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1.
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16 p, 3.6 MB |
The population genomic legacy of the second plague pandemic
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Gopalakrishnan, Shyam (University of Copenhagen. The GLOBE Institute) ;
Ebenesersdóttir, S. Sunna (University of Iceland. Department of Anthropology) ;
Lundstrøm, Inge K.C. (University of Copenhagen. The GLOBE Institute) ;
Turner-Walker, Gordon (National Yunlin University of Science & Technology (Taiwan)) ;
Moore, Kristjan H.S. (deCODE Genetics (Reykjavík, Islàndia)) ;
Luisi, Pierre (Universidad Nacional de Córdoba (Argentina)) ;
Margaryan, Ashot (University of Copenhagen. The GLOBE Institute) ;
Martin, Michael D. (Norwegian University of Science and Technology. NTNU University Museum) ;
Ellegaard, Martin Rene (Norwegian University of Science and Technology. NTNU University Museum) ;
Magnússon, Ólafur þ. (deCODE Genetics (Reykjavík, Islàndia)) ;
Sigurðsson, Ásgeir (deCODE Genetics (Reykjavík, Islàndia)) ;
Snorradóttir, Steinunn (deCODE Genetics (Reykjavík, Islàndia)) ;
Magnúsdóttir, Droplaug N. (deCODE Genetics (Reykjavík, Islàndia)) ;
Laffoon, Jason E. (Leiden University. Department of Archaeological Sciences) ;
van Dorp, Lucy (University College London. Department of Genetics, Evolution and Environment) ;
Liu, Xiaodong (University of Copenhagen. Department of Biology) ;
Moltke, Ida (University of Copenhagen. Department of Biology) ;
Ávila-Arcos, Maria C (Universidad Nacional Autónoma de México. Laboratorio Internacional de Investigación sobre el Genoma Humano) ;
Schraiber, Joshua G. (Illumina Inc. Illumina Artificial Intelligence Laboratory (USA)) ;
Rasmussen, Simon (University of Copenhagen. Novo Nordisk Foundation Center for Protein Research) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Gelabert, Pere (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
de-Dios, Toni (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fotakis, Anna K. (University of Copenhagen. The GLOBE Institute) ;
Iraeta-Orbegozo, Miren (University of Copenhagen. The GLOBE Institute) ;
Vågene, Åshild J. (Max Planck Institute for the Science of Human History) ;
Denham, Sean Dexter (University of Stavanger. Museum of Archaeology) ;
Christophersen, Axel (Norwegian University of Science and Technology. NTNU University Museum) ;
Stenøien, Hans K. (Norwegian University of Science and Technology. NTNU University Museum) ;
Garrett Vieira, Filipe (University of Copenhagen. The GLOBE Institute) ;
Liu, Shanlin (China National GeneBank) ;
Günther, Torsten (Evolutionsbiologisk Centrum EBC (Sweden)) ;
Kivisild, Toomas (University of Tartu. Institute of Genomics) ;
Moseng, Ole Georg (University of South-Eastern Norway. Department of Business, History and Social Sciences) ;
Skar, Birgitte (Norwegian University of Science and Technology. NTNU University Museum) ;
Cheung, Christina (Muséum National d'Histoire Naturelle (París, França)) ;
Sandoval-Velasco, Marcela (University of Copenhagen. The GLOBE Institute) ;
Wales, Nathan (University of York. Department of Archaeology) ;
Schroeder, Hannes (University of Copenhagen. The GLOBE Institute) ;
Campos, Paula F. (Universidade do Porto. Centro Interdisciplinar de Investigação Marinha e Ambiental) ;
Guðmundsdóttir, Valdís B. (University of Iceland. Department of Anthropology) ;
Sicheritz-Ponten, Thomas (AIMST University (Malàisia). Centre of Excellence for Omics-Driven Computational Biodiscovery) ;
Petersen, Bent (AIMST University (Malàisia). Centre of Excellence for Omics-Driven Computational Biodiscovery) ;
Halgunset, Jostein (Biobank1 (Norway)) ;
Gilbert, Edmund (School of Pharmacy and Biomolecular Sciences (Ireland)) ;
Cavalleri, Gianpiero L. (FutureNeuro SFI Research Centre (Ireland)) ;
Hovig, Eivind (University of Oslo. Center for Bioinformatics) ;
Kockum, Ingrid (Karolinska Institutet (Estocolm, Suècia). Department of Clinical Neuroscience) ;
Olsson, Tomas (Karolinska Institutet (Estocolm, Suècia). Department of Clinical Neuroscience) ;
Alfredsson, Lars (Karolinska Institutet (Estocolm, Suècia)) ;
Hansen, Thomas F. (Copenhagen Mental Health Services. Institute of Biological Psychiatry) ;
Werge, Thomas (Copenhagen Mental Health Services. Institute of Biological Psychiatry) ;
Willerslev, Eske (University of Cambridge. Department of Zoology) ;
Balloux, François (University College London. Department of Genetics, Evolution and Environment) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Lalueza-Fox, Carles (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Nielsen, Rasmus (University of California. Department of Integrative Biology) ;
Stefánsson, Kári (deCODE Genetics (Reykjavík, Islàndia)) ;
Helgason, Agnar (deCODE Genetics (Reykjavík, Islàndia)) ;
Gilbert, M. Thomas P. (Norwegian University of Science and Technology. University Museum)
Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%. [...]
