Cell Genomics (Jun 2022)
Population dynamics and genetic connectivity in recent chimpanzee history
- Claudia Fontsere,
- Martin Kuhlwilm,
- Carlos Morcillo-Suarez,
- Marina Alvarez-Estape,
- Jack D. Lester,
- Paolo Gratton,
- Joshua M. Schmidt,
- Paula Dieguez,
- Thierry Aebischer,
- Paula Álvarez-Varona,
- Anthony Agbor,
- Samuel Angedakin,
- Alfred K. Assumang,
- Emmanuel A. Ayimisin,
- Emma Bailey,
- Donatienne Barubiyo,
- Mattia Bessone,
- Andrea Carretero-Alonso,
- Rebecca Chancellor,
- Heather Cohen,
- Emmanuel Danquah,
- Tobias Deschner,
- Andrew Dunn,
- Jef Dupain,
- Villard E. Egbe,
- Olga Feliu,
- Annemarie Goedmakers,
- Anne-Céline Granjon,
- Josephine Head,
- Daniela Hedwig,
- Veerle Hermans,
- R. Adriana Hernandez-Aguilar,
- Inaoyom Imong,
- Sorrel Jones,
- Jessica Junker,
- Parag Kadam,
- Mike Kaiser,
- Mbangi Kambere,
- Magloire V. Kambale,
- Ammie K. Kalan,
- Ivonne Kienast,
- Deo Kujirakwinja,
- Kevin Langergraber,
- Juan Lapuente,
- Bradley Larson,
- Anne Laudisoit,
- Kevin Lee,
- Manuel Llana,
- Miquel Llorente,
- Sergio Marrocoli,
- David Morgan,
- Felix Mulindahabi,
- Mizuki Murai,
- Emily Neil,
- Sonia Nicholl,
- Stuart Nixon,
- Emma Normand,
- Chris Orbell,
- Lucy J. Ormsby,
- Liliana Pacheco,
- Alex Piel,
- Laura Riera,
- Martha M. Robbins,
- Aaron Rundus,
- Crickette Sanz,
- Lilah Sciaky,
- Volker Sommer,
- Fiona A. Stewart,
- Nikki Tagg,
- Luc Roscelin Tédonzong,
- Els Ton,
- Joost van Schijndel,
- Virginie Vergnes,
- Erin G. Wessling,
- Jacob Willie,
- Roman M. Wittig,
- Yisa G. Yuh,
- Kyle Yurkiw,
- Klaus Zuberbuehler,
- Jochen Hecht,
- Linda Vigilant,
- Christophe Boesch,
- Aida M. Andrés,
- David A. Hughes,
- Hjalmar S. Kühl,
- Esther Lizano,
- Mimi Arandjelovic,
- Tomas Marques-Bonet
Affiliations
- Claudia Fontsere
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Corresponding author
- Martin Kuhlwilm
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
- Carlos Morcillo-Suarez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Marina Alvarez-Estape
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Jack D. Lester
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Paolo Gratton
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
- Joshua M. Schmidt
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK; School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Thierry Aebischer
- University of Fribourg, Fribourg, Switzerland
- Paula Álvarez-Varona
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Alfred K. Assumang
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Emmanuel A. Ayimisin
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Emma Bailey
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Donatienne Barubiyo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Andrea Carretero-Alonso
- Fundación Rainfer, Fuente el Saz de Jarama, Madrid, Spain
- Rebecca Chancellor
- Depts of Anthropology & Sociology and Psychology, West Chester University, West Chester, PA, USA
- Heather Cohen
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Wild Chimpanzee Foundation (WCF), Deutscher Platz 6, 04103 Leipzig, Germany
- Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Andrew Dunn
- Wildlife Conservation Society (WCS), 2300 Southern Boulevard, Bronx, NY 10460, USA
- Jef Dupain
- Antwerp Zoo Foundation-KMDA, Royal Zoological Society of Antwerp, Antwerp, Belgium
- Villard E. Egbe
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Olga Feliu
- Research Department, Fundació MONA, Riudellots de la Selva, Girona, Spain
- Annemarie Goedmakers
- Chimbo Foundation, Huningspaed 6. 8567 LL Oudemirdum, the Netherlands
- Anne-Céline Granjon
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Daniela Hedwig
- The Elephant Listening Project, K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
- Veerle Hermans
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- R. Adriana Hernandez-Aguilar
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal; Serra Húnter Professor, Department of Social Psychology and Quantitative Psychology, University of Barcelona, Barcelona, Spain
- Inaoyom Imong
- Wildlife Conservation Society (WCS), 2300 Southern Boulevard, Bronx, NY 10460, USA
- Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; RSPB Centre of Conservation Science, David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
- Jessica Junker
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Parag Kadam
- Greater Mahale Ecosystem Research and Conservation Project (GMERC, LTD), Mpanda, Tanzania
- Mike Kaiser
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Mbangi Kambere
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Magloire V. Kambale
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Ammie K. Kalan
- Greater Mahale Ecosystem Research and Conservation Project (GMERC, LTD), Mpanda, Tanzania; Department of Anthropology, University of Victoria, BC V8P 5C2, Canada
- Ivonne Kienast
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Deo Kujirakwinja
- Wildlife Conservation Society (WCS), 2300 Southern Boulevard, Bronx, NY 10460, USA
- Kevin Langergraber
