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

Irene Lobon (1) , Serena Tucci (2) , Marc de Manuel (1) , Silvia Ghirotto (2) , Andrea Benazzo (2) , Javier Prado-Martinez (3) , Belen Lorente-Galdos (4) , Ki Woong Nam (5) , Marc Dabad (6, 7) , Jessica Hernandez-Rodriguez (1) , David Comas (1) , Arcadi Navarro (1, 8, 9) , Mikkel H Schierup (5) , Aida M Andres (10) , Guido Barbujani (2) , Christina Hvilsom (11) , Tomas Marques-Bonet (1, 12, 9)

1 Departament de Ciencies Experimentals i de la Salut
2 Department of Life Sciences and Biotechnology
3 The Wellcome Trust Sanger Institute [Cambridge]
4 Department of Neuroscience
5 Bioinformatics Research Center
6 BIST - Barcelona Institute of Science and Technology
7 UPF - Universitat Pompeu Fabra [Barcelona]
8 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
9 CRG - Centre for Genomic Regulation - Centre de Regulació Genòmica [Barcelona]
10 Department of Evolutionary Genetics
11 Research and Conservation
12 Catalan Institution of Research and Advanced Studies

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.

Mots clés: bioinformatics; bonobo; chimpanzee; genome diversity; mtArchitect; next-generation sequencing

Domaines: Biodiversité et Ecologie

Irene Lobon, Serena Tucci, Marc de Manuel, Silvia Ghirotto, Andrea Benazzo, et al.. Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions. Genome Biology and Evolution, 2016, 8 (6), pp.2020-2030. ⟨10.1093/gbe/evw124⟩. ⟨hal-01413553⟩