2022 -  10.1016/j.cub.2022.09.023
Current Biology, Vol. 32 (November 2022) , p. 1-9/e1-e6
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2.
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15 p, 1.4 MB |
Identification of African Swine Fever Virus Transcription within Peripheral Blood Mononuclear Cells of Acutely Infected Pigs
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Olesen, Ann Sofie (Statens Serum Institut. Department of Virus & Microbiological Special Diagnostics) ;
Kodama, Miyako (University of Copenhagen. Center for Evolutionary Hologenomics) ;
Lohse, Louise (Statens Serum Institut. Department of Virus & Microbiological Special Diagnostics) ;
Accensi Alemany, Francesc (Universitat Autònoma de Barcelona. Departament de Sanitat i d'Anatomia Animals) ;
Rasmussen, Thomas Bruun (Statens Serum Institut. Department of Virus & Microbiological Special Diagnostics) ;
Lazov, Christina Marie (University of Copenhagen. Department of Veterinary and Animal Sciences) ;
Limborg, Morten T. (University of Copenhagen. Center for Evolutionary Hologenomics) ;
Gilbert, M. Thomas P. (University of Copenhagen. Center for Evolutionary Hologenomics) ;
Bøtner, Anette (Statens Serum Institut. Department of Virus & Microbiological Special Diagnostics) ;
Belsham, Graham J. (University of Copenhagen. Department of Veterinary and Animal Sciences)
African swine fever virus (ASFV) has become widespread in Europe, Asia and elsewhere, thereby causing extensive economic losses. The viral genome includes nearly 200 genes, but their expression within infected pigs has not been well characterized previously. [...]
2021 - 10.3390/v13112333
Viruses, Vol. 13 (november 2021)
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3.
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14 p, 1.7 MB |
Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics
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Tous, Núria (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal) ;
Marcos, Sofia (University of the Basque Country. Applied Genomics and Bioinformatics) ;
Goodarzi Boroojeni, Farshad (Freie Universität Berlin. Department of Veterinary Medicine) ;
Pérez de Rozas, Ana (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal) ;
Zentek, Jürgen (Freie Universität Berlin. Department of Veterinary Medicine) ;
Estonba, Andone (University of the Basque Country. Applied Genomics and Bioinformatics) ;
Sandvang, Dorthe (Animal Health Innovation) ;
Gilbert, M. Thomas P. (Norwegian University of Science and Technology) ;
Esteve-Garcia, Enric (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal) ;
Finn, Robert (European Bioinformatics Institute) ;
Alberdi, Antton (University of Copenhagen. Center for Evolutionary Hologenomics) ;
Tarradas, Joan (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal)
Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. [...]
2022 - 10.3389/fphys.2022.884925
Frontiers in physiology, Vol. 13 (september 2022)
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4.
