other bnAbs, may explain the molecular basis for the widespread observation that sequential exposure favors greater breadth6–8, and such mechanistic insight will be essential for predicting and eliciting broadly protective immune responses.
Published: 2021
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11. Spatiotemporal sensitivity of thermal stress for monitoring canopy hydrological stress in near real-time

Author: Bijan Seyednasrollah, James S. Clark, Jean-Christophe Domec, Department of Organismic and Evolutionary Biology, Harvard University [Cambridge], School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University [Flagstaff], Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Nicholas School of the Environment, and Duke University [Durham]
Subjects: 0106 biological sciences, Canopy, Atmospheric Science, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], evapotranspiration, Energy balance, Flux, Atmospheric sciences, 01 natural sciences, Stress (mechanics), remote sensing, Hydrology (agriculture), Evapotranspiration, 0105 earth and related environmental sciences, Global and Planetary Change, Forestry, Vegetation, 15. Life on land, thermal stress, 13. Climate action, [SDE]Environmental Sciences, Soil water, bayesian, hierarchical modeling, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Monitoring drought in real-time using minimal field data is a challenge for ecosystem management and conservation. Most methods require extensive data collection and in-situ calibration and accuracy is difficult to evaluate. Here, we demonstrated how the space-borne canopy "thermal stress", defined as surface-air temperature difference, provides a reliable surrogate for drought-induced water stress in vegetation. Using physics-based relationships that accommodate uncertainties, we showed how changes in canopy water flux from ground-based measurements relate to both the surface energy balance and remotely-sensed thermal stress. Field measurements of evapotranspiration in the southeastern and northwestern US verify this approach based on sensitivity of evapotranspiration to thermal stress in a large range of atmospheric and climate conditions. We found that a 1 degrees C change in the thermal stress is comparable to 1-1.2 mm day(-1) of evapotranspiration, depending on site and climate conditions. We quantified temporal and spatial sensitivity of evapotranspiration to the thermal stress and showed that it has the strongest relationship with evapotranspiration during warm and dry seasons, when monitoring drought is essential. Using only air and surface temperatures, we predicted the inter-annual anomaly in thermal stress across the contiguous United States over the course of 15 years and compared it with conventional drought indices. Among drought metrics that were considered in this study, the thermal stress had the highest correlation values. Our sensitivity results demonstrated that the thermal stress is a particularly strong indicator of water-use in warm seasons and regions. This simple metric can be used at varying time-scales to monitor surface evapotranspiration and drought in large spatial extents in near real-time.
Published: 2019
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12. Self-organized biotectonics of termite nests

Author: Alexander Heyde, Guy Theraulaz, Lijie Guo, Lakshminarayanan Mahadevan, Christian Jost, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-CHU Toulouse [Toulouse]-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), Centre de Recherches sur la Cognition Animale - UMR5169 (CRCA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Mind & Brain Institut (TMBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, and Theraulaz, Guy
Subjects: 0106 biological sciences, 0301 basic medicine, [INFO.INFO-CC]Computer Science [cs]/Computational Complexity [cs.CC], Theoretical computer science, ecophysiology, [SDV.NEU.PC] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, morphogenesis, collective animal behavior, Isoptera, 010603 evolutionary biology, 01 natural sciences, Stigmergy, Nesting Behavior, 03 medical and health sciences, [NLIN.NLIN-AO] Nonlinear Sciences [physics]/Adaptation and Self-Organizing Systems [nlin.AO], Nest, termite nests, Animals, Architecture, [NLIN.NLIN-AO]Nonlinear Sciences [physics]/Adaptation and Self-Organizing Systems [nlin.AO], stigmergy, Multidisciplinary, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Models, Theoretical, Tree traversal, 030104 developmental biology, Physical Sciences, [INFO.INFO-CC] Computer Science [cs]/Computational Complexity [cs.CC], Collective animal behavior, Tomography, X-Ray Computed
Abstract: International audience; The termite nest is one of the architectural wonders of the living world, built by the collective action of workers in a colony. Each nest has several characteristic structural motifs that allow for efficient ventilation, cooling, and traversal. We use tomography to quantify the nest architecture of the African termite Apicotermes lamani , consisting of regularly spaced floors connected by scattered linear and helicoidal ramps. To understand how these elaborate structures are built and arranged, we formulate a minimal model for the spatiotemporal evolution of three hydrodynamic fields—mud, termites, and pheromones—linking environmental physics to collective building behavior using simple local rules based on experimental observations. We find that floors and ramps emerge as solutions of the governing equations, with statistics consistent with observations of A. lamani nests. Our study demonstrates how a local self-reinforcing biotectonic scheme is capable of generating an architecture that is simultaneously adaptable and functional, and likely to be relevant for a range of other animal-built structures.
Published: 2021
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13. Population variation in miRNAs and isomiRs and their impact on human immunity to infection

Author: Lluis Quintana-Murci, Katherine J. Siddle, Maxime Rotival, Julien Pothlichet, Martin Silvert, Hélène Quach, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Ecole Doctorale Complexité du Vivant (ED515), Sorbonne Université (SU), Chaire Génomique humaine et évolution, Collège de France (CdF (institution)), The laboratory of L.Q.-M. is supported by the Institut Pasteur, the Collège de France, the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10- LABX-62-IBEID) and 'Milieu Intérieur' (ANR-10-LABX-69-01), and the Fondation pour la Recherche Médicale (Equipe FRM DEQ20180339214). This project was funded by the European Research Council under the European Union’s Seventh Framework Programme (FP/2007–2013)/ERC grant agreement 281297., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), European Project: 281297,EC:FP7:ERC,ERC-2011-StG_20101109,EVOIMMUNOPOP(2012), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Harvard University, and Collège de France - Chaire Génomique humaine et évolution
Subjects: Gene isoform, lcsh:QH426-470, Quantitative Trait Loci, Population, miR-QTLs, Black People, Biology, Infections, Monocytes, White People, 03 medical and health sciences, 0302 clinical medicine, IsomiR, Immune system, microRNA, RNA Isoforms, Humans, education, lcsh:QH301-705.5, Gene, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Genome, Human, Research, Immunity, TLR7, Human genetics, MicroRNAs, lcsh:Genetics, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, lcsh:Biology (General), 030220 oncology & carcinogenesis, miRNAs, Isoforms
Abstract: Background MicroRNAs (miRNAs) are key regulators of the immune system, yet their variation and contribution to intra- and inter-population differences in immune responses is poorly characterized. Results We generate 977 miRNA-sequencing profiles from primary monocytes from individuals of African and European ancestry following activation of three TLR pathways (TLR4, TLR1/2, and TLR7/8) or infection with influenza A virus. We find that immune activation leads to important modifications in the miRNA and isomiR repertoire, particularly in response to viral challenges. These changes are much weaker than those observed for protein-coding genes, suggesting stronger selective constraints on the miRNA response to stimulation. This is supported by the limited genetic control of miRNA expression variability (miR-QTLs) and the lower occurrence of gene-environment interactions, in stark contrast with eQTLs that are largely context-dependent. We also detect marked differences in miRNA expression between populations, which are mostly driven by non-genetic factors. On average, miR-QTLs explain approximately 60% of population differences in expression of their cognate miRNAs and, in some cases, evolve adaptively, as shown in Europeans for a miRNA-rich cluster on chromosome 14. Finally, integrating miRNA and mRNA data from the same individuals, we provide evidence that the canonical model of miRNA-driven transcript degradation has a minor impact on miRNA-mRNA correlations, which are, in our setting, mainly driven by co-transcription. Conclusion Together, our results shed new light onto the factors driving miRNA and isomiR diversity at the population level and constitute a useful resource for evaluating their role in host differences of immunity to infection.
Published: 2020
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14. Development and growth of the pelvic fin in the extant coelacanth Latimeria chalumnae

Author: Mathieu Santin, Paul Tafforeau, Marc Herbin, Gaël Clément, Hugo Dutel, Rohan Mansuit, Anthony Herrel, Centre de Recherche en Paléontologie - Paris (CR2P), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Laboratory for evolutionary morphology, Kobe University, European Synchrotron Radiation Facility (ESRF), Centre de Neuro-Imagerie de Recherche (CENIR), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Center for NeuroImaging Research-Human MRI Neuroimaging core facility for clinical research [ICM Paris] (CENIR), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Histology, Pelvis, 03 medical and health sciences, Endoskeleton, 0302 clinical medicine, medicine, Animals, Coelacanth, Ecology, Evolution, Behavior and Systematics, Phylogeny, ComputingMilieux_MISCELLANEOUS, Appendage, Pelvic girdle, biology, Ossification, Fossils, Latimeria, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Fish fin, Fishes, Actinistia, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, Anatomy, biology.organism_classification, Biological Evolution, Magnetic Resonance Imaging, 030104 developmental biology, Animal Fins, medicine.symptom, 030217 neurology & neurosurgery, Biotechnology
Abstract: The ontogeny of the paired appendages has been extensively studied in lungfishes and tetrapods, but remains poorly known in coelacanths. Recent work has shed light on the anatomy and development of the pectoral fin in Latimeria chalumnae. Yet, information on the development of the pelvic fin and girdle is still lacking. Here, we described the development of the pelvic fin and girdle in Latimeria chalumnae based on 3D reconstructions generated from conventional and X-ray synchrotron microtomography, as well as MRI acquisitions. As in other jawed vertebrates, the development of the pelvic fin occurs later than that of the pectoral fin in Latimeria. Many elements of the endoskeleton are not yet formed at the earliest stage sampled. The four mesomeres are already formed in the fetus, but only the most proximal radial elements (preaxial radial 0-1) are formed and individualized at this stage. We suggest that all the preaxial radial elements in the pelvic and pectoral fin of Latimeria are formed through the fragmentation of the mesomeres. We document the progressive ossification of the pelvic girdle, and the presence of a trabecular system in the adult. This trabecular system likely reinforces the cartilaginous girdle to resist the muscle forces exerted during locomotion. Finally, the presence of a preaxial element in contact with the pelvic girdle from the earliest stage of development onward questions the mono-basal condition of the pelvic fin in Latimeria. However, the particular shape of the mesomeres may explain the presence of this element in contact with the girdle.
Published: 2020
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15. How Does Masticatory Muscle Architecture Covary with Mandibular Shape in Domestic Dogs?

