Ancient admixture from an extinct ape lineage into bonobos
Admixture is a recurrent phenomenon in humans and other great ape populations. Genetic information from extinct hominins allows us to study historical interactions with modern humans and discover adaptive functions of gene flow. Here, we investigate whole genomes from bonobo and chimpanzee populations for signatures of gene flow from unknown archaic populations, finding evidence for an ancient admixture event between bonobos and a divergent lineage. This result reveals a complex population history in our closest living relatives, probably several hundred thousand years ago. We reconstruct up to 4.8% of the genome of this ‘ghost’ ape, which represents genomic data of an extinct great ape population. Genes contained in archaic fragments might confer functional consequences for the immunity, behaviour and physiology of bonobos. Finally, comparing the landscapes of introgressed regions in humans and bonobos, we find that a recurrent depletion of introgression is rare, suggesting that genomic incompatibilities arose seldom in these lineages.
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Springer Nature
2019-04-29
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Subjects: | Evolutionary biology, Evolutionary genetics, Genetic hybridization, Population genetics, |
Online Access: | http://hdl.handle.net/10261/207229 http://dx.doi.org/10.13039/501100001659 http://dx.doi.org/10.13039/501100001871 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100011033 |
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dig-ibe-es-10261-2072292020-12-13T00:08:26Z Ancient admixture from an extinct ape lineage into bonobos Kuhlwilm, Martin Han, Sojung Sousa, Vitor C. Excoffier, Laurent Marqués-Bonet, Tomàs German Research Foundation Fundação para a Ciência e a Tecnologia (Portugal) Swiss National Science Foundation European Commission Fundación "la Caixa" Generalitat de Catalunya Agencia Estatal de Investigación (España) Ministerio de Ciencia, Innovación y Universidades (España) Evolutionary biology Evolutionary genetics Genetic hybridization Population genetics Admixture is a recurrent phenomenon in humans and other great ape populations. Genetic information from extinct hominins allows us to study historical interactions with modern humans and discover adaptive functions of gene flow. Here, we investigate whole genomes from bonobo and chimpanzee populations for signatures of gene flow from unknown archaic populations, finding evidence for an ancient admixture event between bonobos and a divergent lineage. This result reveals a complex population history in our closest living relatives, probably several hundred thousand years ago. We reconstruct up to 4.8% of the genome of this ‘ghost’ ape, which represents genomic data of an extinct great ape population. Genes contained in archaic fragments might confer functional consequences for the immunity, behaviour and physiology of bonobos. Finally, comparing the landscapes of introgressed regions in humans and bonobos, we find that a recurrent depletion of introgression is rare, suggesting that genomic incompatibilities arose seldom in these lineages. We thank A. M. Andres, B. Vernot and L. J. Kuhlwilm for comments and discussion, and M. de Manuel for help with the data. M.K. was supported by a DFG fellowship (KU 3467/1-1). V.C.S. was supported by the Fundação para a Ciência e a Tecnologia (project UID/BIA/00329/2013) and EU Horizon 2020 programme (Marie Skłodowska-Curie grant 799729). L.E. was supported by the Swiss National Science Foundation (number 310030B-166605). T.M.-B. was supported by BFU2017-86471-P (MINECO/FEDER, UE), a U01 MH106874 grant, the Howard Hughes International Early Career programme, Obra Social >La Caixa> and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). 2020-04-13T08:59:40Z 2020-04-13T08:59:40Z 2019-04-29 2020-04-13T08:59:40Z artículo http://purl.org/coar/resource_type/c_6501 doi: 10.1038/s41559-019-0881-7 e-issn: 2397-334X Nature Ecology & Evolution 3: 957-965 (2019) http://hdl.handle.net/10261/207229 10.1038/s41559-019-0881-7 http://dx.doi.org/10.13039/501100001659 http://dx.doi.org/10.13039/501100001871 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100011033 #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/H2020/799729 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/BFU2017-86471-P BFU2017-86471-P/AEI/10.13039/501100011033 http://doi.org/10.1038/s41559-019-0881-7 Sí none Springer Nature |
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Evolutionary biology Evolutionary genetics Genetic hybridization Population genetics Evolutionary biology Evolutionary genetics Genetic hybridization Population genetics |
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Evolutionary biology Evolutionary genetics Genetic hybridization Population genetics Evolutionary biology Evolutionary genetics Genetic hybridization Population genetics Kuhlwilm, Martin Han, Sojung Sousa, Vitor C. Excoffier, Laurent Marqués-Bonet, Tomàs Ancient admixture from an extinct ape lineage into bonobos |
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Admixture is a recurrent phenomenon in humans and other great ape populations. Genetic information from extinct hominins allows us to study historical interactions with modern humans and discover adaptive functions of gene flow. Here, we investigate whole genomes from bonobo and chimpanzee populations for signatures of gene flow from unknown archaic populations, finding evidence for an ancient admixture event between bonobos and a divergent lineage. This result reveals a complex population history in our closest living relatives, probably several hundred thousand years ago. We reconstruct up to 4.8% of the genome of this ‘ghost’ ape, which represents genomic data of an extinct great ape population. Genes contained in archaic fragments might confer functional consequences for the immunity, behaviour and physiology of bonobos. Finally, comparing the landscapes of introgressed regions in humans and bonobos, we find that a recurrent depletion of introgression is rare, suggesting that genomic incompatibilities arose seldom in these lineages. |
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German Research Foundation |
author_facet |
German Research Foundation Kuhlwilm, Martin Han, Sojung Sousa, Vitor C. Excoffier, Laurent Marqués-Bonet, Tomàs |
format |
artículo |
topic_facet |
Evolutionary biology Evolutionary genetics Genetic hybridization Population genetics |
author |
Kuhlwilm, Martin Han, Sojung Sousa, Vitor C. Excoffier, Laurent Marqués-Bonet, Tomàs |
author_sort |
Kuhlwilm, Martin |
title |
Ancient admixture from an extinct ape lineage into bonobos |
title_short |
Ancient admixture from an extinct ape lineage into bonobos |
title_full |
Ancient admixture from an extinct ape lineage into bonobos |
title_fullStr |
Ancient admixture from an extinct ape lineage into bonobos |
title_full_unstemmed |
Ancient admixture from an extinct ape lineage into bonobos |
title_sort |
ancient admixture from an extinct ape lineage into bonobos |
publisher |
Springer Nature |
publishDate |
2019-04-29 |
url |
http://hdl.handle.net/10261/207229 http://dx.doi.org/10.13039/501100001659 http://dx.doi.org/10.13039/501100001871 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100011033 |
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