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13 p, 1.1 MB |
Arctic-adapted dogs emerged at the Pleistocene-Holocene transition
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Sinding, Mikkel-Holger S. (University of Copenhagen. The GLOBE Institute) ;
Gopalakrishnan, Shyam (University of Copenhagen. The GLOBE Institute) ;
Ramos-Madrigal, Jazmín (University of Copenhagen. The GLOBE Institute) ;
de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Pitulko, Vladimir (Russian Academy of Sciences. Institute for the History of Material Culture) ;
Kuderna, Lukas (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Feuerborn, Tatiana (University of Copenhagen. The GLOBE Institute) ;
Frantz, Laurent (University of Oxford. The Palaeogenomics and Bio-Archaeology Research Network) ;
Garrett Vieira, Filipe (University of Copenhagen. The GLOBE Institute) ;
Niemann, Jonas (University of Copenhagen. The GLOBE Institute) ;
Samaniego Castruita, José Alfredo (University of Copenhagen. The GLOBE Institute) ;
Carøe, Christian (University of Copenhagen. The GLOBE Institute) ;
Andersen-Ranberg, Emilie Ulrikka (University of Greenland. The Qimmeq Project) ;
Jordan, Peter (University of Groningen. Arctic Centre and Groningen Institute of Archaeology) ;
Pavlova, Elena (Arctic and Antarctic Research Institute (St. Petersburg, Russia)) ;
Nikolskiy, Pavel (Russian Academy of Sciences. Geological Institute) ;
Kasparov, Aleksei (Russian Academy of Sciences. Institute for the History of Material Culture) ;
Ivanova, Varvara (VNIIOkeangeologia Research Institute) ;
Willerslev, Eske (University of Copenhagen. The GLOBE Institute) ;
Skoglund, Pontus (Harvard Medical School. Department of Genetics) ;
Fredholm, Merete (University of Copenhagen. Department of Veterinary and Animal Sciences) ;
Wennerberg, Sanne Eline (Government of Greenland. Ministry of Fisheries, Hunting and Agriculture) ;
Heide-Jørgensen, Mads Peter (Greenland Institute of Natural Resources) ;
Dietz, Rune (Aarhus University. Department of Bioscience) ;
Sonne, Christian (University of Greenland. The Qimmeq Project) ;
Meldgaard, Morten (University of Copenhagen. The GLOBE Institute) ;
Dalén, Love (Centre for Palaeogenetics) ;
Larson, Greger (University of Oxford. The Palaeogenomics and Bio-Archaeology Research Network) ;
Petersen, Bent (University of Copenhagen. The GLOBE Institute) ;
Sicheritz-Ponten, Thomas (AIMST University (Malàisia). Centre of Excellence for Omics-Driven Computational Biodiscovery) ;
Bachmann, Lutz (University of Oslo. Natural History Museum) ;
Wiig, Øystein (University of Oslo. Natural History Museum) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Hansen, Anders Johannes (University of Copenhagen. The GLOBE Institute) ;
Gilbert, M. Thomas P. (University of Copenhagen. The GLOBE Institute)
Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. [...]
2020 - 10.1126/science.aaz8599
Science, Vol. 368, Issue 6498 (June 2020) , p. 1495-1499
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5.
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7 p, 1.4 MB |
The Earth BioGenome Project 2020: Starting the clock
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Lewin, Harris A. (University of California Davis. Department of Evolution and Ecology (USA)) ;
Richards, Stephen (University of California Davis. Genome Center) ;
Aiden, Erez (Baylor College of Medicine) ;
Allende, Miguel L. (Universidad de Chile. Center for Genome Regulation) ;
Archibald, John M. (Dalhousie University. Department of Biochemistry & Molecular Biology) ;
Bálint, Miklós M. (Senckenberg Leibniz Institution for Biodiversity and Earth System Research. LOEWE Centre of Translational Biodiversity Genomics) ;
Barker, Katharine M. (Smithsonian Institution. National Museum of Natural History) ;
Baumgartnerk, Bridget (Revive & Restore (USA)) ;
Belov, Katherine (University of Sydney. School of Life and Environmental Sciences) ;
Bertorelle, Giorgio (University of Ferrara. Department of Life Sciences and Biotechnology) ;
Blaxter, Mark (Wellcome Sanger Institute (Cambridge)) ;
Cai, Jing (Northwestern Polytechnical University. School of Ecology and Environment (China)) ;
Caperello, Nicolette (University of California Davis. Genome Center) ;
Carlson, Keith (University of California Santa Barbara) ;
Castilla-Rubio, Juan Carlos (Spacetime Ventures (Brazil)) ;
Chaw, Shu-Miaw (Academia Sinica. Biodiversity Research Center (Taiwan)) ;
Chen, Lei (Northwestern Polytechnical University. School of Ecology and Environment (China)) ;
Childers, Anna K. (US Department of Agriculture. Beltsville Agricultural Research Center) ;
Coddington, Jonathan A. (Smithsonian Institution. National Museum of Natural History) ;
Conde, Dalia A. (University of Southern Denmark. Department of Biology) ;
Corominas, Montserrat (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ;
Crandall, Keith A. (George Washington University. Department of Biostatistics & Bioinformatics) ;
Crawford, Andrew J. (Universidad de los Andes. Department of Biological Sciences (Colombia)) ;
