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12 p, 1.3 MB |
Real-time genomics for One Health
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Urban, Lara (Helmholtz Zentrum Muenchen) ;
Perlas Puente, Albert (Helmholtz Zentrum Muenchen) ;
Francino, Olga (Nano1Health, S.L.) ;
Martí-Carreras, Joan (Nano1Health, S.L.) ;
Muga, Brenda (University of Otago. Department of Anatomy) ;
Mwangi, Jenniffer W. (Machakos University. Biological Department) ;
Okalebo, Laura Boykin (BioTeam, Inc. (USA)) ;
Stanton, Jo-Ann (University of Otago. Department of Anatomy) ;
Black, Amanda (Lincoln University. Bioprotection Aotearoa) ;
Waipara, Nick (Plant and Food Research (New Zealand)) ;
Fontsere, Claudia (University of Copenhagen. The Globe Institute. Center for Evolutionary Hologenomics) ;
Eccles, David (Malaghan Institute of Medical Research. Hugh Green Cytometry Centre) ;
Urel, Harika (Helmholtz Zentrum Muenchen) ;
Reska, Tim (Helmholtz Zentrum Muenchen) ;
Morales, Hernan (University of Copenhagen. The Globe Institute. Center for Evolutionary Hologenomics) ;
Palmada-Flores, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Watsa, Mrinalini (San Diego Zoo Wildlife Alliance) ;
Libke, Zane (Instituto Nacional de Biodiversidad (Ecuador)) ;
Erkenswick, Gideon (Field Projects International (USA)) ;
van Oosterhout, Cock (University of East Anglia)
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. [...]
2023 -  10.15252/msb.202311686
Molecular systems biology, Vol. 19, Issue 6 (June 2023) , art. e11686
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39 p, 4.4 MB |
Population dynamics and genetic connectivity in recent chimpanzee history
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Fontsere, Claudia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Kuhlwilm, Martin (University of Vienna. Human Evolution and Archaeological Sciences) ;
Morcillo-Suarez, Carlos (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Alvarez-Estape, Marina (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Lester, Jack D. (Max Planck Institute for Evolutionary Anthropology) ;
Gratton, Paolo (Università di Roma "Tor Vergata". Dipartimento di Biologia) ;
Schmidt, Joshua M. (The University of Adelaide. School of Biological Sciences) ;
Dieguez, Paula (German Centre for Integrative Biodiversity Research (Halle-Jena-Leipzig, Alemanya)) ;
Aebischer, Thierry (University of Fribourg) ;
Álvarez-Varona, Paula (Jane Goodall Institute Spain and Senegal) ;
Agbor, Anthony (Max Planck Institute for Evolutionary Anthropology) ;
Angedakin, Samuel (Max Planck Institute for Evolutionary Anthropology) ;
Assumang, Alfred K. (Kwame Nkrumah University of Science and Technology. Department of Wildlife and Range Management) ;
Ayimisin, Emmanuel A. (Max Planck Institute for Evolutionary Anthropology) ;
Bailey, Emma (Max Planck Institute for Evolutionary Anthropology) ;
Barubiyo, Donatienne (Max Planck Institute for Evolutionary Anthropology) ;
Bessone, Mattia (Max Planck Institute for Evolutionary Anthropology) ;
Carretero-Alonso, Andrea (Fundación Rainfer) ;
Chancellor, Rebecca (West Chester University. Depts of Anthropology and Sociology and Psychology) ;
Cohen, Heather (Wild Chimpanzee Foundation) ;
Danquah, Emmanuel (Kwame Nkrumah University of Science and Technology. Department of Wildlife and Range Management) ;
Deschner, Tobias (Max Planck Institute for Evolutionary Anthropology) ;
Dunn, Andrew (Wildlife Conservation Society) ;
Dupain, Jef (Antwerp Zoo Foundation) ;
Egbe, Villard E. (Max Planck Institute for Evolutionary Anthropology) ;
Feliu, Olga (Fundació MONA) ;
Goedmakers, Annemarie (Chimbo Foundation) ;
Granjon, Anne-Céline (Max Planck Institute for Evolutionary Anthropology) ;
Head, Josephine (Max Planck Institute for Evolutionary Anthropology) ;
Hedwig, Daniela (Cornell University. K. Lisa Yang Center for Conservation) ;
