Demographic History of the Genus Pan Inferred fromWhole Mitochondrial Genome Reconstructions.

The genus Pan is the closestgenus to ourownandit includestwospecies, Panpaniscus (bonobos) andPan troglodytes (chimpanzees). The later is constitutedby four subspecies, all highly endangered. The study of the Pan genera hasbeen incessantly complicated by the intricate relationshipamongsubspecies and the statistical limitations imposedby the reducednumber of samples or genomicmarkers 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 hithertomost complete Pan mitochondrial genomedataset 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 subsetofoursamples,we comparednuclear versusmitochondrialgenomesandwefoundthat chimpanzee subspecieshavedifferent patterns of nuclear andmitochondrial 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. [ABSTRACT FROM AUTHOR]