Population dynamics and genetic connectivity in recent chimpanzee history
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.
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Elsevier
2022-06-01
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Online Access: | http://hdl.handle.net/10261/304440 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/100000011 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100001821 http://dx.doi.org/10.13039/501100004189 |
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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. |
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Fundación "la Caixa" Fontsere, Claudia Kuhlwilm, Martin Morcillo-Suárez, Carlos Alvarez-Estape, Marina Lester, Jack D. Gratton, Paolo Schmidt, Joshua M. Dieguez, Paula Aebischer, Thierry Álvarez-Varona, Paula Agbor, Anthony Angedakin, Samuel Assumang, Alfred K. Ayimisin, Emmanuel Ayuk Bailey, Emma Barubiyo, Donatienne Bessone, Mattia Carretero-Alonso, Andrea Chancellor, Rebecca Cohen, Heather Danquah, Emmanuel Deschner, Tobias Dunn, Andrew Dupain, Jef Egbe, Villard E. Feliú, Olga Goedmakers, Annemarie Granjon, Anne‐Céline Head, Josephine Hedwig, Daniela Hermans, Veerle Hernandez-Aguilar, R. Adriana Imong, Inaoyom Jones, Sorrel Junker, Jessica Kadam, Parag Kaiser, Mike Kambere, Mbangi Kambale, Magloire V. Kalan, Ammie K. Kienast, Ivonne Kujirakwinja, Deo Langergraber, Kevin E. Lapuente, Juan Larson, Bradley Laudisoit, Anne Lee, Kevin Llana, Manuel Llorente, Miquel Marrocol, iSergio Morgan, David Mulindahabi, Felix Murai, Mizuki Neil, Emily Nicholl, Sonia Nixon, Stuart Normand, Emma Orbell, Chris Ormsby, Lucy Jayne Pacheco, Liliana Piel, Alex Riera, Laura Robbins, Martha M. Rundus, Aaron Sanz, Crickette Sciaky, Lilah Sommer, Volker Stewart, Fiona Tagg, Nikki Tédonzong, Luc Roscelin Ton, Els van Schijndel, Joost Vergnes, Virginie Wessling, Erin G. Willie, Jacob Wittig, Roman M. Yuh, Yisa G. Yurkiw, Kyle Zuberbuehler, Klaus Hecht, Jochen Vigilant, Linda Boesch, Christophe Andrés, Aida M. Hughes, David A. Kühl, Hjalmar Lizano, Esther Arandjelovic, Mimi Marqués-Bonet, Tomàs |
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Fontsere, Claudia Kuhlwilm, Martin Morcillo-Suárez, Carlos Alvarez-Estape, Marina Lester, Jack D. Gratton, Paolo Schmidt, Joshua M. Dieguez, Paula Aebischer, Thierry Álvarez-Varona, Paula Agbor, Anthony Angedakin, Samuel Assumang, Alfred K. Ayimisin, Emmanuel Ayuk Bailey, Emma Barubiyo, Donatienne Bessone, Mattia Carretero-Alonso, Andrea Chancellor, Rebecca Cohen, Heather Danquah, Emmanuel Deschner, Tobias Dunn, Andrew Dupain, Jef Egbe, Villard E. Feliú, Olga Goedmakers, Annemarie Granjon, Anne‐Céline Head, Josephine Hedwig, Daniela Hermans, Veerle Hernandez-Aguilar, R. Adriana Imong, Inaoyom Jones, Sorrel Junker, Jessica Kadam, Parag Kaiser, Mike Kambere, Mbangi Kambale, Magloire V. Kalan, Ammie K. Kienast, Ivonne Kujirakwinja, Deo Langergraber, Kevin E. Lapuente, Juan Larson, Bradley Laudisoit, Anne Lee, Kevin Llana, Manuel Llorente, Miquel Marrocol, iSergio Morgan, David Mulindahabi, Felix Murai, Mizuki Neil, Emily Nicholl, Sonia Nixon, Stuart Normand, Emma Orbell, Chris Ormsby, Lucy Jayne Pacheco, Liliana Piel, Alex Riera, Laura Robbins, Martha M. Rundus, Aaron Sanz, Crickette Sciaky, Lilah Sommer, Volker Stewart, Fiona Tagg, Nikki Tédonzong, Luc Roscelin Ton, Els van Schijndel, Joost Vergnes, Virginie Wessling, Erin G. Willie, Jacob Wittig, Roman M. Yuh, Yisa G. Yurkiw, Kyle Zuberbuehler, Klaus Hecht, Jochen Vigilant, Linda Boesch, Christophe Andrés, Aida M. Hughes, David A. Kühl, Hjalmar Lizano, Esther Arandjelovic, Mimi Marqués-Bonet, Tomàs |
