"Nature never intends the generation of a monster."

John Bramhall, Bishop of Derry, in debate with Thomas Hobbes (1645)

In 1607, after being held captive by the Portuguese in West Africa's Congo Basin for nearly 18 years, the English sailor Andrew Battell returned home with lurid tales of "ape monsters". The larger of the two creatures Battell described, according to the edited volume later published by travel writer Samuel Purchas, Purchas His Pilgrimes, "is in all proportion like a man", but "more like a giant in stature...and has a man's face, hollow-eyed, with long haire upon his browes". These marauding beasts "goe many together, and kill many (villagers)...they are so strong, that ten men cannot hold one of them". Battell's narrative, much of which was received second hand and sure to be highly imaginative, was nevertheless one of Western society's earliest introductions to our evolutionary cousins, the great apes.

Simia quam similis turpissima bestia nobis ("How similar the ape, this ugliest of beasts, is to ourselves"). What the Roman poet Ennius presented in the 2nd century BC was a refrain that could be heard repeatedly during the subsequent two millennia whenever Europeans encountered this being that so threatened the line separating human and animal. The common depiction of non-human primates in the West as representations of sin and the Devil, wickedness, frivolity, impulsivity and violence would ultimately say more about our own discomfort at being reminded of similar qualities in ourselves than their nature.

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But it is the depiction of the ape as monster that is even more revealing. When Bishop John Bramhall challenged Thomas Hobbes' position on free will in 1645 by insisting that "Nature never intends the generation of a monster," he wasn't referring to apes but to what today we would call a mutant; something fundamentally unnatural and far removed from ourselves. For Battell, and those who came after him, to use this term repeatedly for describing great apes suggests that the experience was so profoundly disturbing that the only recourse was to relegate them to some narrow island of the mind where any similarities with humans could be ignored. The ape, to adopt lines from Shakespeare written at the time, was "a perfidious...howling...abominable monster", little more than "a born devil, on whose nature nurture can never stick".

As it turns out, William Shakespeare's The Tempest (1611), generally accepted to be the Bard's final production, was ideally timed for the playwright to have encountered the story of these ape monsters. As science writer Dale Peterson has shown, enclosed in the same edited volume that contained Battell's narrative was the report of a tragic shipwreck in the Bermuda islands that Shakespeare is known to have used while developing his script. While the play has been widely interpreted as a commentary on 17th-century British colonialism, the relationship between the part-human, part-animal Caliban and his master Prospero - a deposed duke, marooned on an island prison, who has learned to manipulate the natural world - suggests that Shakespeare may have been asking deeper questions about human nature during a time of systemic change. Caliban, portrayed as an ugly, selfish and disloyal wretch who forges a plot to murder his master in his sleep, embodies nearly all of the characteristics usually imposed on apes and is referred to as a "monster" no fewer than 45 times.

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The kind of exotic travel narrative that Purchas sought out in Battell or that Shakespeare chose as his swansong came at a unique time in Western history, between the publication of Nicolaus Copernicus' new model of the Universe in 1543 and Galileo Galilei's confirmation of his insights in 1632. As the new physics and cosmological discoveries were destabilising humanity's central position in the celestial order, biology and the discovery of great apes began to fracture a previously ordered hierarchy in the natural world. In time, the "beasts" and "killers" that travellers such as Battell encountered in distant lands would give rise to a new generation of monsters, ones that would only loom closer as a disoriented public struggled to maintain their balance during a period of rapid change.

While it seems clear that the larger of Battell's two "monsters" was most likely a gorilla, the "lesser" figure he referenced could have been either a chimpanzee or a bonobo, since both are endemic to that region of Africa. All three species, along with humans and orang-utans, comprise the Hominidae family, more commonly known as great apes (the more distantly related gibbon, the only ape with a consistently monogamous lifestyle, is in a separate taxonomic category).