Di Palma, Federica (Genome British Columbia (Vancouver)) ;
Durbin, Richard (University of Cambridge. Department of Genetics) ;
Ebenezer, ThankGod E. (Wellcome Genome Campus. European Bioinformatics Institute) ;
Edwards, Scott (Harvard University. Department of Organismic and Evolutionary Biology) ;
Fedrigo, Olivier (The Rockefeller University. Laboratory of the Neurogenetics of Language (USA)) ;
Flicek, Paul (Wellcome Trust Sanger Institute (Regne Unit)) ;
Formenti, Giulio (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Gibbs, Richard A. (Baylor College of Medicine. Human Genome Sequencing Center) ;
Gilbert, M. Thomas P. (University of Copenhagen. The GLOBE Institute) ;
Goldstein, Melissa M. (George Washington University. Department of Health Policy and Management) ;
Marshall Graves, Jennifer A. (University of Canberra. Institute for Applied Ecology) ;
Greely, Henry (Stanford University. Stanford Law School) ;
Grigoriev, Igor (United States. Department of Energy. Joint Genome Institute) ;
Hackett, Kevin J. (United States. Department of Agriculture. Agricultural Research Service) ;
Hall, Neil (Norwich Research Park. Earlham Institute (UK)) ;
Haussler, David (University of California Santa Cruz. Genome Institute (USA)) ;
Helgen, Kristofer M. (Australian Museum Research Institute) ;
Hogg, Carolyn J. (University of Sydney. School of Life and Environmental Sciences) ;
Isobe, Sachiko (Kazusa DNA Research Institute. Department of Frontier Research and Development) ;
Jakobsen, Kjetill Sigurd (University of Oslo. Department of Biosciences) ;
Janke, Axel (Senckenberg Leibniz Institution for Biodiversity and Earth System Research. LOEWE Centre of Translational Biodiversity Genomics) ;
Jarvis, Erich (The Rockefeller University. Laboratory of the Neurogenetics of Language (USA)) ;
Johnson, Warren E. (Smithsonian Conservation Biology Institute) ;
Jones, Steven J. M. (Canada's Michael Smith Genome Sciences Centre) ;
Karlsson, Elinor K. (University of Massachusetts Medical School. Bioinformatics and Integrative Biology) ;
Kersey, Paul J. (Royal Botanic Gardens Kew) ;
Kim, Jin-Hyoung (Korea Polar Research Institute. Division of Life Sciences) ;
Kress, W. John (Smithsonian Institution. National Museum of Natural History) ;
Kuraku, Shigehiro (National Institute of Genetics. Department of Genomics and Evolutionary Biology) ;
Lawniczak, Mara K. N. (Wellcome Sanger Institute (Cambridge)) ;
Leebens-Mack, James H. (University of Georgia. Department of Plant Biology) ;
Li, Xueyan (Chinese Academy of Sciences. Kunming Institute of Zoology) ;
Lindblad-Toh, Kerstin (Uppsala University. Department of Medical Biochemistry & Microbiology) ;
Liu, Xin (Beijing Genomics Institute-Shenzhen) ;
Lopez, Jose V. (Nova Southeastern University. Department of Biological Sciences) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Mazard, Sofhie (Macquarie University. Bioplatforms Australia) ;
Mazet, Jonna (University of California Davis. One Health Institute) ;
Mazzoni, Camila J. (Berlin Center for Genomics in Biodiversity Research) ;
Myers, Eugene W. (Max Planck Institute of Molecular Cell Biology and Genetics (Germany)) ;
O'Neill, Rachel J. (University of Connecticut. Institute for Systems Genomics) ;
Paez, Sadye (The Rockefeller University. Laboratory of the Neurogenetics of Language (USA)) ;
Park, Hyun (Korea University. Division of Biotechnology) ;
Robinson, Gene (University of Illinois at Urbana−Champaign. Department of Entomology) ;
Roquet, Cristina (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia) ;
Ryder, Oliver A (University of California San Diego. Department of Evolution, Behavior, and Ecology (USA)) ;
Sabir, Jamal S. M. (King Abdulaziz University. Department of Biological Sciences (Saudi Arabia)) ;
Shaffer, Howard Bradley (University of California, Los Angeles. Department of Ecology and Evolutionary Biology) ;
Shank, Timothy M. (Woods Hole Oceanographic Institution) ;
Sherkow, Jacob S. (University of Illinois at Urbana−Champaign. Department of Entomology) ;
Soltis, Pamela (University of Florida. Florida Museum of Natural History) ;
Tang, Boping (Yancheng Teachers University. School of Wetlands (China)) ;
Tedersoo, Leho (University of Tartu. Center of Mycology and Microbiology) ;
Uliano da Silva, Marcela (Wellcome Sanger Institute (Cambridge)) ;
Wang, Kun (Northwestern Polytechnical University. School of Ecology and Environment (China)) ;
Wei, Xiaofeng (Beijing Genomics Institute-Shenzhen) ;
Wetzer, Regina (University of Southern California, Los Angeles. Biological Sciences) ;
Wilson, Julia L. (Wellcome Sanger Institute (Cambridge)) ;
Xu, Xun (Beijing Genomics Institute-Shenzhen) ;
Yang, Huanming (Beijing Genomics Institute-Shenzhen) ;
Yoder, Anne (Duke University, Durham. Department of Biology) ;
Zhang, Guojie (Beijing Genomics Institute-Shenzhen)
2022 - 10.1073/pnas.2115635118
Proceedings of the National Academy of Sciences of the United States of America, Vol. 119, Num. 4 (2022) , art. e2115635118
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6.
