Chimpanzee genomic diversity reveals ancient admixture with bonobos

Abstract

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We have analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from ten countries in Africa. We find that chimpanzee population sub-structure makes genetic information a good predictor of geographic origin at country and regional scales. Most strikingly, multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200 and 550 thousand years ago (Kya), probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another possibly more recent contact (after 200 Kya), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.

The mitochondrial ancestor of bonobos and the origin of their major haplogroups

“…Although previous genome studies suggested no gene flow between bonobos and any of the chimpanzee groups [2,3], some gene flow from chimpanzees to bonobos might have occurred after 0.65 Ma [4]. However mtDNA haplotypes of bonobos analyzed in this study coalesced to form one root (Figs 2, 4 and 5) and clearly separated from the haplotypes of chimpanzees.…”

“…Other four studies also suggested that TMRCA of bonobos by mtDNA was at around 0.5 Ma [4,5,6] (Table 5). If these estimations are true, three quarters or two-thirds of the bonobos’ genetic history remains unknown.…”

Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

“…If in fact Africans are closer to chimpanzees or carrying more ancestral alleles in general, the conclusion of gene flow into non-Africans would become invalid. We examined this by measuring genetic distance between 1000 genomes and 10 previously sequenced chimpanzee genomes (49). Using the random 255K SNPs set, we found closer hom distance between Africans and chimpanzees than between non-Africans and chimpanzees ( Supplementary Fig.…”

The evolution of the Cercopithecini: a (post)modern synthesis

“…12,13 The other approach is built on hypotheses about climatic change and habitat shift. [60][61][62][63] In the context of the biological species concept, which defines species in terms of reproductive isolation, instances of gene flow between species were dismissed as failures of the barriers to mismating, and most of the discussion about hybrids has focused on their infertility or inviability. Recent studies using more sophisticated molecular "chromosome painting" techniques indicate that the history of the tribe has been more complicated than these two frameworks indicate.…”

“…De Manuel et al 62 have shown that low levels of gene exchange between bonobos and chimpanzees continued between 550 and 200 kya after their original divergence, although bonobos ultimately contributed less than 1% to the Pan troglodytes genome. De Manuel et al 62 have shown that low levels of gene exchange between bonobos and chimpanzees continued between 550 and 200 kya after their original divergence, although bonobos ultimately contributed less than 1% to the Pan troglodytes genome.…”