Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions

Lobón, Irene et al.

Detalles Bibliográficos
Autores: Lobón, Irene, Manuel, Marc de, Hernandez, Jessica, Comas, David, Navarro, Arcadi, Marqués-Bonet, Tomàs
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/150570
Acceso en línea:http://hdl.handle.net/10261/150570
Access Level:acceso abierto
Palabra clave:Genome diversity
Chimpanzees
Bonobo
Bioinformatics
Next-generation sequencing
mtArchitect
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spelling Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome ReconstructionsLobón, IreneManuel, Marc deHernandez, JessicaComas, DavidNavarro, ArcadiMarqués-Bonet, TomàsGenome diversityChimpanzeesBonoboBioinformaticsNext-generation sequencingmtArchitectLobón, Irene et al.The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81–1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41–0.78] with further internal separations at 0.32 Mya [0.22–0.43] and 0.16 Mya [0.17–0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.The authors thank Luca Betti for drawing the map of the Chimpanzees distribution, Stefania Rubbini for helping with the dataset management, T.M-B is supported by ICREA ( www.icrea.cat ), EMBO YIP ( www.embo.org ) 2013, MINECO BFU2014-55090-P (FEDER), BFU2015-7116-ERC and BFU2015-6215-ERCU01 MH106874 grant, Fundacio Zoo Barcelona and Secretaria d Universitats i Recerca del Departament d Economia i Coneixement de la Generalitat de Catalunya. S.T. was supported by the Young Researcher Fellowship (5×1000 Year 2010 and Unicredit 2013 Funds) from the University of Ferrara.Peer reviewedOxford University PressGeneralitat de CatalunyaEMBOMinisterio de Economía y Competitividad (España)European CommissionFundació Barcelona ZooUniversità degli Studi di FerraraConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]201720172016info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/150570reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2014-55090-Pinfo:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2015-7116-ERCinfo:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2015-6215-ERChttps://doi.org/10.1093/gbe/evw124Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1505702026-05-22T06:33:51Z
dc.title.none.fl_str_mv Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions
title Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions
spellingShingle Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions
Lobón, Irene
Genome diversity
Chimpanzees
Bonobo
Bioinformatics
Next-generation sequencing
mtArchitect
title_short Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions
title_full Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions
title_fullStr Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions
title_full_unstemmed Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions
title_sort Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions
dc.creator.none.fl_str_mv Lobón, Irene
Manuel, Marc de
Hernandez, Jessica
Comas, David
Navarro, Arcadi
Marqués-Bonet, Tomàs
author Lobón, Irene
author_facet Lobón, Irene
Manuel, Marc de
Hernandez, Jessica
Comas, David
Navarro, Arcadi
Marqués-Bonet, Tomàs
author_role author
author2 Manuel, Marc de
Hernandez, Jessica
Comas, David
Navarro, Arcadi
Marqués-Bonet, Tomàs
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Generalitat de Catalunya
EMBO
Ministerio de Economía y Competitividad (España)
European Commission
Fundació Barcelona Zoo
Università degli Studi di Ferrara
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Genome diversity
Chimpanzees
Bonobo
Bioinformatics
Next-generation sequencing
mtArchitect
topic Genome diversity
Chimpanzees
Bonobo
Bioinformatics
Next-generation sequencing
mtArchitect
description Lobón, Irene et al.
publishDate 2016
dc.date.none.fl_str_mv 2016
2017
2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/150570
url http://hdl.handle.net/10261/150570
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2014-55090-P
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2015-7116-ERC
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2015-6215-ERC
https://doi.org/10.1093/gbe/evw124
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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