Research published last month by the online journal PLoS Genetics is the latest to emphasise our close relationship to the great apes. In direct contradiction to the idea of apes as monsters (or even perhaps its ultimate rationale), it adds to the multiple genetic analyses carried out over the past 20 years that found that the two Pan species - P. troglodytes (chimps) and P. paniscus (bonobos) - share about 98.8 per cent of their DNA with humans. The "monsters" of yore are but minor variations of ourselves. However, the latest study moves the percentage even closer and raises intriguing questions about what the rate of evolutionary change in our closest relatives might tell us about human origins.

The study was the product of an international team who, for the first time, constructed a comprehensive family tree of all living primate species from the mouse lemur to the great apes. By conducting a comparative analysis of 54 nuclear gene regions - DNA that is passed on through sexual reproduction - the resulting phylogeny creates a temporal map that places each of the 186 species into an evolutionary relationship with all the others over a period of 90 million years.

As the genetic and fossil data have shown, Homo and Pan shared a common ancestor until about 6.5 million years ago. Following this speciation event, bonobos and chimpanzees then split from their common ancestor approximately 1.5 million years ago. Conventional wisdom has always been that humans are equally related to both species, the same way that you would be equally related to cousins born to different aunts on the same side of your family. Despite this identical relationship, however, chimpanzees have long been the preferred models for testing assumptions about what the Homo-Pan ancestor would have been like.

"Until now the strategy of many anthropologists has been to marginalise the bonobo," says Frans de Waal, a leading primatologist who studies great ape behaviour and cognition at Emory University's Yerkes National Primate Research Center in Atlanta, Georgia. De Waal has done more than any other researcher to bring attention to this close relative: among its ranks, female alliances intimidate males, sexual behaviour is as diverse as our own, and cooperation replaces aggression as the norm in social interactions.

"Perhaps this new genetic analysis will finally open the eyes of many that we have for four decades been hearing an overly narrow perspective on human evolution," he says.

"Ever since Raymond Dart, anthropologists have been seriously invested in a theory of humans as aggressive, tying human progress to warfare and all of our accomplishments to defeating so-called 'lesser' tribes."

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Dart was the progenitor of this "we are the champions" literature, beginning in 1925, when he built his dark vision of human evolution on the back of one of the most important scientific discoveries in history, made the previous year: the 2.8 million-year-old hominin fossil Australopithecus africanus, then the earliest known member of the human lineage ever discovered. Ironically, he had never wanted to go to Africa and viewed his position there as a demotion, marooned to the backwaters with little hope for career advancement. His fortuitous discovery of a juvenile skull, the "Taung child", was a major breakthrough that confirmed a prediction made by Charles Darwin as early as 1871.

But if Dart thought his ship had come in, it was an illusion. Few of his colleagues were looking to Africa for important discoveries, and certainly not to South Africa. Asia is where hominin evolution was expected to have occurred and Dart, along with his child-sized skull, was a laughing stock. Isolated and rejected by his colleagues, but sitting on a treasure trove of readily accessible fossil material, Dart began to imagine. Like the deposed Prospero, manipulating the reality of his island prison and populating his loneliness with phantasms, he fashioned a monstrous creature that would serve him in the years to come.

Caves are ideal environments for fostering the transformation of bone into rock and maintaining stable conditions for the preservation of fossil remains. It was in just such a cave that Dart's "killer-ape" was born. As more australopithecine fossils were discovered, protected in these subterranean lairs, it was revealed that they were often associated with the discarded remains of partially consumed mammals. It was unlikely that such an assemblage could have developed by chance and Dart interpreted these animals as victims of our hominin forebears, who were now revealed to be "confirmed killers".

As Dart would describe in the article "The predatory transition from ape to man", the human lineage was therefore descended from "carnivorous creatures, that seized living quarries by violence, battered them to death, tore apart their broken bodies, dismembered them limb from limb, slaking their ravenous thirst with the hot blood of victims and greedily devouring livid writhing flesh". Standing over the imagined carnage, Dart saw that Man had emerged, red in tooth and claw, with a lust for death.

This ancestral Caliban, a creature that longed for bloody violence (to "batter his skull, or paunch him with a stake, or cut his wesand (windpipe) with thy knife") was, for Dart, the beginning of human domination over nature. But he was far from the only anthropologist depicting violent and predatory habits in the human past. The horrors of the Second World War offered such stuff as nightmares are made on, and in the following decades researchers increasingly turned to the "Dark Continent" to find causal explanations for the worst excesses of human violence.

