A new DNA study shows Homo floresiensis genes don't live on in a group of people living near where the extinct hominin was discovered.

The Indonesian island of Flores may be famous as the home of a tiny enigmatic extinct human, but its present-day pygmy population has a few mysteries of its own.

Key points:

• Groups of pygmy people live near a site where fossils of a short-statured species of hominin called Homo floresiensis were found
• Whether present-day inhabitants are descendants of Homo floresiensis was up for debate
• New DNA analysis shows no ancestral link between current population and Homo floresiensis
• Short stature evolved twice in two separate lineages of hominins on Flores

Even though current inhabitants live just a few kilometres from the cave that housed fossils of the long-dead Homo floresiensis — also dubbed the "hobbit" for its miniature size — they are not descendants of the extinct hominin.

Instead, short stature independently evolved in human inhabitants of the island at least twice, separated by tens of thousands of years.

The international study was published in Science today.

Indonesia today is home to hundreds of ethnic groups spread across thousands of volcanic islands. But it has a long history of habitation by people other than our own species, Homo sapiens.

It's thought that an ancient human species known as Homo erectus colonised the island of Java from around 1.7 million years to 23,000 years ago, and Homo floresiensis lived on Flores from roughly 190,000 to 50,000 years ago.

Modern humans are a relatively recent addition to the gang, arriving in Sumatra around 73,000 to 63,000 years ago and going on to colonise other islands shortly afterwards.

 

Fossils suggest the hobbit stood a tad over a metre tall.

And they bred with hominin species that are extinct today. We carry the signatures of those ancient dalliances in the form of Neanderthal and Denisovan genetic material woven in with our own.

But what about other long-dead hominins, such as the hobbit?

The long and the short of it

At first glance, modern Flores pygmies appear like they might harbour some of the extinct hobbit DNA.

Homo floresiensis stood just over a metre tall. The current pygmy population averages around 1.45 metres.

(To be classified a pygmy population, average male adult height must be no taller than 1.5 metres).

The question of whether or not they're related — and if today's pygmy population can attribute their short stature to hobbit ancestors — has sparked intense debate within archaeological circles.

To find out, Princeton University evolutionary biologist Serena Tucci and her colleagues compared DNA from 32 pygmy adults from the village of Rampasasa with sequences from modern humans from around the world, as well as Neanderthals and Denisovans.

They found Neanderthal and Denisovan DNA within the pygmy genomes — which was expected — but nothing out of the ordinary that might point to another archaic hominin, said study co-author and University of Queensland geneticist Peter Visscher.

"They kind of fit in where you'd probably expect them to fit in, in terms of ancestry, when you compare that group of people to other populations in South-East Asia, Oceania and so on," he said.

"It would be really surprising if we saw patterns of DNA that can't be explained by modern humans or Neanderthals or Denisovans. But that's not what we found."

In other words, there were no strange or unknown stretches of genetic material that could be attributed to Homo floresiensis.

 

Homo floresiensis had a tiny head, holding a brain that was around a third the volume of ours.

Ideally, geneticists looking for signs of Homo floresiensis DNA in present-day populations would refer to a hobbit genome, like they can with Neanderthal and Denisovan genomes.

But despite their best attempts, no-one's successfully taken DNA from Homo floresiensis fossils, said Debbie Argue, a palaeoanthropologist at the Australian National University who was not involved with the study.

"At least three labs have tried," Dr Argue said.

"DNA doesn't preserve well in tropical regions. It's been a disappointment to all of us because if we had DNA, we'd nail it."

Island living produces shorter stature

Instead of being a genetic legacy of Homo floresiensis interbreeding, the current population's short stature is due to natural selection that took place over the past 30,000 years or so.

Human height is determined by a whole multitude of gene variants. Some of these give you a bit more height while others decrease stature.

"We looked at the variants in the pygmy population and asked: 'Are they enriched for height-decreasing gene variants?'" Professor Visscher said.

"That's exactly what we found — more height-decreasing variants in the Flores sample than other samples from South-East Asia and Oceania."

Short stature is found in isolated populations of mammals, including humans, all over the world.

For instance, dwarfed species of elephants also once called Flores home.

One subspecies tipped the scales at just 300 kilograms as an adult — around an 18th of the weight of a present-day adult male Asian elephant.

 

The Liang Bua cave in Flores, where the hobbit's remains were discovered, also contained stegodon fossils.

Some evolutionary biologists call this tendency to smaller body size the "island rule", Professor Visscher said.

"If you look at island populations in Europe, for example, the same kind of phenomenon was seen for the population on the island of Sardinia in the Mediterranean.

"The Sardinians aren't a pygmy population, but they are quite small."

Evolutionary enigma of shrinking

But why isolated groups tend to shrink is still an evolutionary enigma.

"Maybe it's to do with predation or depending on the diet you have, which means it's better to have a smaller body size," Professor Visscher said.

Indeed, Dr Argue suggests Homo floresiensis bucked the island dwarfism trend and didn't shrink over time. Rather, it may have grown taller.

A million-year-old adult jaw bone, found at a site called Mata Menge in central Flores and reported in 2016, appeared to come from an individual that was similar in shape to Homo floresiensis.

"But it was 22 per cent smaller than Homo floresiensis jaws," Dr Argue said.

"If anything, Homo floresiensis could have increased in size."

Still, precisely why people living on Flores are smaller than those on surrounding islands is a mystery worth investigating, said Bastien Llamas, a palaeogeneticist at the University of Adelaide who wasn't involved with the study.

"The pygmy population on Flores Island is one population on one island in Indonesia.

"But there have been many other humans living in the same area on other islands that haven't become small.

"So something is going on in that population that's quite different from other humans [nearby], and the study suggests selection on multiple gene variants led to short stature."

And while there doesn't seem to be traces of hobbit DNA in the present-day pygmy population on Flores, it's not necessarily the case for groups living elsewhere in Indonesia, Dr Llamas said.

"What I'm curious to see is if you look at other Indonesian populations around, is there any hobbit or Homo erectus DNA in them?"