spellingShingle |
Fontsere, Claudia Kuhlwilm, Martin Morcillo-Suárez, Carlos Alvarez-Estape, Marina Lester, Jack D. Gratton, Paolo Schmidt, Joshua M. Dieguez, Paula Aebischer, Thierry Álvarez-Varona, Paula Agbor, Anthony Angedakin, Samuel Assumang, Alfred K. Ayimisin, Emmanuel Ayuk Bailey, Emma Barubiyo, Donatienne Bessone, Mattia Carretero-Alonso, Andrea Chancellor, Rebecca Cohen, Heather Danquah, Emmanuel Deschner, Tobias Dunn, Andrew Dupain, Jef Egbe, Villard E. Feliú, Olga Goedmakers, Annemarie Granjon, Anne‐Céline Head, Josephine Hedwig, Daniela Hermans, Veerle Hernandez-Aguilar, R. Adriana Imong, Inaoyom Jones, Sorrel Junker, Jessica Kadam, Parag Kaiser, Mike Kambere, Mbangi Kambale, Magloire V. Kalan, Ammie K. Kienast, Ivonne Kujirakwinja, Deo Langergraber, Kevin E. Lapuente, Juan Larson, Bradley Laudisoit, Anne Lee, Kevin Llana, Manuel Llorente, Miquel Marrocol, iSergio Morgan, David Mulindahabi, Felix Murai, Mizuki Neil, Emily Nicholl, Sonia Nixon, Stuart Normand, Emma Orbell, Chris Ormsby, Lucy Jayne Pacheco, Liliana Piel, Alex Riera, Laura Robbins, Martha M. Rundus, Aaron Sanz, Crickette Sciaky, Lilah Sommer, Volker Stewart, Fiona Tagg, Nikki Tédonzong, Luc Roscelin Ton, Els van Schijndel, Joost Vergnes, Virginie Wessling, Erin G. Willie, Jacob Wittig, Roman M. Yuh, Yisa G. Yurkiw, Kyle Zuberbuehler, Klaus Hecht, Jochen Vigilant, Linda Boesch, Christophe Andrés, Aida M. Hughes, David A. Kühl, Hjalmar Lizano, Esther Arandjelovic, Mimi Marqués-Bonet, Tomàs Population dynamics and genetic connectivity in recent chimpanzee history |
author_sort |
Fontsere, Claudia |
title |
Population dynamics and genetic connectivity in recent chimpanzee history |
title_short |
Population dynamics and genetic connectivity in recent chimpanzee history |
title_full |
Population dynamics and genetic connectivity in recent chimpanzee history |
title_fullStr |
Population dynamics and genetic connectivity in recent chimpanzee history |
title_full_unstemmed |
Population dynamics and genetic connectivity in recent chimpanzee history |
title_sort |
population dynamics and genetic connectivity in recent chimpanzee history |
publisher |
Elsevier |
publishDate |
2022-06-01 |
url |
http://hdl.handle.net/10261/304440 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/100000011 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100001821 http://dx.doi.org/10.13039/501100004189 |
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dig-ibe-es-10261-3044402023-03-28T07:17:34Z Population dynamics and genetic connectivity in recent chimpanzee history Fontsere, Claudia Kuhlwilm, Martin Morcillo-Suárez, Carlos Alvarez-Estape, Marina Lester, Jack D. Gratton, Paolo Schmidt, Joshua M. Dieguez, Paula Aebischer, Thierry Álvarez-Varona, Paula Agbor, Anthony Angedakin, Samuel Assumang, Alfred K. Ayimisin, Emmanuel Ayuk Bailey, Emma Barubiyo, Donatienne Bessone, Mattia Carretero-Alonso, Andrea Chancellor, Rebecca Cohen, Heather Danquah, Emmanuel Deschner, Tobias Dunn, Andrew Dupain, Jef Egbe, Villard E. Feliú, Olga Goedmakers, Annemarie Granjon, Anne‐Céline Head, Josephine Hedwig, Daniela Hermans, Veerle Hernandez-Aguilar, R. Adriana Imong, Inaoyom Jones, Sorrel Junker, Jessica Kadam, Parag Kaiser, Mike Kambere, Mbangi Kambale, Magloire