Hermans, Veerle (Royal Zoological Society of Antwerp) ;
Hernandez-Aguilar, R. Adriana (Universitat de Barcelona. Departament de Psicologia Social i Psicologia Quantitativa) ;
Imong, Inaoyom (Wildlife Conservation Society) ;
Jones, Sorrel (RSPB Centre of Conservation Science) ;
Junker, Jessica (German Centre for Integrative Biodiversity Research (Halle-Jena-Leipzig, Alemanya)) ;
Kadam, Parag (Greater Mahale Ecosystem Research and Conservation Project) ;
Kaiser, Mike (Max Planck Institute for Evolutionary Anthropology) ;
Kambere, Mbangi (Max Planck Institute for Evolutionary Anthropology) ;
Kambale, Magloire V. (Max Planck Institute for Evolutionary Anthropology) ;
Kalan, Ammie K. (University of Victoria. Department of Anthropology) ;
Kienast, Ivonne (Max Planck Institute for Evolutionary Anthropology) ;
Kujirakwinja, Deo (Wildlife Conservation Society) ;
Langergraber, Kevin (Arizona State University) ;
Lapuente, Juan (Max Planck Institute for Evolutionary Anthropology) ;
Larson, Bradley (Max Planck Institute for Evolutionary Anthropology) ;
Laudisoit, Anne (Evolutionary Ecology group) ;
Lee, Kevin (Arizona State University. School of Human Evolution and Social Change) ;
Llana, Manuel (Jane Goodall Institute Spain and Senegal) ;
Llorente, Miquel (Universitat de Girona. Departament de Psicologia) ;
Marrocoli, Sergio (Max Planck Institute for Evolutionary Anthropology) ;
Morgan, David (Lester E. Fisher Center for the Study and Conservation of Apes) ;
Mulindahabi, Felix (Wildlife Conservation Society) ;
Murai, Mizuki (Max Planck Institute for Evolutionary Anthropology) ;
Neil, Emily (Max Planck Institute for Evolutionary Anthropology) ;
Nicholl, Sonia (Max Planck Institute for Evolutionary Anthropology) ;
Nixon, Stuart (Chester Zoo) ;
Normand, Emma (Wild Chimpanzee Foundation) ;
Orbell, Chris (Panthera) ;
Ormsby, Lucy J. (Max Planck Institute for Evolutionary Anthropology) ;
Pacheco, Liliana (Centres Molina) ;
Piel, Alex (University College London. Department of Anthropology) ;
Riera, Laura (Fundació MONA) ;
Robbins, Martha M. (Max Planck Institute for Evolutionary Anthropology) ;
Rundus, Aaron (West Chester University. Department of Psychology) ;
Sanz, Crickette (Wildlife Conservation Society) ;
Sciaky, Lilah (Max Planck Institute for Evolutionary Anthropology) ;
Sommer, Volker (Primate Project) ;
Stewart, Fiona A. (Liverpool John Moores University. School of Biological & Environmental Sciences) ;
Tagg, Nikki (Royal Zoological Society of Antwerp) ;
Tédonzong, Luc Roscelin (Royal Zoological Society of Antwerp) ;
Ton, Els (Chimbo Foundation) ;
van Schijndel, Joost (Chimbo Foundation) ;
Vergnes, Virginie (Wild Chimpanzee Foundation) ;
Wessling, Erin G. (Harvard University. Department of Human Evolutionary Biology) ;
Willie, Jacob (Ghent University. Department of Biology) ;
Wittig, Roman M. (Taï Chimpanzee Project) ;
Yuh, Yisa G. (University of Concordia. Department of Geography, Planning and Environmental Studies) ;
Yurkiw, Kyle (Max Planck Institute for Evolutionary Anthropology) ;
Zuberbuehler, Klaus (University of St. Andrews. School of Psychology and Neuroscience) ;
Hecht, Jochen (Institut de Ciència i Tecnologia de Barcelona) ;
Vigilant, Linda (Max Planck Institute for Evolutionary Anthropology) ;
Boesch, Christophe (Max Planck Institute for Evolutionary Anthropology) ;
Andrés, Aida M. (University College London. Department of Genetics, Evolution and Environment) ;
Hughes, David A. (University of Bristol. Bristol Medical School) ;
Kühl, Hjalmar S. (German Centre for Integrative Biodiversity Research (Halle-Jena-Leipzig, Alemanya)) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Arandjelovic, Mimi (German Centre for Integrative Biodiversity Research (Halle-Jena-Leipzig, Alemanya)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. [...]