Author: Cécile Callou, Jacques Barrat, Elodie Monchâtre-Leroy, Colline Brassard, Marilaine Merlin, Claude Guintard, Raphaël Cornette, Anthony Herrel, Muséum national d'Histoire naturelle (MNHN), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), SIERDAH, Laboratoire de la rage et pathologie des animaux sauvages (LERPAS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), and Harvard University [Cambridge]
Subjects: 0106 biological sciences, 0301 basic medicine, Muscle size, [SDV]Life Sciences [q-bio], Mandible, Anatomy, Biology, 010603 evolutionary biology, 01 natural sciences, Masticatory force, 03 medical and health sciences, Skull, 030104 developmental biology, medicine.anatomical_structure, Form and function, medicine, Masticatory muscle, Mastication, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Muscle force
Abstract: Despite the considerable scientific interest in the variability and patterns of integration in the dog skull, how these patterns impact or are driven by function remains largely unexplored. Since the mandible is directly involved in mastication, it can be expected to be directly related to the development of the adductor and abductor muscles. Here, we explore whether variation in the architecture and size of the masticatory muscles is associated with the variation in mandibular shape in dogs. We obtained muscle data from the dissection of 48 dogs from different breeds and morphotypes to explore the architecture of the muscles and used 3D geometric morphometric approaches to quantify the shape of the mandible. Covariations between the masticatory muscles and mandibular shape were explored using two-block partial least square analyses (2B-PLS). Our results show there is a strong covariation between mandibular shape and masticatory muscles mass (rPLS from 0.70 to 0.74 for the first axis representing more than 90% of the total covariance) and physiological cross-sectional area (rPLS from 0.64 to 0.73 for the first axis representing more than 80% of the total covariance), irrespective of whether size is taken into account or not. These results suggest muscle size and thus attachment area requirements for individual muscles are likely drivers of mandibular shape. Moreover, mandible shape is likely to be a good predictor of muscle force. Finally, it appears that domestication of dogs has not resulted in a disuse phenotype characterized by a decoupling between form and function.
Published: 2020
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16. Evolving Teeth Within a Stable Masticatory Apparatus in Orkney Mice

Author: Ronan Ledevin, Louise Souquet, Lionel Hautier, Sabrina Renaud, Sylvie Agret, Anthony Herrel, Helder Gomes Rodrigues, Samuel Ginot, Julien Claude, PaleoEnvironnements et PaleobioSphere (PEPS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Paléontologie-Paléobiologie-Phylogénie (UMR CNRS 5554), Université Montpellier 2 - Sciences et Techniques (UM2), 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), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], and Museum of Zoology, University of Cambridge
Subjects: 0106 biological sciences, 0301 basic medicine, Molar, Morphometrics, Orthodontics, geography, geography.geographical_feature_category, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Mandible, Biology, 010603 evolutionary biology, 01 natural sciences, Masticatory force, Bite force quotient, stomatognathic diseases, 03 medical and health sciences, 030104 developmental biology, Biting, stomatognathic system, Archipelago, Mastication, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics
Abstract: Mice from the Orkney archipelago exhibit an important diversity regarding molar shape. While on some islands mice display a usual dental pattern, teeth from other islands display additional cusplets and unusual phenotypes that may constitute case studies for evaluating the potential functional relevance of dental changes. We developed a multifaceted approach combining 2D and 3D geometric morphometrics, dental topography, dental wear, biomechanics, estimations of masticatory muscles force, and in vivo bite force on wild-derived lab descendants exemplifying the two extreme dental morphologies. The two strains differed in the geometry of the upper and lower tooth rows, and in the topography of the upper row only. Surprisingly, the most unusual tooth morphology appeared as the least complex because tooth simplification overwhelmed the signal provided by the occurrence of additional cusplets. No difference in bite force nor muscle force was evidenced, showing that the important change in dental morphology was accommodated without major changes in the rest of the masticatory apparatus. The evolution of unusual dental phenotypes was possibly fueled by drift and inbreeding in small and isolated populations on remote islands of the archipelago. No functional counter-selection impeded this diversification, since the unusual dental phenotypes did not disrupt occlusion and mastication.
Published: 2018
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17. Iso/Anisohydry: A Plant–Environment Interaction Rather Than a Simple Hydraulic Trait

Author: Uri Hochberg, Fulton E. Rockwell, N. Michele Holbrook, Hervé Cochard, Department of Organismic and Evolutionary Biology, Harvard University, Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Harvard University [Cambridge], and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, Ecological niche, anisohydric, Management science, isohydric, Foundation (engineering), Water, Plant Science, 15. Life on land, Biology, 01 natural sciences, Terminology, Plant Leaves, 03 medical and health sciences, 030104 developmental biology, Plant Stomata, Trait, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Vitis, Plant Physiological Phenomena, hydraulic, 010606 plant biology & botany, Simple (philosophy)
Abstract: International audience; Plants are frequently classified as isohydric or anisohydric in an attempt to portray their water relations strategy or ecological niche. However, despite the popularity of the iso/anisohydric classification, the underlying biology remains unclear. We use here a simple hydraulic model and the extensive literature on grapevine hydraulics to illustrate that the iso/anisohydric classification of a plant depends on the definition used and the environment in which it is grown, rather than describing an intrinsic property of the plant itself. We argue that abandoning the iso/anisohydric terminology and returning to a more fundamental hydraulic framework would provide a stronger foundation for species comparisons and ecological predictions.
Published: 2018
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18. Three-axis optical force plate for studies in small animal locomotor mechanics

Author: Hsieh, S [Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 (United States)]
Published: 2006
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19. Diversity buffers winegrowing regions from climate change losses

Author: Thierry Lacombe, Benjamin I. Cook, Cornelis van Leeuwen, Elizabeth M. Wolkovich, Amber Parker, Ignacio Morales-Castilla, Kimberly A. Nicholas, Iñaki García de Cortázar-Atauri, Universidad de Alcalá - University of Alcalá (UAH), Harvard University [Cambridge], Department of Organismic and Evolutionary Biology, Agroclim (AGROCLIM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), Columbia University [New York], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lincoln University, Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lund University Centre for Sustainability Studies (LUCSUS), and University of British Columbia (UBC)
Subjects: Climate Change, [SDV]Life Sciences [q-bio], Climate change, phenology, Intraspecific competition, Crop, 03 medical and health sciences, agrobiodiversity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Vitis, Cultivar, resilience, climate change adaptation, 030304 developmental biology, agriculture, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Agroforestry, business.industry, Phenology, 04 agricultural and veterinary sciences, Biodiversity, 15. Life on land, Adaptation, Physiological, Geography, SI Correction, 13. Climate action, Agriculture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Agricultural biodiversity, Seasons, business, Diversity (business)
Abstract: Agrobiodiversity—the variation within agricultural plants, animals, and practices—is often suggested as a way to mitigate the negative impacts of climate change on crops [S. A. Woodet al.,Trends Ecol. Evol.30, 531–539 (2015)]. Recently, increasing research and attention has focused on exploiting the intraspecific genetic variation within a crop [Hajjaret al.,Agric. Ecosyst. Environ.123, 261–270 (2008)], despite few relevant tests of how this diversity modifies agricultural forecasts. Here, we quantify how intraspecific diversity, via cultivars, changes global projections of growing areas. We focus on a crop that spans diverse climates, has the necessary records, and is clearly impacted by climate change: winegrapes (predominantlyVitis viniferasubspeciesvinifera). We draw on long-term French records to extrapolate globally for 11 cultivars (varieties) with high diversity in a key trait for climate change adaptation—phenology. We compared scenarios where growers shift to more climatically suitable cultivars as the climate warms or do not change cultivars. We find that cultivar diversity more than halved projected losses of current winegrowing areas under a 2 °C warming scenario, decreasing areas lost from 56 to 24%. These benefits are more muted at higher warming scenarios, reducing areas lost by a third at 4 °C (85% versus 58%). Our results support the potential of in situ shifting of cultivars to adapt agriculture to climate change—including in major winegrowing regions—as long as efforts to avoid higher warming scenarios are successful.
Published: 2020
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20. Genomic architecture and introgression shape a butterfly radiation

Author: Marcus R. Kronforst, Daniel E. Neafsey, Gilson R. P. Moreira, Brian A. Counterman, W. Owen McMillan, David B. Jaffe, John W. Davey, Michael Miyagi, Bernardo J. Clavijo, Gonzalo García-Accinelli, Nathaniel B. Edelman, Andrew J. Blumberg, Riccardo Papa, Robert D. Reed, Mark Blaxter, Steven M. Van Belleghem, Camilo Salazar, James Mallet, Richard Challis, Federica Di Palma, Paul B. Frandsen, Nick Patterson, Kanchon K. Dasmahapatra, Sujai Kumar, Mathieu Chouteau, Chris D. Jiggins, Mathieu Joron, Rebecca B. Dikow, John Wakeley, The Genome Analysis Centre (TGAC), Smithsonian Institution, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS), Institute of Evolutionary Biology, Invasive Species Branch, United States Geological Survey (USGS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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), Harvard University, Broad Institute [Cambridge], Harvard University-Massachusetts Institute of Technology (MIT), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), ANR-18-CE02-0019,Supergene,Les conséquences de l'évolution d'un supergène(2018), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Harvard University [Cambridge], Massachusetts Institute of Technology (MIT)-Harvard University [Cambridge], Norwich Research Park, Laboratoire Ecologie, évolution, interactions des systèmes amazoniens (LEEISA), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), and Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, Introgression, [SDV]Life Sciences [q-bio], Genome, Insect, Genes, Insect, Genome, Gene, 01 natural sciences, Coalescent theory, Gene flow, Adaptive radiation, Heliconius, Wings, Animal, Phylogeny, Allele, 0303 health sciences, Multidisciplinary, Gene rearrangement, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Papilionoidea, Genomics, Biological Evolution, Phylogenetics, Incompatibility, Butterflies, Gene Flow, Genetic Speciation, Locus (genetics), [SDV.BID]Life Sciences [q-bio]/Biodiversity, Speciation (biology), Biology, Genetic Introgression, 010603 evolutionary biology, Article, 03 medical and health sciences, Gene density, Animals, 030304 developmental biology, Butterfly, Nonhuman, biology.organism_classification, Species differentiation, Evolutionary biology, Chromosome Inversion
Abstract: We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genusHeliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny forHeliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and high gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.
Published: 2019
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21. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