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For the American primatologist Sherwood Washburn, Australopithecus africanus was "already a hunter", but through him emerged a killing instinct honed by evolution. "Man is naturally aggressive," wrote Washburn in Man the Hunter. "He naturally enjoys the destruction of other creatures...Other human beings were simply the most dangerous game." Joining him was Nobel prizewinning ethologist Konrad Lorenz, who wrote in On Aggression that our tool-bearing australopithecine ancestors "promptly used their new weapon to kill not only game, but fellow members of their species as well". Completing the raiding party was the science populariser Robert Ardrey, who recrafted Dart's vision for a new generation of readers in the 1960s with his book African Genesis. "We were born of risen apes, not fallen angels," he wrote, "and the apes were armed killers besides."

That there was little in the way of fossil evidence supporting these pessimistic conclusions didn't seem to have been noticed. "Virtually all our theories about human origins were relatively unconstrained by fossil data," says David Pilbeam, a palaeoanthropologist at Harvard University, in Current Argument on Early Man (1980). "Our theories have often said far more about the theorists than about what actually happened."

What actually did happen, something that would have to wait until the mid-1970s to be established, was altogether different. The animal remains that Dart found scattered throughout hominin caves were actually the leftovers from African carnivores such as lions and leopards. Australopithecines had not been the predators; they were the prey. While some of them may have fashioned basic stone tools, they most likely used these as cutting implements to carve up animals that had already been killed by larger, more dangerous hunters.

But by then the myth of the killer-ape had caught hold and Dart's conjuration had mesmerised millions. Already popular in comic books and adventure novels, now moviegoers witnessed the origin story of this monster in the opening sequence of Stanley Kubrick's 2001: A Space Odyssey (1968). Choreographed by Dart's student Phillip Tobias, the scene depicts a ragged australopithecine who raises a discarded femur against his brother and employs it to commit the world's first murder. Afterwards, in an ecstasy of violence, this would-be Cain hurls the bone skywards where, in a multimillion-year jump, it becomes an orbiting spacecraft. The metaphor is unmistakable: through aggression, selfishness and the tools of violence lay the secret to humanity's success. The wages of sin may be death, but the compound interest was paid out in dividends of human progress.

"Then suddenly," says Jane Goodall, pioneering primatologist, in Reason for Hope, "we found that chimpanzees could be brutal - that they, like us, had a dark side to their nature." Previously the killer-ape had to be imagined and their tools of violence manipulated to create the monster. But now the carnage was real. The earliest long-term field studies in the 1960s began to reveal P. troglodytes as the monster we'd always known him to be, confirming the worst fears about our own nature. Chimps would engage in all-male raiding parties to patrol their territory and murder outsiders who strayed too near. There were documented cases of infanticide, cannibalism, the murder of group members, as well as the orgiastic ferocity of the hunt. That later research showed these cases to be rare or exaggerated in the media didn't seem to matter. The story to explain humanity's Fall had already been written and the new "killer-ape" could now step into the role.

"Chimpanzee-like violence preceded and paved the way for human war," explains Harvard primatologist Richard Wrangham in his 1996 book Demonic Males: Apes and the Origins of Human Violence, "making modern humans the dazed survivors of a continuous, 5-million-year habit of lethal aggression."

After being confined her whole life to the same island prison as her embittered father, Prospero's youthful daughter Miranda was overjoyed at the prospect of a new life. "How many goodly creatures are there here!" she announced. "O brave new world, that has such people in't!" For those who had grown up expecting monsters, the discovery of bonobos provoked a similar hopeful response in the generation after Dart. The tragedy for many is that they were known about all along but were ignored because they didn't fit the story crafted for human origins.

Even before bonobos were identified as a distinct species in 1929, it was clear that something was different about these apes. In 1925, the same year that Dart was summoning his killer-ape from the subterranean caves of Africa, Robert Yerkes, the American psychologist and primatologist, encountered a remarkably different chimpanzee he named "Prince Chim". This individual was notably more sensitive, altruistic and intelligent than any ape Yerkes had ever encountered. What the great psychologist did not know at the time was that Prince Chim was a bonobo.

