Spooky introgression in the African jungle: Bonobos hybridized with a “ghost” ape

Genetic study finds traces of ancient introgression in bonobo genomes.

Gene flow between distinct species is a common phenomenon. Scientists often observe hybrids in the wild and find evidence for genetic exchange when they look into the genomes of the interbreeding species. But what about ancient hybridization with extinct species? It seems sensible to expect traces of ancient introgression from unknown species in the genomes of extant species. In fact, more and more studies are reporting genetic material from these so-called “ghost lineages” in present-day genomes. A recent paper in the journal Nature Ecology & Evolution found traces of a “ghost” ape in bonobos. Spooky!

A bonobo contemplating the traces of ancient introgression in its genome… © Pierre Fidenci | Wikimedia Commons

 

S* statistic

Martin Kuhlwilm and his colleagues compared 69 genomes of chimpanzees and bonobos to explore patterns of ancient introgression. Chimpanzees have been split into several subspecies based on their distribution, namely the central, western, eastern and Nigeria-Cameroon populations. The map below gives an overview of these subspecies.

The researchers used the S* statistic to find signatures of old gene flow events (for more information about this statistic, you can check this review by Fernando Racimo and others). The analyses revealed an unexpected sharing of genetic variation between central chimpanzees and bonobos, which confirms previous findings.

Distribution of chimpanzee subspecies – western (verus, blue), Nigeria-Cameroon (ellioti, red),
central (troglodytes, green), eastern (schweinfurthii, orange) – and bonobo (pink). Adapted from: de Manuel et al. (2016) Science

 

Ghost Ape

Some genomic regions in the bonobo genomes could not be assigned to any of the chimpanzee populations. Detailed analyses indicated that bonobos received 0.9 to 4.2 percent from an unknown extinct population. The haplotype network below nicely illustrates this finding. The bonobos (red) and chimpanzees (yellow, green, blue and purple) form clearly defined clusters. However, one bonobo haplotype (indicated with the black arrow) is very different from the rest and probably came from a ghost lineage. Inspection of these spooky genomic regions revealed genes involved in immune response and diet, but further research is needed to validate any functional consequences of ancient hybridization.

The haplotype network shows that bonobos (red) and chimpanzees (yellow, green, blue and purple) form clearly defined clusters. However, one bonobo haplotype (indicated with the black arrow) is very different from the rest and probably came from a ghost lineage. Adapted from: Kuhlwilm et al. (2019) Nature Ecology & Evolution

 

Multispecies Introgression

This study shows that the evolutionary history of chimpanzees and bonobos was heavily influenced by introgressive hybridization. Not only did they interbreed among each other, bonobos even received genetic material from an extinct species. I would not be surprised if traces of ancient introgression are also present in the chimpanzee populations. It also illustrates that hybridization is not always restricted to two species, multiple species might be hybridizing. The ecological and evolutionary consequences of multispecies hybridization remain to be investigated. I just published a paper advocating a multispecies perspective on avian hybridization (see blog post here and paper here). Clearly, this perspective is not restricted to birds…

The evolutionary history of chimpanzees and bonobos has been shaped by introgressive hybridization. From: Kuhlwilm et al. (2019) Nature Ecology & Evolution

 

References

de Manuel, M. et al. (2016). Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science, 354(6311), 477-481.

Kuhlwilm, M., Han, S., Sousa, V. C., Excoffier, L., & Marques-Bonet, T. (2019). Ancient admixture from an extinct ape lineage into bonobos. Nature Ecology & Evolution, 3(6), 957.

Ottenburghs, J. (2019). Multispecies hybridization in birds. Avian Research, 10(1), 20.

Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015). Evidence for archaic adaptive introgression in humans. Nature Reviews Genetics, 16(6), 359.