Author: Céline Houssin, James Mallet, Fabrice Legeai, Yann Le Poul, Jérémy Gauthier, Donna Lisa de Silva, Zachariah Gompert, Marianne Elias, Annabel Whibley, Melanie McClure, Claire Lemaitre, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Natural History Museum [Geneva], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Department of Biology [Utah], University of Utah, School of Biological Sciences [Auckland], University of Auckland [Auckland], Institut für Soziologie Ludwig-Maximilians-Universität München (LMU), Ludwig-Maximilians-Universität München (LMU), Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Centre National de la Recherche Scientifique (CNRS)-Université de Guyane (UG)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], CLEARWING ANR‐16‐CE02‐0012, Agence Nationale de la Recherche, RGP0014/2016, Human Frontier Science Program, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, 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), Harvard University, and ANR-16-CE02-0012,CLEARWING,La transparence : origine physique, fonctions adaptatives et évolution chez les papillons transparents(2016)
Subjects: 0106 biological sciences, 0301 basic medicine, Reproductive Isolation, Genotype, Genetic Speciation, Population, Genome, Insect, introgression, Genetic admixture, Introgression, 010603 evolutionary biology, 01 natural sciences, Nymphalidae, Polymorphism, Single Nucleotide, 03 medical and health sciences, Peru, Genetics, Heliconius, Animals, Wings, Animal, education, Hybridization, Ecology, Evolution, Behavior and Systematics, Hybrid, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, education.field_of_study, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Reproductive isolation, differentiation, biology.organism_classification, Ithomiini, 030104 developmental biology, admixture mapping, Genetics, Population, Phenotype, Evolutionary biology, Hybridization, Genetic, Butterflies, mimicry
Abstract: International audience; Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.
Published: 2019
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22. The genetic architecture of adaptation: convergence and pleiotropy in Heliconius wing pattern evolution

Author: Morris, Jake, Navarro, Nicolas, Rastas, Pasi, Rawlins, Lauren D., Sammy, Joshua, Mallet, James, Dasmahapatra, Kanchon K., Department of Biology [York, UK], University of York [York, UK], École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Department of Zoology [Cambridge], University of Cambridge [UK] (CAM), Department of Environment and Geography, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], and Research funded by the Natural Environment Research Council (grant NE/K012886/1), by a NERC studentship, a Heredity fieldwork grant from the Genetics Society and by start-up funds from Harvard University.
Subjects: Genotype, Pigmentation, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Quantitative Trait Loci, Chromosome Mapping, Genetic Variation, Genes, Insect, Quantitative trait, Adaptation, Physiological, Article, Evolutionary genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Phenotype, Peru, Animals, Wings, Animal, Butterflies, Crosses, Genetic
Abstract: 15 pages; International audience; Unravelling the genetic basis of adaptive traits is a major challenge in evolutionary biology. Doing so informs our understanding of evolution towards an adaptive optimum, the distribution of locus effect sizes, and the influence of genetic architecture on the evolvability of a trait. In the Müllerian co-mimics Heliconius melpomene and Heliconius erato some Mendelian loci affecting mimicry shifts are well known. However, several phenotypes in H. melpomene remain to be mapped, and the quantitative genetics of colour pattern variation has rarely been analysed. Here we use quantitative trait loci (QTL) analyses of crosses between H. melpomene races from Peru and Suriname to map, for the first time, the control of the broken band phenotype to WntA and identify a ~100 kb region controlling this variation. Additionally, we map variation in basal forewing red-orange pigmentation to a locus centred around the gene ventral veins lacking (vvl). The locus also appears to affect medial band shape variation as it was previously known to do in H. erato. This adds to the list of homologous regions controlling convergent phenotypes between these two species. Finally we show that Heliconius wing-patterning genes are strikingly pleiotropic among wing pattern traits. Our results demonstrate how genetic architecture can shape, aid and constrain adaptive evolution.
Published: 2019
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23. Cryptic speciation associated with geographic and ecological divergence in two Amazonian Heliconius butterflies

Author: Rosser, Neil Stephen, Freitas, André, Huertas, Blanca, Joron, Mathieu, Lamas, Gerardo, Merot, Claire, Simpson, Fraser, Willmott, Keith R., Mallet, James, Dasmahapatra, Kanchon Kumar, University of York [York, UK], Universität Passau [Passau], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional Mayor de San Marcos (Universidad del Peru) (UNMSM), Florida Museum of Natural History, University of Florida [Gainesville] (UF), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), and Harvard University [Cambridge]
Subjects: [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019
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24. Functional diversity in biters: the evolutionary morphology of the oral jaw system in pacus, piranhas and relatives (Teleostei: Serrasalmidae)

Author: Gregório Kurchevski, Alexandre Lima Godinho, Alessia Huby, Anthony Herrel, Xavier Raick, Bruno Frederich, Régis Vigouroux, Aurélien Lowie, Eric Parmentier, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Hydreco, Laboratoire de Morphologie Fonctionnelle et Evolutive, and Université de Liège
Subjects: 0106 biological sciences, 0301 basic medicine, Teleostei, biology, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Morphology (biology), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Serrasalmidae, stomatognathic diseases, 03 medical and health sciences, Functional diversity, 030104 developmental biology, stomatognathic system, Evolutionary biology, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS
Abstract: Serrasalmid fishes form a highly specialized group of biters that show a large trophic diversity, ranging from pacus able to crush seeds to piranhas capable of cutting flesh. Their oral jaw system has been hypothesized to be forceful, but variation in bite performance and morphology with respect to diet has not previously been investigated. We tested whether herbivorous species have higher bite forces, larger jaw muscles and more robust jaws than carnivorous species. We measured in vivo and theoretical bite forces in 27 serrasalmid species. We compared the size of the adductor mandibulae muscle, the jaw mechanical advantages, the type of jaw occlusion, and the size and shape of the lower jaw. We also examined the association between bite performance and functional morphological traits of the oral jaw system. Contrary to our predictions, carnivorous piranhas deliver stronger bites than their herbivorous counterparts. The size of the adductor mandibulae muscle varies with bite force and muscles are larger in carnivorous species. Our study highlights an underestimated level of functional morphological diversity in a fish group of exclusive biters. We provide evidence that the trophic specialization towards carnivory in piranhas results from changes in the configuration of the adductor mandibulae muscle and the lower jaw shape, which have major effects on bite performance and bite strategy.
Published: 2019
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25. Functional relationship between myology and ecology in carnivores: do forelimb muscles reflect adaptations to prehension?

Author: Stéphane Peigné, Maxime Taverne, Marc Herbin, Christine Böhmer, Anthony Herrel, Anne-Claire Fabre, Département Adaptations du vivant (AVIV), Muséum national d'Histoire naturelle (MNHN), Adaptations et évolution des systèmes ostéomusculaires (AESO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), and Harvard University [Cambridge]
Subjects: 0106 biological sciences, 0303 health sciences, Ecology (disciplines), [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, medicine.anatomical_structure, Evolutionary biology, Myology, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, medicine, Forelimb, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience
Published: 2019
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26. Phenopix: A R package for image-based vegetation phenology

Author: Umberto Morra di Cella, Lisa Wingate, Edoardo Cremonese, Mirco Migliavacca, Matthias Forkel, Gianluca Filippa, Andrew D. Richardson, Enrico Tomelleri, Marta Galvagno, Climate Change Unit, Environmental Protection Agency of Aosta Valley, Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, Interactions Sol Plante Atmosphère (ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de la Recherche Agronomique (INRA), European Academy of Bozen-Bolzano (EURAC), Department of Organismic and Evolutionary Biology, Harvard University [Cambridge], Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), and Interactions Sol Plante Atmosphère (UMR ISPA)
Subjects: 0106 biological sciences, Atmospheric Science, Global and Planetary Change, Data processing, 010504 meteorology & atmospheric sciences, Pixel, Phenology, Digital photography, pixel-based analysis, Forestry, 15. Life on land, Evergreen, phenology, 010603 evolutionary biology, 01 natural sciences, Deciduous, image analysis, Region of interest, Environmental science, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Agronomy and Crop Science, Temperate rainforest, community ecology, 0105 earth and related environmental sciences, Remote sensing
Abstract: In this paper we extensively describe new software available as a R package that allows for the extraction of phenological information from time-lapse digital photography of vegetation cover. The phenopix R package includes all steps in data processing. It enables the user to: draw a region of interest (ROI) on an image; extract red green and blue digital numbers (DN) from a seasonal series of images; depict greenness index trajectories; fit a curve to the seasonal trajectories; extract relevant phenological thresholds (phenophases); extract phenophase uncertainties. The software capabilities are illustrated by analyzing one year of data from a selection of seven sites belonging to the PhenoCam network ( http://phenocam.sr.unh.edu/ ), including an unmanaged subalpine grassland, a tropical grassland, a deciduous needle-leaf forest, three deciduous broad-leaf temperate forests and an evergreen needle-leaf forest. One of the novelties introduced by the package is the spatially explicit, pixel-based analysis, which potentially allows to extract within-ecosystem or within-individual variability of phenology. We examine the relationship between phenophases extracted by the traditional ROI-averaged and the novel pixel-based approaches, and further illustrate potential applications of pixel-based image analysis available in the phenopix R package.
Published: 2016
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27. Immune fingerprinting through repertoire similarity