"Doubtless there are geniuses even among the anthropoid apes," Yerkes observed. "Prince Chim seems to have been an intellectual genius." Yerkes was so struck by his behaviour that he titled the book based on his encounter Almost Human (1925).

Anatomically, bonobos were also found to be strikingly human-like and many initially doubted Dart's claim that Australopithecus africanus was a human ancestor precisely because the skull was so similar to that of the newly discovered bonobo. Subsequent research on bonobos has found regular bipedalism, face-to-face mating (requiring a more ventral orientation of the vagina), reduced limb and body proportions, reduced canines, greater breadth of diet, larger group sizes and reduced competition within groups; all traits shared more closely with humans than chimpanzees. Recent research has also found that bonobos are closer to humans in the genetic expression of hormones promoting sociability and in the brain regions that give rise to empathy. As early as 1933, Harold Coolidge, the anatomist who gave P. paniscus its eventual taxonomic status (and who did the post-mortem on Prince Chim), concluded that this ape "may approach more closely to the common ancestor of chimpanzees and man than does any living chimpanzee".

Bonobos directly contradict the monstrous reflection of human nature reproduced over the subsequent 80 years. While they are far from passive, they reveal a species that succeeds more through mutual aid than through aggressive violence. "From the point of view of individual survival, they are the most successful species among the higher primates," says Takayoshi Kano, a Japanese primatologist who has overseen the longest continuous field study of bonobos in the wild. "They prove that individuals can coexist without relying on competition and dominant-subordinate rank," he writes in The Last Ape (1992).

Such differences suggest that chimpanzees and bonobos have undergone very different selection pressures since they diverged from a common ancestor, unique environments that inscribed unique patterns of genetic information over time. According to Kano, the differences between bonobos and chimpanzees are likely the result of the bonobo habitat remaining "a relatively stable forest environment", whereas chimpanzees adapted to more variable conditions. These differences in habitat may be reflected in the recent PLoS Genetics analysis that suggests chimpanzees have undergone more alterations in their genetic code than the bonobos, an estimated divergence of 12.4 per cent from our Homo-Pan ancestors.

"If that were true," says de Waal, "then bonobos would be our closest relative, with the chimpanzee a close second and gorillas in third place." Statistically, the 12.4 per cent difference does not make bonobos significantly closer to humans than chimpanzees (both Pan species remain sister taxa), but it has evolutionary researchers puzzled over what this could mean about human origins.

"They've found that chimpanzees have one extra substitution for every six between humans and bonobos, and that's strange," says John Hawks, biological anthropologist at the University of Wisconsin-Madison. Chimpanzee nucleotides - the A, C, T or G base pairs that make up the vocabulary of DNA - have been evolving faster, substituting one for another at a higher rate since the two species separated from their common ancestor.

Jonathan Eisen, evolutionary biologist at the University of California, says this coincides with additional research (such as that published in Nature by Tomas Marques-Bonet et al. in 2009) showing an increased genetic substitution rate in chimpanzees compared with humans. More research is needed before any conclusions can be reached, but the study raises important questions about the emphasis on chimpanzees as the model for human origins. "If the rate is higher then they should have indeed diverged more from a common ancestor," says Eisen. "Bonobos might be more similar to the common ancestor of humans, chimps and bonobos than chimpanzees are and thus make a better model for learning about early human evolution."

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In the final scene, Shakespeare has Prospero come to recognise himself in his monster and free him from bondage. "This thing of darkness," he says of Caliban, "I acknowledge mine." Prospero's journey is much like our own. Whatever reason Western society had to be repulsed by apes, whether for destabilising our position at the centre of the natural world or merely because they were so "disproportion'd in manners and in shape" as to remind us of our lowly origin, prithee never mind. The killer-ape is our own creation and by holding on to this myth we are chaining ourselves to a pessimistic vision of human nature. We may be risen apes, but this need not reduce the better angels of our nature. In the end, by releasing Prospero's monster, we are releasing ourselves.