Study: Prehistoric Indonesian Woman Belonged to Extinct Human Lineage

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Fragmentary remains of the human skull.
Fragmentary remains of the human skull found in Leang Panninge in Sulawesi Credit: University of Hasanuddin

A teenage girl who lived 7,300 years ago in Indonesia belonged to an unknown lineage of modern humans, that apparently went extinct, an analysis reported in Nature revealed on Wednesday.

Human history is a story of mysterious migrations and baffling branches. The ancestors of today’s Papuans and ancestors of indigenous Australians split about 37,000 years ago. This girl found in the cave of Leang Panninge in Sulawesi was, genetically, equally related to both, the analysis found.

The inference is that her ancestral lineage split from the Australopapuan line more than 37,000 years ago, Selina Carlhoff of the Max Planck Institute for the Science of Human History, Germany, Adam Brumm of Griffith University, Australia, and colleagues report in Nature.

And she had second ancestral line. “This other ancestry seems to be most closely related to deep East Asian lineages, such as the ancestors of the Onge from the Andaman Islands and Neolithic individuals from China,” lead author Carlhoff says.

Hers is the first ancient genetic evidence from the Oceanic island region called Wallacea, which includes Sulawesi. The team points out that the climatic conditions throughout the region make the recovery of ancient DNA very challenging.

Only two other ancient genomes from the region have been analyzed, both from the mainland: one from Pha Faen, Laos, dated to about 7,900 to 7,700 years ago, and one from Gua Cha in Malaysia, about 4,400 to 4,200 years old. Both seem to have been of “deep Asian” lineage and were most closely related to the Onge, an indigenous Andamanese people. (Like the indigenous Australians, it seems the Onge and by extension, the Sentinelese, have been on their islands since time immemorial – since the first exit from Africa.)

Leang Panninge cave, Sulawesi.Credit: Leang Panninge research team

She died young

The young lady’s remains were found in the cave of Leang Panninge in Sulawesi, Indonesia. Small and slender in build, she died at about age 18-19 and had been buried in a flexed position, which was unusual for the times in this part of the world, Brumm says – though not many pre-Neolithic burials have been found because the climate is terrible for preservation.

Most of the Neolithic dead in that area were laid supine in an extended position like modern burials, he explains

Her grave featured large rocks placed on and around the body, and chunks of ocher pigment, which presumably had symbolic and/or cultural significance, he says. The rock markers, or whatever they were, are not atypical of Neolithic burials in this part of Asia.

Buried with rocks in Leang Panninge Credit: University of Hasanuddin

What killed her, we do not know. “Unfortunately, the remains are quite fragmentary,” Brumm says, adding that her skeleton shows no clear sign of infection or injury. “Childbirth is one possibility,” he adds (maternal and infant mortality rates in the prehistoric world were very high).

In life, she belonged to a pre-ceramic, pre-Neolithic Stone-Age local culture called the Toalean.

It bears adding that the Neolithic revolution – the gradual transition from a life of hunting and gathering to relying on crops and domestic animals – happened at wildly different times in different places. In the Levant it began at least 12,000 years ago, archaeologists generally agree, with spasms of cultivation going back at least 23,000 years. The Chinese were making pottery 20,000 years ago and domesticating millet also about 10,000 years ago. But the Neolithic only reached Southeast Asia much later.

Signals from the Andamans

Long story short, the team compared her genome with present-day peoples from Eastern Asia, Southeast Asia, and Near Oceania: Australians and Papuans. It didn’t match anybody, present-day or ancient, hence the hypothesis that her lineage died out.

Brumm, however, points out that they couldn’t and didn’t test everybody in Sulawesi, let alone the environs. Perhaps if broad testing is done one day, relatives will be found, especially as the island features ethnic diversity.

One of the earliest existing photographs of Great Andamanese known: two men, left one with ocher in his hair. Taken in 1875Credit: Pitt Rivers Museum, Oxford

The antecedents of her lineage could be inferred, though. She was most closely related to present-day indigenous Australians and Papuans. And, she has a component from a deep East Asian (ancient Chinese) lineage, which the indigenous Australians and Papuans do not have.

However, the direct source, as well as the circumstances and timing of this genetic contact, remain unclear.