Author: Meriem Bensouda Koraichi, Thomas Dupic, Anastasia A. Minervina, Mikhail V. Pogorelyy, Thierry Mora, Aleksandra M. Walczak, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Laboratoire de Physique Théorique de l'ENS (LPTENS), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (IBCh RAS), Russian Academy of Sciences [Moscow] (RAS), Pirogov Russian National Research Medical University [Moscow, Russia], Laboratoire de physique de l'ENS - ENS Paris (LPENS (UMR_8023)), École normale supérieure - Paris (ENS Paris), 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), Laboratoire de physique de l'ENS - ENS Paris (LPENS), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)
Subjects: CD4-Positive T-Lymphocytes, Cancer Research, [SDV]Life Sciences [q-bio], QH426-470, Pathology and Laboratory Medicine, Immune Receptors, Biochemistry, White Blood Cells, 0302 clinical medicine, Animal Cells, Medicine and Health Sciences, Public and Occupational Health, Lymphocytes, Precision Medicine, Genetics (clinical), Genetic Fingerprinting, [PHYS]Physics [physics], 0303 health sciences, Immune System Proteins, T Cells, Repertoire, Vaccination and Immunization, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, DNA profiling, Medical Microbiology, Viral Pathogens, 030220 oncology & carcinogenesis, Viruses, Human Cytomegalovirus, Evolutionary Rate, Cellular Types, Pathogens, Identical twins, Research Article, Signal Transduction, Herpesviruses, Evolutionary Immunology, Evolutionary Processes, Immune Cells, Immunology, T cell immunology, Receptors, Antigen, T-Cell, Genetic Fingerprinting and Footprinting, Computational biology, Biology, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Immune system, Similarity (psychology), Genetics, Humans, Quantitative Biology - Genomics, Molecular Biology Techniques, Microbial Pathogens, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genomics (q-bio.GN), Evolutionary Biology, Blood Cells, Models, Statistical, Fingerprint (computing), Organisms, Biology and Life Sciences, Proteins, Cell Biology, Twins, Monozygotic, T Cell Receptors, FOS: Biological sciences, Immune System, Preventive Medicine, DNA viruses, Classifier (UML), Cloning, 030215 immunology
Abstract: Immune repertoires provide a unique fingerprint reflecting the immune history of individuals, with potential applications in precision medicine. However, the question of how personal that information is and how it can be used to identify individuals has not been explored. Here, we show that individuals can be uniquely identified from repertoires of just a few thousands lymphocytes. We present “Immprint,” a classifier using an information-theoretic measure of repertoire similarity to distinguish pairs of repertoire samples coming from the same versus different individuals. Using published T-cell receptor repertoires and statistical modeling, we tested its ability to identify individuals with great accuracy, including identical twins, by computing false positive and false negative rates < 10−6 from samples composed of 10,000 T-cells. We verified through longitudinal datasets that the method is robust to acute infections and that the immune fingerprint is stable for at least three years. These results emphasize the private and personal nature of repertoire data., Author summary Immune repertoires are a trove of personal information: unique to each individual, they are also windows into their past and future health. Thanks to their potential for personalized medicine and progress of sequencing technologies, these repertoires are now routinely sequenced. As a consequence they raise the question of identifiability of samples. In this paper, we estimate the quantity of immune cells needed to associate two samples from the same individual: as little as a finger prick worth of blood can serve as an immune fingerprint that can distinguish even identical twins, without giving away genetic information about non-consenting relatives. We show that this fingerprint is stable through time, and is not erased during infections or vaccinations.
Published: 2021
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28. Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

Author: Kirsten Bomblies, Leandro Quadrana, Ben Hunter, Pierre Baduel, Vincent Colot, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), and Harvard University [Cambridge]
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Acclimatization, Arabidopsis, General Physics and Astronomy, Datasets as Topic, 01 natural sciences, Genome, Mobile elements, Negative selection, Plant evolution, Gene Expression Regulation, Plant, RNA-Seq, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], food and beverages, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Polyploidy in plants, Genome, Plant, Transposable element, Lineage (genetic), Science, MADS Domain Proteins, General Biochemistry, Genetics and Molecular Biology, Article, Evolutionary genetics, Arabidopsis arenosa, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Evolution, Molecular, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Gene, Local adaptation, Whole genome sequencing, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Whole Genome Sequencing, Arabidopsis Proteins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Chemistry, biology.organism_classification, Diploidy, Tetraploidy, 030104 developmental biology, Evolutionary biology, DNA Transposable Elements, lcsh:Q, 010606 plant biology & botany
Abstract: Polyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leverage whole-genome resequencing data available for ~300 individuals of Arabidopsis arenosa, a well characterized natural diploid-autotetraploid plant species, to address these questions. Based on 43,176 TE insertions we detect in these genomes, we demonstrate that relaxed purifying selection rather than transposition bursts is the main driver of TE over-accumulation after WGD. Furthermore, the increased pool of TE insertions in tetraploids is especially enriched within or near environmentally responsive genes. Notably, we show that the major flowering-time repressor gene FLC is disrupted by a TE insertion specifically in the rapid-cycling tetraploid lineage that colonized mainland railways. Together, our findings indicate that tetrasomy leads to an enhanced accumulation of genic TE insertions, some of which likely contribute to local adaptation., Nature Communications, 10 (1), ISSN:2041-1723
Published: 2019
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29. Cranial kinesis in the miniaturised lizard Ablepharus kitaibelii (Squamata: Scincidae)

Author: Anthony Herrel, Vladislav Vergilov, Nikolay Natchev, Patrick Lemell, Stefan Kummer, Christian Josef Beisser, Stephan Handschuh, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), and Harvard University [Cambridge]
Subjects: 0106 biological sciences, Squamata, Physiology, 030310 physiology, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, medicine, Molecular Biology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Cranial kinesis, 0303 health sciences, biology, Osteology, Anatomy, biology.organism_classification, Bite force quotient, Skull, medicine.anatomical_structure, Biting, Insect Science, [SDE]Environmental Sciences, Animal Science and Zoology, Adductor muscles, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ablepharus kitaibelii
Abstract: Cranial kinesis refers to intracranial movements in the vertebrate skull that do not concern the jaw joint, the middle ear or the hypobranchial skeleton. Different kinds of cranial kinesis have been reported for lizards, including mesokinesis, metakinesis, amphikinesis (simultaneous mesokinesis and metakinesis) and streptostyly. Streptostyly is considered relatively widespread within lizards, whereas mesokinesis has been documented only for geckos, varanids and anguids. The present study investigated cranial kinesis in the miniaturised scincid Ablepharus kitaibelii by integrating morphological and experimental data. Based on micro computed tomography, we provide a description of skull osteology. Cranial joints were studied with histology, which results in the first detailed description of cranial joint histology for a member of the Scincidae. Taken together, the morphological data indicate a high potential for amphikinesis and streptostyly, which was also corroborated by skull manipulations. High-speed cinematography demonstrated that mesokinesis occurs during food uptake, processing and intraoral transport cycles. Bite force measurements showed prolonged and reasonably hard biting even at large gape angles. Based on these data, we formulate a model of the amphikinetic A. kitaibelii skull mechanism, which provides an extension of Frazzetta9s quadric-crank model by placing a special emphasis on metakinesis. According to this model, we hypothesise that metakinetic intracranial movements may provide a means for reducing strain in jaw adductor muscles. Presented hypotheses can be addressed and tested in future studies.
Published: 2019
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30. Molecular evidence for the paraphyly of Scolecophidia and its evolutionary implications

Author: Julie Marin, Aurélien Miralles, Nicolas Vidal, Damien Markus, Anthony Herrel, S. Blair Hedges, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Center fo Biodiversity, Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Institut de Chimie Radicalaire (ICR), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Mécanismes Adaptatifs et Evolution (MECADEV), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Paraphyly, Time Factors, Genetic Speciation, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Phylogenetics, Alethinophidia, Animals, Phylogeny, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Scolecophidia, biology, Phylogenetic tree, Snakes, Leptotyphlopidae, biology.organism_classification, Biological Evolution, Typhlopidae, Anomalepididae, 030104 developmental biology, Evolutionary biology, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: The phylogenetic relationships between the three main clades of worm snakes remain controversial. This question is, however, crucial to elucidate the origin of the successful snake radiation, as these burrowing and miniaturized wormlike organisms represent the earliest branching clades within the snake tree. The present molecular phylogenetic study, intended to minimize the amount of missing data, provides fully resolved inter-subfamilial relationships among Typhlopidae. It also brings robust evidence that worm snakes (Scolecophidia) are paraphyletic, with the scolecophidian family Anomalepididae recovered with strong support as sister clade to the 'typical snakes' (Alethinophidia). Ancestral state reconstructions applied to three different traits strongly associated to a burrowing life-style (scolecoidy, absence of retinal cones and microstomy) provide results in favour of a burrowing origin of snakes, and suggest that worm snakes might be the only extant fossorial representatives of the primordial snake incursion towards an underground environment.
Published: 2018
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31. Hearing capacities and morphology of the auditory system in Serrasalmidae (Teleostei: Otophysi)

Author: Mélotte, Geoffrey, Parmentier, Eric, Michel, Christian, Herrel, Anthony, Boyle, Kelly, Université de Liège, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], and Unité de recherche Virologie et Immunologie Moléculaires (VIM)
Subjects: lcsh:R, lcsh:Medicine, Auditory Threshold, Article, Evolution, Molecular, Hearing, Ear, Inner, [SDE]Environmental Sciences, otorhinolaryngologic diseases, Animals, lcsh:Q, Characiformes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, lcsh:Science, ComputingMilieux_MISCELLANEOUS
Abstract: Like all otophysan fishes, serrasalmids (piranhas and relatives) possess a Weberian apparatus that improves their hearing capacities. We compared the hearing abilities among eight species of serrasalmids having different life-history traits: herbivorous vs. carnivorous and vocal vs. mute species. We also made 3D reconstructions of the auditory system to detect potential morphological variations associated with hearing ability. The hearing structures were similar in overall shape and position. All the species hear in the same frequency range and only slight differences were found in hearing thresholds. The eight species have their range of best hearing in the lower frequencies (50–900 Hz). In vocal serrasalmids, the range of best hearing covers the frequency spectrum of their sounds. However, the broad overlap in hearing thresholds among species having different life-history traits (herbivorous vs. carnivorous and vocal vs. non-vocal species) suggests that hearing ability is likely not related to the capacity to emit acoustic signals or to the diet, i.e. the ability to detect sounds is not associated with a given kind of food. The inner ear appears to be highly conservative in this group suggesting that it is shaped by phylogenetic history or by other kinds of constraints such as predator avoidance.
Published: 2018
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32. Habitat characteristics and species interference influence space use and nest-site occupancy: implications for social variation in two sister species