2022 - 10.1016/j.xgen.2022.100133
Cell Genomics, Vol. 2, Issue 6 (June 2022) , art. 100133
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1 p, 5.9 MB |
Ancient and modern genomes unravel the evolutionary history of the rhinoceros family
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Liu, Shanlin (China Agricultural University. Department of Entomology, College of Plant Protection) ;
Westbury, Michael V. (University of Copenhagen. The GLOBE Institute) ;
Dussex, Nicolas (Centre for Palaeogenetics) ;
Kieren, J. Mitchell (University of Adelaide. School of Biological Sciences) ;
Sinding, Mikkel-Holger S. (University of Copenhagen. The GLOBE Institute) ;
Heintzman, Peter D. (UiT The Arctic University of Norway. The Arctic University Museum of Norway) ;
Duchêne, David A. (University of Copenhagen. The GLOBE Institute) ;
Kapp, Joshua D. (University of California. Department of Ecology and Evolutionary Biology) ;
Von Seth, Joahanna (Centre for Palaeogenetics) ;
Heiniger, Holly (School of Biological Sciences, University of Adelaide) ;
Sánchez-Barreiro, Fátima (University of Copenhagen. The GLOBE Institute) ;
Margaryan, Ashot (University of Copenhagen. The GLOBE Institute) ;
André-Olsen, Remi (Stockholm University. Science for Life Laboratory) ;
De Cahsan, Binia (University of Copenhagen. The GLOBE Institute) ;
Meng, Guanliang (China National Genebank) ;
Yang, Chentao (China National Genebank) ;
Chen, Lei (Center for Ecological and Environmental Sciences) ;
Van der Valk, Tom (Uppsala University. Department of Cell and Molecular Biology) ;
Moodley, Yoshan (University of Venda. Department of Zoology) ;
Rookmaaker, Leendert (Rhino Resource Center) ;
Bruford, Michael W. (Cardiff University. School of Biosciences) ;
Ryder, Oliver A (San Diego Zoo Wildlife Alliance) ;
Steiner, Cynthia (San Diego Zoo Wildlife Alliance) ;
Bruins-van Sonsbeek, Linda G. R. (Rotterdam Zoo) ;
Vartanyan, Sergey (Russian Academy of Sciences) ;
Guo, Chunxue (China National Genebank) ;
Cooper, Alan (South Australian Museum) ;
Kosintsev, Pavel (Russian Academy of Sciences) ;
Kirillova, Irina (Russian Academy of Sciences) ;
Lister, Adrian M. (Natural History Museum) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Gopalakrishnan, Shyam (University of Copenhagen. The GLOBE Institute) ;
Dunn, Robert R. (University of Copenhagen. The GLOBE Institute) ;
Lorenzen, Eline D. (University of Copenhagen. The GLOBE Institute) ;
Shapiro, Beth (University of California. Department of Ecology and Evolutionary Biology) ;
Zhang, Guojie (China National Genebank) ;
Antoine, Pierre-Olivier (Université Montpellier. Institut des Sciences de l'Évolution) ;
Dalén, Love (Centre for Palaeogenetics) ;
P. Gilbert, M. Thomas (University of Copenhagen. The GLOBE Institute)
Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. [...]
