The bonobo was first recognised as a distinct taxon in 1928 by German anatomist Ernst Schwarz, based on a skull in the Tervuren Museum in Belgium which had previously been classified as a juvenile chimpanzee (Pan troglodytes). Schwarz published his findings in 1929, classifying the bonobo as a subspecies of chimpanzee, Pan satyrus paniscus. In 1933, American anatomist Harold Coolidge elevated it to species status. Major behavioural differences between bonobos and chimpanzees were first discussed in detail by Tratz and Heck in the early 1950s. Unaware of any taxonomic distinction with the common chimpanzee, American psychologist and primatologist Robert Yerkes had already noticed an unexpected major behavioural difference in the 1920s.
Formerly the bonobo was known as the "pygmy chimpanzee", despite the bonobo having a similar body size to the common chimpanzee. The name "pygmy" was given by the German zoologist Ernst Schwarz in 1929, who classified the species on the basis of a previously mislabeled bonobo cranium, noting its diminutive size compared to chimpanzee skulls.
The name "bonobo" first appeared in 1954, when Austrian zoologist Eduard Paul Tratz and German biologist Heinz Heck proposed it as a new and separate generic term for pygmy chimpanzees. The name is thought to derive from a misspelling on a shipping crate from the town of Bolobo on the Congo River near the location from which the first bonobo specimens were collected in the 1920s.
In 1995, concern over declining numbers of bonobos in the wild led the Zoological Society of Milwaukee (ZSM), in Milwaukee, Wisconsin, with contributions from bonobo scientists around the world, to publish the Action Plan for Pan paniscus: A Report on Free Ranging Populations and Proposals for their Preservation. The Action Plan compiles population data on bonobos from 20 years of research conducted at various sites throughout the bonobo's range. The plan identifies priority actions for bonobo conservation and serves as a reference for developing conservation programs for researchers, government officials, and donor agencies.
During the wars in the 1990s, researchers and international non-governmental organizations (NGOs) were driven out of the bonobo habitat. In 2002, the Bonobo Conservation Initiative initiated the Bonobo Peace Forest Project (supported by the Global Conservation Fund of Conservation International), in cooperation with national institutions, local NGOs, and local communities; the Peace Forest Project works with local communities to establish a linked constellation of community-based reserves managed by local and indigenous people. This model, implemented mainly through DRC organizations and local communities, has helped bring about agreements to protect over 50,000 square miles (130,000 km ) of the bonobo habitat. According to Amy Parish, the Bonobo Peace Forest "is going to be a model for conservation in the 21st century".
Starting in 2003, the U.S. government allocated $54 million to the Congo Basin Forest Partnership. This significant investment has triggered the involvement of international NGOs to establish bases in the region and work to develop bonobo conservation programs. This initiative should improve the likelihood of bonobo survival, but its success still may depend upon building greater involvement and capability in local and indigenous communities.
Nonetheless, the exact timing of the Pan–Homo last common ancestor is contentious, but DNA comparison suggests continual interbreeding between ancestral Pan and Homo groups, post-divergence, until about 4 million years ago. DNA evidence suggests the bonobo and common chimpanzee species diverged approximately 890,000–860,000 years ago due to separation of these two populations possibly due to acidification and the spread of savannas at this time. Currently, these two species are separated by the Congo River, which had existed well before the divergence date, though ancestral Pan may have dispersed across the river using corridors which no longer exist. The first Pan fossils were reported in 2005 from the Middle Pleistocene (after the bonobo–chimpanzee split) of Kenya, alongside early Homo fossils.
Surbeck and Hohmann showed in 2008 that bonobos sometimes do hunt monkey species. Five incidents were observed in a group of bonobos in Salonga National Park, which seemed to reflect deliberate cooperative hunting. On three occasions, the hunt was successful, and infant monkeys were captured and eaten.