Author: Guila Ganem, Claire M. S. Dufour, Neville Pillay, Johan Watson, Etienne Loire, Nico L. Avenant, 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), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], School of Animal, Plant & Environmental Sciences, University of the Witwatersrand [Johannesburg] (WITS), University of the Free State [South Africa], Free State Department of Tourism, Environmental and Economics Affairs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Harvard University, and University of the Free State [South Africa] (UFS)
Subjects: 0106 biological sciences, Sympatry, Rhabdomys, Parapatric speciation, 010603 evolutionary biology, 01 natural sciences, Nest, Ecology, Evolution, Behavior and Systematics, Sociality, Ecological niche, biology, Ecology, 010604 marine biology & hydrobiology, Interspecific competition, 15. Life on land, biology.organism_classification, Écologie des populations, Compétition interspécifique, Écologie animale, L20 - Écologie animale, Social evolution, Nidification, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Comportement animal
Abstract: International audience; Nest-site selection is an important component of species socio-ecology, being a crucial factor in establishment of group living. Consequently, nest-site characteristics together with space-use proxies may reveal the social organization of species, which is critical when direct observation of social interactions is hindered in nature. Importantly, nest-site choice is expected to be under strong selective pressures and the object of intra- and inter-specific competition. Although the bulk of research on sociality focuses on its ecological drivers, our study introduces interspecific competition as a potential factor that could influence social evolution. We investigated the influence of habitat and interspecific competition on the social organization of two sister species of the African four striped mouse (Rhabdomys dilectus dilectus and Rhabdomys bechuanae) in a similar macroenvironment. These species diverged in allopatry and occupy distinct environmental niches. We radiotracked 140 adults to identify their nest-sites, determine nest characteristics and record groups that shared nest-sites. Group cohesion was estimated from nest-site fidelity, group association strength, and home range overlap within versus between group members. We compared the two species in sympatry versus parapatry to determine the impact of species interference on sociality. In parapatry, the two species selected distinct nest-site types, interpreted as different anti-predator strategies: R. bechuanae selected fewer, spaced, less concealed nest-sites whereas R. d. dilectus selected clumped and less visible nest-sites. Rhabdomys bechuanae also showed more cohesive and stable social groups than R. d. dilectus. In sympatry, compared to R. bechuanae, R. d. dilectus occupied similar nest-sites, however slightly more exposed and clumped, and displayed similar nest-site fidelity and group association strength. We conclude that although habitat selection may be an important driver of social divergence in Rhabdomys, species interference, by limiting R. d. dilectus movements and forcing nest-site sharing may induce new ecological pressures that could influence its social evolution.
Published: 2018
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33. Bioconda: sustainable and comprehensive software distribution for the life sciences

Author: Dale R., Gruning B., Sjodin A., Rowe J., Chapman B. A., Tomkins-Tinch C. H., Valieris R., Batut B., Caprez A., Cokelaer T., Yusuf D., Beauchamp K. A., Brinda K., Wollmann T., Corguille G. L., Ryan D., Bretaudeau A., Hoogstrate Y., Pedersen B. S., Heeringen S., Raden M., Luna-Valero S., Soranzo N., Smet M. D., Kuster G. V., Kirchner R., Pantano L., Charlop-Powers Z., Thornton K., Martin M., Beek M. D., Maticzka D., Miladi M., Will S., Gravouil K., Unneberg P., Brueffer C., Blank C., Piro V. C., Wolff J., Antao T., Gladman S., Shlyakhter I., Hollander M., Mabon P., Shen W., Boekel J., Holtgrewe M., Bouvier D., de Ruiter J. R., Cabral J., Choudhary S., Harding N., Kleinkauf R., Enns E., Eggenhofer F., Brown J., Cock P. J. A., Timm H., Thomas C., Zhang X. -O., Chambers M., Turaga N., Seiler E., Brislawn C., Pruesse E., Fallmann J., Kelleher J., Nguyen H., Parsons L., Fang Z., Stovner E. B., Stoler N., Ye S., Wohlers I., Farouni R., Freeberg M., Johnson J. E., Bargull M., Kensche P. R., Webster T. H., Eppley J. M., Stahl C., Rose A. S., Reynolds A., Wang L. -B., Garnier X., Dirmeier S., Knudsen M., Taylor J., Srivastava A., Rai V., Agren R., Junge A., Guimera R. V., Khan A., Schmeier S., He G., Pinello L., Hagglund E., Mikheyev A. S., Preussner J., Waters N. R., Li W., Capellades J., Chande A. T., Pirola Y., Hiltemann S., Bendall M. L., Singh S., Dunn W. A., Drouin A., Domenico T. D., Bruijn I., Larson D. E., Chicco D., Grassi E., Gonnella G., B J., Wang L., Giacomoni F., Clarke E., Blankenberg D., Tran C., Patro R., Laurent S., Gopez M., Sennblad B., Baaijens J. A., Ewels P., Wright P. R., Enache O. M., Roger P., Dampier W., Koppstein D., Devisetty U. K., Rausch T., Cornwell M., Salatino A. E., Seiler J., Jung M., Kornobis E., Cumbo F., Stocker B. K., Moskalenko O., Bogema D. R., Workentine M. L., Newhouse S. J., Leprevost F. D. V., Arvai K., Koster J., Albert-Ludwigs-Universität Freiburg, National Institutes of Health [Bethesda] (NIH), Swedish Defence Research Agency [Stockholm] (FOI), Umeå University, Harvard T.H. Chan School of Public Health, New York University [Abu Dhabi], NYU System (NYU), Harvard University [Cambridge], Hospital Camargo Sao Paulo, Partenaires INRAE, University of Duisburg-Essen, This work was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health (R.D.), the Netherlands Organisation for Scientific Research (NWO) (VENI grant 016.Veni.173.076 to J.K.), the German Research Foundation (SFB 876 to J.K.), and the NYU Abu Dhabi Research Institute for the NYU Abu Dhabi Center for Genomics and Systems Biology, program number CGSB1 (grant to J.R. and A. Yousif)., We thank all contributors, the conda-forge team, and Anaconda Inc. for excellent cooperation. Further, we thank Travis CI (https://travis-ci.com) and Circle CI (https://circleci.com) for providing free Linux and macOS computing capacity. Finally, we thank ELIXIR (https://www.elixir-europe.org) for constant support and donation of staff., Etienne Kornobis (Epigenetic Regulation Unit, Institut Pasteur, Paris, France) fait partie de Bioconda Team, Bioinformatics Group, Department of Computer Science, University of Freiburg [Freiburg], Laboratory of Cellular and Developmental Biology (LCDB), NIDDK, NIH, Department of Organismic and Evolutionary Biology, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Harvard University, Universität Duisburg-Essen = University of Duisburg-Essen [Essen], Dale, R, Gruning, B, Sjodin, A, Rowe, J, Chapman, B, Tomkins-Tinch, C, Valieris, R, Batut, B, Caprez, A, Cokelaer, T, Yusuf, D, Beauchamp, K, Brinda, K, Wollmann, T, Corguille, G, Ryan, D, Bretaudeau, A, Hoogstrate, Y, Pedersen, B, Heeringen, S, Raden, M, Luna-Valero, S, Soranzo, N, Smet, M, Kuster, G, Kirchner, R, Pantano, L, Charlop-Powers, Z, Thornton, K, Martin, M, Beek, M, Maticzka, D, Miladi, M, Will, S, Gravouil, K, Unneberg, P, Brueffer, C, Blank, C, Piro, V, Wolff, J, Antao, T, Gladman, S, Shlyakhter, I, Hollander, M, Mabon, P, Shen, W, Boekel, J, Holtgrewe, M, Bouvier, D, de Ruiter, J, Cabral, J, Choudhary, S, Harding, N, Kleinkauf, R, Enns, E, Eggenhofer, F, Brown, J, Cock, P, Timm, H, Thomas, C, Zhang, X, Chambers, M, Turaga, N, Seiler, E, Brislawn, C, Pruesse, E, Fallmann, J, Kelleher, J, Nguyen, H, Parsons, L, Fang, Z, Stovner, E, Stoler, N, Ye, S, Wohlers, I, Farouni, R, Freeberg, M, Johnson, J, Bargull, M, Kensche, P, Webster, T, Eppley, J, Stahl, C, Rose, A, Reynolds, A, Wang, L, Garnier, X, Dirmeier, S, Knudsen, M, Taylor, J, Srivastava, A, Rai, V, Agren, R, Junge, A, Guimera, R, Khan, A, Schmeier, S, He, G, Pinello, L, Hagglund, E, Mikheyev, A, Preussner, J, Waters, N, Li, W, Capellades, J, Chande, A, Pirola, Y, Hiltemann, S, Bendall, M, Singh, S, Dunn, W, Drouin, A, Domenico, T, Bruijn, I, Larson, D, Chicco, D, Grassi, E, Gonnella, G, B, J, Giacomoni, F, Clarke, E, Blankenberg, D, Tran, C, Patro, R, Laurent, S, Gopez, M, Sennblad, B, Baaijens, J, Ewels, P, Wright, P, Enache, O, Roger, P, Dampier, W, Koppstein, D, Devisetty, U, Rausch, T, Cornwell, M, Salatino, A, Seiler, J, Jung, M, Kornobis, E, Cumbo, F, Stocker, B, Moskalenko, O, Bogema, D, Workentine, M, Newhouse, S, Leprevost, F, Arvai, K, Koster, J, Urology, and Pathology
Subjects: 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Medizin, computer.software_genre, Biochemistry, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, Software system, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Social software engineering, Database, business.industry, Software development, INF/01 - INFORMATICA, Computational Biology, Cell Biology, Software distribution, 030104 developmental biology, Software construction, [SDE]Environmental Sciences, Package development process, Backporting, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Software, 030217 neurology & neurosurgery, Biotechnology
Abstract: International audience; We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi- platform and language-agnostic package manager Conda. Currently, Bioconda o ers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bio- conda improves analysis reproducibility by allowing users to de ne isolated environments with de ned software versions, all of which are easily installed and managed without administrative privileges.
Published: 2018
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34. Personality and performance are affected by age and early life parameters in a small primate

Author: Lucile Rabardel, Anthony Herrel, Pauline B. Zablocki-Thomas, Emmanuelle Pouydebat, Martine Perret, Fabienne Aujard, Isabelle Hardy, École normale supérieure - Lyon (ENS Lyon), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Département Adaptations du vivant (AVIV), Muséum national d'Histoire naturelle (MNHN), Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon), Harvard University, Mécanismes adaptatifs : des organismes aux communautés (MAOAC), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Adaptations et évolution des systèmes ostéomusculaires (AESO), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)
Subjects: 0106 biological sciences, life history, Microcebus murinus, Evolution, Birth weight, media_common.quotation_subject, [SDV]Life Sciences [q-bio], DETERMINANTS, Biology, BEHAVIORAL SYNDROMES, 010603 evolutionary biology, 01 natural sciences, INDIVIDUAL-DIFFERENCES, Behavioral syndrome, Grip strength, SEXUAL-DIMORPHISM, Behavior and Systematics, BITE FORCE, Personality, early life, 0501 psychology and cognitive sciences, 050102 behavioral science & comparative psychology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Original Research, media_common, Nature and Landscape Conservation, phenotypic correlation, Ecology, ANIMAL PERSONALITY, 05 social sciences, MOUSE LEMURS, Biology and Life Sciences, Phenotypic trait, biology.organism_classification, Bite force quotient, Sexual dimorphism, personality, [SDE]Environmental Sciences, MORPHOLOGY, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, REPEATABILITY, performance, Demography
Abstract: A whole suite of parameters is likely to influence the behavior and performance of individuals as adults, including correlations between phenotypic traits or an individual's developmental context. Here, we ask the question whether behavior and physical performance traits are correlated and how early life parameters such as birth weight, litter size, and growth can influence these traits as measured during adulthood. We studied 486 captive gray mouse lemurs (Microcebus murinus) and measured two behavioral traits and two performance traits potentially involved in two functions: exploration behavior with pull strength and agitation score with bite force. We checked for the existence of behavioral consistency in behaviors and explored correlations between behavior, performance, morphology. We analyzed the effect of birth weight, growth, and litter size, while controlling for age, sex, and body weight. Behavior and performance were not correlated with one another, but were both influenced by age. Growth rate had a positive effect on adult morphology, and birth weight significantly affected emergence latency and bite force. Grip strength was not directly affected by early life traits, but bite performance and exploration behavior were impacted by birth weight. This study shows how early life parameters impact personality and performance.
Published: 2018
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35. Bite force and cranial bone strain in four species of lizards

