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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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15 p, 1.8 MB |
Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs
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Alvarez-Estape, Marina (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Pawar, Harvinder (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fontsere, Claudia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Trujillo, Amber (New York University. Department of Anthropology) ;
Gunson, Jessica L. (New York University. Department of Anthropology) ;
Bergl, Richard A. (North Carolina Zoo) ;
Bermejo, Magdalena (Universitat de Barcelona. Departament d'Ecologia i Ciències Ambientals) ;
Linder, Joshua M. (James Madison University. Department of Anthropology) ;
McFarland, Kelley (Triton College) ;
Oates, John F. (University of New York. Department of Anthropology City) ;
Sunderland-Groves, Jacqueline L. (University of British Columbia . Department of Forest Resources Management) ;
Orkin, Joseph (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Higham, James P. (New York University . Department of Anthropology) ;
Viaud-Martinez, Karine A. (Illumina Laboratory Services) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. [...]
2023 - 10.3390/genes14030743
Genes, Vol. 14, Issue 3 (March 2023) , art. 743
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3.
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16 p, 5.0 MB |
Transcriptome innovations in primates revealed by single-molecule long-read sequencing
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Ferrández-Peral, Luis (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Zhan, Xiaoyu (BGI-Shenzhen) ;
Alvarez-Estape, Marina (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Chiva, Cristina (Centre de Regulació Genòmica) ;
Esteller-Cucala, Paula (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
García Perez, Raquel (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Julià, Eva (Centre de Regulació Genòmica) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Fornas, Òscar (Centre de Regulació Genòmica) ;
Sabidó, Eduard (Centre de Regulació Genòmica) ;
Li, Qiye (BGI-Shenzhen) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Zhang, Guojie
Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. [...]
2022 - 10.1101/gr.276395.121
Genome research, Published in Advance July 15, 2022
2 documents
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4.
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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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5.
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14 p, 742.5 KB |
Insights from the rescue and breeding management of Cuvier's gazelle (Gazella cuvieri) through whole-genome sequencing
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Alvarez-Estape, Marina (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fontsere, Claudia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Serres-Armero, Aitor (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Kuderna, Lukas (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Dobrynin, Pavel (ITMO University. Computer Technologies Laboratory) ;
Guidara, Héla (Direction Générale des Forêts (Tunisia)) ;
Pukazhenthi, Budhan S. (Smithsonian Conservation Biology Institute) ;
Koepfli, Klaus-Peter (Smithsonian Conservation Biology Institute) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Moreno, Eulalia (Estación Experimental de Zonas Áridas-CSIC. Departamento de Ecología Funcional y Evolutiva) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont)
Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier's gazelle programme that started in 1975 with only four founding individuals, and after more than four decades of management in captivity, a reintroduction effort was undertaken in Tunisia in 2016, to establish a population in an area historically included within its range. [...]
2022 - 10.1111/eva.13336
Evolutionary applications, Vol. 15, Issue 3 (March 2022) , p. 351-364
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6.
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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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7.
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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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