The bonobo is an omnivorous frugivore; 57% of its diet is fruit, but this is supplemented with leaves, honey, eggs, meat from small vertebrates such as anomalures, flying squirrels and duikers, and invertebrates. The truffle species Hysterangium bonobo is eaten by bonobos. In some instances, bonobos have been shown to consume lower-order primates. Some claim bonobos have also been known to practise cannibalism in captivity, a claim disputed by others. However, at least one confirmed report of cannibalism in the wild of a dead infant was described in 2008. A 2016 paper reported two more instances of infant cannibalism, although it was not confirmed if infanticide was involved.
Relationships of bonobos to humans and other apes can be determined by comparing their genes or whole genomes. While the first bonobo genome was published in 2012, a high-quality reference genome became available only in 2021. The overall nucleotide divergence between chimpanzee and bonobo based on the latter is 0.421 ± 0.086% for autosomes and 0.311 ± 0.060% for the X chromosome. The reference genome predicts 22,366 full-length protein-coding genes and 9,066 noncoding genes, although cDNA sequencing confirmed only 20,478 protein-coding and 36,880 noncoding bonobo genes, similar to the number of genes annotated in the human genome. Overall, 206 and 1,576 protein-coding genes are part of gene families that contracted or expanded in the bonobo genome compared to the human genome, respectively, that is, these genes were lost or gained in the bonobo genome compared to humans.
The first official publication of the sequencing and assembly of the bonobo genome was released in June 2012. The genome of a female bonobo from Leipzig Zoo was deposited with the International Nucleotide Sequence Database Collaboration (DDBJ/EMBL/GenBank) under the EMBL accession number AJFE01000000 after a previous analysis by the National Human Genome Research Institute confirmed that the bonobo genome is about 0.4% divergent from the chimpanzee genome.
According to studies published in 2017 by researchers at The George Washington University, bonobos, along with common chimpanzees, split from the human line about 8 million years ago; moreover, bonobos split from the common chimpanzee line about 2 million years ago.
According to studies published in 2017 by researchers at The George Washington University, the ancestors of the genus Pan split from the human line about 8 million years ago; moreover, bonobos split from the common chimpanzee line about 2 million years ago.
In 2020 the first whole-genome comparison between chimpanzees and bonobos was published and showed genomic aspects that may underlie or have resulted from their divergence and behavioral differences, including selection for genes related to diet and hormones. A 2010 study found that "female bonobos displayed a larger range of tool use behaviours than males, a pattern previously described for chimpanzees but not for other great apes". This finding was affirmed by the results of another 2010 study which also found that "bonobos were more skilled at solving tasks related to theory of mind or an understanding of social causality, while chimpanzees were more skilled at tasks requiring the use of tools and an understanding of physical causality". Bonobos have been found to be more risk-averse compared to chimpanzees, preferring immediate rather than delayed rewards when it comes to foraging. Bonobos also have a weaker spatial memory compared to chimpanzees, with adult bonobos performing comparably to juvenile chimpanzees.
In November 2023, scientists reported, for the first time, evidence that groups of primates, particularly bonobos, are capable of cooperating with each other.
In a study published in November 2023, scientists reported, for the first time, evidence that groups of primates, particularly bonobos, are capable of cooperating with each other. Researchers observed unprecedented cooperation between two distinct bonobo groups in the Congo's Kokolopori Bonobo Reserve, Ekalakala and Kokoalongo, challenging traditional notions of ape societies. Over two years of observation, researchers witnessed 95 encounters between the groups. Contrary to expectations, these interactions resembled those within a single group. During these encounters, the bonobos engaged in behaviors such as grooming, food sharing, and collective defense against threats like snakes. Notably, the two groups, while displaying cooperative tendencies, maintained distinct identities, and there was no evidence of interbreeding or a blending of cultures. The cooperation observed was not arbitrary but evolved through individual bonds formed by exchanging favors and gifts. Some bonobos even formed alliances to target a third individual, demonstrating a nuanced social dynamic within the groups.