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12 p, 1.3 MB |
The genetic impact of an Ebola outbreak on a wild gorilla population
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Fontsere, Claudia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Frandsen, Peter (University of Copenhagen. Department of Biology. Section for Computational and RNA Biology) ;
Hernandez Rodriguez, Jessica (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Niemann, Jonas (University of Copenhagen. Center for Evolutionary Hologenomics. The GLOBE Institute) ;
Hjorth Scharff-Olsen, Camilla (University of Copenhagen. Center for Evolutionary Hologenomics. The GLOBE Institute) ;
Vallet, Dominique (Centre National de la Recherche Scientifique. University of Rennes. ECOBIO: Ecosystems, Biodiversity, Evolution) ;
Le Gouar, Pascaline (Centre National de la Recherche Scientifique. University of Rennes. ECOBIO: Ecosystems, Biodiversity, Evolution) ;
Ménard, Nelly (Centre National de la Recherche Scientifique. University of Rennes. ECOBIO: Ecosystems, Biodiversity, Evolution) ;
Navarro, Arcadi, 1969- (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Siegismund, Hans R. (University of Copenhagen. Department of Biology. Section for Computational and RNA Biology) ;
Hvilsom, Christina (Copenhagen Zoo. Research and Conservation) ;
Gilbert, M. Thomas P. (University of Copenhagen. Center for Evolutionary Hologenomics. The GLOBE Institute) ;
Kuhlwilm, Martin (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Hughes, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Background: Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odzala-Kokoua National Park (Republic of Congo) alone caused a severe decline in the resident western lowland gorilla (Gorilla gorilla gorilla) population, with a 95% mortality rate. [...]
2021 - 10.1186/s12864-021-08025-y
BMC genomics, Vol. 22 (October 2021) , art. 735
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7.
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16 p, 809.0 KB |
A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives
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Westbury, Michael V. (University of Copenhagen. The GLOBE Institute) ;
Barnett, Ross (University of Copenhagen. The GLOBE Institute) ;
Sandoval-Velasco, Marcela (University of Copenhagen. The GLOBE Institute) ;
Gower, Graham (University of Copenhagen. The GLOBE Institute) ;
Garrett Vieira, Filipe (University of Copenhagen. The GLOBE Institute) ;
de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Hansen, Anders Johannes (University of Copenhagen. The GLOBE Institute) ;
Yamaguchi, Nobuyuki (Universiti Malaysia Terengganu. Institute of Tropical Biodiversity and Sustainable Development) ;
Werdelin, Lars (Swedish Museum of Natural History. Department of Palaeobiology) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Gilbert, M. Thomas P. (University of Copenhagen. The GLOBE Institute) ;
Lorenzen, Eline (University of Copenhagen. The GLOBE Institute)
Background: The evolutionary relationships of Felidae during their Early-Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. [...]
2021 - 10.12688/openreseurope.13104.2
Open Research Europe, Vol. 1 (2021) , art. 25
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8.
