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Genome Biol Evol. 2016 Jul 3;8(6):2020-30. doi: 10.1093/gbe/evw124.

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

Author information

1
Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain tomas.marques@upf.edu.
2
Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
3
Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain.
4
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
5
Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
6
Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark.
7
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
8
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.
9
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
10
Research and Conservation, Copenhagen Zoo, Frederiksberg, Denmark.
11
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.

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.

KEYWORDS:

bioinformatics; bonobo; chimpanzee; genome diversity; mtArchitect; next-generation sequencing

PMID:
27345955
PMCID:
PMC4943195
DOI:
10.1093/gbe/evw124
[Indexed for MEDLINE]
Free PMC Article

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