- Recently published research finds that bonobos show a much deeper degree of genetic diversity than previously thought, with the species split into three distinct subgroups that diverged tens of thousands of years ago.
- The study is based on a detailed analysis of the genomes of 30 wild-born captive bonobos, cross-referenced with more limited data from 136 wild bonobos.
- Separation into three genetically isolated groups means that each group is more vulnerable than a single unified population would be, and that loss of any of these groups would result in a significant loss of the species’ genetic diversity.
Bonobos, human’s closest relatives, are classified as an endangered species. Groundbreaking research suggests their vulnerability might be even more severe than previously thought.
In a first-of-its-kind study published in Current Biology, scientists conducted an in-depth analysis of the species’ genetic structure to determine variations within and between bonobo (Pan paniscus) populations.
They found that the diversity in the species is far deeper than previously thought, with bonobos separated into three distinct geographic groups. Genetic analysis shows that these groups have been split from each other for millennia, that they do not mix, and that there is little gene flow across the groups. The researchers say these results indicate a higher vulnerability to extinction and highlight the need to attend to the bonobo substructure “both in terms of research and conservation.”
Understudied apes
Bonobos are exclusively found in the Democratic Republic of Congo, with an estimated population of around 20,000 in a range spanning more than 500,000 square kilometers (193,000 square miles), according to the study. In comparison with other apes, bonobos have been less studied partly because of the social unrest in the country.
Some previous studies have used mitochondrial DNA (mtDNA), to draw conclusions about the presence of differentiated bonobo populations. But these studies, the researchers argue, have been insufficient to build a strong understanding of the genetic substructures of the species.
“mtDNA is highly informative, but it is a single locus and its genealogy reflects only the history of the maternal lineages,” reads the study, highlighting the importance of generating demographic interpretations based on a complete set of genetic information.
Bonobos have long been considered a homogeneous group with low genetic differences between separate populations.
In this study, a team of 11 scientists used much more detailed genomic data to determine the hereditary differences in the bonobos, what their relationships are, and what their evolutionary history is.
Because only noninvasive methods would be possible for the bonobos in their natural habitat, the researchers analyzed the exomes (the protein-coding segment of genes) of 20 bonobos born in the wild but living in captivity. They also analyzed entire DNA sequences of 10 other sanctuary bonobos. They then compared their data with previously published data on 136 wild bonobos.
Lead author Aida Andrés, a genetics scientist at the Max Planck Institute for Evolutionary Anthropology in Germany, tells Mongabay this genomic data allowed scientists to make “fine-scale inferences about the genetic differentiation or high-quality inferences for important parameters such as when populations diverged or how large they have been.”
She says using samples from captive individuals has its own limitations, which includes that it’s difficult to know the geographic origin of the individuals. But by combining their data with previously published DNA information from bonobos of known geographic origin, they were able to determine the geography of each population “with a high degree of certainty.”
Alongside confirming that there are three genetically distinct groups, the study found that the central group of bonobos may have split from the western group some 145,000 years ago and that the two western groups may have diverged 60,000 years ago.
In addition, they found there’s been little mixing of the groups since the split, in part due to habitat fragmentation.
“It is notable that the three bonobo populations are not only genetically differentiated but that they also have substantially different evolutionary histories and have experienced different levels of inbreeding,” reads the study.
It further says the bonobo population in the far west of the range showed evidence of genetic isolation and sporadic gene flow, making it potentially vulnerable to future ecological changes and human activities such as encroachment.
These findings suggest the bonobos are at higher risk than previously thought in several ways, Andrés says. First, because the populations are differentiated and largely isolated from each other, they don’t function as a single, larger population.
“From the point of view of their evolution, they work as a combination of largely separated, smaller populations. This means that if one of the populations disappears, a large amount of genetic variation within the species disappears — and this can reduce substantially the adaptive potential of the species,” Andrés tells Mongabay in an email.
These smaller, isolated populations are also more vulnerable to being completely wiped out than a single unified population would be.
Andrés says it’s important to ensure that the populations are conserved all across their geographic and ecological range.
“Focusing on conserving a subset of the populations risks losing important genetic diversity,” she says.
“Dwindling and isolated populations lose genetic diversity that can help them adapt to changing environments, and because there seems to be little genetic exchange across these populations, it is important that we keep substructure in mind,” Andrés says.
Philip Muruthi, vice president of the African Wildlife Foundation (AWF), which has a bonobo conservation project in the DRC, says deeper understanding of the species is critical for the species’ conservation.
“Now that we know, through this study, that the genetic diversity of the species is deeper than we thought, it also means we have to reconsider our conservation interventions that have treated these critically endangered species as one homogenous group,” says Muruthi, a specialist on species conservation who wasn’t involved in the recent study.
He says genetic variation might mean a difference in ecological preferences among the species and the need for conservation interventions that are specific to each group.
“You can’t conserve species that you don’t understand. This study helps us to understand the bonobos better,” he says.
Muruthi says policymakers should make use of such studies by formulating relevant conservation programs.
“Scientists have been fascinated by these species and have produced a tremendous amount of research; but it’s not enough to just have research,” he says. “National governments in these ape locations should translate these studies into practical conservation initiatives”.
Banner image : A captive bonobo lies in repose at the Frankfurt Zoo. Bonobos, along with chimpanzees, are more closely related to humans than they are to gorillas or any other primate. Image by marfis75 via Flickr (CC BY 2.0).
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Citation:
Han, S., de Filippo, C., Parra, G., Meneu, J. R., Laurent, R., Frandsen, P., … Andrés, A. M. (2024). Deep genetic substructure within bonobos. Current Biology. doi:10.1016/j.cub.2024.09.043
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