On the Indonesian island of Flores, less than a mile from the cave where archaeologists discovered the fossil remains of the small-statured hominin Homo floresiensis, there's a village called Rampasasa that is home to a small population of pygmies. “Pygmy” is the scientific term for a group of people where adult males are less than about 4.7 feet tall but whose bodies have average human proportions. Most of the people living in Rampasasa fit that description.

It would be easy to assume they’re related to the other short-statured residents of Flores, and in fact some of the Rampasasans themselves have made that claim in the past. But a new genetic study says that’s not the case. These people show no signs of H. floresiensis in their ancestry, but their genomes do show evidence of a relatively recent adaptation toward shorter height. That means that people with short stature evolved twice on the same island, tens of thousands of years apart.

The hobbits are gone

Evolutionary biologist Serena Tucci of Princeton University and her colleagues obtained DNA samples from 32 people in Rampasasa. They sequenced the full genomes of 10 of those people and looked for signs of an ancient encounter with H. floresiensis or some other unknown hominin relative.

We don’t have a sample of H. floresiensis DNA, but Tucci and her colleagues used a statistical method that helps identify any segments of a chromosome that have a large number of changes that don’t show up in the rest of the population. Segments that stand out in this analysis could mean that a person’s ancestors once met and mingled with members of another species, like Neanderthals or Denisovans, or even a genetically isolated group of other humans. Tucci and her colleagues were looking for unusual segments that didn’t match up with Neanderthals or Denisovans, because those segments might be traces of H. floresiensis or H. erectus ancestry.

In people from Rampasasa, several sequences matched either Neanderthal or Denisovan genomes. That’s not too surprising, since most human populations outside Africa have some Neanderthal ancestry, and people in island Southeast Asia have the highest prevalence of Denisovan ancestry of any group of modern humans.

But the analysis didn’t find any sequences that seemed to have come from older or more distantly related hominins, like H. floresiensis. Tucci and her colleagues say they can’t rule out small-scale gene flow at some point in the distant past, but the now-extinct Pleistocene hobbits of Flores aren’t direct ancestors of its modern-day residents, despite the similarities in height and the geographical coincidence. So the people of Rampasasa must have evolved their short statures separately.

Rampasasans’ short stature is recent

Height is what’s called a polygenic trait, meaning that the combined effects of many genes influence your height (environment, lifestyle, and nutrition also play important roles). The same person’s genome may include some gene variants, or alleles, associated with increasing height and others associated with decreasing it. Tucci and her colleagues compared the Rampasasan genomes with a list of alleles that have been linked to height in European populations, and they found that those associated with shorter stature tended to be more common in the Flores islanders than in Europeans, which isn’t a surprising result.

And those height-related alleles show up with different frequencies in Rampasasans than in neighboring groups of people—a bigger difference than random genetic drift alone could explain.

Tucci and her colleagues say the Rampasasans’ height could be an example of insular dwarfism (also called island dwarfism), an evolutionary process in which animals living on an island, or in another limited, isolated environment, gradually evolve smaller body sizes than their ancestors. Some biologists have suggested that insular dwarfism is an adaptation to limited food resources or smaller prey animals. If that’s the case for people on Flores today, they’re part of a long evolutionary history of dwarfism on Flores. Besides H. floresiensis, the island was once home to stegodon, a now-extinct pygmy relative of modern elephants.

It’s worth keeping in mind, however, that nutrition and environment also play an important role in determining a person’s height, and Rampasasa is a relatively impoverished village. In 2010, one resident, Viktor Jehabut, 80 years old at the time, told an Associated Press reporter that his family had struggled to find enough food when he was young, and he believed the malnutrition had stunted his growth.

A brief genetic history

The Rampasasans’ DNA also hints at dietary changes in their collective past. The frequencies of alleles in certain regions of their genomes look like what you’d expect if these regions had been the focus of a relatively recent process called a “selective sweep.” This occurs when a single allele offers a significant advantage to members of a species and seems to “sweep” through a population, becoming very common.

On Flores, this seems to have happened with two genes on chromosome 11, FADS1 and FADS2, which code for enzymes involved in processing fatty acids from plants. Tucci and her colleagues call these genes “an evolutionary ‘toggle switch’ in response to changing diet,” and they seem to have been the focus of selective sweeps several times in human history. An allele that leads to less efficient conversion medium-chain fatty acids into long-chain ones has about a 95-percent frequency in the Flores population, which is similar to its frequency in other Southeast Asian groups. That suggests the selective sweep started in a population that contained shared ancestors of both modern groups.

The Rampasasans’ genomes shed new light on that ancestry. Although most of their ancestry comes from East Asian populations, especially Oceanic groups, nearly a quarter comes from New Guinea. Tucci and her colleagues say the Rampasasans’ genetic history suggests that they shared ancestry with today’s Oceanic population and that some time in more recent history, those populations mingled with East Asian groups.

Science, 2018. DOI: 10.1126/science.aar8486 (About DOIs).