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1.
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20 p, 2.9 MB |
Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr)
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Mochales-Riaño, Gabriel (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fontsere, Claudia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Talavera, Adrián (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Burriel-Carranza, Bernat (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Tejero-Cicuéndez, Héctor (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
AlGethami, Raed Hamoud M. (National Center for Wildlife) ;
Shobrak, Mohammed (National Center for Wildlife) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Carranza, Salvador (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. [...]
2023 -  10.1016/j.isci.2023.107481
iScience, Vol. 26, Issue 9 (September 2023) , art. 107481
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2.
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20 p, 2.4 MB |
Ghost admixture in eastern gorillas
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Pawar, Harvinder (Institute of Evolutionary Biology) ;
Rymbekova, Aigerim (University of Vienna. Department of Evolutionary Anthropology) ;
Cuadros-Espinoza, Sebastian (Institute of Evolutionary Biology) ;
Huang, Xin (University of Vienna. Department of Evolutionary Anthropology) ;
de Manuel, Marc (Institute of Evolutionary Biology) ;
van der Valk, Tom (Swedish Museum of Natural History) ;
Lobón, Irene (Institute of Evolutionary Biology) ;
Alvarez-Estape, Marina (Institute of Evolutionary Biology) ;
Haber, Marc (University of Birmingham. Institute of Cancer and Genomic Sciences) ;
Dolgova, Olga (Parque Científico Tecnológico de Bizkaia. Centro de Investigación Cooperativa en Biociencias) ;
Han, Sojung 1984- (Institute of Evolutionary Biology) ;
Esteller-Cucala, Paula (Institute of Evolutionary Biology) ;
Juan, David (Institute of Evolutionary Biology) ;
Ayub, Qasim (Monash University Malaysia) ;
Bautista, Ruben (Wellcome Trust Sanger Institute (Regne Unit)) ;
Kelley, Joanna (University of California. Department of Ecology and Evolutionary Biology) ;
Cornejo, Omar E. (University of California. Department of Ecology and Evolutionary Biology) ;
Lao, Oscar (Institute of Evolutionary Biology) ;
Andrés, Aida M. (University College London. Department of Genetics, Evolution and Environment) ;
Guschanski, Katerina (University of Edinburgh) ;
Ssebide, Benard (Gorilla Doctors) ;
Cranfield, Mike (University of California Davis) ;
Tyler-Smith, Chris (Wellcome Trust Sanger Institute (Regne Unit)) ;
Xue, Yali (Wellcome Trust Sanger Institute (Regne Unit)) ;
Prado-Martinez, Javier (Institute of Evolutionary Biology) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Kuhlwilm, Martin (Institute of Evolutionary Biology)
Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. [...]
2023 - 10.1038/s41559-023-02145-2
Nature ecology & evolution, Vol. 7 (July 2023) , p. 1503-1514
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3.
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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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4.
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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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5.
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12 p, 2.8 MB |
The genomics of ecological flexibility, large brains,and long lives in capuchin monkeys revealedwith fecalFACS
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Orkin, Joseph (University of Calgary. Department of Anthropology and Archaeology) ;
Montague, Michael (University of Pennsylvania. Department of Neuroscience) ;
Tejada-Martinez, Daniela (Thomas Jefferson University. Department of Biochemistry and Molecular Biology) ;
de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
del Campo, Javier (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Cheves Hernandez, Saul (Área de Concervación Guanacaste) ;
Di Fiore, Anthony (University of Texas at Austin. Department of Anthropology and Primate Molecular Ecology and Evolution Laboratory) ;
Fontsere, Claudia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Hodgson, Jason A. (Pennsylvania State University. Department of Anthropology) ;
Janiak, Mareike (University of Calgary. Department of Anthropology and Archaeology) ;
Kuderna, Lukas (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Martino, Maria Pia (Kids Saving the Rainforest Wildlife Rescue Center) ;
Niimura, Yoshihito (The University of Tokyo. Department of Applied Biological Chemistry) ;
Perry, George (Pennsylvania State University. Department of Anthropology) ;
Soto Valverde, Carmen (Kids Saving the Rainforest Wildlife Rescue Center) ;
Tanga, Jia (University of Calgary. Department of Anthropology and Archaeology) ;
Warren, Wesley (University of Missouri. Division of Animal Sciences, School of Medicine) ;
de Magalhaes, Joao Pedro (University of Liverpool. Institute of Ageing and Chronic Disease) ;
Kawamura, Shoji (The University of Tokyo. Department of Integrated Biosciences) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Krawetz, Roman (University of Calgary. Department of Cell Biology and Anatomy) ;
Melin, Amanda D. (University of Calgary. Department of Anthropology and Archaeology)
Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. [...]
2021 - 10.1073/pnas.2010632118
Proceedings of the National Academy of Sciences of the United States of America, Vol. 118, Issue 7 (February 2021) , e2010632118
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6.
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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 documents
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7.
