A New Genetic Study Suggests Modern Flores Island Pygmies and Ancient Hobbits Are Unrelated

The island dwarfism effect seems to have occurred independently in each population, thousands of years apart

Liang Bua cave on Flores Island, where Homo floresiensis remains were discovered in 2003. Nearby is a village where the pygmies live. (Wikimedia Commons)
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Geneticist Serena Tucci sat in the small Indonesian village of Rampasasa on Flores Island, the only woman in a room full of male researchers and pygmy villagers. Smoke from clove cigarettes swirled through the air and the villagers, whose average height was about 4.5 feet, offered their guests palm wine made from the sap of nearby trees. Slowly, with the help of translators working through three different languages, Tucci and her colleagues explained why they wanted to sample the villagers’ blood and saliva.

Clear communication was important, Tucci now says of that 2013 research trip. Scientists have made lots of mistakes in the past when working with the DNA of indigenous people. But once the villagers understood, they were excited. They wanted to know what their genetics could reveal about their personal history. They wanted to know if they were the descendants of the ancient hominins who once inhabited their island, Homo floresiensis, sometimes called hobbits for their resemblance to the fictional Tolkien creatures.

“The discovery of Floresiensis was one of the most important discoveries of the century and the fact that [the modern pygmies] live in a village very close to the cave [where Floresiensis remains were found] makes them even more interesting,” Tucci says.

The results of their research are published today in the journal Science: the modern pygmies have no relation to Homo floresiensis—though they do contain genetic material from Neanderthals and Denisovans, two extinct hominin lineages. While many modern humans have traces of extinct hominins in their DNA, the particular admixture seen in the pygmies is unique, and tells a fascinating story of how populations from different regions—the islands of Southeast Asia and the East Asia coast—mingled on this island.

“We have been unable to obtain DNA from Homo floresiensis. At least three ancient DNA labs have tried,” said Debbie Argue, a paleoanthropologist at Australian National University unaffiliated with the research, by email. “This study used a DNA statistical method to see if the Rampasasa individuals’ DNA had any indication of unidentified hominin lineages. It didn’t, so it puts the nail in the coffin for anyone who still thought that the Homo floresiensis remains were somehow related to modern humans.”

For many paleoanthropologists, that final nail has been a long time in coming. The discovery of the diminutive remains in Liang Bua cave, announced in 2004, ignited the world of paleoanthropology. The skeletons were initially dated to 18,000 years ago, meaning the tiny Flores people could’ve conceivably existed on Indonesia at the same time as modern Homo sapiens. The adult remains were tiny, less than four feet tall, and had plenty of other odd features. Their skulls had a brow ridge, like that of other ancient hominins, but instead of being one continuous hump across their forehead it broke into two sections. Their feet were huge, much more like the feet of apes than humans. The mixture of modern and archaic traits was a puzzle, one that scientists struggled to solve.

“It is the most extreme hominin ever discovered,” wrote paleoanthropologists Marta Mirazon Lahr and Robert Foley in 2004. “An archaic hominin at that date changes our understanding of late human evolutionary geography, biology and culture.”

Several factors made the hobbits particularly fascinating. First, their proximity to another ancient hominin species—Homo erectus. The first fossil remains of the “Upright Man” were discovered on the nearby Indonesian island of Java in 1891. Could the tiny Homo floresiensis be some descendant of Homo erectus? Could its environment have been the reason for it growing so small?

Flores, while in the same archipelago as Java, is separated by an important geological boundary known as Wallace’s Line. “To get from Java to Flores requires multiple crossings of deep channels and treacherous currents, including one of at least 25 kilometers,” writes John Langdon in The Science of Human Evolution: Getting It Right. That means Flores was home to a very limited number of mammals—hominins, rats, and relatives of elephants known as Stegodon—so food resources might have been scarce. Maybe the hobbits were small because it was the only way to survive.

But other scientists disagreed vehemently that the hobbits deserved their own taxonomical category. They argued that the remains belonged to Homo sapiens struck by some unknown affliction: maybe microcephaly (having an abnormally small brain) or a hormonal disease that caused stunted growth. The pathological hypothesis, while never earning full scientific consensus, remained a thorn in the side of researchers who wanted to treat Homo floresiensis as a novel species.

All that seemed to change in 2016, when a new round of dating placed the Homo floresiensis remains at 60,000 to 100,000 years old, rather than only 18,000. A separate group of researchers found more remains on a different part of the island, similar to the Homo floresiensis skeleton in the Liang Bua cave, only these remains were dated to 700,000 years ago. Along with thousands of stone tools dated to nearly 1 million years ago, the growing body of evidence seemed to move solidly in favor of an ancient and strange species of hominin making the island of Flores their home for tens of thousands of years.

If those second round of dates are correct, it’s no surprise that the modern pygmies are unrelated to Homo floresiensis, says study author Ed Green, a biomolecular engineer at the University of California, Santa Cruz. What did surprise him was what they found regarding the genetics of the short-statured people: Their genes that code for height (or lack of it) are in all of us.

“There’s a whole bunch of variation in all human populations, so that if you need to be short, there’s the genetic material [available]. You just select on it and you can be small-statured,” Green says. Basically, the pygmy villagers aren’t special in terms of their genetics; anyone might be significantly shorter if the right genes were selected.

As for how the pygmy people of Rampasasa themselves feel about the study results, that remains to be seen. In a village with no phones or Internet, sharing the data is a bit of a logistical hurdle. “We’re working now to set up a new expedition to Flores to bring the results back,” Tucci says. She’s been working with an illustrator to visually convey the results of the study, so that the villagers will have a memento of their collaboration with the scientists. They’ll also learn more about their own migratory history, how the genetic data shows their ancestors mixing with populations from East Asia and Melanesia. Even if their story doesn’t include the mysterious hobbits, it’s still part of the amazing journey Homo sapiens made across land and sea to all the corners of the world.

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