Ghost admixture in eastern gorillas
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. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility...
| Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | article |
| Publication Date: | 2023 |
| Country: | España |
| Institution: | Universitat Autònoma de Barcelona |
| Repository: | Dipòsit Digital de Documents de la UAB |
| Language: | English |
| OAI Identifier: | oai:ddd.uab.cat:281933 |
| Online Access: | https://ddd.uab.cat/record/281933 https://dx.doi.org/urn:doi:10.1038/s41559-023-02145-2 |
| Access Level: | Open access |
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Ghost admixture in eastern gorillasPawar, Harvinder|||0000-0002-3852-4999Rymbekova, AigerimCuadros-Espinoza, Sebastián|||0000-0002-6240-281XHuang, Xin|||0000-0002-9918-9602de Manuel, Marc|||0000-0002-1245-0127van der Valk, Tom|||0000-0001-6582-3452Lobón, Irene|||0000-0003-1170-9915Alvarez-Estape, Marina|||0000-0001-8242-1092Haber, MarcDolgova, OlgaHan, Sojung|||0000-0002-6113-1042Esteller-Cucala, Paula|||0000-0003-3048-4280Juan, David|||0000-0003-1912-9667Ayub, Qasim|||0000-0003-3291-0917Bautista, RubenKelley, Joanna|||0000-0002-7731-605XCornejo, Omar E.|||0000-0003-4076-4227Lao, OscarAndrés, Aida M.Guschanski, Katerina|||0000-0002-8493-5457Ssebide, BenardCranfield, MikeTyler-Smith, ChrisXue, YaliPrado-Martinez, Javier|||0000-0001-5402-2721Marquès i Bonet, Tomàs|||0000-0002-5597-3075Kuhlwilm, Martin|||0000-0002-0115-1797Archaic 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. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species. 22023-01-0120232023-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/281933https://dx.doi.org/urn:doi:10.1038/s41559-023-02145-2reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengEuropean Commission https://doi.org/10.13039/501100000780 864203Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 PID2021-126004NB-100Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 FI_B100131Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2021/SGR-00177Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 PRE2018-083966open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2819332026-06-06T12:50:31Z |
| dc.title.none.fl_str_mv |
Ghost admixture in eastern gorillas |
| title |
Ghost admixture in eastern gorillas |
| spellingShingle |
Ghost admixture in eastern gorillas Pawar, Harvinder|||0000-0002-3852-4999 |
| title_short |
Ghost admixture in eastern gorillas |
| title_full |
Ghost admixture in eastern gorillas |
| title_fullStr |
Ghost admixture in eastern gorillas |
| title_full_unstemmed |
Ghost admixture in eastern gorillas |
| title_sort |
Ghost admixture in eastern gorillas |
| dc.creator.none.fl_str_mv |
Pawar, Harvinder|||0000-0002-3852-4999 Rymbekova, Aigerim Cuadros-Espinoza, Sebastián|||0000-0002-6240-281X Huang, Xin|||0000-0002-9918-9602 de Manuel, Marc|||0000-0002-1245-0127 van der Valk, Tom|||0000-0001-6582-3452 Lobón, Irene|||0000-0003-1170-9915 Alvarez-Estape, Marina|||0000-0001-8242-1092 Haber, Marc Dolgova, Olga Han, Sojung|||0000-0002-6113-1042 Esteller-Cucala, Paula|||0000-0003-3048-4280 Juan, David|||0000-0003-1912-9667 Ayub, Qasim|||0000-0003-3291-0917 Bautista, Ruben Kelley, Joanna|||0000-0002-7731-605X Cornejo, Omar E.|||0000-0003-4076-4227 Lao, Oscar Andrés, Aida M. Guschanski, Katerina|||0000-0002-8493-5457 Ssebide, Benard Cranfield, Mike Tyler-Smith, Chris Xue, Yali Prado-Martinez, Javier|||0000-0001-5402-2721 Marquès i Bonet, Tomàs|||0000-0002-5597-3075 Kuhlwilm, Martin|||0000-0002-0115-1797 |
| author |
Pawar, Harvinder|||0000-0002-3852-4999 |
| author_facet |
Pawar, Harvinder|||0000-0002-3852-4999 Rymbekova, Aigerim Cuadros-Espinoza, Sebastián|||0000-0002-6240-281X Huang, Xin|||0000-0002-9918-9602 de Manuel, Marc|||0000-0002-1245-0127 van der Valk, Tom|||0000-0001-6582-3452 Lobón, Irene|||0000-0003-1170-9915 Alvarez-Estape, Marina|||0000-0001-8242-1092 Haber, Marc Dolgova, Olga Han, Sojung|||0000-0002-6113-1042 Esteller-Cucala, Paula|||0000-0003-3048-4280 Juan, David|||0000-0003-1912-9667 Ayub, Qasim|||0000-0003-3291-0917 Bautista, Ruben Kelley, Joanna|||0000-0002-7731-605X Cornejo, Omar E.|||0000-0003-4076-4227 Lao, Oscar Andrés, Aida M. Guschanski, Katerina|||0000-0002-8493-5457 Ssebide, Benard Cranfield, Mike Tyler-Smith, Chris Xue, Yali Prado-Martinez, Javier|||0000-0001-5402-2721 Marquès i Bonet, Tomàs|||0000-0002-5597-3075 Kuhlwilm, Martin|||0000-0002-0115-1797 |
| author_role |
author |
| author2 |
Rymbekova, Aigerim Cuadros-Espinoza, Sebastián|||0000-0002-6240-281X Huang, Xin|||0000-0002-9918-9602 de Manuel, Marc|||0000-0002-1245-0127 van der Valk, Tom|||0000-0001-6582-3452 Lobón, Irene|||0000-0003-1170-9915 Alvarez-Estape, Marina|||0000-0001-8242-1092 Haber, Marc Dolgova, Olga Han, Sojung|||0000-0002-6113-1042 Esteller-Cucala, Paula|||0000-0003-3048-4280 Juan, David|||0000-0003-1912-9667 Ayub, Qasim|||0000-0003-3291-0917 Bautista, Ruben Kelley, Joanna|||0000-0002-7731-605X Cornejo, Omar E.|||0000-0003-4076-4227 Lao, Oscar Andrés, Aida M. Guschanski, Katerina|||0000-0002-8493-5457 Ssebide, Benard Cranfield, Mike Tyler-Smith, Chris Xue, Yali Prado-Martinez, Javier|||0000-0001-5402-2721 Marquès i Bonet, Tomàs|||0000-0002-5597-3075 Kuhlwilm, Martin|||0000-0002-0115-1797 |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author |
| description |
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. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species. |
| publishDate |
2023 |
| dc.date.none.fl_str_mv |
2 2023-01-01 2023 2023-01-01 |
| dc.type.none.fl_str_mv |
Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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info:eu-repo/semantics/article |
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article |
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https://ddd.uab.cat/record/281933 https://dx.doi.org/urn:doi:10.1038/s41559-023-02145-2 |
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https://ddd.uab.cat/record/281933 https://dx.doi.org/urn:doi:10.1038/s41559-023-02145-2 |
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Inglés eng |
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Inglés |
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eng |
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European Commission https://doi.org/10.13039/501100000780 864203 Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 PID2021-126004NB-100 Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 FI_B100131 Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2021/SGR-00177 Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 PRE2018-083966 |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf |
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