Tiny Humans Evolved Twice on Flores: Today’s Pygmies Unrelated to Extinct ‘Hobbit’

Insular dwarfism happened not once but twice on the Indonesian island, which was occupied for half a million years before Homo sapiens began to evolve

The skull, left,  of a newly discovered species known as  Homo floresiensis, displayed next to a normal human's skull, right,  at a news conference in Yogyakarta, Indonesia Friday, Nov. 5, 2004.

Pygmies living on the Indonesian island of Flores today are not descendants of the “hobbit,” an enigmatic species of human that once lived there but died out, a large international team of scientists demonstrated Thursday in Science.

Genetic analysis of the modern pygmies showed they do have Neanderthal and Denisovan ancestry – as do neighboring peoples in southeast Asia – but the scientists found no traces of a relationship with Homo floresiensis. The present-day pygmies are a second case of insular dwarfism on the isle, with Homo floresiensis being the first, the team concludes.

“Insular dwarfism” refers to the propensity of large mammals to evolve into smaller forms when geographically isolated, typically on an island.

In the absence of adequate resources to sustain a breeding population of large animals, and in the absence of big predators (which don’t thrive on tiny, isolated islands), and in the absence of competition from similar species – diminution becomes an advantage.

Cyprus once had dwarf hippos; Flores itself was home to a miniature stegodon (primitive elephant), of which, it seems, Homo floresiensis ate. A number of islands have pygmy humans, for instance in the Philippines and Andamans.

By the way, Flores is also home to a giant rat. While big mammals tend to become small on islands, over generations small mammals become bigger.

Morphological drift takes time, and Homo floresiensis may have had a long time to develop its diminution. Scientists continue to spar over the antecedents of this mysterious species, which stood all of 1.1 meter (3.5 foot) tall in adulthood. But at least it is now clear that the population of small people on Flores today is unrelated.

Which doesn’t mean the two species of humans didn’t meet. They may have. “The current archaeological record points to the presence of H. floresiensis on Flores from 100,000 to 60,000 years ago,” lead author Dr. Serena Tucci of Princeton tells Haaretz. “We still don’t know when modern humans arrived there, so it is hard to say.” 

The hobbit emerges

In 2003, a strange fossil skeleton of a strikingly small hominin with an extremely small brain (400 cubic centimeters, compared with our 1,350 cubic centimeters) and enormous feet was found in a cave on Flores. And the fight was on.

Nicknamed the “hobbit” (officially Homo floresiensis), that and subsequent discoveries triggered tooth-and-claw quarrels among scientists over whether “Flores person” was a diseased Homo sapiens who suffered from dwarfism, microcephalism and other physical deformities; whether it descended from Homo erectus; or whether it descended from some other hominin altogether – maybe a far-ranging Homo habilis. They were short, too.

The difficulties in definitively classifying H. floresiensis are legion. One: Extracting usable DNA from ancient bones is extraordinarily tricky. DNA cannot be extracted from fossils, which are bones that underwent mineralization. It can only be extracted, with extraordinary luck and skill, from preserved bones. DNA has not yet been recovered from the H. floresiensis remains.

Another snag in studying the evolution of the wonder that is ourselves is that human fossils are so rare; there are also precious few fossils of floresiensis, and all were found in that one cave. The earliest date back some 100,000 years, the latest to about 50,000 years, Tucci says. (They could have gone extinct much later but we haven’t found the remains. We just don’t know.)

Further confusing the issue is that stone tools have been found on Flores dating back about a million years. The tools were found in the proximity of dwarf stegodon (Stegodon florensis). Ergo, the island was colonized by hominins at least half a million years before Homo sapiens began to evolve, and they seem to have liked to hunt and eat little elephants.

Reconstruction of human, hobbit and Neanderthal women, from left

We cannot know whether the ancestors of H. floresiensis made those tools. If they did, then the “hobbits” arose from a hominin that predated humankind by hundreds of thousands of years, and lived in isolation on the island for at least a million years.

The hobbit on its lonesome

Moving on eons, pygmies now live near the Liang Bua limestone cave where the floresiensis fossils were found. They’re a foot taller on average then the hobbits were, but one might assume they descended from the hobbits.

They did not, the team concludes, after sequencing the genomes of 32 pygmies.

Homo sapiens evidently mixed and matched with Neanderthals and Denisovans, though where and when is enormously complicated. Certain populations today have traces of “ghost ancestors” – which means they have genes of uncertain origin. If an isolated group of people has a gene for a protein that no other living or extinct humans have, the assumption is that the gene came from some unknown ancestor. A famous instance is a unique protein found in saliva among some sub-Saharan Africans.

Lacking hobbit DNA for comparison, the researchers combed the pygmy genome for genes from ancient human lineages. They found Neanderthal genes, Denisovan ancestry – and that’s all, folks. They found no mysterious genes that might have come from H. floresiensis.

Based on existing technological capabilities, they found no compelling evidence that the Flores pygmies harbor traces of admixture with other archaic hominin species, Tucci tells Haaretz.

“There is no indication of gene flow from the hobbit into people living today,” says Richard Green of UC Santa Cruz, one of the scientists who originally found archaic genes in our modern genomes.

We do not know when the ancestors of the pygmies reached Flores, which was no mean feat, nor do we know how long they were isolated. “It is hard to say,” Tucci explains. “We know it was really hard to cross the deep waters that separated Flores from Asia [also called the Wallace line]. Very few mammals were able to cross this line.”

We can say that the pygmies share ancestry with people in East Asia and Island Southeast Asia, Tucci says. They have a more distant relationship with populations in Oceania, including Papuans and Australian Aborigines. “Genetically, they’re not so different from other populations in that part of the world,” Green says.

So the pygmies didn’t get their short genes from the hobbits.

Height has to do with diet, but mainly it is a very heritable trait, the scientists explain. Genes associated with taller or shorter stature have been identified, in Europeans, but that counts too.

So Green and colleagues analyzed the Flores pygmy genomes for genes related to height in Europeans, and found a high frequency of genetic variants associated with decreased height, they report.

Conclusion: The pygmies evolved to be short on that small island by natural selection acting on preexisting genetic variation.

Therefore, “it means that these gene variants were present in a common ancestor of Europeans and the Flores pygmies. They became short by selection acting on this standing variation already present in the population, so there’s little need for genes from an archaic hominin to explain their small stature,” Green sums up.

So, they are saying that human-type beings moved to Flores and underwent insular dwarfism not once but twice. “Weird things happen on islands,” Green says. “With the gene pool cut off from the larger population, an island population is free to evolve in unrestrained directions based on the demands of a small ecosystem.”