2021 - 10.1016/j.cell.2021.07.032
Cell, Vol. 184 (September 2021) , p. 1-12
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19 p, 6.2 MB |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
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Abascal, Federico (Centro Nacional de Investigaciones Oncológicas) ;
Corvelo, André (Centre Nacional d'Anàlisi Genòmica) ;
Cruz, Fernando (Centre Nacional d'Anàlisi Genòmica) ;
Villanueva-Cañas, J. L. (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Vlasova, Anna (Centre de Regulació Genòmica) ;
Marcet-Houben, Marina (Centre de Regulació Genòmica) ;
Martínez-Cruz, B. (Estación Biológica de Doñana) ;
Cheng, J. Y. (Aarhus University. Bioinformatics Research Centre) ;
Prieto, P. (Centre de Regulació Genòmica) ;
Quesada, V. (Universidad de Oviedo. Instituto Universitario de Oncología) ;
Quilez, J. (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Li, G. (Texas A;M University. Department of Veterinary Integrative Biosciences) ;
García, Francisca (Universitat Autònoma de Barcelona. Servei de Cultius Cel·lulars, Producció d'Anticossos i Citometria) ;
Rubio-Camarillo, M. (Centro Nacional de Investigaciones Oncológicas) ;
Frias, Leonor (Centre Nacional d'Anàlisi Genòmica) ;
Ribeca, Paolo (Centre Nacional d'Anàlisi Genòmica) ;
Capella-Gutiérrez, Salvador (Centre de Regulació Genòmica) ;
Rodríguez, J. M. (Centro Nacional de Investigaciones Oncológicas) ;
Câmara, F. (Centre de Regulació Genòmica) ;
Lowy, Ernesto (Centre de Regulació Genòmica) ;
Cozzuto, Luca (Centre de Regulació Genòmica) ;
Erb, I. (Centre de Regulació Genòmica) ;
Tress, M. L. (Centro Nacional de Investigaciones Oncológicas) ;
Rodriguez-Ales, J. L. (Centre de Regulació Genòmica) ;
Ruiz-Orera, J. (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Reverter, F. (Centre de Regulació Genòmica) ;
Casas-Marce, M. (Estación Biológica de Doñana) ;
Soriano, L. (Estación Biológica de Doñana) ;
Arango, Javier R (Universidad de Oviedo. Departamento de Bioquímica y Biología Molecular) ;
Derdak, Sophia (Centre Nacional d'Anàlisi Genòmica) ;
Galán, Beatriz (Centro de Investigaciones Biológicas (Madrid)) ;
Blanc, Julie (Centre Nacional d'Anàlisi Genòmica) ;
Gut, Marta (Centre Nacional d'Anàlisi Genòmica) ;
Lorente-Galdos, Belen (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Andrés Nieto, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
López-Otín, C. (Universidad de Oviedo. Departamento de Bioquímica y Biología Molecular) ;
Valencia, A. (Centro Nacional de Investigaciones Oncológicas) ;
Gut, I. (Centre Nacional d'Anàlisi Genòmica) ;
García, J. L. (Centro de Investigaciones Biológicas (Madrid)) ;
Guigó, R. (Centre de Regulació Genòmica) ;
Murphy, W. J. (Texas A;M University. Department of Veterinary Integrative Biosciences) ;
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Marques-Bonet, Tomas. 1975- (Centre Nacional d'Anàlisi Genòmica) ;
Roma, Guglielmo (Centre de Regulació Genòmica) ;
Notredame, C. (Centre de Regulació Genòmica) ;
Mailund, Thomas (Aarhus University. Bioinformatics Research Centre) ;
Albà, M. Mar (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Gabaldón, Toni (Centre de Regulació Genòmica) ;
Alioto, Tyler Scott (Centre Nacional d'Anàlisi Genòmica) ;
Godoy, J. A. (Estación Biológica de Doñana)
Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. [...]
