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1.
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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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2.
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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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3.
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5 p, 650.3 KB |
HuConTest : Testing Human Contamination in Great Ape Samples
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Kuhlwilm, Martin (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fontsere, Claudia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Han, Sojung 1984- (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Alvarez-Estape, Marina (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in noninvasive samples. [...]
2021 - 10.1093/gbe/evab117
Genome biology and evolution, Vol. 13, Issue 6 (June 2021) , art. evab117
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4.
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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 i Cuartiellas, 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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5.
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17 p, 2.4 MB |
Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures
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García Perez, Raquel (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Esteller-Cucala, Paula (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Mas, Glòria (Centre de Regulació Genòmica) ;
Lobón, Irene (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Di Carlo, Valerio (Centre de Regulació Genòmica) ;
Riera, Meritxell (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Kuhlwilm, Martin (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Navarro i Cuartiellas, Arcadi, 1969- (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Blancher, Antoine (Centre de Physiopathologie Toulouse-Purpan) ;
Di Croce, Luciano (Centre de Regulació Genòmica) ;
Gomez-Skarmeta, José Luis (Centro Andaluz de Biología del Desarrollo) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ChIP-seq for five histone marks, ATAC-seq and RNA-seq, further complemented with whole genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS). [...]
2021 - 10.1038/s41467-021-23397-1
Nature communications, Vol. 12 (May 2021) , art. 3116
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6.
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14 p, 627.9 KB |
Genetic variation in pan species is shaped by demographic history and harbors lineage-specific functions
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Han, Sojung, 1984- (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Andrés, Aida M. (UCL Genetics Institute) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Kuhlwilm, Martin (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Universitat Autònoma de Barcelona
Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the closest living relatives of humans, but the two species show distinct behavioral and physiological differences, particularly regarding female reproduction. [...]
2019 - 10.1093/gbe/evz047
Genome biology and evolution, Vol. 11, Issue 4 (April 2019) , p. 1178-1191
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7.
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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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8.
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8 p, 1.1 MB |
Selective single molecule sequencing and assembly of a human Y chromosome of African origin
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Kuderna, Lukas (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Lizano, Esther (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Julià, Eva (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Gómez-Garrido, Jessica (Centre de Regulació Genòmica) ;
Serres-Armero, Aitor (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Kuhlwilm, Martin (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Antoni Alandes, Regina (Centre de Regulació Genòmica) ;
Alvarez-Estape, Marina (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Heath, Simon (Centre de Regulació Genòmica) ;
Alioto, Tyler Scott (Centre de Regulació Genòmica) ;
Gut, Marta (Centre de Regulació Genòmica) ;
Gut, Ivo (Centre de Regulació Genòmica) ;
Heide Schierup, Mikkel (Aarhus University. Bioinformatics Research Center) ;
Fornas, Òscar (Centre de Regulació Genòmica) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont)
Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly characterized. [...]
2019 - 10.1038/s41467-018-07885-5
Nature communications, Vol. 10 (January 2019) , art. 4
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