Author: Susan E. Evans, Michael J. Fagan, Callum F. Ross, Anthony Herrel, Laura B. Porro, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), and Harvard University [Cambridge]
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Zoology, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Anolis, Bite Force, 03 medical and health sciences, biology.animal, parasitic diseases, Animals, Molecular Biology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Cranial kinesis, Iguana, biology, Strain (chemistry), Lizard, Skull, Lizards, Feeding Behavior, biology.organism_classification, Uromastyx, Bite force quotient, 030104 developmental biology, Biting, Insect Science, [SDE]Environmental Sciences, Animal Science and Zoology, Stress, Mechanical, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: In vivo bone strain data provide direct evidence of strain patterns in the cranium during biting. Compared with those in mammals, in vivo bone strains in lizard skulls are poorly documented. This paper presents strain data from the skulls of Anolis equestris, Gekko gecko, Iguana iguana and Salvator merianae during transducer biting. Analysis of variance was used to investigate effects of bite force, bite point, diet, cranial morphology and cranial kinesis on strain magnitude. Within individuals, the most consistent determinants of variance in bone strain magnitude were gauge location and bite point, with the importance of bite force varying between individuals. Inter-site variance in strain magnitude - strain gradient - was present in all individuals and varied with bite point. Between individuals within species, variance in strain magnitude was driven primarily by variation in bite force, not gauge location or bite point, suggesting that inter-individual variation in patterns of strain magnitude is minimal. Between species, variation in strain magnitude was significantly impacted by bite force and species membership, as well as by interactions between gauge location, species and bite point. Independent of bite force, species differences in cranial strain magnitude may reflect selection for different cranial morphology in relation to feeding function, but what these performance criteria are is not clear. The relatively low strain magnitudes in Iguana and Uromastyx compared with those in other lizards may be related to their herbivorous diet. Cranial kinesis and the presence or absence of postorbital and supratemporal bars are not important determinants of inter-specific variation in strain magnitude.
Published: 2018
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36. Skull Size and Biomechanics are Good Estimators of In Vivo Bite Force in Murid Rodents

Author: Ginot, Samuel, Herrel, Anthony, Claude, Julien, Hautier, Lionel, 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), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Museum of Zoology, University of Cambridge, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Mécanismes Adaptatifs et Evolution (MECADEV), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Muridae, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Muscle, bite force, [SPI.MECA.BIOM]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Biomechanics [physics.med-ph], adaptation, vertebrates, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Rodentia is a species-rich group with diversified modes of life and diets. Although rodent skull morphology has been the focus of a voluminous literature, the functional significance of its variations has yet to be explored in live animals. Myomorphous rodents, including murids, have been suggested to represent “high-performance generalists.” We measured in vivo bite force in 14 species of wild and lab-reared murid rodents of various sizes and diets to investigate potential morphofunctional differences between them. We dissected their skulls and computed a biomechanical model to estimate bite force. We first tested if our model allowed good estimation of in vivo data. Then, using morphological, in vivo and estimated bite force data in a phylogenetic context, we aimed to find the drivers of bite force differences among species. Estimated and in vivo bite forces were strongly correlated, which indicates that (a) biomechanical models allow a good estimation of real performance, and that (b) size and muscular changes (increased mass, fiber length, and PCSA) are the main drivers of bite performance differences. Myomorphous rodents, therefore, may have evolved high bite force through a combination of changes in size and musculature, which gave them a great versatility in their ability to process food. We found mixed results at the intraspecific level, with only some species displaying a good fit between estimated and in vivo measurements. We suggest that limited variation in size and muscular organization, and increased behavioral variation might decrease the precision of bite force estimates within species.
Published: 2018
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37. Later springs green-up faster: the relation between onset and completion of green-up in deciduous forests of North America

Author: Stephen Klosterman, Koen Hufkens, Andrew D. Richardson, Department of Organismic and Evolutionary Biology, Harvard University [Cambridge], Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Faculty of Bioscience Engineering, Universiteit Gent = Ghent University [Belgium] (UGENT), School of Informatics, Computing, and Cyber Systems (SICCS), and Northern Arizona University [Flagstaff]
Subjects: 0106 biological sciences, Atmospheric Science, green-up, 010504 meteorology & atmospheric sciences, Range (biology), [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, ecosystem model, Forests, phenology, 010603 evolutionary biology, 01 natural sciences, Trees, Ecosystem model, medicine, Ecosystem, 0105 earth and related environmental sciences, Transpiration, forest productivity, Ecology, Phenology, 15. Life on land, Seasonality, medicine.disease, Plant Leaves, Deciduous, Productivity (ecology), 13. Climate action, [SDE]Environmental Sciences, North America, Environmental science, Physical geography, Seasons
Abstract: International audience; In deciduous forests, spring leaf phenology controls the onset of numerous ecosystem functions. While most studies have focused on a single annual spring event, such as budburst, ecosystem functions like photosynthesis and transpiration increase gradually after budburst, as leaves grow to their mature size. Here, we examine the "velocity of green-up," or duration between budburst and leaf maturity, in deciduous forest ecosystems of eastern North America. We use a diverse data set that includes 301 site-years of phenocam data across a range of sites, as well as 22 years of direct ground observations of individual trees and 3 years of fine-scale high-frequency aerial photography, both from Harvard Forest. We find a significant association between later start of spring and faster green-up: - 0.47 ± 0.04 (slope ± 1 SE) days change in length of green-up for every day later start of spring within phenocam sites, - 0.31 ± 0.06 days/day for trees under direct observation, and - 1.61 ± 0.08 days/day spatially across fine-scale landscape units. To explore the climatic drivers of spring leaf development, we fit degree-day models to the observational data from Harvard Forest. We find that the default phenology parameters of the ecosystem model PnET make biased predictions of leaf initiation (39 days early) and maturity (13 days late) for red oak, while the optimized model has biases of 1 day or less. Springtime productivity predictions using optimized parameters are closer to results driven by observational data (within 1%) than those of the default parameterization (17% difference). Our study advances empirical understanding of the link between early and late spring phenophases and demonstrates that accurately modeling these transitions is important for simulating seasonal variation in ecosystem productivity.
Published: 2018
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38. Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity

Author: Rika E. Anderson, Colleen M. Cavanaugh, Sintra Reves-Sohn, Julie A. Huber, Julie Reveillaud, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Marine Biological Laboratory, Carleton College, Department of Organismic and Evolutionary Biology, Harvard University [Cambridge], Woods Hole Oceanographic Institution (WHOI), This work was supported by a NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) grant NNX-32709AB75G to JAH, a grant from the Deep Carbon Observatory's Deep Life Initiative to JAH, the NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI contribution 412) and a mobility research grant from GDR3692 'Genomique environnementale', and Reveillaud, Julie
Subjects: 0301 basic medicine, Microbiology (medical), [SDV]Life Sciences [q-bio], 030106 microbiology, Trophosome, Biology, Microbiology, lcsh:Microbial ecology, 03 medical and health sciences, Hydrothermal Vents, Phylogenetics, RNA, Ribosomal, 16S, Gammaproteobacteria, Lamellibrachia, Animals, 14. Life underwater, Symbiosis, Phylogeny, Phylotype, Autotrophic Processes, Phylogenetic tree, Bacteria, Research, fungi, Polychaeta, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 030104 developmental biology, Evolutionary biology, Genes, Bacterial, Candidatus, lcsh:QR100-130, bacteria, RRNA Operon, Metagenomics
Abstract: Background The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR) in the Caribbean Sea were characterized using microscopy, phylogenetic analyses, and a metagenomic approach. Results Bacteria, with a typical Gram negative cell envelope contained within membrane-bound vacuoles, were observed within the trophosome of both tubeworm species. Phylogenetic analysis of the 16S rRNA gene and ITS region suggested MCR individuals harbored highly similar endosymbionts that were > 98% identical, with the exception of two symbionts that showed a 60 bp insertion within the ITS region. All sequences from MCR endosymbionts formed a separate well-supported clade that diverged from those of symbionts of seep and vent vestimentiferans from the Pacific, Gulf of Mexico, and Mediterranean Sea. The metagenomes of the symbionts of two specimens of each tubeworm species were sequenced, and two distinct Gammaproteobacteria metagenome-assembled genomes (MAGs) of more than 4 Mbp assembled. An Average Nucleotide Identity (ANI) of 86.5% between these MAGs, together with distinct 16S rRNA gene and ITS sequences, indicate the presence of multiple endosymbiont phylotypes at the MCR, with one MAG shared between one Escarpia and two Lamellibrachia individuals, indicating these endosymbionts are not specific to either host species. Genes for sulfur and hydrogen oxidation, nitrate reduction (assimilatory and dissimilatory), glycolysis and the Krebs cycle, peptide, sugar, and lipid transporters, and both rTCA and CBB carbon fixation cycles were detected in the MAGs, highlighting key and shared functions with symbiont metagenomes of the vestimentiferans Riftia, Tevnia, and Ridgeia from the Pacific. The potential for a second hydrogen oxidation pathway (via a bidirectional hydrogenase), formate dehydrogenase, a catalase, and several additional peptide transporters were found exclusively in the MCR endosymbiont MAGs. Conclusions The present study adds new evidence that tubeworm endosymbionts can potentially switch from autotrophic to heterotrophic metabolism, or may be mixotrophic, presumably while free-living, and also suggests their versatile metabolic potential may enable both the host and symbionts to exploit a wide range of environmental conditions. Together, the marked gene content and sequence dissimilarity at the rRNA operon and whole genome level between vent and seep symbionts suggest these newly described endosymbionts from the MCR belong to a novel tubeworm endosymbiont genera, introduced as Candidatus Vondammii. Electronic supplementary material The online version of this article (10.1186/s40168-018-0411-x) contains supplementary material, which is available to authorized users.
Published: 2018
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39. The effect of recent competition between the native Anolis oculatus and the invasive A. cristatellus on display behavior