“Previously we thought the earliest input of Asian genes into Wallacea was about 3,500 years ago, when Neolithic farmers came down from Taiwan through the Philippines into Indonesia in the Austronesian expansion. They introduced the first crops and domestic animals and pottery” to the islands, Brumm says.

Supplanting the ‘hobbits’

Asked about the knotty conundrum that is the original human settlement of Australia, Brumm explains that the jury remains out, and he personally isn’t “wedded” to either the long chronology or short chronology, he says.

Fragmentary remains of the human pelvis found at Leang Panninge cave, Sulawesi.Credit: University of Hasanuddin

Note that based on evidence in Israel and Greece, modern humans were roaming beyond Africa for at least 200,000 years. But the early exiters went extinct, all evidence so far indicates. Today’s people beyond sub-Saharan Africa, including the indigenous Australians and Papuans, descend from humans who left later.

How much later? Depends who you ask.

Southeast Asia was clearly thronged with Homo species before modern types arrived: at the least, Homo erectus, which may have begat the wee Flores “hobbit,” Homo Floresiensis, and an equally tiny hominin called Homo Luzoniensis. (These pint-sized archaic hominins on Flores and Luzon were not the same species; but their ancestors evidently both got marooned on islands and underwent island dwarfism.)

View of the Andaman Islands, IndiaCredit: Venkatesh K

Homo erectus died out before modern sapiens arrived in Asia, and we don’t know if modern humans encountered these dwarfed island hominins. It is theoretically possible that the other human species had all died out before modern humans arrived. Or not.

The earliest solid evidence for modern human arrival in Southeast Asia is figurative cave paintings, including a lovely depiction of a warty pig, in Sulawesi dating to 45,500 years ago.

The authors also note the behavioral shift deduced to have taken place in Flores at about that time – between 47,000 to 43,000 years ago. The occupants of the Liang Bua cave, the site where the hobbits were identified, fashioned tools from local volcanic rocks. After the shift, the cave occupants suddenly switched to using much higher-quality rocks like chert flint that was, apparently, not locally sourced.

The thinking is, the makers of the primitive volcanic-rock tools were hobbits. The makers of the quality flint tools were modern humans who may have obtained their stones through prehistoric trading networks, or procured by special trips. Did they use these modern tools to knock out the hobbits? Maybe.

As for the peopling of Australia, Brumm cautiously suggests that Australia was colonized at least 50,000 and possibly up to 65,000 years ago, based on recent (and extremely contentious) dating work at Madjedbebe. The dating there didn’t put doubts to rest, though, because of the technique: OSL.

In short, Brumm feels that dating the first human arrival to Australia at 55,000 years ago is reasonable. There is also a charming theory that today's indigenous Australians are still telling the tale of a volcanic eruption their ancestors witnessed 37,000 years ago.

Excavations at Leang Panninge cave.Credit: Leang Panninge research team

“The archaeological evidence of human presence in Sulawesi around 47,000 years ago combined with the new finding that the Leang Panninge ancestry split off before the ancestors of indigenous Australians and Papuans separated around 37,000 years ago could indicate that this newly described ancestry from Leang Panninge was present in the region near the time of first human settlement,” Carlhoff says.

Which doesn’t mean it was her ancestors who drew that warty pig, she clarifies. But it could have been.

The Denisovan donation

For dessert, let us glance into archaic admixture. The Leang Panninge teenager had substantial Denisovan-related ancestry, but less than Papuan and indigenous Australians, the team writes.

The other two somewhat-sequenced humans, the Pha Faen and Gua Cha hunter-gatherers, had no Denisovan ancestry. (Recent work finds that the highest level of Denisovan ancestry, known so far, is in certain Negrito groups in the Philippines.)

Why did  the Pha Faen and Gua Cha hunter-gatherers have no Denisovan background, while she had some but less Denisovan ancestry than Papuans and indigenous Australians?

One possibility is that the ancestors of the Australians and Papuans had a separate, additional admixture with Denisovans. Another is that her Denisovan ancestry became “diluted” through admixture with the deep Asian lineage carrying less or no such ancestry; that is the possibility the team favors.

Just to confuse the issue, separate studies indicate two, deeply divergent Denisovan lineages in the background of Papuans, the team adds. Nu. It is becoming clearer by the day that when it came to inter-variant sex, our species never was particular.

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