V. Kalan, Ammie K. Kienast, Ivonne Kujirakwinja, Deo Langergraber, Kevin E. Lapuente, Juan Larson, Bradley Laudisoit, Anne Lee, Kevin Llana, Manuel Llorente, Miquel Marrocol, iSergio Morgan, David Mulindahabi, Felix Murai, Mizuki Neil, Emily Nicholl, Sonia Nixon, Stuart Normand, Emma Orbell, Chris Ormsby, Lucy Jayne Pacheco, Liliana Piel, Alex Riera, Laura Robbins, Martha M. Rundus, Aaron Sanz, Crickette Sciaky, Lilah Sommer, Volker Stewart, Fiona Tagg, Nikki Tédonzong, Luc Roscelin Ton, Els van Schijndel, Joost Vergnes, Virginie Wessling, Erin G. Willie, Jacob Wittig, Roman M. Yuh, Yisa G. Yurkiw, Kyle Zuberbuehler, Klaus Hecht, Jochen Vigilant, Linda Boesch, Christophe Andrés, Aida M. Hughes, David A. Kühl, Hjalmar Lizano, Esther Arandjelovic, Mimi Marqués-Bonet, Tomàs Fundación "la Caixa" Ministerio de Ciencia, Innovación y Universidades (España) Ministerio de Economía y Competitividad (España) European Commission Vienna Science and Technology Fund European Research Council Howard Hughes Medical Institute Generalitat de Catalunya Wellcome Trust Centre for Human Genetics Max Planck Society Heinz L. Krekeler Foundation 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. Funding: “la Caixa” Foundation doctoral fellowship program LCF/BQ/DE15/10360006 (to C.F.). FPI (Formación de Personal Investigador) PRE2018-083966 from Ministerio de Ciencia, Universidades e Investigación (to M.A.-E.) and CGL2017-82654-P (MINECO/FEDER, UE) (to E.L.). “la Caixa” Foundation (ID 100010434), fellowship code LCF/BQ/PR19/11700002 (to M.K.). Vienna Science and Technology Fund (WWTF) and the City of Vienna project VRG20-001 (to M.K.). The European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 864203) (to T.M.-B.). BFU2017-86471-P (MINECO/FEDER, UE) (to T.M.-B.). “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M) (to T.M.-B.). Howard Hughes International Early Career (to T.M.-B.). NIH 1R01HG010898-01A1 (to T.M.-B.). Secretaria d’Universitats i Recerca and CERCA Program del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880) (to T.M.-B.). UCL’s Wellcome Trust ISSF3 award 204841/Z/16/Z (to A.M.A. and J.M.S.). Generalitat de Catalunya (2017 SGR-1040) (to M. Llorente). Wellcome Trust Investigator Award 202802/Z/16/Z (to D.A.H.). The Pan African Program: The Cultured Chimpanzee (PanAf) is generously funded by the Max Planck Society, the Max Planck Society Innovation Fund, and the Heinz L. Krekeler Foundation. With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2018-000792-M) Peer reviewed 2023-03-27T12:10:09Z 2023-03-27T12:10:09Z 2022-06-01 2023-03-27T12:10:09Z artículo doi: 10.1016/j.xgen.2022.100133 e-issn: 2666-979X Cell Genomics 2(6): 100133 (2022) (CEX2018-000792-M) http://hdl.handle.net/10261/304440 10.1016/j.xgen.2022.100133 2666-979X http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/100000011 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100001821 http://dx.doi.org/10.13039/501100004189 en #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CGL2017-82654-P/ES/LOS PRIMATES DEL CENOZOICO DE LA PENINSULA IBERICA: EVOLUCION, ASPECTOS PALEOAMBIENTALES Y PALEOBIOGEOGRAFICOS/ info:eu-repo/grantAgreement/EC/H2020/864203 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2017-86471-P/ES/GEO-ESTRATIFICACION DE LA DIVERSIDAD GENOMICA EN GRANDES SIMIOS BASADO EN MUESTRAS NO INVASIVAS/ Publisher's version https://doi.org/10.1016/j.xgen.2022.100133 Sí open application/pdf Elsevier |