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32 p, 22.5 MB |
Towards complete and error-free genome assemblies of all vertebrate species
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Rhie, Arang (National Institutes of Health. National Human Genome Research Institute (USA)) ;
McCarthy, Shane A. (University of Cambridge. Department of Genetics (UK)) ;
Fedrigo, Olivier (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Damas, Joana (University of California Davis. The Genome Center (USA)) ;
Formenti, Giulio (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Koren, Sergey (National Institutes of Health. National Human Genome Research Institute (USA)) ;
Uliano da Silva, Marcela (Leibniz Institute for Zoo and Wildlife Research. Department of Evolutionary Genetics (Germany)) ;
Chow, William (Wellcome Trust Sanger Institute (Regne Unit)) ;
Fungtammasan, Arkarachai (DNAnexus Inc. (USA)) ;
Kim, Juwan (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea)) ;
Lee, Chul (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea)) ;
Ko, Byung June (Seoul National University. Department of Agricultural Biotechnology (Republic of Korea)) ;
Chaisson, Mark (University of Southern California (USA)) ;
Gedman, Gregory L. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA)) ;
Cantin, Lindsey J. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA)) ;
Thibaud-Nissen, Françoise (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Haggerty, Leanne (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Bista, Iliana (University of Cambridge. Department of Genetics (UK)) ;
Smith, Michelle (Wellcome Trust Sanger Institute (Regne Unit)) ;
Haase, Bettina (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Mountcastle, Jacquelyn (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Winkler, Sylke (Max Planck Institute of Molecular Cell Biology and Genetics (Germany)) ;
Paez, Sadye (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Howard, Jason (Novogene (USA)) ;
Vernes, Sonja C. (Donders Institute for Brain, Cognition and Behaviour (The Netherlands)) ;
Lama, Tanya M. (University of Massachusetts. Cooperative Fish and Wildlife Research Unit (USA)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Warren, Wesley (University of Missouri. Bond Life Sciences Center (USA)) ;
Balakrishnan, Christopher N. (East Carolina University. Department of Biology (USA)) ;
Burt, Dave (University of Queensland. UQ Genomics (Australia)) ;
George, Julia M. (Clemson University. Department of Biological Sciences (USA)) ;
Biegler, Matthew T. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA)) ;
Iorns, David (The Genetic Rescue Foundation (New Zealand)) ;
Digby, Andrew (Kākāpō Recovery, Department of Conservation (New Zealand)) ;
Eason, Daryl (Kākāpō Recovery, Department of Conservation (New Zealand)) ;
Robertson, Bruce (University of Otago. Department of Zoology (New Zealand)) ;
Edwards, Taylor (University of Arizona Genetics Core (USA)) ;
Wilkinson, Mark (Natural History Museum. Department of Life Sciences (UK)) ;
Turner, George (Bangor University. School of Natural Sciences (UK)) ;
Meyer, Axel (University of Konstanz. Department of Biology (Germany)) ;
Kautt, Andreas F. (University of Konstanz. Department of Biology (Germany)) ;
Franchini, Paolo (University of Konstanz. Department of Biology (Germany)) ;
Detrich III, H. William (Northeastern University Marine Science Center. Department of Marine and Environmental Sciences (USA)) ;
Svardal, Hannes (University of Antwerp. Department of Biology (Belgium)) ;
Wagner, Maximilian (Karl-Franzens University of Graz. Institute of Biology (Austria)) ;
Naylor, Gavin J. P. (University of Florida. Florida Museum of Natural History (USA)) ;
Pippel, Martin (Max Planck Institute of Molecular Cell Biology and Genetics (Germany)) ;
Malinsky, Milan (University of Basel. Zoological Institute (Switzerland)) ;
Mooney, Mark (Tag.bio (USA)) ;
Simbirsky, Maria (DNAnexus Inc. (USA)) ;
Hannigan, Brett T. (DNAnexus Inc. (USA)) ;
Pesout, Trevor (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Houck, Marlys (San Diego Zoo Global (USA)) ;
Misuraca, Ann (San Diego Zoo Global (USA)) ;
Kingan, Sarah B. (Pacific Biosciences (USA)) ;
Hall, Richard (Pacific Biosciences (USA)) ;
Kronenberg, Zev (Pacific Biosciences (USA)) ;
Sović, Ivan (Pacific Biosciences (USA)) ;
Dunn, Christopher (Pacific Biosciences (USA)) ;
Ning, Zemin (Wellcome Trust Sanger Institute (Regne Unit)) ;
Hastie, Alex (Bionano Genomics (USA)) ;
Lee, Joyce (Bionano Genomics (USA)) ;
Selvaraj, Siddarth (Arima Genomics (USA)) ;
Green, Richard E. (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Putnam, Nicholas H. (Independent Researcher. Santa Cruz (USA)) ;
Gut, Ivo (Centro Nacional de Análisis Genómico. Instituto de Ciencia y Tecnología de Barcelona) ;
Ghurye, Jay (University of Maryland College Park. Department of Computer Science (USA)) ;