- School of Human Evolution and Social Change, Arizona State University, 900 Cady Mall, Tempe, AZ 85287, USA; Institute of Human Origins, Arizona State University, 900 Cady Mall, Tempe, AZ 85287, USA; Arizona State University, PO Box 872402, Tempe, AZ 85287-2402, USA
- Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Bradley Larson
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Anne Laudisoit
- EcoHealth Alliance, 520 Eighth Ave, Suite 1200, New York, NY 10018, USA; Evolutionary Ecology group (EVECO), Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
- Kevin Lee
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; School of Human Evolution and Social Change, Arizona State University, 900 Cady Mall, Tempe, AZ 85287, USA
- Manuel Llana
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Miquel Llorente
- Research Department, Fundació MONA, Riudellots de la Selva, Girona, Spain; Serra Húnter Fellow, Departament de Psicologia, Facultat d’Educació i Psicologia, Universitat de Girona, Girona, Spain
- Sergio Marrocoli
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- David Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, 2001 North Clark Street, Chicago, IL 60614, USA
- Felix Mulindahabi
- Wildlife Conservation Society (WCS), 2300 Southern Boulevard, Bronx, NY 10460, USA
- Mizuki Murai
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Emily Neil
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Sonia Nicholl
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Stuart Nixon
- Chester Zoo, Field Programmes, Cedar House, Caughall Road, Upton-by Chester, CH2 1LH, UK
- Emma Normand
- Wild Chimpanzee Foundation (WCF), 23BP238 Abidjan, Côte d'Ivoire
- Chris Orbell
- Panthera, 8 W 40th St., New York, NY 10018, USA
- Lucy J. Ormsby
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Liliana Pacheco
- Centres Molina, Carrer de Lorena, 61, 08042 Barcelona, Spain
- Alex Piel
- Greater Mahale Ecosystem Research and Conservation Project (GMERC, LTD), Mpanda, Tanzania; University College London, Department of Anthropology, 14 Taviton Street, London, WC1H 0BW, UK
- Laura Riera
- Research Department, Fundació MONA, Riudellots de la Selva, Girona, Spain
- Martha M. Robbins
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Aaron Rundus
- Department of Psychology, West Chester University, West Chester, PA, USA
- Crickette Sanz
- Washington University in Saint Louis, Department of Anthropology, One Brookings Drive, St. Louis, MO 63130, USA; Wildlife Conservation Society, Congo Program, Brazzaville, Republic of Congo
- Lilah Sciaky
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Volker Sommer
- University College London, Department of Anthropology, 14 Taviton Street, London, WC1H 0BW, UK; Primate Project, Serti, Taraba State 663001, Nigeria
- Fiona A. Stewart
- Greater Mahale Ecosystem Research and Conservation Project (GMERC, LTD), Mpanda, Tanzania; University College London, Department of Anthropology, 14 Taviton Street, London, WC1H 0BW, UK; School of Biological & Environmental Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, UK
- Nikki Tagg
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- Luc Roscelin Tédonzong
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- Els Ton
- Chimbo Foundation, Huningspaed 6. 8567 LL Oudemirdum, the Netherlands
- Joost van Schijndel
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Chimbo Foundation, Huningspaed 6. 8567 LL Oudemirdum, the Netherlands
- Virginie Vergnes
- Wild Chimpanzee Foundation (WCF), 23BP238 Abidjan, Côte d'Ivoire
- Erin G. Wessling
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
- Jacob Willie
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium; Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University (UGent), K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
- Roman M. Wittig
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, BP 1301, Abidjan 01, Côte d'Ivoire
- Yisa G. Yuh
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Geography, Planning and Environmental Studies, University of Concordia, 1455 Boulevard de Maisonneuve Ouest, Montréal, QC H3G 1M8, Canada
- Kyle Yurkiw
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Klaus Zuberbuehler
- Université de Neuchâtel, Institut de Biologie, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland; School of Psychology and Neuroscience, University of St. Andrews, St. Andrews, UK
- Jochen Hecht
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Christophe Boesch
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Aida M. Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
- David A. Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
- Hjalmar S. Kühl
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Esther Lizano
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
- Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Corresponding author
- Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain; Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain; Corresponding author
- Journal volume & issue
-
Vol. 2,
no. 6
p. 100133
Abstract
Summary: 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. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.