Author: Claire M. S. Dufour, Anthony Herrel, Jonathan B. Losos, Harvard University (Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology), Département Adaptations du vivant (AVIV), Muséum national d'Histoire naturelle (MNHN), Department of Biology, University of Washington, University of Washington [Seattle], Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA), Evolutionary Morphology of Vertebrates, and Ghent University [Belgium] (UGENT)
Subjects: 0106 biological sciences, 0301 basic medicine, Sympatry, Dewlap extension, media_common.quotation_subject, lcsh:Medicine, Zoology, Introduced species, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Anolis, Competition (biology), 03 medical and health sciences, Character displacement, ComputingMilieux_MISCELLANEOUS, media_common, Push-up display, biology, Invasive species, General Neuroscience, lcsh:R, General Medicine, Interspecific competition, 15. Life on land, biology.organism_classification, Display behavior, Habitat, 030104 developmental biology, Dewlap, [SDE]Environmental Sciences, Anolis cristatellus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences
Abstract: Invasive species are a global threat to biodiversity. Cases where the invasion has been tracked since its beginning are rare, however, such that the first interactions between invasive and native species remain poorly understood. Communication behavior is an integral part of species identity and is subject to selection. Consequently, resource use and direct interference competition between native and invasive species may drive its evolution. Here, we tested the role of interactions between the recently introduced invasive lizardAnolis cristatellusand the nativeAnolis oculatuson variation in behavior and communication in Calibishie (Dominica). From May to June 2016, we filmed 122 adult males of both species displaying in banana farms under two contexts (allopatry and sympatry). We then recorded (i) the proportion of time spent displaying and (ii) the relative frequency of dewlap vs. push-up displays. To control for habitat variation, we measured and compared the habitat characteristics (canopy openness and habitat openness) of 228 males in allopatry and sympatry. While the habitat characteristics and total display-time did not differ between the contexts for the two species, the proportion of display-time spent dewlapping byA. cristatellusdecreased in sympatry. The display ofA. oculatusdid not differ between the contexts, however. Shifts in microhabitat use, predation pressure, or interspecific interference are potential factors which might explain the behavioral changes in display observed inA. cristatellus. This study highlights the role of behavioral traits as a first response of an invasive species to recent competition with a closely related native species.
Published: 2018
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40. An integrated phenology modelling framework in R

Author: Eli K. Melaas, David Basler, Andrew D. Richardson, Tom Milliman, Koen Hufkens, Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Department of Applied Ecology and Environmental Biology, Department of Organismic and Evolutionary Biology, Harvard University [Cambridge], University of New Hampshire (UNH), Boston University [Boston] (BU), School of Informatics, Computing, and Cyber Systems (SICCS), and Northern Arizona University [Flagstaff]
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, PEP725, Phenology, [SDV]Life Sciences [q-bio], Ecological Modeling, modelling, MODIS land surface phenology, PHENOCAM, phenology, R package, USA-NPN, 15. Life on land, Atmospheric sciences, 010603 evolutionary biology, 01 natural sciences, 13. Climate action, [SDE]Environmental Sciences, Environmental science, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences
Abstract: International audience; 1. Phenology is a first-order control on productivity and mediates the biophysical environment by altering albedo, surface roughness length and evapotranspiration. Accurate and transparent modelling of vegetation phenology is therefore key in understanding feedbacks between the biosphere and the climate system. 2. Here, we present the PHENOR R package and modelling framework. The framework leverages measurements of vegetation phenology from four common phenology observation datasets, the PhenoCam network, the USA National Phenology Network (USA-NPN), the Pan European Phenology Project (PEP725), MODIS phenology (MCD12Q2) combined with (global) retrospective and projected climate data. 3. We show an example analysis, using the PHENOR modelling framework, which quickly and easily compares 20 included spring phenology models for three plant functional types. An analysis of model skill using the root mean squared (RMSE) error shows little or no difference regardless of model structure, corroborating previous studies. We argue that addressing this issue will require novel model development combined with easy data assimilation as facilitated by our framework. 4. In conclusion, we hope the PHENOR phenology modelling framework in the R language and environment for statistical computing will facilitate reproducibility and community driven phenology model development, in order to increase their overall predictive power, and leverage an ever growing number of phenology data products.
Published: 2018
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41. Integrating camera imagery, crowdsourcing, and deep learning to improve high-frequency automated monitoring of snow at continental-to-global scales

Author: Margaret Kosmala, Koen Hufkens, Andrew D. Richardson, Department of Organismic and Evolutionary Biology, Harvard University [Cambridge], Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), School of Informatics, Computing, and Cyber Systems (SICCS), and Northern Arizona University [Flagstaff]
Subjects: Satellite Imagery, 010504 meteorology & atmospheric sciences, Computer science, [SDV]Life Sciences [q-bio], 0211 other engineering and technologies, 02 engineering and technology, Forests, 01 natural sciences, Convolutional neural network, Machine Learning, Snow, Multidisciplinary, Data Processing, Contextual image classification, Ecology, Cameras, Terrestrial Environments, Spring, Optical Equipment, [SDE]Environmental Sciences, Medicine, Crowdsourcing, Engineering and Technology, Seasons, Information Technology, Research Article, Computer and Information Sciences, Neural Networks, Imaging Techniques, Science, Equipment, Research and Analysis Methods, Sensitivity and Specificity, Ecosystems, Deep Learning, Artificial Intelligence, Support Vector Machines, Humans, 021101 geological & geomatics engineering, 0105 earth and related environmental sciences, Remote sensing, business.industry, Deep learning, Ecology and Environmental Sciences, Reproducibility of Results, Biology and Life Sciences, Support vector machine, 13. Climate action, Earth Sciences, Artificial intelligence, business, Snow cover, Neuroscience
Abstract: International audience; Snow is important for local to global climate and surface hydrology, but spatial and temporal heterogeneity in the extent of snow cover make accurate, fine-scale mapping and monitoring of snow an enormous challenge. We took 184,453 daily near-surface images acquired by 133 automated cameras and processed them using crowdsourcing and deep learning to determine whether snow was present or absent in each image. We found that the crowdsourced data had an accuracy of 99.1% when compared with expert evaluation of the same imagery. We then used the image classification to train a deep convolutional neural network via transfer learning, with accuracies of 92% to 98%, depending on the image set and training method. The majority of neural network errors were due to snow that was present not being detected. We used the results of the neural networks to validate the presence or absence of snow inferred from the MODIS satellite sensor and obtained similar results to those from other validation studies. This method of using automated sensors, crowdsourcing, and deep learning in combination produced an accurate high temporal dataset of snow presence across a continent. It holds broad potential for real-time large-scale acquisition and processing of ecological and environmental data in support of monitoring, management, and research objectives.
Published: 2018
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42. Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies

Author: Chazot, Nicolas, de-Silva, Donna Lisa, Willmott, Keith, Freitas, André V.L., Lamas, Gerardo, Mallet, James, Giraldo, Carlos E., Uribe, Sandra, Elias, Marianne, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Florida Museum of Natural History, University of Florida [Gainesville] (UF), Universidade Estadual de Campinas (UNICAMP), Universidad Nacional Mayor de San Marcos (UNMSM), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Universidad Catolica de Oriente, Universidad Nacional de Colombia (Sede Medellín), and Universidad Nacional de Colombia
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.BID]Life Sciences [q-bio]/Biodiversity
Abstract: International audience; The Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time-calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework. We found common diversification patterns across the three subtribes, as well as major differences. In Dircennina and Oleriina, our results reveal a congruent pattern of diversification related to the Andes with an Andean origin , which contrasts with the Amazonian origin and multiple Andean colonizations of Godyridina. In each of the three subtribes, a clade diversified in the Northern Andes at a faster rate. Diversification within Amazonia occurred in Oleriina and Godyridina, while virtually no speciation occurred in Dircennina in this region. Dircennina was therefore characterized by higher diversification rates within the Andes compared to non-Andean regions, while in Oleriina and Godyridina, we found no difference between these regions. Our results and discussion highlight the importance of comparative approaches in biogeographic studies.
Published: 2018
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43. Ecological character displacement between a native and an introduced species: the invasion of Anolis cristatellus in Dominica

Author: Jonathan B. Losos, Claire M. S. Dufour, Anthony Herrel, Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Evolutionary Morphology of Vertebrates, Ghent University [Belgium] (UGENT), Harvard University (Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology), Département Adaptations du vivant (AVIV), and Muséum national d'Histoire naturelle (MNHN)
Subjects: 0106 biological sciences, 0301 basic medicine, Ecology, Introduced species, Character displacement, 15. Life on land, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Limb, 03 medical and health sciences, 030104 developmental biology, Interspecific competition, Invasion, [SDE]Environmental Sciences, Lizard, Anolis cristatellus, Perch height, Anolis, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Species invasions are a global scourge. Nonetheless, they provide the appropriate evolutionary setting to rigorously test the role that interspecific competition plays in species evolution. The process of ecological character displacement, in which species diverge in sympatry to minimize resource use overlap, is one example. Here, we examine whether ecological character displacement occurs as the result of a species invasion and, if so, whether morphological adaptations subsequently evolve. We studied the invasion of the lizard Anolis cristatellus in Dominica, where the native Anolis oculatus occurs, and compared nine allopatric and 11 sympatric populations at two scales: across the island, where A. cristatellus invaded since 1998, and in the northeastern region (Calibishie), where the species arrived in 2014. Perch height and diameter, as well as body, limb and toepad traits, were measured on 593 adults. In sympatry, habitat divergence occurred rapidly but was associated with morphological divergence at the island scale only: A. oculatus perched higher and possessed shorter limbs, while A. cristatellus moved downward with associated longer limbs and, in females, fewer toepad lamellae. The different results for the two scales suggest that sympatry is too recent at Calibishie for morphological trait evolution to occur
Published: 2018
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44. Leaf phenology paradox: Why warming matters most where it is already warm

