At first, the skeleton looked like a child’s. Uncovered in the gaping Liang Bua cave on the Indonesian island of Flores, the female hominin would have stood just 3.5 feet tall in life. But she wasn't a youngster, and it soon became clear that the short-statured hominin was something special: a never-before-seen species, which the researchers dubbed Homo floresiensis.
The find, announced in 2004, ignited a debate that has since raged over how this curious hominin and other similar remains, known as the “hobbits,” fit into our family tree. A new paper, published today in the journal Science, is the latest chapter in what study author Richard E. Green calls, “the great mystery that is the hobbit.”
Green, a computational biologist at the University of California, Santa Cruz, along with an international group of colleagues, examined the genetic material of the modern Rampasasa pygmy group, who live near the cave where the hobbit was found. They were curious whether the hobbit DNA lives on in these modern, short-statured people.
“Long story short, the answer is: No,” says Green. “Having looked hard, we don't see any, any evidence for that.” Instead, it seems, groups of Flores residents developed short stature at least twice—the evolutionary adaptations separated by tens of thousands of years.
“Pretty Freaking Interesting”
In recent years, researchers have slowly assembled the story of H. floresiensis. These short-statured hominins likely descended from Homo erectus, who inhabited the region as early as a million years ago. It's unclear exactly when the hobbits roamed Flores, but based on the discovery of a hobbit-like jaw and teeth near the cave, some island inhabitants seem to have achieved their short stature by 700,000 years ago. Hobbit remains date between 100,000 and 60,000 years ago, while analysis of their stone tools places them on the island between 190,000 and 50,000 years ago.
Still, some contended that the hobbit was not a new species at all, suggesting that Down syndrome or dwarfism could explain its diminutive size. This latest work springs from a controversial study published in 2011, in which researchers suggested H. floresiensis suffered from microcephaly, which stunted individuals’ growth. Green opposes this idea, but he says the researchers “did point out a pretty freaking interesting thing.”
They found some striking similarities in the facial proportions of the ancient H. floresiensis and the modern Rampasasa pygmies, who still thrive near the Liang Bua cave. “That just seemed like too much of a coincidence for me,” he says.
At the time, Green was was fresh off composing a draft sequence of the Neanderthal genome. As part of this research, his team identified traces of these ancient hominin genes in modern humans. This was sort of the science “zeitgeist” of the time, he says: “Maybe everything admixes with everything if there is an opportunity.” Maybe the same was true for hobbits.
So Green and his colleagues, including researchers from Europe, Australia, and Indonesia, set out to analyze the modern pygmy genome and determine if their ancestors were or once intermingled with H. floresiensis.
Two Translators, 32 Spit Samples
Since the discovery of H. floresiensis—and possibly even before—the Rampasasa people have believed that their ancestry was tied to the towering “cathedral-like” Liang Bua cave, says Serena Tucci, an author of the new study and researcher at Princeton University. They believe that the hobbit found there is one of their ancestors—and often bring food or flowers to the cave as offerings, she says.
Before collecting samples, the team worked hard to explain its goals and the collection process, Tucci explains, relying on two translators to communicate: one to translate from English to Indonesian and another to translate from Indonesian into the local Manggarai language. Overall, the Rampasasa people were eager to participate in the analysis. “They wanted to know about their history,” she says.
For collection, the researchers randomly selected 32 adults from a group of volunteers, requiring each to spit in a tube for genetic analysis. Of these individuals, they analyzed 10 whole genomes. They then compared the genetic analyses to the DNA of more than 2,500 modern individuals from 225 populations across East Asia, Malaysia, Indonesia, Papua New Guinea, and more.
Because no one has yet successfully extracted DNA from H. floresiensis remains, the researchers couldn't directly compare ancient and modern DNA. Instead, they searched for hobbit traces using a slightly different tack, by asking the question: “What do we find that we can't explain?” says Green. “And the answer is: nothing that looks like what we expect a hobbit to look like.”
This analysis suggests that the Rampasasa people can trace a large part of their ancestry to Near Oceania, a region that includes Papua New Guinea, the Solomon Islands, and the Bismarck Archipelago. Another significant part of their genetics seem to come from a relatively recent migration from East Asia.
There is some evidence of ancient hominins, including traces of Neanderthal and roughly 0.8 percent Denisovan genes. But the researchers couldn't find any additional hominin mixing ancient enough to have come from a species like the hobbit.
“[I] would have very much loved for the answer to be yes,” says Green. “And it just ain't so.”
What's Going On?
“Everywhere we look we find admixture, even in populations we thought were different species,” says Amy Goldberg, a population geneticist at Duke University who was not involved in the research. This latest study, she says, is one of the first times in the modern genomic era when researchers haven't found such interbreeding.
She praises the thoroughness of the new analysis, noting that it's possible that hobbit traces could still be there—just not detectable with current methods. But it's also entirely possible, she says, that short stature developed twice through time.
“We think that many strange things happen on islands,” Tucci explains. Exposed to different food availability and often unusual collections—or an overall lack—of predators, island life grows strikingly different than continental creatures. Many become small, a process known as insular dwarfism. That's likely what happened to the mini hippos of Madagascar and the small elephant cousins that once roamed Flores alongside the hobbit. Yet other creatures get big, like Flores' giant rats, which still scramble across the island today. They're “the size of my cat,” Tucci adds.
But Gerrit Van den Bergh of the University of Wollongong cautions against drawing conclusions about the cause of the shrinkage. It's unclear whether insular dwarfism is actually at play for the Rampasasa people, he says. The Rampasasa people are successful farmers, and so scarcity of food—a common proposed driving force for insular dwarfism—may not play a major role in selection.
“Insular dwarfism is itself a bit of a mystery,” Green agrees. “It's one of these things in science that seems like: 'Well, that should [already] be worked out.'”
“This study, to me, shows that height has a complex architecture,” adds Sohini Ramachandran, a human population geneticist at Brown University who was not involved in the work. It's still unclear why these short statures evolve, she notes. “There's some more exciting future work to do to incorporate these samples into other studies to understand the genetics of that trait.”
The team is now working to communicate their results to the Rampasasa people. “Bringing back the result is a key part of the research,” says Tucci, who is currently collaborating with an Indonesian illustrator to develop an understandable graphic to present to the village. But there is still much more to do. The research seems to raise more questions than it answers, but it is an tantalizing hint to the life and death of the enigmatic H. floresiensis.
“The big mystery remains,” says Green. “What was it?”