Garrison, Erik (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Sims, Ying (Wellcome Trust Sanger Institute (Regne Unit)) ;
Collins, Joanna (Wellcome Trust Sanger Institute (Regne Unit)) ;
Pelan, Sarah (Wellcome Trust Sanger Institute (Regne Unit)) ;
Torrance, James (Wellcome Trust Sanger Institute (Regne Unit)) ;
Tracey, Alan (Wellcome Trust Sanger Institute (Regne Unit)) ;
Wood, Jonathan (Wellcome Trust Sanger Institute (Regne Unit)) ;
Dagnew, Robel E. (University of Southern California (USA)) ;
Guan, Dengfeng (Harbin Institute of Technology. Center for Bioinformatics. School of Computer Science and Technology (China)) ;
London, Sarah E. (University of Chicago. Institute for Mind and Biology. Department of Psychology (USA)) ;
Clayton, David F. (Clemson University. Department of Genetics and Biochemistry (USA)) ;
Mello, Claudio V. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA)) ;
Friedrich, Samantha R. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA)) ;
Lovell, Peter V. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA)) ;
Osipova, Ekaterina (Max Planck Institute for the Physics of Complex Systems (Germany)) ;
Al-Ajli, Farooq O. (Monash University Malaysia. Tropical Medicine and Biology Multidisciplinary Platform (Malaysia)) ;
Secomandi, Simona (University of Milan. Department of Biosciences (Italy)) ;
Kim, Heebal (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea)) ;
Theofanopoulou, Constantina (The Rockefeller University. Laboratory of Neurogenetics of Language (USA)) ;
Hiller, Michael (Goethe-University. Faculty of Biosciences (Germany)) ;
Zhou, Yang (BGI-Shenzhen (China)) ;
Harris, Robert S. (Pennsylvania State University. Department of Biology (USA)) ;
Makova, Kateryna D. (Pennsylvania State University. Department of Biology (USA)) ;
Medvedev, Paul (Pennsylvania State University. Center for Medical Genomics (USA)) ;
Hoffman, Jinna (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Masterson, Patrick (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Clark, Karen (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Martin, Fergal J. (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Howe, Kevin (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Flicek, Paul (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Walenz, Brian P. (National Institutes of Health. National Human Genome Research Institute (USA)) ;
Kwak, Woori (eGnome, Inc. (Republic of Korea)) ;
Clawson, Hiram (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Diekhans, Mark (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Nassar, Luis (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Paten, Benedict (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Kraus, Robert H. S. (Max Planck Institute of Animal Behavior. Department of Migration (Germany)) ;
Crawford, Andrew J. (Universidad de los Andes. Department of Biological Sciences (Colombia)) ;
Gilbert, M. Thomas P. (University of Copenhagen. The GLOBE Institute. Center for Evolutionary Hologenomics (Denmark)) ;
Zhang, Guojie (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics (China)) ;
Venkatesh, Byrappa (A*STAR. Institute of Molecular and Cell Biology (Singapore)) ;
Murphy, Robert W. (Royal Ontario Museum. Centre for Biodiversity (Canada)) ;
Koepfli, Klaus-Peter (Smithsonian Conservation Biology Institute) ;
Shapiro, Beth (Howard Hughes Medical Institute (USA)) ;
Johnson, Warren E. (Smithsonian Conservation Biology Institute) ;
Di Palma, Federica (University of East Anglia. Earlham Institute. Department of Biological Sciences (UK)) ;
Teeling, Emma C. (University College Dublin. School of Biology and Environmental Science (Ireland)) ;
Warnow, Tandy (The University of Illinois at Urbana-Champaign. Department of Computer Science (USA)) ;
Graves, Jennifer Marshall (La Trobe University. School of Life Science (Australia)) ;
Ryder, Oliver A. (University of California San Diego. Department of Evolution, Behavior, and Ecology (USA)) ;
Haussler, David (University of California Santa Cruz. Department of Ecology and Evolutionary Biology (USA)) ;
O'Brien, Stephen J. (ITMO University. Laboratory of Genomics Diversity-Center for Computer Technologies (Russian Federation)) ;
Korlach, Jonas (Pacific Biosciences (USA)) ;
Lewin, Harris A. (University of California Davis. John Muir Institute for the Environment (USA)) ;
Howe, Kerstin (Wellcome Trust Sanger Institute (Regne Unit)) ;
Myers, Eugene W. (Max Planck Institute of Molecular Cell Biology and Genetics (Germany)) ;
Durbin, Richard (University of Cambridge. Department of Genetics (UK)) ;
Phillippy, Adam M. (National Institutes of Health. National Human Genome Research Institute (USA)) ;
Jarvis, Erich (The Rockefeller University. Vertebrate Genome Lab (USA))
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1, 2, 3, 4. [...]
2021 - 10.1038/s41586-021-03451-0
Nature, Vol. 592 (April 2021) , p. 737-746
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9.