Author: Bijan Seyednasrollah, James S. Clark, Jennifer J. Swenson, Jean-Christophe Domec, Department of Organismic and Evolutionary Biology, Harvard University [Cambridge], Nicholas School of the Environment, Duke University [Durham], School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University [Flagstaff], Interactions Sol Plante Atmosphère (UMR ISPA), and Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)
Subjects: 0106 biological sciences, Canopy, green-up, 010504 meteorology & atmospheric sciences, warming, NDVI, multispectral, [SDV]Life Sciences [q-bio], Soil Science, Climate change, land surface temperature, Atmospheric sciences, 010603 evolutionary biology, 01 natural sciences, phenology, forest, Ecosystem, Computers in Earth Sciences, 0105 earth and related environmental sciences, Remote sensing, spring, Phenology, Global warming, Geology, Vegetation, daily vegetation index, 15. Life on land, Evergreen, EVI, Deciduous, climate change, MODIS, 13. Climate action, [SDE]Environmental Sciences, bayesian, southeastern US, Environmental science, hierarchical modeling
Abstract: International audience; Interactions between climate and ecosystem properties that control phenological responses to climate warming and drought are poorly understood. To determine contributions from these interactions, we used space-borne remotely sensed vegetation indices to monitor leaf development across climate gradients and ecoregions in the southeastern United States. We quantified how air temperature, drought severity, and canopy thermal stress contribute to changes in leaf flushing from mountainous to coastal plain regions by developing a hierarchical state-space Bayesian model. We synthesized daily field climate data with daily vegetation indices and canopy surface temperature during spring green-up season at 59 sites in the southeastern United States between 2001 and 2012. Our results demonstrated strong interaction effects between ecosystem properties and climate variables across ecoregions. We found spring green-up is faster in the mountains, while coastal forests express a larger sensitivity to inter-annual temperature anomalies. Despite our detection of a decreasing trend in sensitivity to warming with temperature in all regions, we identified an ecosystem interaction: Deciduous dominated forests are less sensitive to warming than are those with fewer deciduous trees, likely due to the continuous presence of leaves in evergreen species throughout the season. Mountainous forest green-up is more susceptible to intensifying drought and moisture deficit, while coastal areas are relatively resilient. We found that with increasing canopy thermal stress, defined as canopy-air temperature difference, leaf development slows following dry years, and accelerates following wet years.
Published: 2018
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45. Can functional traits help explain the coexistence of two species of Apodemus?

Author: Anthony Herrel, Pascale Chevret, Anne Tresset, Helder Gomes Rodrigues, Elizabeth Kerr, Sabrina Renaud, Raphaël Cornette, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Mécanismes adaptatifs : des organismes aux communautés (MECADEV), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), PaleoEnvironnements et PaleobioSphere (PEPS), 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, Ecologie et évolution des populations, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie et histoire des sociétés (AHS), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Mécanismes Adaptatifs et Evolution (MECADEV), Centre de Recherche en Paléontologie - Paris (CR2P), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie, histoire des sociétés et des peuplements animaux (AHS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and Harvard University
Subjects: 0106 biological sciences, 0301 basic medicine, biology, Ecology, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Apodemus, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2017
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46. A new exceptionally preserved specimen of Dracaenosaurus (Squamata, Lacertidae) from the Oligocene of France as revealed by micro-computed tomography

Author: Marc Louis Augé, Anthony Herrel, Arnau Bolet, Johannes Müller, Jean-Claude Rage, Andrej Čerňanský, Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona (UAB), Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC), École des hautes études en sciences sociales (EHESS), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Mécanismes Adaptatifs et Evolution (MECADEV), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 010506 paleontology, Squamata, biology, Osteology, Lizard, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Paleontology, Postcrania, Anatomy, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Skull, medicine.anatomical_structure, biology.animal, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, medicine, Lacertidae, Crest, Process (anatomy), ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: The best-preserved material of Dracaenosaurus croizeti, an almost complete and previously unpublished skull with a few associated postcranial bones (stylopodium, zeugopodium, and cervical vertebra), is described. The material comes from the locality of Cournon, a late Oligocene site in south-central France. Micro-computed tomography applied to this specimen revealed previously unknown internal osteological characters. Among lacertids, this taxon represents a notable phenomenon: it is an extreme durophagous specialist. Many of the newly observed cranial character states reflect the lifestyle of this lizard, because animals with a hard-shelled diet display a specialized cranial morphology associated with more massive cranial muscles. One unique character for Lacertidae is observed: the parietal-supraoccipital contact is formed by a ventrally deep parietal crest that fits into a bifurcate ascending process of the supraoccipital. In fact, such a connection represents the opposite to the connection in ...
Published: 2017
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47. How Aging Affects Grasping Behavior and Pull Strength in Captive Gray Mouse Lemurs (Microcebus murinus)

Author: Marie Le Brazidec, Boulinguez-Ambroise Grégoire, Emmanuelle Pouydebat, Anthony Herrel, Pauline Thomas, Fabienne Aujard, Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University, Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Adaptations et évolution des systèmes ostéomusculaires (AESO), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Harvard University [Cambridge], Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Mécanismes adaptatifs : des organismes aux communautés (MAOAC), and Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, medicine.medical_specialty, Microcebus murinus, [SDV]Life Sciences [q-bio], Lemur, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Grip strength, 0302 clinical medicine, Feeding behavior, Physical medicine and rehabilitation, biology.animal, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, medicine, Force platform, Young adult, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, biology.organism_classification, Animal ecology, Animal Science and Zoology, Psychology, 030217 neurology & neurosurgery, Prehensile tail
Abstract: Prehension is essential for animal survival and fitness. It is involved in locomotion and feeding behavior and subject to physical and physiological constraints. Studies of prehension in primates have explored the importance of food properties and of the environment, but aging has rarely been studied although prehensile capacity may deteriorate with age in humans. To test the hypothesis that aging affects grasping abilities and to reveal possible behavioral adaptations to this, we quantified behavioral grasping strategies and pull strength in 10 young adult (2–3 yr old) and 10 aged (7–8 yr old) gray mouse lemurs (Microcebus murinus). We assessed grasping strategies in an experimental cage by quantifying grip types used to grasp static and mobile foods. We measured strength using a Kistler triaxial force platform. Our results show that 1) mobile and static foods affected individuals of different ages in similar ways; 2) older individuals used more mouth grasps than young ones; 3) aged individuals made twice as many attempts as young ones when grasping mobile food items but this difference was not significant; and 4) there were no differences in hand grip strength between age classes but young individuals showed a higher foot pull strength compared to old ones. These data suggest that the observed differences in behavior may be due to a decrease in foot grip strength, which in turn influences stability on narrow branches, forcing animals to use their hands to maintain stability and preventing them from using their hands for food-related tasks.
Published: 2017
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48. The effect of food properties on grasping and manipulation in the aquatic frog X enopus laevis

Author: Emmanuelle Pouydebat, Anthony Herrel, Madeleine Aumont, Thierry Decamps, Aude Anzeraey, Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Adaptations et évolution des systèmes ostéomusculaires (AESO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Harvard University, and Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Arboreal locomotion, biology, Physiology, Ecology, [SDV]Life Sciences [q-bio], Xenopus, Zoology, Context (language use), Aquatic Science, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Predation, 03 medical and health sciences, Aquatic species, 030104 developmental biology, Insect Science, Animal Science and Zoology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Prehensile tail, ComputingMilieux_MISCELLANEOUS
Abstract: The ability to grasp an object is fundamental from an evolutionary perspective. Involved in many daily activities, grasping has been extensively studied in primates and other mammals. Yet, other groups of tetrapods, including anurans, have also evolved significant forelimb prehensile capacities that are often thought to have originated in an arboreal context. However, grasping is also observed in aquatic species. Yet, how aquatic frogs use their forelimbs to capture and manipulate prey remains largely unknown. The aim of this study is to explore how the grasping and manipulation of food items in aquatic frogs is impacted by food properties such as size and mobility. To do so we use the aquatic frog Xenopus laevis and quantified the use of the hands and fingers while processing mobile and stationary prey of different sizes (small, intermediate, and large prey). Our results show that X. laevis is able to individualize the digits and that the mobility and the length of the prey significantly influence the kind of grasping pattern used. Grasping abilities are thus not specific to terrestrial, nor arboreal species. These results illustrate how prey properties impact grasping and manipulation strategies in an aquatic frog and shed further light on the ecological contexts that may have given rise to the origin of grasping in frogs.
Published: 2017
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49. Morphological integration in the appendicular skeleton of two domestic taxa: the horse and donkey

Author: Anthony Herrel, Pauline Hanot, Raphaël Cornette, Claude Guintard, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Mécanismes Adaptatifs et Evolution (MECADEV), SIERDAH, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Appendicular skeleton, Evolution, [SDV]Life Sciences [q-bio], Anatomical structures, Diversification (marketing strategy), Biology, Breeding, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Bone and Bones, 03 medical and health sciences, Specialization (functional), [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Forelimb, medicine, Animals, Horses, Selection, Genetic, ComputingMilieux_MISCELLANEOUS, General Environmental Science, Morphometrics, General Immunology and Microbiology, Ecology, [SDV.BA]Life Sciences [q-bio]/Animal biology, General Medicine, Equidae, Biological Evolution, Hindlimb, 030104 developmental biology, medicine.anatomical_structure, Taxon, Morphological integration, Evolutionary biology, Female, Donkey, General Agricultural and Biological Sciences, Locomotion
Abstract: Organisms are organized into suites of anatomical structures that typically covary when developmentally or functionally related, and this morphological integration plays a determinant role in evolutionary processes. Artificial selection on domestic species causes strong morphological changes over short time spans, frequently resulting in a wide and exaggerated phenotypic diversity. This raises the question of whether integration constrains the morphological diversification of domestic species and how natural and artificial selection may impact integration patterns. Here, we study the morphological integration in the appendicular skeleton of domestic horses and donkeys, using three-dimensional geometric morphometrics on 75 skeletons. Our results indicate that a strong integration is inherited from developmental mechanisms which interact with functional factors. This strong integration reveals a specialization in the locomotion of domestic equids, partly for running abilities. We show that the integration is stronger in horses than in donkeys, probably because of a greater degree of specialization and predictability of their locomotion. Thus, the constraints imposed by integration are weak enough to allow important morphological changes and the phenotypic diversification of domestic species.
Published: 2017
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50. Xylem tension relaxation under water does not lead to refilling in embolized grapevine petioles

Author: Herrera, José C., Cochard, Hervé, Badel, Eric, Hochberg, Uri, Division of Viticulture and Pomology, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant - Clermont Auvergne (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Department of Organismic and Evolutionary Biology, Harvard University [Cambridge], Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), and Harvard University
Subjects: Vegetal Biology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biologie végétale
Abstract: Xylem tension relaxation under water does not lead to refilling in embolized grapevine petioles. 3rd Xylem International Meeting
Published: 2017

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