2016 - 10.1186/s13059-016-1090-1
Genome biology, Vol. 17 (2016) , art. 251
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13 p, 1.8 MB |
Historical genomes reveal the genomic consequences of recent population decline in eastern gorillas
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van der Valk, Tom (Uppsala University. Department of Ecology and Genetics (Sweden)) ;
Díez-del-Molino, David (Swedish Museum of Natural History. Department of Bioinformatics and Genetics (Sweden)) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Guschanski, Katerina (Uppsala University. Department of Ecology and Genetics (Sweden)) ;
Dalén, Love (Swedish Museum of Natural History. Department of Bioinformatics and Genetics (Sweden))
Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3, 4, 5, 6, 7]. [...]
2019 - 10.1016/j.cub.2018.11.055
Current biology, Vol. 29, Issue 1 (January 2019) , p. 165-170
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18 p, 2.3 MB |
The genomic footprints of the fall and recovery of the crested ibis
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Feng, Shaohong (University of Chinese Academy of Sciences) ;
Fang, Qi (China National GeneBank) ;
Barnett, Ross (Københavns Universitet. Sektion for GeoGenetik) ;
Li, Cai (China National GeneBank) ;
Han, Sojung 1984- (Institute of Evolutionary Biology) ;
Kuhlwilm, Martin (Institute of Evolutionary Biology) ;
Zhou, Long (China National GeneBank) ;
Pan, Hailin (China National GeneBank) ;
Deng, Yuan (China National GeneBank) ;
Chen, Guangji (University of Chinese Academy of Sciences) ;
Gamauf, Anita (Naturhistorisches Museum Wien) ;
Woog, Friederike (Staatliches Museum für Naturkunde) ;
Prys-Jones, Robert (The Natural History Museum) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
P. Gilbert, M. Thomas (Københavns Universitet. Sektion for GeoGenetik) ;
Zhang, Guojie (China National GeneBank)
Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1, 2, 3, 4]. [...]
2019 - 10.1016/j.cub.2018.12.008
Current biology, Vol. 29, issue 2 (Jan. 2019) , p. 340-349
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15 p, 3.0 MB |
Single-cell transcriptome conservation in cryopreserved cells and tissues
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Guillaumet-Adkins, Amy (Centre de Regulació Genòmica) ;
Rodríguez-Esteban, Gustavo (Centre de Regulació Genòmica) ;
Mereu, Elisabetta (Centre de Regulació Genòmica) ;
Mendez-Lago, Maria (Centre de Regulació Genòmica) ;
Jaitin, Diego A. (Weizmann Institute of Science (Israel). Department of Immunology) ;
Villanueva, Alberto (Hospital Universitari de Bellvitge) ;
Vidal, August (Institut d'Investigació Biomèdica de Bellvitge) ;
Martinez-Marti, Alex (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Felip, Enriqueta (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Vivancos, Ana (Vall d'Hebron Institut d'Oncologia) ;
Keren-Shaul, Hadas (Weizmann Institute of Science (Israel). Department of Immunology) ;
Heath, Simon (Centre de Regulació Genòmica) ;
Gut, Marta (Centre de Regulació Genòmica) ;
Amit, Ido (Weizmann Institute of Science (Israel). Department of Immunology) ;
Gut, Ivo (Centre de Regulació Genòmica) ;
Heyn, Holger (Centre de Regulació Genòmica)
A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps. [...]
2017 - 10.1186/s13059-017-1171-9
Genome biology, Vol. 18 (march 2017)
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