title: Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.
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.
authors.affiliation: Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain tomas.marques@upf.edu.
authors.forename: Irene
authors.initials: I
authors.lastname: Lobon
authors.affiliation: Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
authors.forename: Serena
authors.initials: S
authors.lastname: Tucci
authors.affiliation: Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain.
authors.forename: Marc
authors.initials: M
authors.lastname: de Manuel
authors.affiliation: Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Ghirotto
authors.affiliation: Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Benazzo
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
authors.forename: Javier
authors.initials: J
authors.lastname: Prado-Martinez
authors.affiliation: Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
authors.forename: Belen
authors.initials: B
authors.lastname: Lorente-Galdos
authors.affiliation: Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark.
authors.forename: Kiwoong
authors.initials: K
authors.lastname: Nam
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Marc
authors.initials: M
authors.lastname: Dabad
authors.affiliation: Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain.
authors.forename: Jessica
authors.initials: J
authors.lastname: Hernandez-Rodriguez
authors.affiliation: Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Comas
authors.affiliation: Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
authors.forename: Arcadi
authors.initials: A
authors.lastname: Navarro
authors.affiliation: Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark.
authors.forename: Mikkel H
authors.initials: MH
authors.lastname: Schierup
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Aida M
authors.initials: AM
authors.lastname: Andres
authors.affiliation: Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
authors.forename: Guido
authors.initials: G
authors.lastname: Barbujani
authors.affiliation: Research and Conservation, Copenhagen Zoo, Frederiksberg, Denmark.
authors.forename: Christina
authors.initials: C
authors.lastname: Hvilsom
authors.affiliation: Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain tomas.marques@upf.edu.
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D054629:Genome, Mitochondrial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019974:Pan paniscus / Q000235:genetics*; D002679:Pan troglodytes / Q000235:genetics*; D010802:Phylogeny
keywords: bioinformatics; bonobo; chimpanzee; genome diversity; mtArchitect; next-generation sequencing