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14 p, 1.8 MB |
Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
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Barnett, Ross (University of Copenhagen. Section for Evolutionary Genomics) ;
Westbury, Michael V. (University of Copenhagen. Section for Evolutionary Genomics) ;
Sandoval-Velasco, Marcela (University of Copenhagen. Section for Evolutionary Genomics) ;
Garrett Vieira, Filipe (University of Copenhagen. Section for Evolutionary Genomics) ;
Jeon, Sungwon (Ulsan National Institute of Science and Technology. Department of Biomedical Engineering) ;
Zazula, Grant (Government of Yukon. Yukon Palaeontology Program) ;
Martin, Michael (Norwegian University of Science and Technology. Department of Natural History) ;
Ho, Simon Y. W. (University of Sydney. School of Life and Environmental Sciences) ;
Mather, Niklas (University of Sydney. School of Life and Environmental Sciences) ;
Gopalakrishnan, Shyam (University of Copenhagen. Center for Evolutionary Hologenomics) ;
Ramos-Madrigal, Jazmín (University of Copenhagen. Center for Evolutionary Hologenomics) ;
de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Zepeda Mendoza, Marie Lisandra (University of Birmingham. Institute of Microbiology and Infection) ;
Antunes, Agostinho (University of Porto. Department of Biology) ;
Baez, Aldo Carmon (University of Copenhagen. Section for Evolutionary Genomics) ;
De Cahsan, Binia (University of Copenhagen. Center for Evolutionary Hologenomics) ;
Larson, Greger (University of Oxford. The Palaeogenomics and Bio-Archaeology Research Network) ;
O'Brien, Stephen J. (Nova Southeastern University. Guy Harvey Oceanographic Center) ;
Eizirik, Eduardo (Instituto Pró-Carnívoros) ;
Johnson, Warren E. (Walter Reed Army Institute of Research) ;
Koepfli, Klaus-Peter (Smithsonian Conservation Biology Institute. Center for Species Survival) ;
Wilting, Andreas (Leibniz Institute for Zoo and Wildlife Research) ;
Fickel, Jöms (University of Potsdam. Institute for Biochemistry and Biology) ;
Dalén, Love (Swedish Museum of Natural History. Department of Bioinformatics and Genetics) ;
Lorenzen, Eline D. (University of Copenhagen. Center for Evolutionary Hologenomics) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Hansen, Anders J. (University of Copenhagen. Section for GeoGenetics) ;
Zhang, Guojie (Chinese Academy of Sciences. Kunming Institute of Zoology) ;
Bhak, Jong (Personal Genomics Institute. Genome Research Foundation) ;
Yamaguchi, Nobuyuki (Universiti Malaysia Terengganu. Institute of Tropical Biodiversity and Sustainable Development) ;
Gilbert, M. Thomas P. (University of Copenhagen. Center for Evolutionary Hologenomics)
Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. [...]
2020 - 10.1016/j.cub.2020.09.051
Current Biology, Vol. 30, Issue 24 (December 2020) , p. ages 5018-5025.e5
2 documentos
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10.
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8 p, 2.5 MB |
The evolutionary history of extinct and living lions
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de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Barnett, Ross (University of Copenhagen) ;
Sandoval-Velasco, Marcela (University of Copenhagen) ;
Yamaguchi, Nobuyuki (University Malaysia Terengganu) ;
Garrett Vieira, Filipe (University of Copenhagen) ;
Zepeda Mendoza, Marie Lisandra (University of Birmingham) ;
Liu, Shiping (BGI-Shenzhen) ;
Martin, Michael (Norwegian University of Science and Technology) ;
Sinding, Mikkel-Holger S. (University of Copenhagen) ;
Mak, Sarah S. T. (University of Copenhagen) ;
Carøe, Christian (University of Copenhagen) ;
Liu, Shanlin (BGI-Shenzhen) ;
Guo, Chunxue (BGI-Shenzhen) ;
Zheng, Jiao (University of Chinese. Academy of Sciences) ;
Zazula, Grant (Government of Yukon) ;
Baryshnikov, Gennady (Russian Academy of Sciences) ;
Eizirik, Eduardo (Instituto Pró-Carnívoros) ;
Koepfli, Klaus-Peter (Smithsonian Conservation Biology Institute) ;
Johnson, Warren E. (Walter Reed Army Institute of Research) ;
Antunes, Agostinho (University of Porto) ;
Sicheritz-Ponten, Thomas (Asian Institute of Medicine, Science and Technology) ;
Gopalakrishnan, Shyam (University of Copenhagen) ;
Larson, Greger (University of Oxford) ;
Yang, Huanming (James D. Watson Institute of Genome Science) ;
O'Brien, Stephen J. (Nova Southeastern University) ;
Hansen, Anders J. (University of Copenhagen) ;
Zhang, Guojie (Chinese Academy of Sciences) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Gilbert, M. Thomas P. (Norwegian University of Science and Technology)
Lions were once the most globally widespread mammal species, with distinct populations in Africa, Eurasia, and America. We generated a genomic dataset that included 2 extinct Pleistocene cave lions, 12 lions from historically extinct populations in Africa and the Middle East, and 6 modern lions from Africa and India. [...]
2020 - 10.1073/pnas.1919423117
Proceedings of the National Academy of Sciences of the United States of America, Vol. 117, Num. 20 (May 2020) , p. 10927-10934
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