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11 p, 571.9 KB |
Multiple genomic events altering Hominin SIGLEC biology and innate immunity predated the common ancestor of humans and archaic Hominins
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Khan, Naazneen (University of California. Glycobiology Research and Training Center. Department of Medicine (USA)) ;
de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Peyregne, Stephane (Max Planck Institute for Evolutionary Anthropology. Department of Evolutionary Genetics) ;
Do, Raymond (University of California. Glycobiology Research and Training Center. Department of Medicine (USA)) ;
Prufer, Kay (Max Planck Institute for Evolutionary Anthropology. Department of Evolutionary Genetics) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Varki, Nissi (University of California. Glycobiology Research and Training Center. Department of Medicine (USA)) ;
Gagneux, Pascal (University of California. Glycobiology Research and Training Center. Department of Medicine (USA)) ;
Varki, Ajit (University of California. Glycobiology Research and Training Center. Department of Medicine (USA))
Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface "self-associated molecular patterns" that modulate innate immunity via engagement of CD33-related-Siglec receptors. [...]
2020 - 10.1093/gbe/evaa125
Genome biology and evolution, Vol. 12, Issue 7 (July 2020) , p. 1040-1050
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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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9.
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13 p, 1.5 MB |
Plasmodium vivax Malaria viewed through the lens of an eradicated European strain
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van Dorp, Lucy (University College London. UCL Genetics Institute (UK)) ;
Gelabert Xirinachs, Pere (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Rieux, Adrien (Coopération Internationale en Recherche Agronomique pour le Développement (France)) ;
de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
de-Dios, Toni (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Gopalakrishnan, Shyam (University of Copenhagen. The GLOBE Institute (Denmark)) ;
Carøe, Christian (University of Copenhagen. The GLOBE Institute (Denmark)) ;
Sandoval Velasco, Marcela (University of Copenhagen. The GLOBE Institute (Denmark)) ;
Fregel, Rosa (Universidad de La Laguna. Departamento de Bioquímica, Microbiología, Biología Celular y Genética) ;
Olalde, Iñigo (Harvard Medical School. Department of Genetics (USA)) ;
Escosa, Raúl (Consorci de Polítiques Ambientals de les Terres de l'Ebre) ;
Aranda Pallero, Carles (Consell Comarcal del Baix Llobregat. Servei de Control de Mosquits) ;
Huijben, Silvie (Barcelona Institute for Global Health (ISGlobal)) ;
Mueller, Ivo (Barcelona Institute for Global Health (ISGlobal)) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Balloux, François (University College London. UCL Genetics Institute (UK)) ;
Gilbert, M. Thomas P. (University of Copenhagen. The GLOBE Institute (Denmark)) ;
Lalueza-Fox, Carles (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. [...]
2020 - 10.1093/molbev/msz264
Molecular biology and evolution, Vol. 37, Issue 3 (March 2020) , p. 773-785
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10.
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19 p, 6.6 MB |
Evolutionary history, genomic adaptation to toxic diet, and extinction of the Carolina Parakeet
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Gelabert, Pere (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Sandoval Velasco, Marcela (University of Copenhagen. The GLOBE Institute) ;
Serres, Aitor (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
de Manuel, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Renom, Pere (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Margaryan, Ashot (University of Copenhagen. The GLOBE Institute) ;
Stiller, Josefin (University of Copenhagen. Department of Biology) ;
de-Dios, Toni (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fang, Qi (BGI-Shenzhen (China)) ;
Feng, Shaohong (BGI-Shenzhen (China)) ;
Mañosa, Santi (Universitat de Barcelona. Institut de Recerca de la Biodiversitat (IRBio)) ;
Pacheco, George (University of Copenhagen. The GLOBE Institute) ;
Ferrando-Bernal, Manuel (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Shi, Guolin (Northwestern Polytechnical University. Center of Special Environmental Biomechanics & Biomedical Engineering) ;
Hao, Fei (Northwestern Polytechnical University. Center of Special Environmental Biomechanics & Biomedical Engineering) ;
Chen, Xianqing (Northwestern Polytechnical University. Center for Ecological and Environmental Sciences) ;
Petersen, Bent (AIMST University (Malàisia). Centre of Excellence for Omics-Driven Computational Biodiscovery) ;
Olsen, Remi-André (Stockholm University. Department of Biochemistry and Biophysics) ;
Navarro, Arcadi, 1969- (Institució Catalana de Recerca i Estudis Avançats) ;
Deng, Yuan (BGI-Shenzhen (China)) ;
Dalén, Love (Swedish Museum of Natural History. Department of Bioinformatics and Genetics) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Zhang, Guojie (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics) ;
Antunes, Agostinho (University of Porto. Department of Biology) ;
Gilbert, M. Thomas P. (NTNU University Museum (Norway)) ;
Lalueza-Fox, Carles (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. [...]
2020 - 10.1016/j.cub.2019.10.066
Current biology, Vol. 30, Issue 1 (January 2020) , p. 108-114
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