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Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions

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dc.contributor.author Lobón, Irene
dc.contributor.author Tucci, Serena
dc.contributor.author de Manuel, Marc
dc.contributor.author Ghirotto, Silvia
dc.contributor.author Benazzo, Andrea
dc.contributor.author Prado Martínez, Javier, 1987-
dc.contributor.author Lorente-Galdós, Belén, 1981-
dc.contributor.author Nam, Kiwoong
dc.contributor.author Dabad, Marc
dc.contributor.author Hernández Rodríguez, Jéssica, 1983-
dc.contributor.author Comas, David, 1969-
dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-
dc.contributor.author Schierup, Mikkel H.
dc.contributor.author Andrés Morán, Aida, 1976-
dc.contributor.author Barbujani, Guido
dc.contributor.author Hvilsom, Christina
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.date.accessioned 2016-12-15T08:14:31Z
dc.date.available 2016-12-15T08:14:31Z
dc.date.issued 2016
dc.identifier.citation Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J et al. Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions. Genome Biol Evol. 2016 Jul 3;8(6):2020-30. DOI: 10.1093/gbe/evw124.
dc.identifier.issn 1759-6653
dc.identifier.uri http://hdl.handle.net/10230/27770
dc.description.abstract 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.
dc.description.sponsorship 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/nConeixement de la Generalitat de Catalunya. S.T. was supported by the Young Researcher Fellowship (51000 Year 2010 and Unicredit 2013 Funds) from the University of Ferrara
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Genome Biology and Evolution. 2016 Jul 3;8(6):2020-30
dc.rights © Irene Lobon [et al.] 2016. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution License
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.subject.other Genòmica
dc.subject.other Ximpanzés
dc.title Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/gbe/evw124
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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